water molecules diffusing: Topics by Science.gov

Sample records for water molecules diffusing

Interplay between translational diffusion and large-amplitude angular jumps of water molecules

NASA Astrophysics Data System (ADS)

Liu, Chao; Zhang, Yangyang; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

2018-05-01

Understanding the microscopic mechanism of water molecular translational diffusion is a challenging topic in both physics and chemistry. Here, we report an investigation on the interplay between the translational diffusion and the large-amplitude angular jumps of water molecules in bulk water using molecular dynamics simulations. We found that large-amplitude angular jumps are tightly coupled to the translational diffusions. Particularly, we revealed that concurrent rotational jumps of spatially neighboring water molecules induce inter-basin translational jumps, which contributes to the fast component of the water translational diffusion. Consequently, the translational diffusion shows positional heterogeneity; i.e., the neighbors of the water molecules with inter-basin translational jumps have larger probability to diffuse by inter-basin translational jumps. Our control simulations showed that a model water molecule with moderate hydrogen bond strength can diffuse much faster than a simple Lennard-Jones particle in bulk water due to the capability of disturbing the hydrogen bond network of the surrounding water molecules. Our results added to the understanding of the microscopic picture of the water translational diffusion and demonstrated the unique features of water diffusion arising from their hydrogen bond network structure compared with those of the simple liquids.
Diffusion and mobility of atomic particles in a liquid

NASA Astrophysics Data System (ADS)

Smirnov, B. M.; Son, E. E.; Tereshonok, D. V.

2017-11-01

The diffusion coefficient of a test atom or molecule in a liquid is determined for the mechanism where the displacement of the test molecule results from the vibrations and motion of liquid molecules surrounding the test molecule and of the test particle itself. This leads to a random change in the coordinate of the test molecule, which eventually results in the diffusion motion of the test particle in space. Two models parameters of interaction of a particle and a liquid are used to find the activation energy of the diffusion process under consideration: the gas-kinetic cross section for scattering of test molecules in the parent gas and the Wigner-Seitz radius for test molecules. In the context of this approach, we have calculated the diffusion coefficient of atoms and molecules in water, where based on experimental data, we have constructed the dependence of the activation energy for the diffusion of test molecules in water on the interaction parameter and the temperature dependence for diffusion coefficient of atoms or molecules in water within the models considered. The statistically averaged difference of the activation energies for the diffusion coefficients of different test molecules in water that we have calculated based on each of the presented models does not exceed 10% of the diffusion coefficient itself. We have considered the diffusion of clusters in water and present the dependence of the diffusion coefficient on the cluster size. The accuracy of the presented formulas for the diffusion coefficient of atomic particles in water is estimated to be 50%.
CO2 diffusion in champagne wines: a molecular dynamics study.

PubMed

Perret, Alexandre; Bonhommeau, David A; Liger-Belair, Gérard; Cours, Thibaud; Alijah, Alexander

2014-02-20

Although diffusion is considered as the main physical process responsible for the nucleation and growth of carbon dioxide bubbles in sparkling beverages, the role of each type of molecule in the diffusion process remains unclear. In the present study, we have used the TIP5P and SPC/E water models to perform force field molecular dynamics simulations of CO2 molecules in water and in a water/ethanol mixture respecting Champagne wine proportions. CO2 diffusion coefficients were computed by applying the generalized Fick's law for the determination of multicomponent diffusion coefficients, a law that simplifies to the standard Fick's law in the case of champagnes. The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 × 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. The remarkable agreement between the theoretical CO2 diffusion coefficients obtained within the TIP5P water/ethanol mixture and the experimental data specific to Champagne wines makes us infer that the diffusion coefficient in these emblematic hydroalcoholic sparkling beverages is expected to remain roughly constant whathever their proportions in sugars, glycerol, or peptides.
Structural and water diffusion of poly(acryl amide)/poly(vinyl alcohol) blend films: Experiment and molecular dynamics simulations.

PubMed

Wang, Yanen; Wei, Qinghua; Wang, Shuzhi; Chai, Weihong; Zhang, Yingfeng

2017-01-01

To study the effects of composition ratios and temperature on the diffusion of water molecules in PVA/PAM blend films, five simulation models of PVA/PAM with ten water molecules at different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using a molecular dynamics (MD) simulation. The diffusion behavior of water molecules in blends were investigated from the aspects of the diffusion coefficient, free volume, pair correlation function (PCF) and trajectories of water molecules, respectively. And the hydrophilicity of blend composite was studied based on the contact angle and equilibrium water content (EWC) of the blend films. The simulation results show that the diffusion coefficient of water molecules and fractional free volume (FFV) of blend membranes increase with the addition of PAM, and a higher temperature can also improve the diffusion of water molecules. Additionally, the analysis of PCFs reveals the main reason why the diffusion coefficient of water in blend system increases with the addition of PAM. The measurement results of contact angle and EWC of blend films indicate that the hydrophilicity of blend films decreases with the addition of PAM, but the EWC of blends increases with the addition of PAM. Copyright © 2016 Elsevier Inc. All rights reserved.
Diffusion of aqueous solutions of ionic, zwitterionic, and polar solutes

NASA Astrophysics Data System (ADS)

Teng, Xiaojing; Huang, Qi; Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2018-06-01

The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations. The decrease in the diffusivity of water with the concentration of simple ions and urea can be described by a simple model in which the water molecules hydrogen bonded to the solutes are considered to diffuse at the same rate as the solutes, while the remainder of the water molecules are considered to be bulk and diffuse at almost the same rate as pure water. On the other hand, the decrease in the diffusivity of water with the concentration of TMAO is apparently affected by a decrease in the diffusion rate of the bulk water molecules in addition to the decrease due to the water molecules hydrogen bonded to TMAO. In other words, TMAO enhances the viscosity of water, while urea barely affects it. Overall, this separation of water molecules into those that are hydrogen bonded to solute and those that are bulk can provide a useful means of understanding the short- and long-range effects of solutes on water.
Study of water diffusion on single-supported bilayer lipid membranes by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Bai, M.; Miskowiec, A.; Hansen, F. Y.; Taub, H.; Jenkins, T.; Tyagi, M.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.; Wang, S.-K.

2012-05-01

High-energy-resolution quasielastic neutron scattering has been used to elucidate the diffusion of water molecules in proximity to single bilayer lipid membranes supported on a silicon substrate. By varying sample temperature, level of hydration, and deuteration, we identify three different types of diffusive water motion: bulk-like, confined, and bound. The motion of bulk-like and confined water molecules is fast compared to those bound to the lipid head groups (7-10 H2O molecules per lipid), which move on the same nanosecond time scale as H atoms within the lipid molecules.
Relationship between diffusivity of water molecules inside hydrating tablets and their drug release behavior elucidated by magnetic resonance imaging.

PubMed

Kikuchi, Shingo; Onuki, Yoshinori; Kuribayashi, Hideto; Takayama, Kozo

2012-01-01

We reported previously that sustained release matrix tablets showed zero-order drug release without being affected by pH change. To understand drug release mechanisms more fully, we monitored the swelling and erosion of hydrating tablets using magnetic resonance imaging (MRI). Three different types of tablets comprised of polyion complex-forming materials and a hydroxypropyl methylcellulose (HPMC) were used. Proton density- and diffusion-weighted images of the hydrating tablets were acquired at intervals. Furthermore, apparent self-diffusion coefficient maps were generated from diffusion-weighted imaging to evaluate the state of hydrating tablets. Our findings indicated that water penetration into polyion complex tablets was faster than that into HPMC matrix tablets. In polyion complex tablets, water molecules were dispersed homogeneously and their diffusivity was relatively high, whereas in HPMC matrix tablets, water molecule movement was tightly restricted within the gel. An optimal tablet formulation determined in a previous study had water molecule penetration and diffusivity properties that appeared intermediate to those of polyion complex and HPMC matrix tablets; water molecules were capable of penetrating throughout the tablets and relatively high diffusivity was similar to that in the polyion complex tablet, whereas like the HPMC matrix tablet, it was well swollen. This study succeeded in characterizing the tablet hydration process. MRI provides profound insight into the state of water molecules in hydrating tablets; thus, it is a useful tool for understanding drug release mechanisms at a molecular level.
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

PubMed Central

Miao, Yinglong; Baudry, Jerome

2011-01-01

Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site. PMID:21943431
Temperature dependence of water diffusion pools in brain white matter.

PubMed

Dhital, Bibek; Labadie, Christian; Stallmach, Frank; Möller, Harald E; Turner, Robert

2016-02-15

Water diffusion in brain tissue can now be easily investigated using magnetic resonance (MR) techniques, providing unique insights into cellular level microstructure such as axonal orientation. The diffusive motion in white matter is known to be non-Gaussian, with increasing evidence for more than one water-containing tissue compartment. In this study, freshly excised porcine brain white matter was measured using a 125-MHz MR spectrometer (3T) equipped with gradient coils providing magnetic field gradients of up to 35,000 mT/m. The sample temperature was varied between -14 and +19 °C. The hypothesis tested was that white matter contains two slowly exchanging pools of water molecules with different diffusion properties. A Stejskal-Tanner diffusion sequence with very short gradient pulses and b-factors up to 18.8 ms/μm(2) was used. The dependence on b-factor of the attenuation due to diffusion was robustly fitted by a biexponential function, with comparable volume fractions for each component. The diffusion coefficient of each component follows Arrhenius behavior, with significantly different activation energies. The measured volume fractions are consistent with the existence of three water-containing compartments, the first comprising relatively free cytoplasmic and extracellular water molecules, the second of water molecules in glial processes, and the third comprising water molecules closely associated with membranes, as for example, in the myelin sheaths and elsewhere. The activation energy of the slow diffusion pool suggests proton hopping at the surface of membranes by a Grotthuss mechanism, mediated by hydrating water molecules. Copyright © 2015 Elsevier Inc. All rights reserved.
Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate

PubMed Central

Grudinin, Sergei; Büldt, Georg; Gordeliy, Valentin; Baumgaertner, Artur

2005-01-01

Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is ∼95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR. PMID:15731388
Molecular dynamics study of rhodamine 6G diffusion at n-decane-water interfaces.

PubMed

Popov, Piotr; Steinkerchner, Leo; Mann, Elizabeth K

2015-05-01

Two-dimensional diffusion of a rhodamine 6G fluorescent tracer molecule at the n-decane-water interface was studied with all-atom molecular dynamics simulations. In agreement with experimental data, we find increased mobility of the tracer at the n-decane-water interfaces in comparison to its mobility in bulk water. Orientational ordering of water and n-decane molecules near the interface is observed, and may change the interfacial viscosity as suggested to explain the experimental data. However, the restricted rotational motion of the rhodamine molecule at the interface suggests that the Saffman-Delbrück model may be a more appropriate approximation of rhodamine diffusion at n-decane-water interfaces, and, without any decrease in interfacial viscosity, suggests faster diffusion consistent with both experimental and simulation values.
Investigation of the dynamics of aqueous proline solutions using neutron scattering and molecular dynamics simulations.

PubMed

Malo de Molina, Paula; Alvarez, Fernando; Frick, Bernhard; Wildes, Andrew; Arbe, Arantxa; Colmenero, Juan

2017-10-18

We applied quasielastic neutron scattering (QENS) techniques to samples with two different contrasts (deuterated solute/hydrogenated solvent and the opposite label) to selectively study the component dynamics of proline/water solutions. Results on diluted and concentrated solutions (31 and 6 water molecules/proline molecule, respectively) were analyzed in terms of the susceptibility and considering a recently proposed model for water dynamics [Arbe et al., Phys. Rev. Lett., 2016, 117, 185501] which includes vibrations and the convolution of localized motions and diffusion. We found that proline molecules not only reduce the average diffusion coefficient of water but also extend the time/frequency range of the crossover region ('cage') between the vibrations and purely diffusive behavior. For the high proline concentration we also found experimental evidence of water heterogeneous dynamics and a distribution of diffusion coefficients. Complementary molecular dynamics simulations show that water molecules start to perform rotational diffusion when they escape the cage regime but before the purely diffusive behavior is established. The rotational diffusion regime is also retarded by the presence of proline molecules. On the other hand, a strong coupling between proline and water diffusive dynamics which persists with decreasing temperature is directly observed using QENS. Not only are the temperature dependences of the diffusion coefficients of both components the same, but their absolute values also approach each other with increasing proline concentration. We compared our results with those reported using other techniques, in particular using dielectric spectroscopy (DS). A simple approach based on molecular hydrodynamics and a molecular treatment of DS allows rationalizing the a priori puzzling inconsistency between QENS and dielectric results regarding the dynamic coupling of the two components. The interpretation proposed is based on general grounds and therefore should be applicable to other biomolecular solutions.
Molecular Dynamics Simulations of the Oil-Detachment from the Hydroxylated Silica Surface: Effects of Surfactants, Electrostatic Interactions, and Water Flows on the Water Molecular Channel Formation.

PubMed

Tang, Jian; Qu, Zhou; Luo, Jianhui; He, Lanyan; Wang, Pingmei; Zhang, Ping; Tang, Xianqiong; Pei, Yong; Ding, Bin; Peng, Baoliang; Huang, Yunqing

2018-02-15

The detachment process of an oil molecular layer situated above a horizontal substrate was often described by a three-stage process. In this mechanism, the penetration and diffusion of water molecules between the oil phase and the substrate was proposed to be a crucial step to aid in removal of oil layer/drops from substrate. In this work, the detachment process of a two-dimensional alkane molecule layer from a silica surface in aqueous surfactant solutions is studied by means of molecular dynamics (MD) simulations. By tuning the polarity of model silica surfaces, as well as considering the different types of surfactant molecules and the water flow effects, more details about the formation of water molecular channel and the expansion processes are elucidated. It is found that for both ionic and nonionic type surfactant solutions, the perturbation of surfactant molecules on the two-dimensional oil molecule layer facilitates the injection and diffusion of water molecules between the oil layer and silica substrate. However, the water channel formation and expansion speed is strongly affected by the substrate polarity and properties of surfactant molecules. First, only for the silica surface with relative stronger polarity, the formation of water molecular channel is observed. Second, the expansion speed of the water molecular channel upon the ionic surfactant (dodecyl trimethylammonium bromide, DTAB and sodium dodecyl benzenesulfonate, SDBS) flooding is more rapidly than the nonionic surfactant system (octylphenol polyoxyethylene(10) ether, OP-10). Third, the water flow speed may also affect the injection and diffusion of water molecules. These simulation results indicate that the water molecular channel formation process is affected by multiple factors. The synergistic effects of perturbation of surfactant molecules and the electrostatic interactions between silica substrate and water molecules are two key factors aiding in the injection and diffusion of water molecules and helpful for the oil detachment from silica substrate.
Effective diffusion coefficient including the Marangoni effect

NASA Astrophysics Data System (ADS)

Kitahata, Hiroyuki; Yoshinaga, Natsuhiko

2018-04-01

Surface-active molecules supplied from a particle fixed at the water surface create a spatial gradient of the molecule concentration, resulting in Marangoni convection. Convective flow transports the molecules far from the particle, enhancing diffusion. We analytically derive the effective diffusion coefficient associated with the Marangoni convection rolls. The resulting estimated effective diffusion coefficient is consistent with our numerical results and the apparent diffusion coefficient measured in experiments.
Communication: Modeling of concentration dependent water diffusivity in ionic solutions: Role of intermolecular charge transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Yi; Berkowitz, Max L., E-mail: maxb@unc.edu, E-mail: ykanai@unc.edu; Kanai, Yosuke, E-mail: maxb@unc.edu, E-mail: ykanai@unc.edu

2015-12-28

The translational diffusivity of water in solutions of alkali halide salts depends on the identity of ions, exhibiting dramatically different behavior even in solutions of similar salts of NaCl and KCl. The water diffusion coefficient decreases as the salt concentration increases in NaCl. Yet, in KCl solution, it slightly increases and remains above bulk value as salt concentration increases. Previous classical molecular dynamics simulations have failed to describe this important behavior even when polarizable models were used. Here, we show that inclusion of dynamical charge transfer among water molecules produces results in a quantitative agreement with experiments. Our results indicatemore » that the concentration-dependent diffusivity reflects the importance of many-body effects among the water molecules in aqueous ionic solutions. Comparison with quantum mechanical calculations shows that a heterogeneous and extended distribution of charges on water molecules around the ions due to ion-water and also water-water charge transfer plays a very important role in controlling water diffusivity. Explicit inclusion of the charge transfer allows us to model accurately the difference in the concentration-dependent water diffusivity between Na{sup +} and K{sup +} ions in simulations, and it is likely to impact modeling of a wide range of systems for medical and technological applications.« less
b matrix errors in echo planar diffusion tensor imaging

PubMed Central

Boujraf, Saïd; Luypaert, Robert; Osteaux, Michel

2001-01-01

Diffusion‐weighted magnetic resonance imaging (DW‐MRI) is a recognized tool for early detection of infarction of the human brain. DW‐MRI uses the signal loss associated with the random thermal motion of water molecules in the presence of magnetic field gradients to derive parameters that reflect the translational mobility of the water molecules in tissues. If diffusion‐weighted images with different values of b matrix are acquired during one individual investigation, it is possible to calculate apparent diffusion coefficient maps that are the elements of the diffusion tensor. The diffusion tensor elements represent the apparent diffusion coefficient of protons of water molecules in each pixel in the corresponding sample. The relation between signal intensity in the diffusion‐weighted images, diffusion tensor, and b matrix is derived from the Bloch equations. Our goal is to establish the magnitude of the error made in the calculation of the elements of the diffusion tensor when the imaging gradients are ignored. PACS number(s): 87.57. –s, 87.61.–c PMID:11602015
Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

NASA Astrophysics Data System (ADS)

Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

2018-05-01

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.
Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less
Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

DOE PAGES

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.; ...

2018-05-09

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less
Nuclear magnetic resonance relaxation and diffusion measurements as a proxy for soil properties

NASA Astrophysics Data System (ADS)

Duschl, Markus; Pohlmeier, Andreas; Galvosas, Petrik; Vereecken, Harry

2013-04-01

Nuclear Magnetic Resonance (NMR) relaxation and NMR diffusion measurements are two of a series of fast and non-invasive NMR applications widely used e.g. as well logging tools in petroleum exploration [1]. For experiments with water, NMR relaxation measures the relaxation behaviour of former excited water molecules, and NMR diffusion evaluates the self-diffusion of water. Applied in porous media, both relaxation and diffusion measurements depend on intrinsic properties of the media like pore size distribution, connectivity and tortuosity of the pores, and water saturation [2, 3]. Thus, NMR can be used to characterise the pore space of porous media not only in consolidated sediments but also in soil. The physical principle behind is the relaxation of water molecules in an external magnetic field after excitation. In porous media water molecules in a surface layer of the pores relax faster than the molecules in bulk water because of interactions with the pore wall. Thus, the relaxation in smaller pores is generally faster than in bigger pores resulting in a relaxation time distribution for porous media with a range of pore sizes like soil [4]. In NMR diffusion experiments, there is an additional encoding of water molecules by application of a magnetic field gradient. Subsequent storage of the magnetization and decoding enables the determination of the mean square displacement and therefore of the self-diffusion of the water molecules [5]. Employing various relaxation and diffusion experiments, we get a measure of the surface to volume ratio of the pores and the tortuosity of the media. In this work, we show the characterisation of a set of sand and soil samples covering a wide range of textural classes by NMR methods. Relaxation times were monitored by the Carr-Purcell-Meiboom-Gill sequence and analysed using inverse Laplace transformation. Apparent self-diffusion constants were detected by a 13-intervall pulse sequence and variation of the storage time. We correlated the results with various soil properties like texture, water retention parameters, and hydraulic conductivity. This way we show that we can predict soil properties by NMR measurements and that we are able use results of NMR measurements as a proxy without the need of direct measurements. [1] Song, Y.-Q., Vadose Zone Journal, 9 (2010) [2] Stingaciu, L. R., et al., Water Resources Research, 46 (2010) [3] Vogt, C., et al., Journal of Applied Geophysics, 50 (2002) [4] Barrie, P. J., Annual Reports on NMR Spectroscopy, 41 (2000) [5] Stallmach, F., Galvosas, P., Annual Reports on NMR Spectroscopy, 61 (2007)

Diffusion of flexible, charged, nanoscopic molecules in solution: Size and pH dependence for PAMAM dendrimer

NASA Astrophysics Data System (ADS)

Maiti, Prabal K.; Bagchi, Biman

2009-12-01

In order to understand self-diffusion (D) of a charged, flexible, and porous nanoscopic molecule in water, we carry out very long, fully atomistic molecular dynamics simulation of PAMAM dendrimer up to eight generations in explicit salt water under varying pH. We find that while the radius of gyration (Rg) varies as N1/3, the self-diffusion constant (D ) scales, surprisingly, as N-α, with α =0.39 at high pH and 0.5 at neutral pH, indicating a dramatic breakdown of Stokes-Einstein relation for diffusion of charged nanoscopic molecules. The variation in D as a function of radius of gyration demonstrates the importance of treating water and ions explicitly in the diffusion process of a flexible nanoscopic molecule. In agreement with recent experiments, the self-diffusion constant increases with pH, revealing the importance of dielectric friction in the diffusion process. The shape of a dendrimer is found to fluctuate on a nanosecond time scale. We argue that this flexibility (and also the porosity) of the dendrimer may play an important role in determining the mean square displacement of the dendrimer and the breakdown of the Stokes-Einstein relation between diffusion constant and the radius.
Proline induced disruption of the structure and dynamics of water.

PubMed

Yu, Dehong; Hennig, Marcus; Mole, Richard A; Li, Ji Chen; Wheeler, Cheryl; Strässle, Thierry; Kearley, Gordon J

2013-12-21

We use quasi-elastic neutron scattering spectroscopy to study the diffusive motion of water molecules at ambient temperature as a function of the solute molar fraction of the amino acid, proline. We validate molecular dynamics simulations against experimental quasielastic neutron scattering data and then use the simulations to reveal, and understand, a strong dependence of the translational self-diffusion coefficient of water on the distance to the amino acid molecule. An analysis based on the juxtaposition of water molecules in the simulation shows that the rigidity of proline imposes itself on the local water structure, which disrupts the hydrogen-bond network of water leading to an increase in the mean lifetime of hydrogen bonds. The net effect is some distortion of the proline molecule and a slowing down of the water mobility.
Complimentary aspects of diffusion imaging and fMRI: II. Elucidating contributions to the fMRI signal with diffusion sensitization.

PubMed

Mulkern, Robert V; Haker, Steven J; Maier, Stephan E

2007-07-01

Tissue water molecules reside in different biophysical compartments. For example, water molecules in the vasculature reside for variable periods of time within arteries, arterioles, capillaries, venuoles and veins, and may be within blood cells or blood plasma. Water molecules outside of the vasculature, in the extravascular space, reside, for a time, either within cells or within the interstitial space between cells. Within these different compartments, different types of microscopic motion that water molecules may experience have been identified and discussed. These range from Brownian diffusion to more coherent flow over the time scales relevant to functional magnetic resonance imaging (fMRI) experiments, on the order of several 10s of milliseconds. How these different types of motion are reflected in magnetic resonance imaging (MRI) methods developed for "diffusion" imaging studies has been an ongoing and active area of research. Here we briefly review the ideas that have developed regarding these motions within the context of modern "diffusion" imaging techniques and, in particular, how they have been accessed in attempts to further our understanding of the various contributions to the fMRI signal changes sought in studies of human brain activation.
Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition.

PubMed

Gupta, Rini; Chandra, Amalendu

2007-07-14

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.
Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.

PubMed

Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma

2015-11-01

Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time. Copyright © 2015 Elsevier Inc. All rights reserved.
Diffusion Rates of Organic Molecules in Secondary Organic Aerosol Particle

NASA Astrophysics Data System (ADS)

Bertram, A. K.; Chenyakin, Y.; Song, M.; Grayson, J. W.; Ullmann, D.; Evoy, E.; Renbaum-Wolff, L.; Liu, P.; Zhang, Y.; Kamal, S.; Martin, S. T.

2016-12-01

Information on the diffusion rates of organic molecules in secondary organic aerosol (SOA) particles are needed when predicting their size distribution, growth rates, photochemistry and heterogeneous chemistry. We have used two approaches to determine diffusion rates of organic molecules in SOA particles and proxies of SOA. In the first approach, we measured viscosities and then predicted diffusion rates using the Stokes-Einstein relation. In the second approach, we measured diffusion rates directly using a technique referred to as fluorescence recovery after photobleaching. Results from these measurements, including diffusion coefficients as a function of water activity, will be presented and the implications discussed.
Atomistic modeling of water diffusion in hydrolytic biomaterials.

PubMed

Gautieri, Alfonso; Mezzanzanica, Andrea; Motta, Alberto; Redealli, Alberto; Vesentini, Simone

2012-04-01

One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.
Diffusion properties of NAA in human corpus callosum as studied with diffusion tensor spectroscopy.

PubMed

Upadhyay, Jaymin; Hallock, Kevin; Erb, Kelley; Kim, Dae-Shik; Ronen, Itamar

2007-11-01

In diffusion tensor imaging (DTI) the anisotropic movement of water is exploited to characterize microstructure. One confounding issue of DTI is the presence of intra- and extracellular components contributing to the measured diffusivity. This causes an ambiguity in determining the underlying cause of diffusion properties, particularly the fractional anisotropy (FA). In this study an intracellular constituent, N-acetyl aspartate (NAA), was used to probe intracellular diffusion, while water molecules were used to probe the combined intra- and extracellular diffusion. NAA and water diffusion measurements were made in anterior and medial corpus callosum (CC) regions, which are referred to as R1 and R2, respectively. FA(NAA) was found to be greater than FA(Water) in both CC regions, thus indicating a higher degree of anisotropy within the intracellular space in comparison to the combined intra- and extracellular spaces. A decreasing trend in the FA of NAA and water was observed between R1 and R2, while the radial diffusivity (RD) for both molecules increased. The increase in RD(NAA) is particularly significant, thus explaining the more significant decrease in FA(NAA) between the two regions. It is suggested that diffusion tensor spectroscopy of NAA can potentially be used to further characterize microscopic anatomic organization in white matter. Copyright 2007 Wiley-Liss, Inc.
Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.
Translational diffusion of cumene and 3-methylpentane on free surfaces and pore walls studied by time-of-flight secondary ion mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souda, Ryutaro

2010-12-07

Mobility of molecules in confined geometry has been studied extensively, but the origins of finite size effects on reduction of the glass transition temperature, T{sub g}, are controversial especially for supported thin films. We investigate uptake of probe molecules in vapor-deposited thin films of cumene, 3-methylpentane, and heavy water using secondary ion mass spectrometry and discuss roles of individual molecular motion during structural relaxation and glass-liquid transition. The surface mobility is found to be enhanced for low-density glasses in the sub-T{sub g} region because of the diffusion of molecules on pore walls, resulting in densification of a film via poremore » collapse. Even for high-density glasses without pores, self-diffusion commences prior to the film morphology change at T{sub g}, which is thought to be related to decoupling between translational diffusivity and viscosity. The diffusivity of deeply supercooled liquid tends to be enhanced when it is confined in pores of amorphous solid water. The diffusivity of molecules is further enhanced at temperatures higher than 1.2-1.3 T{sub g} irrespective of the confinement.« less
Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water

NASA Astrophysics Data System (ADS)

Tan, Pan; Liang, Yihao; Xu, Qin; Mamontov, Eugene; Li, Jinglai; Xing, Xiangjun; Hong, Liang

2018-06-01

Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.
Isothermal dehydration of thin films of water and sugar solutions

NASA Astrophysics Data System (ADS)

Heyd, R.; Rampino, A.; Bellich, B.; Elisei, E.; Cesàro, A.; Saboungi, M.-L.

2014-03-01

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.
Isothermal dehydration of thin films of water and sugar solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heyd, R.; Rampino, A.; Laboratory of Physical and Macromolecular Chemistry, University of Trieste, Via Giorgieri 1, 34127 Trieste

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose webmore » of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.« less
Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations.

PubMed

Mermigkis, Panagiotis G; Tsalikis, Dimitrios G; Mavrantzas, Vlasis G

2015-10-28

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D(eff), of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D(eff) is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D(eff) as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D(eff) (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.
Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G.; Mavrantzas, Vlasis G.

2015-10-01

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, Deff, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, Deff is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for Deff as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on Deff (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.
Transport Mechanism of Guest Methane in Water-Filled Nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bui, Tai; Phan, Anh; Cole, David R.

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less
Transport Mechanism of Guest Methane in Water-Filled Nanopores

DOE PAGES

Bui, Tai; Phan, Anh; Cole, David R.; ...

2017-05-11

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less
Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.
Kinetics of proton migration in liquid water.

PubMed

Chen, Hanning; Voth, Gregory A; Agmon, Noam

2010-01-14

We have utilized multistate empirical valence bond (MS-EVB3) simulations of protonated liquid water to calculate the relative mean-square displacement (MSD) and the history-independent time correlation function, c(t), of the hydrated proton center of excess charge (CEC) with respect to the water molecule on which it has initially resided. The MSD is nonlinear for the first 15 ps, suggesting that the relative diffusion coefficient increases from a small value, D(0), at short separations to its larger bulk value, D(infinity), at large separations. With the ensuing distance-dependent diffusion coefficient, D(r), the time dependence of both the MSD and c(t) agrees quantitatively with the solution of a diffusion equation for reversible geminate recombination. This suggests that the relative motion of the CEC is not independent from the nearby water molecules, in agreement with theoretical and experimental observations that large water clusters participate in the mechanism of proton mobility.
Quantification of the Intracellular Life Time of Water Molecules to Measure Transport Rates of Human Aquaglyceroporins.

PubMed

Palmgren, Madelene; Hernebring, Malin; Eriksson, Stefanie; Elbing, Karin; Geijer, Cecilia; Lasič, Samo; Dahl, Peter; Hansen, Jesper S; Topgaard, Daniel; Lindkvist-Petersson, Karin

2017-12-01

Orthodox aquaporins are transmembrane channel proteins that facilitate rapid diffusion of water, while aquaglyceroporins facilitate the diffusion of small uncharged molecules such as glycerol and arsenic trioxide. Aquaglyceroporins play important roles in human physiology, in particular for glycerol metabolism and arsenic detoxification. We have developed a unique system applying the strain of the yeast Pichia pastoris, where the endogenous aquaporins/aquaglyceroporins have been removed and human aquaglyceroporins AQP3, AQP7, and AQP9 are recombinantly expressed enabling comparative permeability measurements between the expressed proteins. Using a newly established Nuclear Magnetic Resonance approach based on measurement of the intracellular life time of water, we propose that human aquaglyceroporins are poor facilitators of water and that the water transport efficiency is similar to that of passive diffusion across native cell membranes. This is distinctly different from glycerol and arsenic trioxide, where high glycerol transport efficiency was recorded.

Water barrier properties of starch films reinforced with cellulose nanocrystals obtained from sugarcane bagasse.

PubMed

Slavutsky, Aníbal M; Bertuzzi, María A

2014-09-22

Water transport in edible films based on hydrophilic materials such as starch, is a complex phenomenon due to the strong interaction of sorbed water molecules with the polymeric structure. Cellulose nanocrystals (CNC) were obtained from sugarcane bagasse. Starch and starch/CNC films were formulated and their water barrier properties were studied. The measured film solubility, contact angle, and water sorption isotherm indicated that reinforced starch/CNC films have a lower affinity to water molecules than starch films. The effects that the driving force and the water activity (aw) values at each side of the film have on permeability were analyzed. Permeability, diffusivity, and solubility coefficients indicated that the permeation process depends mostly on the tortuous pathway formed by the incorporation of CNC and therefore were mainly controlled by water diffusion. The interaction between CNC and starch chain is favoured by the chemical similarities of both molecules. Copyright © 2014 Elsevier Ltd. All rights reserved.
Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

2015-02-01

Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.
Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Malek, Kourosh; Odijk, Theo; Coppens, Marc-Olivier

2005-07-01

The dynamics of water and sodium counter-ions (Na+) in a C2221 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm2 ns-1, when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.
Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide

DOE PAGES

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O.; ...

2015-11-03

We studied the dynamics of water in polyethylene oxide (PEO)/LiCl solution with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. Furthermore, the measured diffusion coefficient of interfacial water remained 5–10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li +. Detailed analysis of MD trajectories suggests that Li + is favorably found at the surface of the hydration layer, and the probability to find the caged Li + configuration formed by themore » PEO is lower than for the noncaged Li +-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li + hydration complexes. Moreover, performing the MD simulation with different ions (Na + and K +) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.« less
Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O.; Jalarvo, Niina H.; Hong, Kunlun; Han, Youngkyu; Smith, Gregory S.; Do, Changwoo

2015-11-01

The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li+ . Detailed analysis of MD trajectories suggests that Li+ is favorably found at the surface of the hydration layer, and the probability to find the caged Li+ configuration formed by the PEO is lower than for the noncaged Li+-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li+ hydration complexes. Performing the MD simulation with different ions (Na+ and K+ ) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.
Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide.

PubMed

Zhang, Zhe; Ohl, Michael; Diallo, Souleymane O; Jalarvo, Niina H; Hong, Kunlun; Han, Youngkyu; Smith, Gregory S; Do, Changwoo

2015-11-06

The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li(+). Detailed analysis of MD trajectories suggests that Li(+) is favorably found at the surface of the hydration layer, and the probability to find the caged Li(+) configuration formed by the PEO is lower than for the noncaged Li(+)-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li(+) hydration complexes. Performing the MD simulation with different ions (Na(+) and K(+)) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.
Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.
The bubble method of water purification

NASA Astrophysics Data System (ADS)

Smirnov, B. M.; Babaeva, N. Yu.; Naidis, G. V.; Panov, V. A.; Saveliev, A. S.; Son, E. E.; Tereshonok, D. V.

2018-02-01

The processes of water purification from admixture molecules are analyzed. The purification rate is limited due to a low diffusion coefficient of the admixture molecules in water. At non-small concentrations of the admixture molecules, the water purication can proceed through association of molecules in condensed nanoparticles which fall on the bottom of the water volume. The rate of association may be increased in an external electric field, but in reality this cannot change significantly the rate of the purification process. The bubble method of water purification is considered, where air bubbles formed at the bottom of the water volume, transfer admixture molecules to the interface. This method allows one to clean small water volumes fast. This mechanism of water purification is realized experimentally and exhibits the promises of the bubble purification method.
Dynamics of water in synthetic saponite clays: Effect of trivalent ion substitution

NASA Astrophysics Data System (ADS)

Mitra, S.; Prabhudesai, S. A.; Chakrabarty, D.; Sharma, V. K.; Vicente, M. A.; Embs, J. P.; Mukhopadhyay, R.

2013-06-01

Saponite clay belongs to the phyllosilicate family and is comprised of layers of Si(IV) tetrahedra and Al(III) or Mg(II) octahedra with definite interlayer spacing. In these systems, the trivalent ion substitutions in the tetrahedral layers lead to negative charge on the layers. Here we report the dynamics of water contained in [Si6.97Al1.03][Ni6.00]O20(OH)4[Na1.03]·28H2O (SAP-1) and [Si7.13Fe0.86][Ni6.00]O20(OH)4[Na0.86]·14H2O (SAP-2) saponite clays in the temperature range 200-310 K as studied by quasielastic neutron scattering technique. Particularly the effect of the ion substitution towards the dynamics of water is addressed here. Data analysis is carried out using the relaxing cage model. The existence of distribution in relaxation times indicated that the water molecules in saponite clay have a different local environment which leads to complex diffusion behavior. It is found that water exists in a supercooled state in the temperature range up to 235 K. However, some of the water molecules are found to be immobile in the temperature range 240-285 K. The fraction of immobile water decreases with increase in temperature. At higher temperatures, some of the water molecules in the hydration shells or those near the surface start participating in the diffusion process and at 293 K, almost all water molecules contribute to the dynamics. Diffusivity of water in both SAP-1 and SAP-2 are found to be lower in comparison to the bulk, and within the two samples of saponite clay diffusivity in SAP-1 is found to be lower compared to SAP-2; this has been explained on the basis of the charge on the tetrahedral layers and the charge balancing cations in the interlayer spacing.
Physics, Techniques and Review of Neuroradiological Applications of Diffusion Kurtosis Imaging (DKI).

PubMed

Marrale, M; Collura, G; Brai, M; Toschi, N; Midiri, F; La Tona, G; Lo Casto, A; Gagliardo, C

2016-12-01

In recent years many papers about diagnostic applications of diffusion tensor imaging (DTI) have been published. This is because DTI allows to evaluate in vivo and in a non-invasive way the process of diffusion of water molecules in biological tissues. However, the simplified description of the diffusion process assumed in DTI does not permit to completely map the complex underlying cellular components and structures, which hinder and restrict the diffusion of water molecules. These limitations can be partially overcome by means of diffusion kurtosis imaging (DKI). The aim of this paper is the description of the theory of DKI, a new topic of growing interest in radiology. DKI is a higher order diffusion model that is a straightforward extension of the DTI model. Here, we analyze the physics underlying this method, we report our MRI acquisition protocol with the preprocessing pipeline used and the DKI parametric maps obtained on a 1.5 T scanner, and we review the most relevant clinical applications of this technique in various neurological diseases.
Laser absorption spectroscopy of water vapor confined in nanoporous alumina: wall collision line broadening and gas diffusion dynamics.

PubMed

Svensson, Tomas; Lewander, Märta; Svanberg, Sune

2010-08-02

We demonstrate high-resolution tunable diode laser absorption spectroscopy (TDLAS) of water vapor confined in nanoporous alumina. Strong multiple light scattering results in long photon pathlengths (1 m through a 6 mm sample). We report on strong line broadening due to frequent wall collisions (gas-surface interactions). For the water vapor line at 935.685 nm, the HWHM of confined molecules are about 4.3 GHz as compared to 2.9 GHz for free molecules (atmospheric pressure). Gas diffusion is also investigated, and in contrast to molecular oxygen (that moves rapidly in and out of the alumina), the exchange of water vapor is found very slow.
Dynamics of two-dimensional monolayer water confined in hydrophobic and charged environments.

PubMed

Kumar, Pradeep; Han, Sungho

2012-09-21

We perform molecular dynamics simulations to study the effect of charged surfaces on the intermediate and long time dynamics of water in nanoconfinements. Here, we use the transferable interaction potential with five points (TIP5P) model of a water molecule confined in both hydrophobic and charged surfaces. For a single molecular layer of water between the surfaces, we find that the temperature dependence of the lateral diffusion constant of water up to very high temperatures remains Arrhenius with a high activation energy. In case of charged surfaces, however, the dynamics of water in the intermediate time regime is drastically modified presumably due to the transient coupling of dipoles of water molecules with electric field fluctuations induced by charges on the confining surfaces. Specifically, the lateral mean square displacements display a distinct super-diffusive behavior at intermediate time scale, defined as the time scale between ballistic and diffusive regimes. This change in the intermediate time-scale dynamics in the charged confinement leads to the enhancement of long-time dynamics as reflected in increasing diffusion constant. We introduce a simple model for a possible explanation of the super-diffusive behavior and find it to be in good agreement with our simulation results. Furthermore, we find that confinement and the surface polarity enhance the low frequency vibration in confinement compared to bulk water. By introducing a new effective length scale of coupling between translational and orientational motions, we find that the length scale increases with the increasing strength of the surface polarity. Further, we calculate the correlation between the diffusion constant and the excess entropy and find a disordering effect of polar surfaces on the structure of water. Finally, we find that the empirical relation between the diffusion constant and the excess entropy holds for a monolayer of water in nanoconfinement.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G.; Institute of Chemical Engineering and High Temperature Chemical Processes, GR 26500 Patras

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrixmore » and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D{sub eff}, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D{sub eff} is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D{sub eff} as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D{sub eff} (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.« less
Water imbibition by mica pores: what happens when capillary flow is suppressed?

NASA Astrophysics Data System (ADS)

Fang, Chao; Qiao, Rui

2017-11-01

The imbibition of liquids into porous media plays a critical role in numerous applications. Most prior studies focused on imbibition driven by capillary flows. In this work, we study the imbibition of water into slit-shaped mica pores filled with pressurized methane using molecular simulations. Despite that capillary flow is suppressed by the high gas pressure, water is imbibed into the pore as monolayer liquid films. Since the classical hydrodynamic flow is not readily applicable for the monolayer water film propagating on the mica wall and the imbibition is driven by the strong affinity of water molecules to the mica walls, the observed imbibition is best taken as surface hydration. We show that the dynamics of water's imbibition front follows a simple diffusive scaling law. The effective diffusion coefficient of the imbibition front, however, is more than ten times larger than the diffusion coefficient of the water molecules in the water film adsorbed on the mica walls. Using a molecular theory originally developed for the spreading of monolayer films on solid substrates, we clarify the mechanism underlying the rapid water imbibition observed here.
Tracing compartment exchange by NMR diffusometry: Water in lithium-exchanged low-silica X zeolites

NASA Astrophysics Data System (ADS)

Lauerer, A.; Kurzhals, R.; Toufar, H.; Freude, D.; Kärger, J.

2018-04-01

The two-region model for analyzing signal attenuation in pulsed field gradient (PFG) NMR diffusion studies with molecules in compartmented media implies that, on their trajectory, molecules get from one region (one type of compartment) into the other one with a constant (i.e. a time-invariant) probability. This pattern has proved to serve as a good approach for considering guest diffusion in beds of nanoporous host materials, with the two regions ("compartments") identified as the intra- and intercrystalline pore spaces. It is obvious, however, that the requirements of the application of the two-region model are not strictly fulfilled given the correlation between the covered diffusion path lengths in the intracrystalline pore space and the probability of molecular "escape" from the individual crystallites. On considering water diffusion in lithium-exchanged low-silica X zeolite, we are now assuming a different position since this type of material is known to offer "traps" in the trajectories of the water molecules. Now, on attributing the water molecules in the traps and outside of the traps to these two types of regions, we perfectly comply with the requirements of the two-region model. We do, moreover, benefit from the option of high-resolution measurements owing to the combination of magic angle spinning (MAS) with PFG NMR. Data analysis via the two-region model under inclusion of the influence of nuclear magnetic relaxation yields satisfactory agreement between experimental evidence and theoretical estimates. Limitations in accuracy are shown to result from the fact that mass transfer outside of the traps is too complicated for being adequately reflected by simple Fick's laws with but one diffusivity.
Influence of humidity on performance and microscopic dynamics of an ionic liquid in supercapacitor

NASA Astrophysics Data System (ADS)

Osti, Naresh C.; Dyatkin, Boris; Thompson, Matthew W.; Tiet, Felix; Zhang, Pengfei; Dai, Sheng; Tyagi, Madhusudan; Cummings, Peter T.; Gogotsi, Yury; Wesolowski, David J.; Mamontov, Eugene

2017-08-01

We investigated the influence of water molecules on the diffusion, dynamics, and electrosorption of a room temperature ionic liquid (RTIL), [BMI m+] [T f2N-] , confined in carbide-derived carbon with a bimodal nanoporosity. Water molecules in pores improved power densities and rate handling abilities of these materials in supercapacitor electrode configurations. We measured the water-dependent microscopic dynamics of the RTIL cations using quasielastic neutron scatting (QENS). The ionic liquid demonstrated greater mobility with increasing water uptake, facilitated by the nanoporous carbon environment, up to a well-defined saturation point. We concluded that water molecules displaced RTIL ions attached to the pore surfaces and improved the diffusivity of the displaced cations. This effect consequently increased capacitance and rate handling of the electrolyte in water-containing pores. Our findings suggest the possible effect of immiscible co-solvents on energy and power densities of energy storage devices, as well as the operating viability of nonaqueous supercapacitor electrolytes in humid environments.
[See the thinking brain: a story about water].

PubMed

Le Bihan, D

2008-01-01

Among the astonishing Einstein's papers from 1905, there is one which unexpectedly gave birth to a powerful method to explore the brain. Molecular diffusion was explained by Einstein on the basis of the random translational motion of molecules which results from their thermal energy. In the mid 1980s it was shown that water diffusion in the brain could be imaged using MRI. During their random displacements water molecules probe tissue structure at a microscopic scale, interacting with cell membranes and, thus, providing unique information on the functional architecture of tissues. A dramatic application of diffusion MRI has been brain ischemia, following the discovery that water diffusion drops immediately after the onset of an ischemic event, when brain cells undergo swelling through cytotoxic edema. On the other hand, water diffusion is anisotropic in white matter, because axon membranes limit molecular movement perpendicularly to the fibers. This feature can be exploited to map out the orientation in space of the white matter tracks and image brain connections. More recently, it has been shown that diffusion MRI could accurately detect cortical activation. As the diffusion response precedes by several seconds the hemodynamic response captured by BOLD fMRI, it has been suggested that water diffusion could reflect early neuronal events, such as the transient swelling of activated cortical cells. If confirmed, this discovery will represent a significant breakthrough, allowing non invasive access to a direct physiological marker of brain activation. This approach will bridge the gap between invasive optical imaging techniques in neuronal cell cultures, and current functional neuroimaging approaches in humans, which are based on indirect and remote blood flow changes.
Diffusion of biomass pyrolysis products in H-ZSM-5 by molecular dynamics simulations

DOE PAGES

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; ...

2016-12-13

Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5more » zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p-xylene: o-xylene: m-xylene ≈ 83:3:1 at 700 K. Furthermore, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.« less
Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

PubMed

Choudhuri, Jyoti Roy; Chandra, Amalendu

2014-10-07

We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.
Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

USDA-ARS?s Scientific Manuscript database

Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

Diffusion MRI at 25: Exploring brain tissue structure and function

PubMed Central

Bihan, Denis Le; Johansen-Berg, Heidi

2013-01-01

Diffusion MRI (or dMRI) came into existence in the mid-1980s. During the last 25 years, diffusion MRI has been extraordinarily successful (with more than 300,000 entries on Google Scholar for diffusion MRI). Its main clinical domain of application has been neurological disorders, especially for the management of patients with acute stroke. It is also rapidly becoming a standard for white matter disorders, as diffusion tensor imaging (DTI) can reveal abnormalities in white matter fiber structure and provide outstanding maps of brain connectivity. The ability to visualize anatomical connections between different parts of the brain, non-invasively and on an individual basis, has emerged as a major breakthrough for neurosciences. The driving force of dMRI is to monitor microscopic, natural displacements of water molecules that occur in brain tissues as part of the physical diffusion process. Water molecules are thus used as a probe that can reveal microscopic details about tissue architecture, either normal or in a diseased state. PMID:22120012
Diffusion coefficients of nitric oxide in water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pokharel, Sunil; Pantha, Nurapati; Adhikari, N. P.

2016-09-01

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute-solute, solute-solvent and solvent-solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.
Diffusion coefficients in organic-water solutions and comparison with Stokes-Einstein predictions

NASA Astrophysics Data System (ADS)

Evoy, E.; Kamal, S.; Bertram, A. K.

2017-12-01

Diffusion coefficients of organic species in particles containing secondary organic material (SOM) are necessary for predicting the growth and reactivity of these particles in the atmosphere. Previously, the Stokes-Einstein equation combined with viscosity measurements have been used to predict these diffusion coefficients. However, the accuracy of the Stokes-Einstein equation for predicting diffusion coefficients in SOM-water particles has not been quantified. To test the Stokes-Einstein equation, diffusion coefficients of fluorescent organic probe molecules were measured in citric acid-water and sorbitol-water solutions. These solutions were used as proxies for SOM-water particles found in the atmosphere. Measurements were performed as a function of water activity, ranging from 0.26-0.86, and as a function of viscosity ranging from 10-3 to 103 Pa s. Diffusion coefficients were measured using fluorescence recovery after photobleaching. The measured diffusion coefficients were compared with predictions made using the Stokes-Einstein equation combined with literature viscosity data. Within the uncertainties of the measurements, the measured diffusion coefficients agreed with the predicted diffusion coefficients, in all cases.
Water Dynamics in Nafion Fuel Cell Membranes: the Effects of Confinement and Structural Changes on the Hydrogen Bond Network

PubMed Central

Moilanen, David E.; Piletic, Ivan R.; Fayer, Michael D.

2008-01-01

The complex environments experienced by water molecules in the hydrophilic channels of Nafion membranes are studied by ultrafast infrared pump-probe spectroscopy. A wavelength dependent study of the vibrational lifetime of the O-D stretch of dilute HOD in H2O confined in Nafion membranes provides evidence of two distinct ensembles of water molecules. While only two ensembles are present at each level of membrane hydration studied, the characteristics of the two ensembles change as the water content of the membrane changes. Time dependent anisotropy measurements show that the orientational motions of water molecules in Nafion membranes are significantly slower than in bulk water and that lower hydration levels result in slower orientational relaxation. Initial wavelength dependent results for the anisotropy show no clear variation in the time scale for orientational motion across a broad range of frequencies. The anisotropy decay is analyzed using a model based on restricted orientational diffusion within a hydrogen bond configuration followed by total reorientation through jump diffusion. PMID:18728757
Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and (13)C NMR Spectroscopy.

PubMed

Bonhommeau, David A; Perret, Alexandre; Nuzillard, Jean-Marc; Cilindre, Clara; Cours, Thibaud; Alijah, Alexander; Liger-Belair, Gérard

2014-12-18

The diffusion coefficients of carbon dioxide (CO2) and ethanol (EtOH) in carbonated hydroalcoholic solutions and Champagne wines are evaluated as a function of temperature by classical molecular dynamics (MD) simulations and (13)C NMR spectroscopy measurements. The excellent agreement between theoretical and experimental diffusion coefficients suggest that ethanol is the main molecule, apart from water, responsible for the value of the CO2 diffusion coefficients in typical Champagne wines, a result that could likely be extended to most sparkling wines with alike ethanol concentrations. CO2 and EtOH hydrodynamical radii deduced from viscometry measurements by applying the Stokes-Einstein relationship are found to be mostly constant and in close agreement with MD predictions. The reliability of our approach should be of interest to physical chemists aiming to model transport phenomena in supersaturated aqueous solutions or water/alcohol mixtures.
Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

2013-08-01

In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.
Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

PubMed

Liu, Liyan; Zhang, Ruifeng; Liu, Ying; Tan, Wei; Zhu, Guorui

2018-05-28

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.
Is the wall of a cellulose fiber saturated with liquid whether or not permeable with CO2 dissolved molecules? Application to bubble nucleation in champagne wines.

PubMed

Liger-Belair, Gérard; Topgaard, Daniel; Voisin, Cédric; Jeandet, Philippe

2004-05-11

In this paper, the transversal diffusion coefficient D perpendicular of CO2 dissolved molecules through the wall of a hydrated cellulose fiber was approached, from the liquid bulk diffusion coefficient of CO2 dissolved molecules modified by an obstruction factor. The porous network between the cellulose microfibrils of the fiber wall was assumed being saturated with liquid. We retrieved information from previous NMR experiments on the self-diffusion of water in cellulose fibers to reach an order of magnitude for the transversal diffusion coefficient of CO2 molecules through the fiber wall. A value of about D perpendicular approximately 0.2D0 was proposed, D0 being the diffusion coefficient of CO2 molecules in the liquid bulk. Because most of bubble nucleation sites in a glass poured with carbonated beverage are cellulose fibers cast off from paper or cloth which floated from the surrounding air, or remaining from the wiping process, this result directly applies to the kinetics of carbon dioxide bubble formation from champagne and sparkling wines. If the cellulose fiber wall was impermeable with regard to CO2 dissolved molecules, it was suggested that the kinetics of bubbling would be about three times less than it is.
The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions

NASA Astrophysics Data System (ADS)

Nguyen, Mary; Rick, Steven W.

2018-06-01

The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.
Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.
Water-Mediated Proton Hopping on an Iron Oxide Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merte, L. R.; Peng, Guowen; Bechstein, Ralf

2012-05-18

The diffusion of hydrogen atoms across solid oxide surfaces is often assumed to be accelerated by the presence of water molecules. Here we present a high-resolution, high-speed scanning tunneling microscopy (STM) study of the diffusion of H atoms on an FeO thin film. STM movies directly reveal a water-mediated hydrogen diffusion mechanism on the oxide surface at temperatures between 100 and 300 kelvin. Density functional theory calculations and isotope-exchange experiments confirm the STM observations, and a proton-transfer mechanism that proceeds via an H3O+-like transition state is revealed. This mechanism differs from that observed previously for rutile TiO2(110), where water dissociationmore » is a key step in proton diffusion.« less
Thermodynamic properties and diffusion of water + methane binary mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

2014-03-14

Thermodynamic and diffusion properties of water + methane mixtures in a single liquid phase are studied using NVT molecular dynamics. An extensive comparison is reported for the thermal pressure coefficient, compressibilities, expansion coefficients, heat capacities, Joule-Thomson coefficient, zero frequency speed of sound, and diffusion coefficient at methane concentrations up to 15% in the temperature range of 298–650 K. The simulations reveal a complex concentration dependence of the thermodynamic properties of water + methane mixtures. The compressibilities, heat capacities, and diffusion coefficients decrease with increasing methane concentration, whereas values of the thermal expansion coefficients and speed of sound increase. Increasing methanemore » concentration considerably retards the self-diffusion of both water and methane in the mixture. These effects are caused by changes in hydrogen bond network, solvation shell structure, and dynamics of water molecules induced by the solvation of methane at constant volume conditions.« less
Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rønnest, A. K.; Peters, G. H.; Hansen, F. Y., E-mail: flemming@kemi.dtu.dk

2016-04-14

Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for allmore » water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 10{sup 8}–10{sup 9} V m{sup −1}, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ∼1 V (∼2 ⋅ 10{sup 8} V m{sup −1}) when in the fluid phase with a monovalent counter-ion and ∼1.4 V (∼2.8 ⋅ 10{sup 8} V m{sup −1}) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) membranes but comparable to the number inferred for 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) membranes. Some of the properties of the DMPG membrane are compared with those of the neutral zwitterionic DMPC bilayer membrane at 303 K and 1 atm, which is the same reduced temperature with respect to the gel-to-fluid transition temperature as 310 K is for the DMPG bilayer membrane.« less
Structure and Dynamics of Confined Alcohol-Water Mixtures.

PubMed

Bampoulis, Pantelis; Witteveen, Jorn P; Kooij, E Stefan; Lohse, Detlef; Poelsema, Bene; Zandvliet, Harold J W

2016-07-26

The effect of confinement between mica and graphene on the structure and dynamics of alcohol-water mixtures has been studied in situ and in real time at the molecular level by atomic force microscopy (AFM) at room temperature. AFM images reveal that the adsorbed molecules are segregated into faceted alcohol-rich islands on top of an ice layer on mica, surrounded by a pre-existing multilayer water-rich film. These faceted islands are in direct contact with the graphene surface, revealing a preferred adsorption site. Moreover, alcohol adsorption at low relative humidity (RH) reveals a strong preference of the alcohol molecules for the ordered ice interface. The growth dynamics of the alcohol islands is governed by supersaturation, temperature, the free energy of attachment of molecules to the island edge and two-dimensional (2D) diffusion. The measured diffusion coefficients display a size dependence on the molecular size of the alcohols, and are about 6 orders of magnitude smaller than the bulk diffusion coefficients, demonstrating the effect of confinement on the behavior of the alcohols. These experimental results provide new insights into the behavior of multicomponent fluids in confined geometries, which is of paramount importance in nanofluidics and biology.
Dynamics of Phenanthrenequinone on Carbon Nano-Onion Surfaces Probed by Quasielastic Neutron Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anjos, Daniela M; Mamontov, Eugene; Brown, Gilbert M

We used quasielastic neutron scattering (QENS) to study the dynamics of phenanthrenequinone (PQ) on the surface of onion-like carbon (OLC), or so called carbon onions, as a function of surface coverage and temperature. For both the high- and low-coverage samples, we observed two diffusion processes; a faster process and nearly an order of magnitude slower process. On the high-coverage surface, the slow diffusion process is of long-range translational character, whereas the fast diffusion process is spatially localized on the length scale of ~ 4.7 . On the low-coverage surface, both diffusion processes are spatially localized; on the same length scalemore » of ~ 4.7 for the fast diffusion and a somewhat larger length scale for the slow diffusion. Arrhenius temperature dependence is observed except for the long-range diffusion on the high-coverage surface. We attribute the fast diffusion process to the generic localized in-cage dynamics of PQ molecules, and the slow diffusion process to the long-range translational dynamics of PQ molecules, which, depending on the coverage, may be either spatially restricted, or long-range. On the low-coverage surface, uniform surface coverage is not attained, and the PQ molecules experience the effect of spatial constraints on their long-range translational dynamics. Unexpectedly, the dynamics of PQ molecules on OLC as a function of temperature and surface coverage bears qualitative resemblance to the dynamics of water molecules on oxide surfaces, including practically temperature-independent residence times for the low-coverage surface. The dynamics features that we observed may be universal across different classes of surface adsorbates.« less
Molecular dynamics simulations reveal that water diffusion between graphene oxide layers is slow

DOE PAGES

Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; ...

2016-07-08

Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in spacing from about 0.7 nm to 0.8 nm and an increase in mass ofmore » about 14% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. As a result, slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.« less
Kinetic Monte Carlo simulations of water ice porosity: extrapolations of deposition parameters from the laboratory to interstellar space.

PubMed

Clements, Aspen R; Berk, Brandon; Cooke, Ilsa R; Garrod, Robin T

2018-02-21

Dust grains in cold, dense interstellar clouds build up appreciable ice mantles through the accretion and subsequent surface chemistry of atoms and molecules from the gas. These mantles, of thicknesses on the order of 100 monolayers, are primarily composed of H 2 O, CO, and CO 2 . Laboratory experiments using interstellar ice analogues have shown that porosity could be present and can facilitate diffusion of molecules along the inner pore surfaces. However, the movement of molecules within and upon the ice is poorly described by current chemical kinetics models, making it difficult either to reproduce the formation of experimental porous ice structures or to extrapolate generalized laboratory results to interstellar conditions. Here we use the off-lattice Monte Carlo kinetics model MIMICK to investigate the effects that various deposition parameters have on laboratory ice structures. The model treats molecules as isotropic spheres of a uniform size, using a Lennard-Jones potential. We reproduce experimental trends in the density of amorphous solid water (ASW) for varied deposition angle, rate and surface temperature; ice density decreases when the incident angle or deposition rate is increased, while increasing temperature results in a more-compact water ice. The models indicate that the density behaviour at higher temperatures (≥80 K) is dependent on molecular rearrangement resulting from thermal diffusion. To reproduce trends at lower temperatures, it is necessary to take account of non-thermal diffusion by newly-adsorbed molecules, which bring kinetic energy both from the gas phase and from their acceleration into a surface binding site. Extrapolation of the model to conditions appropriate to protoplanetary disks, in which direct accretion of water from the gas-phase may be the dominant ice formation mechanism, indicate that these ices may be less porous than laboratory ices.
Diffusion of water in the endosperm tissue of wheat grains as studied by pulsed field gradient nuclear magnetic resonance.

PubMed

Callaghan, P T; Jolley, K W; Lelievre, J

1979-10-01

Pulsed field gradient nuclear magnetic resonance has been used to measure water self-diffusion coefficients in the endosperm tissue of wheat grains as a function of the tissue water content. A model that confines the water molecules to a randomly oriented array of capillaries with both transverse dimension less than 100 nm has been used to fit the data and give a unique diffusion coefficient at each water content. The diffusion rates vary from 1.8 x 10(-10) m2s-1 at the lowest to 1.2 x 10(-9) m2s-1 at the highest moisture content. This variation can be explained in terms of an increase in water film thickness from approximately 0.5 to approximately 2.5 nm over the moisture range investigated (200-360 mg g-1).
Generation of various radicals in nitrogen plasma and their behavior in media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uhm, Han S., E-mail: hsuhm@kw.ac.kr

2015-12-15

Research on the generation of radicals in nitrogen plasma shows that the most dominant radicals are excited nitrogen molecules in the metastable state of N{sub 2}(A{sub 3}∑{sub u}{sup +}). Hydroxyl molecules are generated from the dissociation of water molecules upon contact with excited nitrogen molecules. The estimated densities of various radicals in nitrogen plasma with an electron temperature of 1 eV are presented in this study. The behavior of these radicals in media is also investigated. Excited nitrogen molecules in the N{sub 2}(A{sub 3}∑{sub u}{sup +}) state from a plasma jet are injected into water, after which the molecules disappear instantaneouslymore » within a few tens of nm, producing hydroxyl molecules. Hydrogen peroxide, hydrogen dioxide, and nitrogen monoxide molecules can diffuse much deeper into water, implying the possibility that a chemical reaction between hydrogen dioxide and nitrogen monoxide molecules produces hydroxyl molecules in deep water, even though density in this case may not be very high.« less
Sucrose diffusion in aqueous solution

PubMed Central

Murray, Benjamin J.

2016-01-01

The diffusion of sugar in aqueous solution is important both in nature and in technological applications, yet measurements of diffusion coefficients at low water content are scarce. We report directly measured sucrose diffusion coefficients in aqueous solution. Our technique utilises a Raman isotope tracer method to monitor the diffusion of non-deuterated and deuterated sucrose across a boundary between the two aqueous solutions. At a water activity of 0.4 (equivalent to 90 wt% sucrose) at room temperature, the diffusion coefficient of sucrose was determined to be approximately four orders of magnitude smaller than that of water in the same material. Using literature viscosity data, we show that, although inappropriate for the prediction of water diffusion, the Stokes–Einstein equation works well for predicting sucrose diffusion under the conditions studied. As well as providing information of importance to the fundamental understanding of diffusion in binary solutions, these data have technological, pharmaceutical and medical implications, for example in cryopreservation. Moreover, in the atmosphere, slow organic diffusion may have important implications for aerosol growth, chemistry and evaporation, where processes may be limited by the inability of a molecule to diffuse between the bulk and the surface of a particle. PMID:27364512

Kinetics and equilibrium of solute diffusion into human hair.

PubMed

Wang, Liming; Chen, Longjian; Han, Lujia; Lian, Guoping

2012-12-01

The uptake kinetics of five molecules by hair has been measured and the effects of pH and physical chemical properties of molecules were investigated. A theoretical model is proposed to analyze the experimental data. The results indicate that the binding affinity of solute to hair, as characterized by hair-water partition coefficient, scales to the hydrophobicity of the solute and decreases dramatically as the pH increases to the dissociation constant. The effective diffusion coefficient of solute depended not only on the molecular size as most previous studies suggested, but also on the binding affinity as well as solute dissociation. It appears that the uptake of molecules by hair is due to both hydrophobic interaction and ionic charge interaction. Based on theoretical considerations of the cellular structure, composition and physical chemical properties of hair, quantitative-structure-property-relationships (QSPR) have been proposed to predict the hair-water partition coefficient (PC) and the effective diffusion coefficient (D (e)) of solute. The proposed QSPR models fit well with the experimental data. This paper could be taken as a reference for investigating the adsorption properties for polymeric materials, fibres, and biomaterials.
Pectins filled with LDH-antimicrobial molecules: preparation, characterization and physical properties.

PubMed

Gorrasi, Giuliana; Bugatti, Valeria; Vittoria, Vittoria

2012-06-05

Nanohybrids of layered double hydroxide (LDH) with intercalated active molecules: benzoate, 2,4-dichlorobenzoate, para-hydroxybenzoate and ortho-hydroxybenzoate, were incorporated into pectins from apples through high energy ball milling in the presence of water. Cast films were obtained and analysed. X-ray diffraction analysis showed a complete destructuration of all nanohybrids in the pectin matrix. Thermogravimetric analysis showed a better thermal resistance of pectin in the presence of fillers, especially para-hydroxybenzoate and ortho-hydroxybenzoate. Mechanical properties showed an improvement of elastic modulus in particular for LDH-para-hydroxybenzoate nanohybrid, due probably to a better interaction between pectin matrix and nanohybrid layers. Barrier properties (sorption and diffusion) to water vapour showed improvement in the dependence on the intercalated active molecule, the best improvement was achieved for composites containing para-hydroxybenzoate molecules, suggesting that the interaction between the filler phase and the polymer plays an important role in sorption and diffusion phenomena. Incorporation of these active molecules gave antimicrobial properties to the composite films giving opportunities in the field of active packaging. Copyright © 2012 Elsevier Ltd. All rights reserved.
Anomalous Diffusion of Water in Lamellar Membranes Formed by Pluronic Polymers

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Ohl, Michael; Han, Youngkyu; Smith, Gregory; Do, Changwoo; Biology; Soft-Matter Division, Oak Ridge National Laboratory Team; Julich CenterNeutron Science Team

Water diffusion is playing an important role in polymer systems. We calculated the water diffusion coefficient at different layers along z-direction which is perpendicular to the lamellar membrane formed by Pluronic block copolymers (L62: (EO6-PO34-EO6)) with the molecular dynamics simulation trajectories. Water molecules at bulk layers are following the normal diffusion, while that at hydration layers formed by polyethylene oxide (PEO) and hydrophobic layers formed by polypropylene oxide (PPO) are following anomalous diffusion. We find that although the subdiffusive regimes at PEO layers and PPO layers are the same, which is the fractional Brownian motion, however, the dynamics are different, i.e. diffusion at the PEO layers is much faster than that at the PPO layers, and meanwhile it exhibits a normal diffusive approximation within a short time period which is governed by the localized free self-diffusion, but becomes subdiffusive after t >8 ps, which is governed by the viscoelastic medium. The Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy; and Zhe Zhang gratefully acknowledges financial support from Julich Center for Neutron Science.
Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.
Development and application of an exchange model for anisotropic water diffusion in the microporous MOF aluminum fumarate

NASA Astrophysics Data System (ADS)

Splith, Tobias; Fröhlich, Dominik; Henninger, Stefan K.; Stallmach, Frank

2018-06-01

Diffusion of water in aluminum fumarate was studied by means of pulsed field gradient (PFG) nuclear magnetic resonance (NMR). Due to water molecules exchanging between the intracrystalline anisotropic pore space and the isotropic intercrystalline void space the model of intracrystalline anisotropic diffusion fails to describe the experimental PFG NMR data at high observation times. Therefore, the two-site exchange model developed by Kärger is extended to the case of exchange between an anisotropic and an isotropic site. This extended exchange model is solved by numerical integration. It describes the experimental data very well and yields values for the intracrystalline diffusion coefficient and the mean residence times of the respective sites. Further PFG NMR studies were performed with coatings consisting of small aluminum fumarate crystals, which are used in adsorptive heat transformation applications. The diffusion coefficients of water in the small crystal coating are compared to the values expected from the extended two-site exchange model and from the model of long-range diffusion.
Defusing Diffusion

ERIC Educational Resources Information Center

Dou, Remy; Hogan, DaNel; Kossover, Mark; Spuck, Timothy; Young, Sarah

2013-01-01

Diffusion has often been taught in science courses as one of the primary ways by which molecules travel, particularly within organisms. For years, classroom teachers have used the same common demonstrations to illustrate this concept (e.g., placing drops of food coloring in a beaker of water). Most of the time, the main contributor to the motion…
Diffusion-weighted magnetic resonance imaging reveals the effects of different cooling temperatures on the diffusion of water molecules and perfusion within human skeletal muscle.

PubMed

Yanagisawa, O; Fukubayashi, T

2010-11-01

To evaluate the effect of local cooling on the diffusion of water molecules and perfusion within muscle at different cooling temperatures. Magnetic resonance diffusion-weighted (DW) images of the leg (seven males) were obtained before and after 30 min cooling (0, 10, and 20°C), and after a 30 min recovery period. Two types of apparent diffusion coefficient (ADC; ADC1, reflecting both water diffusion and perfusion within muscle, and ADC2, approximating the true water diffusion coefficient) of the ankle dorsiflexors were calculated from DW images. T2-weighted images were also obtained to calculate T2 values of the ankle dorsiflexors. The skin temperature was measured before, during, and after cooling. Both ADC values significantly decreased after cooling under all cooling conditions; the rate of decrease depended on the cooling temperature used (ADC1: -36% at 0°C, -27.8% at 10°C, and -22.6% at 20°C; ADC2: -26% at 0°C, -21.1% at 10°C, and -14.6% at 20°C). These significant decreases were maintained during the recovery period. Conversely, the T2 value showed no significant changes. Under all cooling conditions, skin temperature significantly decreased during cooling; the rate of decrease depended on the cooling temperature used (-74.8% at 0°C, -51.1% at 10°C, and -26.8% at 20°C). Decreased skin temperatures were not restored to pre-cooling values during the recovery period under any cooling conditions. Local cooling decreased the water diffusion and perfusion within muscle with decreased skin temperature; the rates of decrease depended on the cooling temperature used. These decreases were maintained for 30 min after cooling. Copyright © 2010 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.
Climate change and cutaneous water loss of birds.

PubMed

Williams, Joseph B; Muñoz-Garcia, Agustí; Champagne, Alex

2012-04-01

There is a crucial need to understand how physiological systems of animals will respond to increases in global air temperature. Water conservation may become more important for some species of birds, especially those living in deserts. Lipids of the stratum corneum (SC), the outer layer of the epidermis, create the barrier to water vapor diffusion, and thus control cutaneous water loss (CWL). An appreciation of the ability of birds to change CWL by altering lipids of the skin will be important to predict responses of birds to global warming. The interactions of these lipids are fundamental to the modulation of water loss through skin. Cerebrosides, with their hexose sugar moiety, are a key component of the SC in birds, but how these lipids interact with other lipids of the SC, or how they form hydrogen bonds with water molecules, to form a barrier to water vapor diffusion remains unknown. An understanding of how cerebrosides interact with other lipids of the SC, and of how the hydroxyl groups of cerebrosides interact with water molecules, may be a key to elucidating the control of CWL by the SC.
Understanding of Relationship between Phospholipid Membrane Permeability and Self-Diffusion Coefficients of Some Drugs and Biologically Active Compounds in Model Solvents.

PubMed

Blokhina, Svetlana V; Volkova, Tatyana V; Golubev, Vasiliy A; Perlovich, German L

2017-10-02

In this work we measured self-diffusion coefficients of 5 drugs (aspirin, caffeine, ethionamide, salicylic acid, and paracetamol) and 11 biologically active compounds of similar structure in deuterated water and 1-octanol by NMR. It has been found that an increase in the van der Waals volume of the molecules of the studied substances result in reduction of their diffusion mobility in both solvents. The analysis of the experimental data showed the influence of chemical nature and structural isomerization of the molecules on the diffusion mobility. Apparent permeability coefficients of the studied compounds were determined using an artificial phospholipid membrane made of egg lecithin as a model of in vivo absorption. Distribution coefficients in 1-octanol/buffer pH 7.4 system were measured. For the first time the model of the passive diffusion through the phospholipid membrane was validated based on the experimental data. To this end, the passive diffusion was considered as an additive process of molecule passage through the aqueous boundary layer before the membrane and 1-octanol barrier simulating the lipid layer of the membrane.
Water dynamics in hardened ordinary Portland cement paste or concrete: from quasielastic neutron scattering.

PubMed

Bordallo, Heloisa N; Aldridge, Laurence P; Desmedt, Arnaud

2006-09-14

Portland cement reacts with water to form an amorphous paste through a chemical reaction called hydration. In concrete the formation of pastes causes the mix to harden and gain strength to form a rock-like mass. Within this process lies the key to a remarkable peculiarity of concrete: it is plastic and soft when newly mixed, strong and durable when hardened. These qualities explain why one material, concrete, can build skyscrapers, bridges, sidewalks and superhighways, houses, and dams. The character of the concrete is determined by the quality of the paste. Creep and shrinkage of concrete specimens occur during the loss and gain of water from cement paste. To better understand the role of water in mature concrete, a series of quasielastic neutron scattering (QENS) experiments were carried out on cement pastes with water/cement ratio varying between 0.32 and 0.6. The samples were cured for about 28 days in sealed containers so that the initial water content would not change. These experiments were carried out with an actual sample of Portland cement rather than with the components of cement studied by other workers. The QENS spectra differentiated between three different water interactions: water that was chemically bound into the cement paste, the physically bound or "glassy water" that interacted with the surface of the gel pores in the paste, and unbound water molecules that are confined within the larger capillary pores of cement paste. The dynamics of the "glassy" and "unboud" water in an extended time scale, from a hundred picoseconds to a few nanoseconds, could be clearly differentiated from the data. While the observed motions on the picosecond time scale are mainly stochastic reorientations of the water molecules, the dynamics observed on the nanosecond range can be attributed to long-range diffusion. Diffusive motion was characterized by diffusion constants in the range of (0.6-2) 10(-9) m(2)/s, with significant reduction compared to the rate of diffusion for bulk water. This reduction of the water diffusion is discussed in terms of the interaction of the water with the calcium silicate gel and the ions present in the pore water.
Water Diffusion through a Titanium Dioxide/Poly(Carbonate Urethane) Nanocomposite for Protecting Cultural Heritage: Interactions and Viscoelastic Behavior

PubMed Central

Abbate, Mario; D’Orazio, Loredana

2017-01-01

Water diffusion through a TiO2/poly (carbonate urethane) nanocomposite designed for the eco-sustainable protection of outdoor cultural heritage stonework was investigated. Water is recognized as a threat to heritage, hence the aim was to gather information on the amount of water uptake, as well as of species of water molecules absorbed within the polymer matrix. Gravimetric and vibrational spectroscopy measurements demonstrated that diffusion behavior of the nanocomposite/water system is Fickian, i.e., diffusivity is independent of concentration. The addition of only 1% of TiO2 nanoparticles strongly betters PU barrier properties and water-repellency requirement is imparted. Defensive action against penetration of water free from, and bonded through, H-bonding association arises from balance among TiO2 hydrophilicity, tortuosity effects and quality of nanoparticle dispersion and interfacial interactions. Further beneficial to antisoiling/antigraffiti action is that water-free fraction was found to be desorbed at a constant rate. In environmental conditions, under which weathering processes are most likely to occur, nanocomposite Tg values remain suitable for heritage treatments. PMID:28902179
Anomalous cation diffusion in salt-doped confined bilayer ice.

PubMed

Qiu, Hu; Xue, Minmin; Shen, Chun; Guo, Wanlin

2018-05-17

The diffusive dynamics of aqueous electrolyte solutions in nanoconfined spaces has attracted considerable attention due to their potential applications in desalination, biosensors and supercapacitors. Here we show by molecular dynamics simulations that lithium and sodium ions diffuse at a rate at least an order of magnitude higher than that of water molecules when the ions are trapped in an ice bilayer confined between two parallel plates. This novel picture is in sharp contrast to the prevailing view that the diffusion rate of ions is comparable to or even lower than that of water in both bulk and confined solutions. The predicted high ion mobility stems from frequent lateral hopping of ions along the coordination sites inside the hydrogen-bonding network connecting the two water layers of the ice bilayer. This anomalous diffusion should provide new insights into the physics of confined aqueous electrolytes.
Highly Viscous States Affect the Browning of Atmospheric Organic Particulate Matter

PubMed Central

2018-01-01

Initially transparent organic particulate matter (PM) can become shades of light-absorbing brown via atmospheric particle-phase chemical reactions. The production of nitrogen-containing compounds is one important pathway for browning. Semisolid or solid physical states of organic PM might, however, have sufficiently slow diffusion of reactant molecules to inhibit browning reactions. Herein, organic PM of secondary organic material (SOM) derived from toluene, a common SOM precursor in anthropogenically affected environments, was exposed to ammonia at different values of relative humidity (RH). The production of light-absorbing organonitrogen imines from ammonia exposure, detected by mass spectrometry and ultraviolet–visible spectrophotometry, was kinetically inhibited for RH < 20% for exposure times of 6 min to 24 h. By comparison, from 20% to 60% RH organonitrogen production took place, implying ammonia uptake and reaction. Correspondingly, the absorption index k across 280 to 320 nm increased from 0.012 to 0.02, indicative of PM browning. The k value across 380 to 420 nm increased from 0.001 to 0.004. The observed RH-dependent behavior of ammonia uptake and browning was well captured by a model that considered the diffusivities of both the large organic molecules that made up the PM and the small reactant molecules taken up from the gas phase into the PM. Within the model, large-molecule diffusivity was calculated based on observed SOM viscosity and evaporation. Small-molecule diffusivity was represented by the water diffusivity measured by a quartz-crystal microbalance. The model showed that the browning reaction rates at RH < 60% could be controlled by the low diffusivity of the large organic molecules from the interior region of the particle to the reactive surface region. The results of this study have implications for accurate modeling of atmospheric brown carbon production and associated influences on energy balance. PMID:29532020
Highly Viscous States Affect the Browning of Atmospheric Organic Particulate Matter.

PubMed

Liu, Pengfei; Li, Yong Jie; Wang, Yan; Bateman, Adam P; Zhang, Yue; Gong, Zhaoheng; Bertram, Allan K; Martin, Scot T

2018-02-28

Initially transparent organic particulate matter (PM) can become shades of light-absorbing brown via atmospheric particle-phase chemical reactions. The production of nitrogen-containing compounds is one important pathway for browning. Semisolid or solid physical states of organic PM might, however, have sufficiently slow diffusion of reactant molecules to inhibit browning reactions. Herein, organic PM of secondary organic material (SOM) derived from toluene, a common SOM precursor in anthropogenically affected environments, was exposed to ammonia at different values of relative humidity (RH). The production of light-absorbing organonitrogen imines from ammonia exposure, detected by mass spectrometry and ultraviolet-visible spectrophotometry, was kinetically inhibited for RH < 20% for exposure times of 6 min to 24 h. By comparison, from 20% to 60% RH organonitrogen production took place, implying ammonia uptake and reaction. Correspondingly, the absorption index k across 280 to 320 nm increased from 0.012 to 0.02, indicative of PM browning. The k value across 380 to 420 nm increased from 0.001 to 0.004. The observed RH-dependent behavior of ammonia uptake and browning was well captured by a model that considered the diffusivities of both the large organic molecules that made up the PM and the small reactant molecules taken up from the gas phase into the PM. Within the model, large-molecule diffusivity was calculated based on observed SOM viscosity and evaporation. Small-molecule diffusivity was represented by the water diffusivity measured by a quartz-crystal microbalance. The model showed that the browning reaction rates at RH < 60% could be controlled by the low diffusivity of the large organic molecules from the interior region of the particle to the reactive surface region. The results of this study have implications for accurate modeling of atmospheric brown carbon production and associated influences on energy balance.
Morphology Effect on Proton Dynamics in Nafion® 117 and Sulfonated Polyether Ether Ketone

NASA Astrophysics Data System (ADS)

Leong, Jun Xing; Diño, Wilson Agerico; Ahmad, Azizan; Daud, Wan Ramli Wan; Kasai, Hideaki

2016-09-01

We report results of our experimental and theoretical studies on the dynamics of proton conductivity in Nafion® 117 and self-fabricated sulfonated polyether ether ketone (SPEEK) membranes. Knowing that the presence of water molecules in the diffusion process results in a lower energy barrier, we determined the diffusion barriers and corresponding tunneling probabilities of Nafion® 117 and SPEEK system using a simple theoretical model that excludes the medium (water molecules) in the initial calculations. We then propose an equation that relates the membrane conductivity to the tunneling probability. We recover the effect of the medium by introducing a correction term into the proposed equation, which takes into account the effect of the proton diffusion distance and the hydration level. We have also experimentally verified that the proposed equation correctly explain the difference in conductivity between Nafion® 117 and SPEEK. We found that membranes that are to be operated in low hydration environments (high temperatures) need to be designed with short diffusion distances to enhance and maintain high conductivity.
NMR Water Self–Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions

PubMed Central

Bai, Ruiliang; Basser, Peter J.; Briber, Robert M.; Horkay, Ferenc

2013-01-01

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced. PMID:24409001
NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions.

PubMed

Bai, Ruiliang; Basser, Peter J; Briber, Robert M; Horkay, Ferenc

2014-03-15

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca 2+ and Na + . Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na + on the mobility of water molecules was practically undetectable. By contrast, addition of Ca 2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.
Early detection of response to radiation therapy in patients with brain malignancies using conventional and high b-value diffusion-weighted magnetic resonance imaging.

PubMed

Mardor, Yael; Pfeffer, Raphael; Spiegelmann, Roberto; Roth, Yiftach; Maier, Stephan E; Nissim, Ouzi; Berger, Raanan; Glicksman, Ami; Baram, Jacob; Orenstein, Arie; Cohen, Jack S; Tichler, Thomas

2003-03-15

To study the feasibility of using diffusion-weighted magnetic resonance imaging (DWMRI), which is sensitive to the diffusion of water molecules in tissues, for detection of early tumor response to radiation therapy; and to evaluate the additional information obtained from high DWMRI, which is more sensitive to low-mobility water molecules (such as intracellular or bound water), in increasing the sensitivity to response. Standard MRI and DWMRI were acquired before and at regular intervals after initiating radiation therapy for 10 malignant brain lesions in eight patients. One week posttherapy, three of six responding lesions showed an increase in the conventional DWMRI parameters. Another three responding lesions showed no change. Four nonresponding lesions showed a decrease or no change. The early change in the diffusion parameters was enhanced by using high DWMRI. When high DWMRI was used, all responding lesions showed increase in the diffusion parameter and all nonresponding lesions showed no change or decrease. Response was determined by standard MRI 7 weeks posttherapy. The changes in the diffusion parameters measured 1 week after initiating treatment were correlated with later tumor response or no response (P <.006). This correlation was increased to P <.0006 when high DWMRI was used. The significant correlation between changes in diffusion parameters 1 week after initiating treatment and later tumor response or no response suggests the feasibility of using DWMRI for early, noninvasive prediction of tumor response. The ability to predict response may enable early termination of treatment in nonresponding patients, prevent additional toxicity, and allow for early changes in treatment.
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

PubMed Central

Zhang, Chao; Knyazev, Denis G.; Vereshaga, Yana A.; Ippoliti, Emiliano; Nguyen, Trung Hai; Carloni, Paolo; Pohl, Peter

2012-01-01

Fast lateral proton migration along membranes is of vital importance for cellular energy homeostasis and various proton-coupled transport processes. It can only occur if attractive forces keep the proton at the interface. How to reconcile this high affinity to the membrane surface with high proton mobility is unclear. Here, we tested whether a minimalistic model interface between an apolar hydrophobic phase (n-decane) and an aqueous phase mimics the biological pathway for lateral proton migration. The observed diffusion span, on the order of tens of micrometers, and the high proton mobility were both similar to the values previously reported for lipid bilayers. Extensive ab initio simulations on the same water/n-decane interface reproduced the experimentally derived free energy barrier for the excess proton. The free energy profile GH+ adopts the shape of a well at the interface, having a width of two water molecules and a depth of 6 ± 2RT. The hydroniums in direct contact with n-decane have a reduced mobility. However, the hydroniums in the second layer of water molecules are mobile. Their in silico diffusion coefficient matches that derived from our in vitro experiments, (5.7 ± 0.7) × 10-5 cm2 s-1. Conceivably, these are the protons that allow for fast diffusion along biological membranes. PMID:22675120
Electrically tunable spatially variable switching in ferroelectric liquid crystal/water system

NASA Astrophysics Data System (ADS)

Choudhary, A.; Coondoo, I.; Prakash, J.; Sreenivas, K.; Biradar, A. M.

2009-04-01

An unusual switching phenomenon in the region outside conducting patterned area in ferroelectric liquid crystal (FLC) containing about 1-2 wt % of water has been observed. The presence of water in the studied heterogeneous system was confirmed by Fourier transform infrared spectroscopy. The observed optical studies have been emphasized on the "spatially variable switching" phenomenon of the molecules in the nonconducting region of the cell. The observed phenomenon is due to diffusion of water between the smectic layers of the FLC and the interaction of the curved electric field lines with the FLC molecules in the nonconducting region.

Diffusion of gas mixtures in the sI hydrate structure

NASA Astrophysics Data System (ADS)

Waage, Magnus H.; Trinh, Thuat T.; van Erp, Titus S.

2018-06-01

Replacing methane with carbon dioxide in gas hydrates has been suggested as a way of harvesting methane, while at the same time storing carbon dioxide. Experimental evidence suggests that this process is facilitated if gas mixtures are used instead of pure carbon dioxide. We studied the free energy barriers for diffusion of methane, carbon dioxide, nitrogen, and hydrogen in the sI hydrate structure using molecular simulation techniques. Cage hops between neighboring cages were considered with and without a water vacancy and with a potential inclusion of an additional gas molecule in either the initial or final cage. Our results give little evidence for enhanced methane and carbon dioxide diffusion if nitrogen is present as well. However, the inclusion of hydrogen seems to have a substantial effect as it diffuses rapidly and can easily enter occupied cages, which reduces the barriers of diffusion for the gas molecules that co-occupy a cage with hydrogen.
Effects of microwave electric fields on the translational diffusion of dipolar molecules in surface potential: A simulation study

NASA Astrophysics Data System (ADS)

Kapranov, Sergey V.; Kouzaev, Guennadi A.

2018-01-01

Variations of effective diffusion coefficient of polar molecules exposed to microwave electric fields in a surface potential are studied by solving coupled stochastic differential equations of motion with a deterministic component of the surface force. Being an essential tool for the simulation interpretation, a theoretical approach to effective diffusion in surface potential is first developed. The effective diffusion coefficient is represented as the product of the normal diffusion coefficient and potential-dependent correction function, whose temperature dependence is close to the Arrhenius form. The analytically found zero-diffusion condition defines the state of thermal equilibrium at the surface. The diffusion of a water-like dipole molecule in the potential of graphite surface is simulated in the field-free conditions and in the presence of the alternating electric fields of various magnitude intensities and frequencies. Temperature dependence of the correction function exhibits field-induced variations of the effective Lennard-Jones energy parameter. It demonstrates maximum departure from the zero-field value at certain frequencies and intensities, which is associated with variations in the rotational dynamics. A concept of the amplitude-frequency resonance put forward to interpret the simulation results is explained using a heuristic reasoning and is corroborated by semi-quantitative considerations in terms of the Dissado-Hill cluster theory of dielectric relaxation.
The ionic DTI model (iDTI) of dynamic diffusion tensor imaging (dDTI)

PubMed Central

Makris, Nikos; Gasic, Gregory P.; Garrido, Leoncio

2014-01-01

Measurements of water molecule diffusion along fiber tracts in CNS by diffusion tensor imaging (DTI) provides a static map of neural connections between brain centers, but does not capture the electrical activity along axons for these fiber tracts. Here, a modification of the DTI method is presented to enable the mapping of active fibers. It is termed dynamic diffusion tensor imaging (dDTI) and is based on a hypothesized “anisotropy reduction due to axonal excitation” (“AREX”). The potential changes in water mobility accompanying the movement of ions during the propagation of action potentials along axonal tracts are taken into account. Specifically, the proposed model, termed “ionic DTI model”, was formulated as follows.•First, based on theoretical calculations, we calculated the molecular water flow accompanying the ionic flow perpendicular to the principal axis of fiber tracts produced by electrical conduction along excited myelinated and non-myelinated axons.•Based on the changes in molecular water flow we estimated the signal changes as well as the changes in fractional anisotropy of axonal tracts while performing a functional task.•The variation of fractional anisotropy in axonal tracts could allow mapping the active fiber tracts during a functional task. Although technological advances are necessary to enable the robust and routine measurement of this electrical activity-dependent movement of water molecules perpendicular to axons, the proposed model of dDTI defines the vectorial parameters that will need to be measured to bring this much needed technique to fruition. PMID:25431757
Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films.

PubMed

McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J

2016-09-01

The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability.
Direct molecular diffusion and micro-mixing for rapid dewatering of LiBr solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bigham, S; Isfahani, RN; Moghaddam, S

2014-03-01

A slow molecular diffusion rate often limits the desorption process of an absorbate molecule from a liquid absorbent. To enhance the desorption rate, the absorbent is often boiled to increase the liquid vapor interfacial area. However, the growth of bubbles generated during the nucleate boiling process still remains mass-diffusion limited. Here, it is shown that a desorption rate higher than that of boiling can be achieved, if the vapor absorbent interface is continuously replenished with the absorbate-rich solution to limit the concentration boundary layer growth. The study is conducted in a LiBr-water-solution, in which the water molecules' diffusion rate ismore » quite slow. The manipulation of the vapor solution interface concentration distribution is enabled by the mechanical confinement of the solution flow within microchannels, using a hydrophobic vapor-venting membrane and the implementation of microstructures on the flow channel's bottom wall. The microstructures stretch and fold the laminar streamlines within the solution film and produce vortices. The vortices continuously replace the concentrated solution at the vapor solution interface with the water-rich solution brought from the bottom and middle of the flow channel. The physics of the process is described using a combination of experimental and numerical studies. Published by Elsevier Ltd.« less
The influence of trehalose on hydrophobic interactions of small nonpolar solute: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Paul, Subrata; Paul, Sandip

2013-07-01

Molecular dynamics simulations were carried out to investigate the influences of aqueous trehalose solution on the hydrophobic interactions between neopentane molecules. In this study, we consider six different trehalose concentrations ranging from 0% to 56%. We observe that with increasing trehalose concentration the dispersion of solute neopentane takes place. The neopentane-neopentane association constant value decreases with addition of trehalose. Our preferential interaction calculations suggest that with increasing trehalose concentration neopentane interacts preferentially with water over trehalose. Site-site neopentane-trehalose rdfs indicate that trehalose molecules are expelled out from the neopentane surface. Also observed are (i) trehalose induced second shell collapse of water network (ii) decrease in average number of water-water and water-trehalose hydrogen bonds with increasing trehalose concentration. We also find that addition of trehalose decreases the translational motion of all the solution species. The decrease in diffusion coefficient value is more pronounced for trehalose. We, further, observe that the ratio of the diffusion coefficient values of water and trehalose increases with increasing trehalose concentration.
Water Diffusion Mechanism in Carbon Nanotube and Polyamide Nanocomposite Reverse Osmosis Membranes: A Possible Percolation-Hopping Mechanism

NASA Astrophysics Data System (ADS)

Araki, Takumi; Cruz-Silva, Rodolfo; Tejima, Syogo; Ortiz-Medina, Josue; Morelos-Gomez, Aaron; Takeuchi, Kenji; Hayashi, Takuya; Terrones, Mauricio; Endo, Morinobu

2018-02-01

This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. The mechanism of water diffusion across reverse osmosis nanocomposite membranes made of carbon nanotubes (CNTs) and aromatic polyamide is not completely understood despite its high potential for desalination applications. While most of the groups have proposed that superflow inside the CNT might positively impact the water flow across membranes, here we show theoretical evidence that this is not likely the case in composite membranes because CNTs are usually oriented parallel to the membrane surface, not to mention that sometimes the nanotube cores are occluded. Instead, we propose an oriented diffusion mechanism that explains the high water permeation by decreasing the diffusion path of water molecules across the membranes, even in the presence of CNTs that behave as impermeable objects. Finally, we provide a comprehensive description of the molecular dynamics occurring in water desalination membranes by considering the bond polarizability caused by dynamic charge transfer and explore the use of molecular-dynamics-derived stochastic diffusion simulations. The proposed water diffusion mechanism offers an alternative and most likely explanation for the high permeation phenomena observed in CNTs and PA nanocomposite membranes, and its understanding can be helpful to design the next generation of reverse osmosis desalination membranes.
Cumulant expansions for measuring water exchange using diffusion MRI

NASA Astrophysics Data System (ADS)

Ning, Lipeng; Nilsson, Markus; Lasič, Samo; Westin, Carl-Fredrik; Rathi, Yogesh

2018-02-01

The rate of water exchange across cell membranes is a parameter of biological interest and can be measured by diffusion magnetic resonance imaging (dMRI). In this work, we investigate a stochastic model for the diffusion-and-exchange of water molecules. This model provides a general solution for the temporal evolution of dMRI signal using any type of gradient waveform, thereby generalizing the signal expressions for the Kärger model. Moreover, we also derive a general nth order cumulant expansion of the dMRI signal accounting for water exchange, which has not been explored in earlier studies. Based on this analytical expression, we compute the cumulant expansion for dMRI signals for the special case of single diffusion encoding (SDE) and double diffusion encoding (DDE) sequences. Our results provide a theoretical guideline on optimizing experimental parameters for SDE and DDE sequences, respectively. Moreover, we show that DDE signals are more sensitive to water exchange at short-time scale but provide less attenuation at long-time scale than SDE signals. Our theoretical analysis is also validated using Monte Carlo simulations on synthetic structures.
Structures of water molecules in carbon nanotubes under electric fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji

2015-03-28

Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electricmore » field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.« less
Continuous Diffusion Model for Concentration Dependence of Nitroxide EPR Parameters in Normal and Supercooled Water.

PubMed

Merunka, Dalibor; Peric, Miroslav

2017-05-25

Electron paramagnetic resonance (EPR) spectra of radicals in solution depend on their relative motion, which modulates the Heisenberg spin exchange and dipole-dipole interactions between them. To gain information on radical diffusion from EPR spectra demands both reliable spectral fitting to find the concentration coefficients of EPR parameters and valid expressions between the concentration and diffusion coefficients. Here, we measured EPR spectra of the 14 N- and 15 N-labeled perdeuterated TEMPONE radicals in normal and supercooled water at various concentrations. By fitting the EPR spectra to the functions based on the modified Bloch equations, we obtained the concentration coefficients for the spin dephasing, coherence transfer, and hyperfine splitting parameters. Assuming the continuous diffusion model for radical motion, the diffusion coefficients of radicals were calculated from the concentration coefficients using the standard relations and the relations derived from the kinetic equations for the spin evolution of a radical pair. The latter relations give better agreement between the diffusion coefficients calculated from different concentration coefficients. The diffusion coefficients are similar for both radicals, which supports the presented method. They decrease with lowering temperature slower than is predicted by the Stokes-Einstein relation and slower than the rotational diffusion coefficients, which is similar to the diffusion of water molecules in supercooled water.
Vibrational dephasing and frequency shifts of hydrogen-bonded pyridine-water complexes

NASA Astrophysics Data System (ADS)

Kalampounias, A. G.; Tsilomelekis, G.; Boghosian, S.

2015-01-01

In this paper we present the picosecond vibrational dynamics and Raman shifts of hydrogen-bonded pyridine-water complexes present in aqueous solutions in a wide concentration range from dense to extreme dilute solutions. We studied the vibrational dephasing and vibrational frequency modulation by calculating time correlation functions of vibrational relaxation by fits in the frequency domain. The concentration induced variations in bandwidths, band frequencies and characteristic dephasing times have been estimated and interpreted as effects due to solute-solvent interactions. The time-correlation functions of vibrational dephasing were obtained for the ring breathing mode of both "free" and hydrogen-bonded pyridine molecules and it was found that sufficiently deviate from the Kubo model. There is a general agreement in the whole concentration range with the modeling proposed by the Rothschild approach, which applies to complex liquids. The results have shown that the reorientation of pyridine aqueous solutions is very slow and hence in both scattering geometries only vibrational dephasing is probed. It is proposed that the spectral changes depend on the perturbations induced by the dynamics of the water molecules in the first hydration cell and water in bulk, while at extreme dilution conditions, the number of bulk water molecules increases and the interchange between molecules belonging to the first hydration cell may not be the predominant modulation mechanism. The evolution of several parameters, such as the characteristic times, the percentage of Gaussian character in the peak shape and the a parameter are indicative of drastic variations at extreme dilution revealing changes in the vibrational relaxation of the pyridine complexes in the aqueous environment. The higher dilution is correlated to diffusion of water molecules into the reference pyridine system in agreement with the jump diffusion model, while at extreme dilutions, almost all pyridine molecules are elaborated in hydrogen bonding. The results are discussed in the framework of the current phenomenological status of the field.
Diffusion Magnetic Resonance Imaging: What Water Tells Us about Biological Tissues

PubMed Central

Le Bihan, Denis; Iima, Mami

2015-01-01

Since its introduction in the mid-1980s, diffusion magnetic resonance imaging (MRI), which measures the random motion of water molecules in tissues, revealing their microarchitecture, has become a pillar of modern neuroimaging. Its main clinical domain has been the diagnosis of acute brain stroke and neurogical disorders, but it is also used in the body for the detection and management of cancer lesions. It can also produce stunning maps of white matter tracks in the brain, with the potential to aid in the understanding of some psychiatric disorders. However, in order to exploit fully the potential of this method, a deeper understanding of the mechanisms that govern the diffusion of water in tissues is needed. PMID:26204162
Sugar-influenced water diffusion, interaction, and retention in clay interlayer nanopores probed by theoretical simulations and experimental spectroscopies

NASA Astrophysics Data System (ADS)

Aristilde, Ludmilla; Galdi, Stephen M.; Kelch, Sabrina E.; Aoki, Thalia G.

2017-08-01

Understanding the hydrodynamics in clay nanopores is important for gaining insights into the trapping of water, nutrients, and contaminants in natural and engineered soils. Previous investigations have focused on the interlayer organization and molecular diffusion coefficients (D) of cations and water molecules in cation-saturated interlayer nanopores of smectite clays. Little is known, however, about how these interlayer dynamic properties are influenced by the ubiquitous presence of small organic compounds such as sugars in the soil environment. Here we probed the effects of glucose molecules on montmorillonite interlayer properties. Molecular dynamics simulations revealed re-structuring of the interlayer organization of the adsorptive species. Water-water interactions were disrupted by glucose-water H-bonding interactions. ;Dehydration; of the glucose-populated nanopore led to depletion in the Na solvation shell, which resulted in the accumulation of both Na ions (as inner-sphere complexes) and remaining hydrated water molecules at the mineral surface. This accumulation led to a decrease in both DNa and Dwater. In addition, the reduction in Dglucose as a function of increasing glucose content can be explained by the aggregation of glucose molecules into organic clusters H-bonded to the mineral surface on both walls of the nanopore. Experimental nuclear magnetic resonance and X-ray diffraction data were consistent with the theoretical predictions. Compared to clay interlayers devoid of glucose, increased intensities and new peaks in the 23Na nuclear magnetic resonance spectra confirmed increasing immobilization of Na as a function of increasing glucose content. And, the X-ray diffraction data indicated a reduced collapse of glucose-populated interlayers exposed to decreasing moisture conditions, which led to the maintenance of hydrated clay nanopores. The coupling of theoretical and experimental findings sheds light on the molecular to nanoscale mechanisms that control the enhanced trapping of water molecules and solutes within sugar-enriched clay nanopores.
Effect of Sodium Dodecyl Sulfate Adsorption on the Behavior of Water inside Single Walled Carbon Nanotubes with Dissipative Particle Dynamics Simulation.

PubMed

Vo, Minh D; Papavassiliou, Dimitrios V

2016-04-15

Dissipative particle dynamics (DPD) simulations were utilized to investigate the ability of sodium dodecyl sulfate (SDS) to adsorb inside a single-walled, arm-chair carbon nanotube (SWCNT), as well as the effect of surfactant on the properties of water inside the SWCNT. The diameter of the SWCNT varied from 1 to 5 nm. The radial and axial density profiles of water inside the SWCNTs were computed and compared with published molecular dynamics results. The average residence time and diffusivity were also calculated to show the size effect on mobility of water inside the SWCNT. It was found that nanotubes with diameter smaller than 3 nm do not allow SDS molecules to enter the SWCNT space. For larger SWCNT diameter, SDS adsorbed inside and outside the nanotube. When SDS was adsorbed in the hollow part of the SWCNT, the behavior of water inside the nanotube was found to be significantly changed. Both radial and axial density profiles of water inside the SWCNT fluctuated strongly and were different from those in bulk phase. In addition, SDS molecules increased the retention of water beads inside SWCNT (d ≥ 3nm) while water diffusivity was decreased.
Free energy barriers for escape of water molecules from protein hydration layer.

PubMed

Roy, Susmita; Bagchi, Biman

2012-03-08

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these "slow" water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.
Translational and Rotational Diffusion in Water in the Gigapascal Range

NASA Astrophysics Data System (ADS)

Bove, L. E.; Klotz, S.; Strässle, Th.; Koza, M.; Teixeira, J.; Saitta, A. M.

2013-11-01

First measurements of the self-dynamics of liquid water in the GPa range are reported. The GPa range has here become accessible through a new setup for the Paris-Edinburgh press specially conceived for quasielastic neutron scattering studies. A direct measurement of both the translational and rotational diffusion coefficients of water along the 400 K isotherm up to 3 GPa, corresponding to the melting point of ice VII, is provided and compared with molecular dynamics simulations. The translational diffusion is observed to strongly decrease with pressure, though its variation slows down for pressures higher than 1 GPa and decouples from that of the shear viscosity. The rotational diffusion turns out to be insensitive to pressure. Through comparison with structural data and molecular dynamics simulations, we show that this is a consequence of the rigidity of the first neighbors shell and of the invariance of the number of hydrogen bonds of a water molecule under high pressure. These results show the inadequacy of the Stokes-Einstein-Debye equations to predict the self-diffusive behavior of water at high temperature and high pressure, and challenge the usual description of hot dense water behaving as a simple liquid.
The effect of bioadhesive on the interfacial compatibility and pervaporation performance of composite membranes by MD and GCMC simulation.

PubMed

Wang, Baohe; Nie, Yan; Ma, Jing

2018-03-01

Combing molecular dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulation, the effect of bioadhesive transition layer on the interfacial compatibility of the pervaporation composite membranes, and the pervaporation performance toward penetrant molecules were investigated. In our previous experimental study, the structural stability and permeability selectivity of the composite membranes were considerably enhanced by the introduction of bioadhesive carbopol (CP). In the present study, the interfacial compatibility and the interfacial energies between the chitosan (CS) separation layer, CP transition layer and the support layer were investigated, respectively. The mobility of polymer chains, free volume in bulk and interface regions were evaluated by the mean-square displacement (MSD) and free volume voids (FFV) analysis. The diffusion and sorption behavior of water/ethanol molecules in bulk and interface regions were characterized. The simulation results of membrane structure have good consistency, indicating that the introduction of CP transition layer improved the interfacial compatibility and interaction between the separation layer and the support layer. Comparing the bulk region of the separation layer, the mobility and free volume of the polymer chain in the interface region decreased and thus reduced the swelling of CS active layer, revealing the increased diffusion selectivity toward the permeated water and ethanol molecules. The strong hydrogen bonds interaction between the COOH of the CP transition layer and water molecules increased the adsorption of water molecules in the interface region. The simulation results were quite consistent with the experimental results. Copyright © 2018 Elsevier Inc. All rights reserved.
Two-dimensional description of surface-bounded exospheres with application to the migration of water molecules on the Moon

NASA Astrophysics Data System (ADS)

Schorghofer, Norbert

2015-05-01

On the Moon, water molecules and other volatiles are thought to migrate along ballistic trajectories. Here, this migration process is described in terms of a two-dimensional partial differential equation for the surface concentration, based on the probability distribution of thermal ballistic hops. A random-walk model, a corresponding diffusion coefficient, and a continuum description are provided. In other words, a surface-bounded exosphere is described purely in terms of quantities on the surface, which can provide computational and conceptual advantages. The derived continuum equation can be used to calculate the steady-state distribution of the surface concentration of volatile water molecules. An analytic steady-state solution is obtained for an equatorial ring; it reveals the width and mass of the pileup of molecules at the morning terminator.
Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

PubMed

Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

2018-06-05

The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.
Reaction Kinetics of Water Molecules with Oxygen Vacancies on Rutile TiO 2(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Nikolay G.; Kimmel, Gregory A.

2015-09-16

The formation of bridging hydroxyls (OHb) via reactions of water molecules with oxygen vacancies (VO) on reduced TiO 2(110) surfaces is studied using infrared reflection-absorption spectroscopy (IRAS), electron-stimulated desorption (ESD), and photon-stimulated desorption (PSD). Narrow IRAS peaks at 2737 cm-1 and 3711 cm -1 are observed for stretching vibrations of OD b and OH b on TiO 2(110), respectively. IRAS measurements with s- and p-polarized light demonstrate that the bridging hydroxyls are oriented normal to the (110) surface. The IR peaks disappear after the sample is exposed to O 2 or annealed in the temperature range of 400 – 600more » K (correlating with the temperature at which pairs of OHb’s reform water and then desorb), which is consistent with their identification as bridging hydroxyls. We have studied the kinetics of water reacting with the vacancies by monitoring the formation of bridging hydroxyls (using IRAS) as a function of the annealing temperature for a small amount of water initially dosed on the TiO 2(110) at low temperature. Separate experiments have also monitored the loss of water molecules (using water ESD) and vacancies (using the CO photooxidation reaction) due to the reactions of water molecules with the vacancies. All three techniques show that the reaction rate becomes appreciable for T > 150 K and that the reactions largely complete for T > 250 K. The temperature-dependent water-VO reaction kinetics are consistent with a Gaussian distribution of activation energies with E a = 0.545 eV, ΔE a(FWHM) = 0.125 eV, and a “normal” prefactor, v = 10 12 s -1. In contrast, a single activation energy with a physically reasonable prefactor does not fit the data well. Our experimental activation energy is close to theoretical estimates for the diffusion of water molecules along the Ti 5c rows on the reduced TiO 2(110) surface, which suggests that the diffusion of water controls the water – V O reaction rate.« less

Predict the glass transition temperature and plasticization of β-cyclodextrin/water binary system by molecular dynamics simulation.

PubMed

Zhou, Guohui; Zhao, Tianhai; Wan, Jie; Liu, Chengmei; Liu, Wei; Wang, Risi

2015-01-12

The glass transition temperature, diffusion behavior and plasticization of β-cyclodextrin (β-CD), and three amorphous β-CD/water mixtures (3%, 5% and 10% [w/w] water, respectively) were investigated by molecular dynamics simulation, which were performed using Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field and isothermal-isobaric ensembles. The specific volumes of four amorphous cells were obtained as a function of temperature. The glass transition temperatures (T(g)) were estimated to be 334.25 K, 325.12 K, 317.32 K, and 305.41 K for amorphous β-CD containing 0%, 3%, 5% and 10% w/w water, respectively, which compares well with the values observed in published literature. The radial distribution function was computed to elucidate the intermolecular interactions between amorphous β-CD and water, which acts as a plasticizer. These results indicate that the hydrogen bond interactions of oxygen in hydroxyl ions was higher than oxygen in acetal groups in β-CD amorphous mixtures with that in water, due to less accessibility of ring oxygens to the surrounding water molecules. The mobility of water molecules was investigated over various temperature ranges, including the rubbery and glassy phases of the β-CD/water mixtures, by calculating the diffusion coefficients and the fractional free volume. In β-CD amorphous models, the higher mobility of water molecules was observed at temperatures above Tg, and almost no change was observed at temperatures below T(g). Copyright © 2014 Elsevier Ltd. All rights reserved.
Water organization between oppositely charged surfaces: Implications for protein sliding along DNA a)

NASA Astrophysics Data System (ADS)

Marcovitz, Amir; Naftaly, Aviv; Levy, Yaakov

2015-02-01

Water molecules are abundant in protein-DNA interfaces, especially in their nonspecific complexes. In this study, we investigated the organization and energetics of the interfacial water by simplifying the geometries of the proteins and the DNA to represent them as two equally and oppositely charged planar surfaces immersed in water. We found that the potential of mean force for bringing the two parallel surfaces into close proximity comprises energetic barriers whose properties strongly depend on the charge density of the surfaces. We demonstrated how the organization of the water molecules into discretized layers and the corresponding energetic barriers to dehydration can be modulated by the charge density on the surfaces, salt, and the structure of the surfaces. The 1-2 layers of ordered water are tightly bound to the charged surfaces representing the nonspecific protein-DNA complex. This suggests that water might mediate one-dimensional diffusion of proteins along DNA (sliding) by screening attractive electrostatic interactions between the positively charged molecular surface on the protein and the negatively charged DNA backbone and, in doing so, reduce intermolecular friction in a manner that smoothens the energetic landscape for sliding, and facilitates the 1D diffusion of the protein.
Diffusivity measurements of volatile organics in levitated viscous aerosol particles

NASA Astrophysics Data System (ADS)

Bastelberger, Sandra; Krieger, Ulrich K.; Luo, Beiping; Peter, Thomas

2017-07-01

Field measurements indicating that atmospheric secondary organic aerosol (SOA) particles can be present in a highly viscous, glassy state have spurred numerous studies addressing low diffusivities of water in glassy aerosols. The focus of these studies is on kinetic limitations of hygroscopic growth and the plasticizing effect of water. In contrast, much less is known about diffusion limitations of organic molecules and oxidants in viscous matrices. These may affect atmospheric chemistry and gas-particle partitioning of complex mixtures with constituents of different volatility. In this study, we quantify the diffusivity of a volatile organic in a viscous matrix. Evaporation of single particles generated from an aqueous solution of sucrose and small amounts of volatile tetraethylene glycol (PEG-4) is investigated in an electrodynamic balance at controlled relative humidity (RH) and temperature. The evaporative loss of PEG-4 as determined by Mie resonance spectroscopy is used in conjunction with a radially resolved diffusion model to retrieve translational diffusion coefficients of PEG-4. Comparison of the experimentally derived diffusivities with viscosity estimates for the ternary system reveals a breakdown of the Stokes-Einstein relationship, which has often been invoked to infer diffusivity from viscosity. The evaporation of PEG-4 shows pronounced RH and temperature dependencies and is severely depressed for RH ≲ 30 %, corresponding to diffusivities < 10-14 cm2 s-1 at temperatures < 15 °C. The temperature dependence is strong, suggesting a diffusion activation energy of about 300 kJ mol-1. We conclude that atmospheric volatile organic compounds can be subject to severe diffusion limitations in viscous organic aerosol particles. This may enable an important long-range transport mechanism for organic material, including pollutant molecules such as polycyclic aromatic hydrocarbons (PAHs).
First Principles Study for Proton Transport and Diffusion Behavior in Hydrous Hexagonal WO3

NASA Astrophysics Data System (ADS)

Liu, Chi-Ping; Zhou, Fei; Ozolins, Vidvuds; QPAM Team

2013-03-01

Proton transport is of great importance in biological species and energy storage and conversion systems. Previous studies have shown fast proton conduction in liquids and polymers but seldom in inorganic materials. In this work, first principles density functional theory (DFT) reveals that the formation of hydronium and water chains inside the hexagonal channels plays the key roles for the anomalously fast proton transport, by following modified Grotthuss mechanism. Our DFT study shows the detailed microscopic proton diffusion mechanism along the channel in hydrous WO3 with 50% water composition, which is proper for water chain formation. The water chain in the channel serves as a possible diffusion media for hydronium (H3O +) . With the continuous formation and cleavage of hydrogen bonds in the channel, the hydronium diffuses by hydrogen bonds exchange between water molecules. This mechanism is very similar with Grotthuss relay mechanism for proton transport in liquid. The possible proton diffusion were studied for hydronium is either far away from the water chain bond defect or next to H2O defect at the end of water chain. The diffusion barriers for both conditions are around 150 meV to 200 meV, and water defects reorganization in the chain is the rate-limited step for proton diffusion. These small diffusion barriers could explain the fast 1-D proton transport in hydrous WO3 channel. Further studies about fast proton transport in other inorganic materials could be an important topic in not only biochemistry but also clean energy applications like fuel cell applications.
Diffusion coefficients of organic molecules in sucrose-water solutions and comparison with Stokes-Einstein predictions

NASA Astrophysics Data System (ADS)

Chenyakin, Yuri; Ullmann, Dagny A.; Evoy, Erin; Renbaum-Wolff, Lindsay; Kamal, Saeid; Bertram, Allan K.

2017-02-01

The diffusion coefficients of organic species in secondary organic aerosol (SOA) particles are needed to predict the growth and reactivity of these particles in the atmosphere. Previously, viscosity measurements, along with the Stokes-Einstein relation, have been used to estimate the diffusion rates of organics within SOA particles or proxies of SOA particles. To test the Stokes-Einstein relation, we have measured the diffusion coefficients of three fluorescent organic dyes (fluorescein, rhodamine 6G and calcein) within sucrose-water solutions with varying water activity. Sucrose-water solutions were used as a proxy for SOA material found in the atmosphere. Diffusion coefficients were measured using fluorescence recovery after photobleaching. For the three dyes studied, the diffusion coefficients vary by 4-5 orders of magnitude as the water activity varied from 0.38 to 0.80, illustrating the sensitivity of the diffusion coefficients to the water content in the matrix. At the lowest water activity studied (0.38), the average diffusion coefficients were 1.9 × 10-13, 1.5 × 10-14 and 7.7 × 10-14 cm2 s-1 for fluorescein, rhodamine 6G and calcein, respectively. The measured diffusion coefficients were compared with predictions made using literature viscosities and the Stokes-Einstein relation. We found that at water activity ≥ 0.6 (which corresponds to a viscosity of ≤ 360 Pa s and Tg/T ≤ 0.81), predicted diffusion rates agreed with measured diffusion rates within the experimental uncertainty (Tg represents the glass transition temperature and T is the temperature of the measurements). When the water activity was 0.38 (which corresponds to a viscosity of 3.3 × 106 Pa s and a Tg/T of 0.94), the Stokes-Einstein relation underpredicted the diffusion coefficients of fluorescein, rhodamine 6G and calcein by a factor of 118 (minimum of 10 and maximum of 977), a factor of 17 (minimum of 3 and maximum of 104) and a factor of 70 (minimum of 8 and maximum of 494), respectively. This disagreement is significantly smaller than the disagreement observed when comparing measured and predicted diffusion coefficients of water in sucrose-water mixtures.
Ion pair and solvation dynamics of [Bmim][BF4 ] + water system.

PubMed

Cascão, João; Silva, Wagner; Ferreira, Ana S D; Cabrita, Eurico J

2018-02-01

In this work, 1-butyl-3-methylimidazolium tetrafluoroborate/water mixtures were analysed over the whole water composition (x w ) in order to study the rotational and translational behaviour of the ions. We employed a multinuclear NMR approach to determine anion/cation/water diffusion coefficients and longitudinal relaxation rates at different water content. In neat ionic liquids (IL), the cation diffuses faster than the anion, and at low x w , anions and cations share almost the same diffusion coefficient, but above a critical water concentration, the anion begins to diffuse faster than the cation. We identified this composition as approximately 10% x w where the ions share the same diffusion coefficient. We found that the water at this composition seems to have a much more dramatic effect in the rotational diffusion of the anion that decreases substantially and approaches that of the anion in the diluted IL. Translational and rotational dynamics of the ions suggest that water is first incorporated in pockets in the nanostructure of the IL allowing the ions to maintain most of the cation/anion interactions present in neat IL but already disrupting some anion/cation interactions due to preferential interaction with the anion. HOESY and NOESY data show that water displays contacts both with the cation and the anion in a positive NOE regime in contrary to the negative regime found for the cation/anion and cation/cation cross-relaxation. This is in accordance with the high relative diffusion coefficient of water and suggests that water molecules can exchange between preferential location sites that allow water to maintain contacts both with the anion and cation. Copyright © 2017 John Wiley & Sons, Ltd.
Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Pusheng; Asher, Sanford A.

1999-01-01

The separation of macromolecules such as polymers and DNA by means of electrophoresis, gel permeation chromatography or filtration exploits size-dependent differences in the time it takes for the molecules to migrate through a random porous network. Transport through the gel matrices, which usually consist of full swollen crosslinked polymers, depends on the relative size of the macromolecule compared with the pore radius. Sufficiently small molecules are thought to adopt an approximately spherical conformation when diffusing through the gel matrix, whereas larger ones are forced to migrate in a snake-like fashion. Molecules of intermediate size, however, can get temporarily trapped in the largest pores of the matrix, where the molecule can extend and thus maximize its conformational entropy. This `entropic trapping' is thought to increase the dependence of diffusion rate on molecular size. Here we report the direct experimental verification of this phenomenon. Bragg diffraction from a hydrogel containing a periodic array of monodisperse water voids confirms that polymers of different weights partition between the hydrogel matrix and the water voids according to the predictions of the entropic trapping theory. Our approach might also lead to the design of improved separation media based on entropic trapping.
Osmosis and solute-solvent drag: fluid transport and fluid exchange in animals and plants.

PubMed

Hammel, H T; Schlegel, Whitney M

2005-01-01

In 1903, George Hulett explained how solute alters water in an aqueous solution to lower the vapor pressure of its water. Hulett also explained how the same altered water causes osmosis and osmotic pressure when the solution is separated from liquid water by a membrane permeable to the water only. Hulett recognized that the solute molecules diffuse toward all boundaries of the solution containing the solute. Solute diffusion is stopped at all boundaries, at an open-unopposed surface of the solution, at a semipermeable membrane, at a container wall, or at the boundary of a solid or gaseous inclusion surrounded by solution but not dissolved in it. At each boundary of the solution, the solute molecules are reflected, they change momentum, and the change of momentum of all reflected molecules is a pressure, a solute pressure (i.e., a force on a unit area of reflecting boundary). When a boundary of the solution is open and unopposed, the solute pressure alters the internal tension in the force bonding the water in its liquid phase, namely, the hydrogen bond. All altered properties of the water in the solution are explained by the altered internal tension of the water in the solution. We acclaim Hulett's explanation of osmosis, osmotic pressure, and lowering of the vapor pressure of water in an aqueous solution. His explanation is self-evident. It is the necessary, sufficient, and inescapable explanation of all altered properties of the water in the solution relative to the same property of pure liquid water at the same externally applied pressure and the same temperature. We extend Hulett's explanation of osmosis to include the osmotic effects of solute diffusing through solvent and dragging on the solvent through which it diffuses. Therein lies the explanations of (1) the extravasation from and return of interstitial fluid to capillaries, (2) the return of luminal fluid in the proximal and distal convoluted tubules of a kidney nephron to their peritubular capillaries, (3) the return of interstitial fluid to the vasa recta, (4) return of aqueous humor to the episcleral veins, and (5) flow of phloem from source to sink in higher plants and many more examples of fluid transport and fluid exchange in animal and plant physiology. When a membrane is permeable to water only and when it separates differing aqueous solutions, the flow of water is from the solution with the lower osmotic pressure to the solution with the higher osmotic pressure.
An optical conveyor for molecules.

PubMed

Weinert, Franz M; Braun, Dieter

2009-12-01

Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.
Hydration and rotational diffusion of levoglucosan in aqueous solutions

NASA Astrophysics Data System (ADS)

Corezzi, S.; Sassi, P.; Paolantoni, M.; Comez, L.; Morresi, A.; Fioretto, D.

2014-05-01

Extended frequency range depolarized light scattering measurements of water-levoglucosan solutions are reported at different concentrations and temperatures to assess the effect of the presence and distribution of hydroxyl groups on the dynamics of hydration water. The anhydro bridge, reducing from five to three the number of hydroxyl groups with respect to glucose, considerably affects the hydration properties of levoglucosan with respect to those of mono and disaccharides. In particular, we find that the average retardation of water dynamics is ≈3-4, that is lower than ≈5-6 previously found in glucose, fructose, trehalose, and sucrose. Conversely, the average number of retarded water molecules around levoglucosan is 24, almost double that found in water-glucose mixtures. These results suggest that the ability of sugar molecules to form H-bonds through hydroxyl groups with surrounding water, while producing a more effective retardation, it drastically reduces the spatial extent of the perturbation on the H-bond network. In addition, the analysis of the concentration dependence of the hydration number reveals the aptitude of levoglucosan to produce large aggregates in solution. The analysis of shear viscosity and rotational diffusion time suggests a very short lifetime for these aggregates, typically faster than ≈20 ps.
Hydration of polar and nonpolar molecules at the surface of amorphous solid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souda, Ryutaro

2004-10-15

On the basis of time-of-flight secondary ion mass spectrometry, properties of amorphous solid water above the glass transition temperature (136 K) and the hydration of polar (HCOOH,C{sub 3}H{sub 7}OH) and nonpolar (C{sub 6}H{sub 14},C{sub 6}F{sub 14}) molecules on the D{sub 2}O-ice surface have been investigated. No evidence was obtained for the irreversible transition of the amorphous solid water into the crystalline phase: the self-diffusion of water molecules occurs above 140 K irrespective of the preparation temperatures of the water-ice film ranging from 15 K to 165 K, whereas the morphology of the film changes drastically at 165 K due tomore » the evolution of liquidlike water. It is also demonstrated that the change in conformation of the hydrated HCOOH molecule, as well as the occurrence of hydrophilic/hydrophobic hydration of the C{sub 3}H{sub 7}OH molecule, can be analyzed successfully from the temperature evolutions of the secondary-ion intensities. These polar molecules basically stay on the surface and tend to quench the morphological change of the water film due to the reduction of surface tension. The nonpolar C{sub 6}H{sub 14} and C{sub 6}F{sub 14} molecules readily dissolve in the D{sub 2}O layer below 100 K and dehydration of the incorporated molecules occurs at 165 K concomitantly with the evolution of the liquidlike water. It is thus concluded that the hydrophobic hydration of nonpolar molecules is intimately related to the properties of water films.« less
Atom Resolved Electron Microscpe Images of Polyvinylidene Fluoride Nanofibers for Water Desalination

NASA Astrophysics Data System (ADS)

Liu, Suqi; Reneker, Darrell

Ultra-thin nanofibers of polyvinylidene fluoride (PVDF), observed with an aberration corrected transmission electron microscope, in a through focus series of 50 images, revealed three-dimensional positions and motions of some molecular segments. The x,y positions of fluorine atoms in the PVDF segments were observed at high resolution as described in (DOI: 10.1039/c5nr01619c). The methods described in (DOI:10.1038/nature11074) were used to measure the positions of fluorine atoms along the observation direction of the microscope. PVDF is widely used to separate salt ions from water in reverse osmosis systems. The observed separation depends on the atomic scale positions and motions of segments of the PVDF molecules. Conformational changes and the associated changes in the directions of the dipole moments of PVDF segments distinguish the diffusion of dipolar water molecules from diffusion of salt ions to accomplish desalination. Authors thank Coalescence Filtration Nanofibers Consortium at The University of Akron for support.
Using light transmission to watch hydrogen diffuse

PubMed Central

Pálsson, Gunnar K.; Bliersbach, Andreas; Wolff, Max; Zamani, Atieh; Hjörvarsson, Björgvin

2012-01-01

Because of its light weight and small size, hydrogen exhibits one of the fastest diffusion rates in solid materials, comparable to the diffusion rate of liquid water molecules at room temperature. The diffusion rate is determined by an intricate combination of quantum effects and dynamic interplay with the displacement of host atoms that is still only partially understood. Here we present direct observations of the spatial and temporal changes in the diffusion-induced concentration profiles in a vanadium single crystal and we show that the results represent the experimental counterpart of the full time and spatial solution of Fick's diffusion equation. We validate the approach by determining the diffusion rate of hydrogen in a single crystal vanadium (001) film, with net diffusion in the [110] direction. PMID:22692535
Using light transmission to watch hydrogen diffuse

NASA Astrophysics Data System (ADS)

Pálsson, Gunnar K.; Bliersbach, Andreas; Wolff, Max; Zamani, Atieh; Hjörvarsson, Björgvin

2012-06-01

Because of its light weight and small size, hydrogen exhibits one of the fastest diffusion rates in solid materials, comparable to the diffusion rate of liquid water molecules at room temperature. The diffusion rate is determined by an intricate combination of quantum effects and dynamic interplay with the displacement of host atoms that is still only partially understood. Here we present direct observations of the spatial and temporal changes in the diffusion-induced concentration profiles in a vanadium single crystal and we show that the results represent the experimental counterpart of the full time and spatial solution of Fick's diffusion equation. We validate the approach by determining the diffusion rate of hydrogen in a single crystal vanadium (001) film, with net diffusion in the [110] direction.
An elemental mercury diffusion coefficient for natural waters determined by molecular dynamics simulation.

PubMed

Kuss, Joachim; Holzmann, Jörg; Ludwig, Ralf

2009-05-01

Mercury is a priority pollutant as its mobility between the hydrosphere and the atmosphere threatens the biosphere globally. The air-water gas transfer of elemental mercury (Hg0) is controlled by its diffusion through the water-side boundary layer and thus by its diffusion coefficient, D(Hg), the value of which, however, has not been established. Here, the diffusion of Hg0 in water was modeled by molecular dynamics (MD) simulation and the diffusion coefficient subsequently determined. Therefore the movement of either Hg(0) or xenon and 1000 model water molecules (TIP4P-Ew) were traced for time spans of 50 ns. The modeled D(Xe) of the monatomic noble gas agreed well with measured data; thus, MD simulation was assumed to be a reliable approach to determine D(Hg) for monatomic Hg(0) as well. Accordingly, Hg(0) diffusion was then simulated for freshwater and seawater, and the data were well-described by the equation of Eyring. The activation energies for the diffusion of Hg0 in freshwater was 17.0 kJ mol(-1) and in seawater 17.8 kJ mol(-1). The newly determined D(Hg) is clearly lower than the one previously used for an oceanic mercury budget. Thus, its incorporation into the model should lead to lower estimates of global ocean mercury emissions.
High-ionic-strength electroosmotic flows in uncharged hydrophobic nanochannels.

PubMed

Kim, Daejoong; Darve, Eric

2009-02-01

We report molecular dynamics simulation results of high-ionic-strength electroosmotic flows inside uncharged nanochannels. The possibility of this unusual electrokinetic phenomenon has been discussed by Dukhin et al. [A. Dukhin, S. Dukhin, P. Goetz, Langmuir 21 (2005) 9990]. Our computed velocity profiles clearly indicate the presence of a net flow with a maximum velocity around 2 m/s. We found the apparent zeta potential to be -29.7+/-6.8 mV, using the Helmholtz-Smoluchowski relation and the measured mean velocity. This value is comparable to experimentally measured values in Dukhin et al. and references therein. We also investigate the orientations of water molecules in response to an electric field by computing polarization density. Water molecules in the bulk region are oriented along the direction of the external electric field, while their near-wall orientation shows oscillations. The computation of three-dimensional density distributions of sodium and chloride ions around each individual water molecule show that chloride ions tend to concentrate near a water molecule, whereas sodium ions are diffusely distributed.
Pore-size dependence and characteristics of water diffusion in slitlike micropores

DOE PAGES

Diallo, S. O.

2015-07-16

The temperature dependence of the dynamics of water inside microporous activated carbon fibers (ACF) is investigated by means of incoherent elastic and quasielastic neutron-scattering techniques. The aim is to evaluate the effect of increasing pore size on the water dynamics in these primarily hydrophobic slit-shaped channels. Using two different micropore sizes (similar to 12 and 18 angstrom, denoted, respectively, ACF-10 and ACF-20), a clear suppression of the mobility of the water molecules is observed as the pore gap or temperature decreases. Suppression, we found, is accompanied by a systematic dependence of the average translational diffusion coefficient D-r and relaxation timemore » [tau(0)] of the restricted water on pore size and temperature. We observed D-r values and tested against a proposed scaling law, in which the translational diffusion coefficient D-r of water within a porous matrix was found to depend solely on two single parameters, a temperature-independent translational diffusion coefficient D-c associated with the water bound to the pore walls and the ratio theta of this strictly confined water to the total water inside the pore, yielding unique characteristic parameters for water transport in these carbon channels across the investigated temperature range.« less
Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers.

PubMed

Elola, M Dolores; Rodriguez, Javier

2018-06-07

We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
3D diffusion model within the collagen apatite porosity: An insight to the nanostructure of human trabecular bone

PubMed Central

Bini, Fabiano; Pica, Andrada; Marinozzi, Andrea; Marinozzi, Franco

2017-01-01

Bone tissue at nanoscale is a composite mainly made of apatite crystals, collagen molecules and water. This work is aimed to study the diffusion within bone nanostructure through Monte-Carlo simulations. To this purpose, an idealized geometric model of the apatite-collagen structure was developed. Gaussian probability distribution functions were employed to design the orientation of the apatite crystals with respect to the axes (length L, width W and thickness T) of a plate-like trabecula. We performed numerical simulations considering the influence of the mineral arrangement on the effective diffusion coefficient of water. To represent the hindrance of the impermeable apatite crystals on the water diffusion process, the effective diffusion coefficient was scaled with the tortuosity, the constrictivity and the porosity factors of the structure. The diffusion phenomenon was investigated in the three main directions of the single trabecula and the introduction of apatite preferential orientation allowed the creation of an anisotropic medium. Thus, different diffusivities values were observed along the axes of the single trabecula. We found good agreement with previous experimental results computed by means of a genetic algorithm. PMID:29220377
Anomalous diffusion of water molecules at grain boundaries in ice Ih.

PubMed

Moreira, Pedro Augusto Franco Pinheiro; Veiga, Roberto Gomes de Aguiar; Ribeiro, Ingrid de Almeida; Freitas, Rodrigo; Helfferich, Julian; de Koning, Maurice

2018-05-23

Using ab initio and classical molecular dynamics simulations, we study pre-melting phenomena in pristine coincident-site-lattice grain boundaries (GBs) in proton-disordered hexagonal ice Ih at temperatures just below the melting point Tm. Concerning pre-melt-layer thicknesses, the results are consistent with the available experimental estimates for low-disorder impurity-free GBs. With regard to molecular mobility, the simulations provide a key new insight: the translational motion of the water molecules is found to be subdiffusive for time scales from ∼10 ns up to at least 0.1 μs. Moreover, the fact that the anomalous diffusion occurs even at temperatures just below Tm where the bulk supercooled liquid still diffuses normally suggests that it is related to the confinement of the GB pre-melt layers by the surrounding crystalline environment. Furthermore, we show that this behavior can be characterized by continuous-time random walk models in which the waiting-time distributions decay according to power-laws that are very similar to those describing dynamics in glass-forming systems.

INMS measures an influx of molecules from Saturn's rings

NASA Astrophysics Data System (ADS)

Perry, M. E.

2017-12-01

In 1984, Connerney and Waite proposed water influx from Saturn's rings to explain the low electron densities measured during Pioneer and Voyager radio occultation experiments. Charge exchange with this minor species depleted the H+ ions and provided a faster path to electron recombination. With ice the primary constituent of the rings, water was the most likely in-falling molecule. During the Grand Finale orbits, Cassini's Ion and Neutral Mass Spectrometer (INMS) detected and quantified an influx from the rings. Unexpectedly, the primary influx molecules are CH4 and a heavier carbon-bearing species. Water was detected, but quantities were factors of ten lower than these other species. Distribution in both altitude and latitude are consistent with a ring influx. The concentration of the minor species in Saturn's atmosphere shows that they enter Saturn's atmosphere from the top. Both molecules have their highest concentrations at the highest altitudes, with concentrations >0.4% at 3,500 km altitude and only 0.02% at 2,700 km. Molecules from the rings deorbit to Saturn's atmosphere at altitudes near 4,000 km, consistent with the INMS measurements. The latitudinal dependence of the minor species indicates that their source is near the equatorial plane. At high altitudes, the minor species were observed primarily at zero latitude, where the 28u species was six times more concentrated than at 5° latitude. At lower altitudes, the peaking ratio was 1, indicating that the species had diffused and was fully mixed into Saturn's H2 atmosphere. The lighter molecule, CH4, diffuses more rapidly than the 28u species. INMS also detected both of these species during the earlier F-ring passes, finding that the neutrals were centered at the ring plane and extended 3,000 km (half width, half max) north and south.
Dynamics of Hydration Water in Sugars and Peptides Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perticaroli, Stefania; Nakanishi, Masahiro; Pashkovski, Eugene

2013-01-01

We analyzed solute and solvent dynamics of sugars and peptides aqueous solutions using extended epolarized light scattering (EDLS) and broadband dielectric spectroscopies (BDS). Spectra measured with both techniques reveal the same mechanism of rotational diffusion of peptides molecules. In the case of sugars, this solute reorientational relaxation can be isolated by EDLS measurements, whereas its ontribution to the dielectric spectra is almost negligible. In the presented analysis, we characterize the hydration water in terms of hydration number and retardation ratio between relaxation times of hydration and bulk water. Both techniques provide similar estimates of . The retardation imposed on themore » hydration water by sugars is 3.3 1.3 and involves only water molecules hydrogen-bonded (HB) to solutes ( 3 water molecules per sugar OH-group). In contrast, polar peptides cause longer range erturbations beyond the first hydration shell, and between 2.8 and 8, increasing with the number of chemical groups engaged in HB formation. We demonstrate that chemical heterogeneity and specific HB interactions play a crucial role in hydration dynamics around polar solutes. The obtained results help to disentangle the role of excluded volume and enthalpic contributions in dynamics of hydration water at the interface with biological molecules.« less
Quantifying atom addition reactions on amorphous solid water: a review of recent laboratory advances

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-06-01

Complex organic molecules found in space are mostly formed on and in the ice mantle covering interstellar dust grains. In clouds where ionizing irradiation is insignificant, chemical reactions on the ice mantle are dominated by thermal processes. Modeling of grain surface chemistry requires detailed information from the laboratory, including sticking coefficients, binding energies, diffusion energy barriers, mechanism of reaction, and chemical desorption rates. In this talk, recent laboratory advances in obtaining these information would be reviewed. Specifically, this talk will focus on the efforts in our group in: 1) Determining the mechanism of atomic hydrogen addition reactions on amorphous solid water (ASW); 2) Measuring the chemical desorption coefficient of H+O3-->O2+OH using the time-resolved scattering technique; and 3) Measuring the diffusion energy barrier of volatile molecules on ASW. Further laboratory studies will be suggested.This research was supported by NSF Astronomy & Astrophysics Research Grant #1615897.
Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.
Structural inhomogeneity of interfacial water at lipid monolayers revealed by surface-specific vibrational pump-probe spectroscopy.

PubMed

Bonn, Mischa; Bakker, Huib J; Ghosh, Avishek; Yamamoto, Susumu; Sovago, Maria; Campen, R Kramer

2010-10-27

We report vibrational lifetime measurements of the OH stretch vibration of interfacial water in contact with lipid monolayers, using time-resolved vibrational sum frequency (VSF) spectroscopy. The dynamics of water in contact with four different lipids are reported and are characterized by vibrational relaxation rates measured at 3200, 3300, 3400, and 3500 cm(-1). We observe that the water molecules with an OH frequency ranging from 3300 to 3500 cm(-1) all show vibrational relaxation with a time constant of T(1) = 180 ± 35 fs, similar to what is found for bulk water. Water molecules with OH groups near 3200 cm(-1) show distinctly faster relaxation dynamics, with T(1) < 80 fs. We successfully model the data by describing the interfacial water containing two distinct subensembles in which spectral diffusion is, respectively, rapid (3300-3500 cm(-1)) and absent (3200 cm(-1)). We discuss the potential biological implications of the presence of the strongly hydrogen-bonded, rapidly relaxing water molecules at 3200 cm(-1) that are decoupled from the bulk water system.
Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin

PubMed Central

Sachdeva, Shivangi; Kolimi, Narendar; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

2016-01-01

Capsular polysaccharides (CPSs) are major bacterial virulent determinants that facilitate host immune evasion. E. coli group1 K30CPS is noncovalently attached to bacterial surface by Wzi, a lectin. Intriguingly, structure based phylogenetic analysis indicates that Wzi falls into porin superfamily. Molecular dynamics (MD) simulations further shed light on dual role of Wzi as it also functions as a bidirectional passive water specific porin. Such a functional role of Wzi was not realized earlier, due to the occluded pore. While five water specific entry points distributed across extracellular & periplasmic faces regulate the water diffusion involving different mechanisms, a luminal hydrophobic plug governs water permeation across the channel. Coincidently, MD observed open state structure of “YQF” triad is seen in sugar-binding site of sodium-galactose cotransporters, implicating its involvement in K30CPS surface anchorage. Importance of Loop 5 (L5) in membrane insertion is yet another highlight. Change in water diffusion pattern of periplasmic substitution mutants suggests Wzi’s role in osmoregulation by aiding in K30CPS hydration, corroborating earlier functional studies. Water molecules located inside β-barrel of Wzi crystal structure further strengthens the role of Wzi in osmoregulation. Thus, interrupting water diffusion or L5 insertion may reduce bacterial virulence. PMID:27320406
Dynamics and Solubility of He and CO 2 in Brine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Tuan Anh; Tenney, Craig M.

2016-09-01

Molecular dynamics simulation was implemented using LAMMPS simulation package (1) to study the diffusivity of He 3 and CO 2 in NaCl aqueous solution. To simulate at infinite dilute gas concentration, we placed one He 3 or CO 2 molecule in an initial simulation box of 24x24x33Å 3 containing 512 water molecules and a certain number of NaCl molecules depending on the concentration. Initial configuration was set up by placing water, NaCl, and gas molecules into different regions in the simulation box. Calculating diffusion coefficient for one He or CO 2 molecule consistently yields poor results. To overcome this, formore » each simulation at specific conditions (i.e., temperature, pressure, and NaCl concentration), we conducted 50 simulations initiated from 50 different configurations. These configurations are obtained by performing the simulation starting from the initial configuration mentioned above in the NVE ensemble (i.e., constant number of particles, volume, and energy). for 100,000 time steps and collecting one configuration every 2,000 times step. The output temperature of this simulation is about 500K. The collected configurations were then equilibrated for 2ns in the NPT ensemble (i.e., constant number of particles, pressure, and temperature) followed by 9ns simulations in the NVT ensemble (i.e., constant number of particles, volume, and temperature). The time step is 1fs for all simulations.« less
A kinetic model for heterogeneous condensation of vapor on an insoluble spherical particle.

PubMed

Luo, Xisheng; Fan, Yu; Qin, Fenghua; Gui, Huaqiao; Liu, Jianguo

2014-01-14

A kinetic model is developed to describe the heterogeneous condensation of vapor on an insoluble spherical particle. This new model considers two mechanisms of cluster growth: direct addition of water molecules from the vapor and surface diffusion of adsorbed water molecules on the particle. The effect of line tension is also included in the model. For the first time, the exact expression of evaporation coefficient is derived for heterogeneous condensation of vapor on an insoluble spherical particle by using the detailed balance. The obtained expression of evaporation coefficient is proved to be also correct in the homogeneous condensation and the heterogeneous condensation on a planar solid surface. The contributions of the two mechanisms to heterogeneous condensation including the effect of line tension are evaluated and analysed. It is found that the cluster growth via surface diffusion of adsorbed water molecules on the particle is more important than the direct addition from the vapor. As an example of our model applications, the growth rate of the cap shaped droplet on the insoluble spherical particle is derived. Our evaluation shows that the growth rate of droplet in heterogeneous condensation is larger than that in homogeneous condensation. These results indicate that an explicit kinetic model is benefit to the study of heterogeneous condensation on an insoluble spherical particle.
Variations of water's local-structure induced by solvation of NaCl

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhang, Feng-Shou; Huang, Yu-Gai; Fang, Xia

2010-03-01

The researches on the structure of water and its changes induced by solutes are of enduring interests. The changes of the local structure of liquid water induced by NaCl solute under ambient conditions are studied and presented quantitatively with some order parameters and visualized with 2-body and 3-body correlation functions. The results show that, after the NaCl are solvated, the translational order t of water is decreased for the suppression of the second hydration shells around H2O molecules; the tetrahedral order (q) of water is also decreased and its favorite distribution peak moves from 0.76 to 0.5. In addition, the orientational freedom k and the diffusion coefficient D of water molecules are reduced because of new formed hydrogen-bonding structures between water and solvated ions.
The effects of charge, polymerization, and cluster size on the diffusivity of dissolved Si species in pore water

NASA Astrophysics Data System (ADS)

Yokoyama, Tadashi; Sakuma, Hiroshi

2018-03-01

Silicon (Si) is the most abundant cation in crustal rocks. The charge and degree of polymerization of dissolved Si significantly change depending on solution pH and Si concentration. We used molecular dynamics (MD) simulations to predict the self-diffusion coefficients of dissolved Si, DSi, for 15 monomeric and polymeric species at ambient temperature. The results showed that DSi decreased with increasing negative charge and increasing degree of polymerization. The relationship between DSi and charge (Z) can be expressed by DSi/10-6 = 2.0 + 9.8e0.47Z, and that between DSi and number of polymerization (NSi) by DSi/10-6 = 9.7/NSi0.56. The results also revealed that multiple Si molecules assembled into a cluster and D decreased as the cluster size increased. Experiments to evaluate the diffusivity of Si in pore water revealed that the diffusion coefficient decreased with increasing Si concentration, a result consistent with the MD simulations. Simulation results can now be used to quantitatively assess water-rock interactions and water-concrete reactions over a wide range of environmentally relevant conditions.
The behaviour of water and sodium chloride solution confined into asbestos nanotube

NASA Astrophysics Data System (ADS)

Fomin, Yu. D.; Ryzhov, V. N.; Tsiok, E. N.

2016-08-01

We present the molecular simulation study of the behaviour of water and sodium chloride solution confined in lizardite asbestos nanotube which is a typical example of hydrophilic confinement. The local structure and orientational and dynamic properties are studied. It is shown that at low enough temperatures there is a well-defined orientational ordering of the water molecules. At high local densities corresponding to the maxima of the density distribution function, the water molecules are oriented parallel to the axis of the tube. It is also shown that the diffusion coefficient drops about two orders of magnitude comparing to the bulk case. The behaviour of sodium chloride solutions is also considered and the formation of double layer is observed.
Scaling behaviour for the water transport in nanoconfined geometries

PubMed Central

Chiavazzo, Eliodoro; Fasano, Matteo; Asinari, Pietro; Decuzzi, Paolo

2014-01-01

The transport of water in nanoconfined geometries is different from bulk phase and has tremendous implications in nanotechnology and biotechnology. Here molecular dynamics is used to compute the self-diffusion coefficient D of water within nanopores, around nanoparticles, carbon nanotubes and proteins. For almost 60 different cases, D is found to scale linearly with the sole parameter θ as D(θ)=DB[1+(DC/DB−1)θ], with DB and DC the bulk and totally confined diffusion of water, respectively. The parameter θ is primarily influenced by geometry and represents the ratio between the confined and total water volumes. The D(θ) relationship is interpreted within the thermodynamics of supercooled water. As an example, such relationship is shown to accurately predict the relaxometric response of contrast agents for magnetic resonance imaging. The D(θ) relationship can help in interpreting the transport of water molecules under nanoconfined conditions and tailoring nanostructures with precise modulation of water mobility. PMID:24699509
Molecular dynamics simulation of the diffusion of uranium species in clay pores.

PubMed

Liu, Xiao-yu; Wang, Lu-hua; Zheng, Zhong; Kang, Ming-liang; Li, Chun; Liu, Chun-li

2013-01-15

Molecular dynamics simulations were carried out to investigate the diffusive behavior of aqueous uranium species in montmorillonite pores. Three uranium species (UO(2)(2+), UO(2)CO(3), UO(2)(CO(3))(2)(2-)) were confirmed in both the adsorbed and diffuse layers. UO(2)(CO(3))(3)(4-) was neglected in the subsequent analysis due to its scare occurrence. The species-based diffusion coefficients in montmorillonite pores were then calculated, and compared with the water mobility and their diffusivity in aqueous solution/feldspar nanosized fractures. Three factors were considered that affected the diffusive behavior of the uranium species: the mobility of water, the self-diffusion coefficient of the aqueous species, and the electrostatic forces between the negatively charged surface and charged molecules. The mobility of U species in the adsorbed layer decreased in the following sequence: UO(2)(2+)>UO(2)CO(3)>UO(2)(CO(3))(2)(2-). In the diffuse layer, we obtained the highest diffusion coefficient for UO(2)(CO(3))(2)(2-) with the value of 5.48×10(-10) m(2) s(-1), which was faster than UO(2)(2+). For these two charged species, the influence of electrostatic forces on the diffusion of solutes in the diffuse layer is overwhelming, whereas the influence of self-diffusion and water mobility is minor. Our study demonstrated that the negatively charged uranyl carbonate complex must be addressed in the safety assessment of potential radioactive waste disposal systems. Copyright © 2012 Elsevier B.V. All rights reserved.
Insight into the molecular mechanism of water evaporation via the finite temperature string method.

PubMed

Musolino, Nicholas; Trout, Bernhardt L

2013-04-07

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.
Diffusion through Pig Gastric Mucin: Effect of Relative Humidity

PubMed Central

Runnsjö, Anna; Dabkowska, Aleksandra P.; Sparr, Emma; Kocherbitov, Vitaly; Arnebrant, Thomas; Engblom, Johan

2016-01-01

Mucus covers the epithelium found in all intestinal tracts, where it serves as an important protecting barrier, and pharmaceutical drugs administrated by the oral, rectal, vaginal, ocular, or nasal route need to penetrate the mucus in order to reach their targets. Furthermore, the diffusion in mucus as well as the viscosity of mucus in the eyes, nose and throat can change depending on the relative humidity of the surrounding air. In this study we have investigated how diffusion through gels of mucin, the main protein in mucus, is affected by changes in ambient relative humidity (i.e. water activity). Already a small decrease in water activity was found to give rise to a significant decrease in penetration rate through the mucin gel of the antibacterial drug metronidazole. We also show that a decrease in water activity leads to decreased diffusion rate in the mucin gel for the fluorophore fluorescein. This study shows that it is possible to alter transport rates of molecules through mucus by changing the water activity in the gel. It furthermore illustrates the importance of considering effects of the water activity in the mucosa during development of potential pharmaceuticals. PMID:27336158
First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

NASA Astrophysics Data System (ADS)

Yang, Yu; Zhang, Ping

2015-05-01

Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.
Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.

1997-01-01

The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.
Boron nitride nanotube as a delivery system for platinum drugs: Drug encapsulation and diffusion coefficient prediction.

PubMed

Khatti, Zahra; Hashemianzadeh, Seyed Majid

2016-06-10

Molecular dynamics (MD) simulation has been applied to investigate a drug delivery system based on boron nitride nanotubes, particularly the delivery of platinum-based anticancer drugs. For this propose, the behavior of carboplatin drugs inserted in boron nitride nanotubes (BNNT) as a carrier was studied. The diffusion rate of water molecules and carboplatin was investigated inside functionalized and pristine boron nitride nanotubes. The penetration rate of water and drug in functionalized BNNT was higher than that in pristine BNNT due to favorable water-mediated hydrogen bonding in hydroxyl edge-functionalized BNNT. Additionally, the encapsulation of multiple carboplatin drugs inside functionalized boron nitride nanotubes with one to five drug molecules confined inside the nanotube cavity was examined. At high drug loading, the hydrogen bond formation between adjacent drugs and the non-bonded van der Waals interaction between carboplatin and functionalized BNNT inner surface were found to be influential in drug displacement within the functionalized BNNT cavity for higher drug-loading capacity. Copyright © 2016 Elsevier B.V. All rights reserved.
NMR investigation of the short-chain ionic surfactant-water systems.

PubMed

Popova, M V; Tchernyshev, Y S; Michel, D

2004-02-03

The structure and dynamics of surfactant molecules [CH3(CH2)7COOK] in heavy water solutions were investigated by 1H and 2H NMR. A double-exponential attenuation of the spin-echo amplitude in a Carr-Purcell-Meiboom-Gill experiment was found. We expect correspondence to both bounded and monomeric states. At high concentrations in the NMR self-diffusion measurements also a double-exponential decay of the spin-echo signal versus the square of the dc magnetic gradient was observed. The slow component of the diffusion process is caused by micellar aggregates, while the fast component is the result of the self-diffusion of the monomers through the micelles. The self-diffusion studies indicate that the form of micelles changes with increasing total surfactant concentration. The critical temperature range for self-association is reflected in the 1H transverse relaxation.
Using Perturbation Theory to Compute the Morphological Similarity of Diffusion Tensors

PubMed Central

Bansal, Ravi; Staib, Lawrence H.; Xu, Dongrong; Laine, Andrew F.; Royal, Jason; Peterson, Bradley S.

2008-01-01

Computing the morphological similarity of Diffusion Tensors (DTs) at neighboring voxels within a DT image, or at corresponding locations across different DT images, is a fundamental and ubiquitous operation in the post-processing of DT images. The morphological similarity of DTs typically has been computed using either the Principal Directions (PDs) of DTs (i.e., the direction along which water molecules diffuse preferentially) or their tensor elements. Although comparing PDs allows the similarity of one morphological feature of DTs to be visualized directly in eigenspace, this method takes into account only a single eigenvector, and it is therefore sensitive to the presence of noise in the images that can introduce error into the estimation of that vector. Although comparing tensor elements, rather than PDs, is comparatively more robust to the effects of noise, the individual elements of a given tensor do not directly reflect the diffusion properties of water molecules. We propose a measure for computing the morphological similarity of DTs that uses both their eigenvalues and eigenvectors, and that also accounts for the noise levels present in DT images. Our measure presupposes that DTs in a homogeneous region within or across DT images are random perturbations of one another in the presence of noise. The similarity values that are computed using our method are smooth (in the sense that small changes in eigenvalues and eigenvectors cause only small changes in similarity), and they are symmetric when differences in eigenvalues and eigenvectors are also symmetric. In addition, our method does not presuppose that the corresponding eigenvectors across two DTs have been identified accurately, an assumption that is problematic in the presence of noise. Because we compute the similarity between DTs using their eigenspace components, our similarity measure relates directly to both the magnitude and the direction of the diffusion of water molecules. The favorable performance characteristics of our measure offer the prospect of substantially improving additional post-processing operations that are commonly performed on DTI datasets, such as image segmentation, fiber tracking, noise filtering, and spatial normalization. PMID:18450533

Voxel-Wise Comparisons of the Morphology of Diffusion Tensors Across Groups of Experimental Subjects

PubMed Central

Bansal, Ravi; Staib, Lawrence H.; Plessen, Kerstin J.; Xu, Dongrong; Royal, Jason; Peterson, Bradley S.

2007-01-01

Water molecules in the brain diffuse preferentially along the fiber tracts within white matter, which form the anatomical connections across spatially distant brain regions. A diffusion tensor (DT) is a probabilistic ellipsoid composed of 3 orthogonal vectors, each having a direction and an associated scalar magnitude, that represent the probability of water molecules diffusing in each of those directions. The 3D morphologies of DTs can be compared across groups of subjects to reveal disruptions in structural organization and neuroanatomical connectivity of the brains of persons with various neuropsychiatric illnesses. Comparisons of tensor morphology across groups have typically been performed on scalar measures of diffusivity, such as Fractional Anisotropy (FA), rather than directly on the complex 3D morphologies of DTs. Scalar measures, however, are related in nonlinear ways to the eigenvalues and eigenvectors that create the 3D morphologies of DTs. We present a mathematical framework that permits the direct comparison across groups of mean eigenvalues and eigenvectors of individual DTs. We show that group-mean eigenvalues and eigenvectors are multivariate Gaussian distributed, and we use the Delta method to compute their approximate covariance matrices. Our results show that the theoretically computed Mean Tensor (MT) eigenvectors and eigenvalues match well with their respective true values. Furthermore, a comparison of synthetically generated groups of DTs highlights the limitations of using FA to detect group differences. Finally, analyses of in vivo DT data using our method reveal significant between-group differences in diffusivity along fiber tracts within white matter, whereas analyses based on FA values failed to detect some of these differences. PMID:18006284
Diffusion and related transport mechanisms in brain tissue

NASA Astrophysics Data System (ADS)

Nicholson, Charles

2001-07-01

Diffusion plays a crucial role in brain function. The spaces between cells can be likened to the water phase of a foam and many substances move within this complicated region. Diffusion in this interstitial space can be accurately modelled with appropriate modifications of classical equations and quantified from measurements based on novel micro-techniques. Besides delivering glucose and oxygen from the vascular system to brain cells, diffusion also moves informational substances between cells, a process known as volume transmission. Deviations from expected results reveal how local uptake, degradation or bulk flow may modify the transport of molecules. Diffusion is also essential to many therapies that deliver drugs to the brain. The diffusion-generated concentration distributions of well-chosen molecules also reveal the structure of brain tissue. This structure is represented by the volume fraction (void space) and the tortuosity (hindrance to diffusion imposed by local boundaries or local viscosity). Analysis of these parameters also reveals how the local geometry of the brain changes with time or under pathological conditions. Theoretical and experimental approaches borrow from classical diffusion theory and from porous media concepts. Earlier studies were based on radiotracers but the recent methods use a point-source paradigm coupled with micro-sensors or optical imaging of macromolecules labelled with fluorescent tags. These concepts and methods are likely to be applicable elsewhere to measure diffusion properties in very small volumes of highly structured but delicate material.
Design and validation of diffusion MRI models of white matter

NASA Astrophysics Data System (ADS)

Jelescu, Ileana O.; Budde, Matthew D.

2017-11-01

Diffusion MRI is arguably the method of choice for characterizing white matter microstructure in vivo. Over the typical duration of diffusion encoding, the displacement of water molecules is conveniently on a length scale similar to that of the underlying cellular structures. Moreover, water molecules in white matter are largely compartmentalized which enables biologically-inspired compartmental diffusion models to characterize and quantify the true biological microstructure. A plethora of white matter models have been proposed. However, overparameterization and mathematical fitting complications encourage the introduction of simplifying assumptions that vary between different approaches. These choices impact the quantitative estimation of model parameters with potential detriments to their biological accuracy and promised specificity. First, we review biophysical white matter models in use and recapitulate their underlying assumptions and realms of applicability. Second, we present up-to-date efforts to validate parameters estimated from biophysical models. Simulations and dedicated phantoms are useful in assessing the performance of models when the ground truth is known. However, the biggest challenge remains the validation of the “biological accuracy” of estimated parameters. Complementary techniques such as microscopy of fixed tissue specimens have facilitated direct comparisons of estimates of white matter fiber orientation and densities. However, validation of compartmental diffusivities remains challenging, and complementary MRI-based techniques such as alternative diffusion encodings, compartment-specific contrast agents and metabolites have been used to validate diffusion models. Finally, white matter injury and disease pose additional challenges to modeling, which are also discussed. This review aims to provide an overview of the current state of models and their validation and to stimulate further research in the field to solve the remaining open questions and converge towards consensus.
Design and validation of diffusion MRI models of white matter

PubMed Central

Jelescu, Ileana O.; Budde, Matthew D.

2018-01-01

Diffusion MRI is arguably the method of choice for characterizing white matter microstructure in vivo. Over the typical duration of diffusion encoding, the displacement of water molecules is conveniently on a length scale similar to that of the underlying cellular structures. Moreover, water molecules in white matter are largely compartmentalized which enables biologically-inspired compartmental diffusion models to characterize and quantify the true biological microstructure. A plethora of white matter models have been proposed. However, overparameterization and mathematical fitting complications encourage the introduction of simplifying assumptions that vary between different approaches. These choices impact the quantitative estimation of model parameters with potential detriments to their biological accuracy and promised specificity. First, we review biophysical white matter models in use and recapitulate their underlying assumptions and realms of applicability. Second, we present up-to-date efforts to validate parameters estimated from biophysical models. Simulations and dedicated phantoms are useful in assessing the performance of models when the ground truth is known. However, the biggest challenge remains the validation of the “biological accuracy” of estimated parameters. Complementary techniques such as microscopy of fixed tissue specimens have facilitated direct comparisons of estimates of white matter fiber orientation and densities. However, validation of compartmental diffusivities remains challenging, and complementary MRI-based techniques such as alternative diffusion encodings, compartment-specific contrast agents and metabolites have been used to validate diffusion models. Finally, white matter injury and disease pose additional challenges to modeling, which are also discussed. This review aims to provide an overview of the current state of models and their validation and to stimulate further research in the field to solve the remaining open questions and converge towards consensus. PMID:29755979
Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

PubMed Central

SHETTY, ANIL N.; CHIANG, SHARON; MALETIC-SAVATIC, MIRJANA; KASPRIAN, GREGOR; VANNUCCI, MARINA; LEE, WESLEY

2016-01-01

In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal–Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain. PMID:27441031
Dynamical properties of the hydration shell of fully deuterated myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Achterhold, Klaus; Parak, Fritz G.; Ostermann, Andreas

2011-10-15

Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 {sup 1}H{sub 2}O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 A{sup -1} and a temperature range from 4 to 297 K. We used neutrons with a wavelength of {lambda}{alpha}E 6 A and an energy resolution of about 65 {mu}eV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra causedmore » by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjoelander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time {tau}{sub 0} in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time {tau}{sub 1} in a nonbound state followed again by the oscillatory motions for {tau}{sub 0} and so forth. We used the general formulation with no simplifications as {tau}{sub 0}>>{tau}{sub 1} or {tau}{sub 1}>>{tau}{sub 0}. At room temperature, we obtained {tau}{sub 0} {alpha}E 104 ps and {tau}{sub 1} {alpha}E 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.« less
Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

PubMed

Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

2013-02-01

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.
Thermal desorption of formamide and methylamine from graphite and amorphous water ice surfaces

NASA Astrophysics Data System (ADS)

Chaabouni, H.; Diana, S.; Nguyen, T.; Dulieu, F.

2018-04-01

Context. Formamide (NH2CHO) and methylamine (CH3NH2) are known to be the most abundant amine-containing molecules in many astrophysical environments. The presence of these molecules in the gas phase may result from thermal desorption of interstellar ices. Aims: The aim of this work is to determine the values of the desorption energies of formamide and methylamine from analogues of interstellar dust grain surfaces and to understand their interaction with water ice. Methods: Temperature programmed desorption (TPD) experiments of formamide and methylamine ices were performed in the sub-monolayer and monolayer regimes on graphite (HOPG) and non-porous amorphous solid water (np-ASW) ice surfaces at temperatures 40-240 K. The desorption energy distributions of these two molecules were calculated from TPD measurements using a set of independent Polanyi-Wigner equations. Results: The maximum of the desorption of formamide from both graphite and ASW ice surfaces occurs at 176 K after the desorption of H2O molecules, whereas the desorption profile of methylamine depends strongly on the substrate. Solid methylamine starts to desorb below 100 K from the graphite surface. Its desorption from the water ice surface occurs after 120 K and stops during the water ice sublimation around 150 K. It continues to desorb from the graphite surface at temperatures higher than160 K. Conclusions: More than 95% of solid NH2CHO diffuses through the np-ASW ice surface towards the graphitic substrate and is released into the gas phase with a desorption energy distribution Edes = 7460-9380 K, which is measured with the best-fit pre-exponential factor A = 1018 s-1. However, the desorption energy distribution of methylamine from the np-ASW ice surface (Edes = 3850-8420 K) is measured with the best-fit pre-exponential factor A = 1012 s-1. A fraction of solid methylamine monolayer of roughly 0.15 diffuses through the water ice surface towards the HOPG substrate. This small amount of methylamine desorbs later with higher binding energies (5050-8420 K) that exceed that of the crystalline water ice (Edes = 4930 K), which is calculated with the same pre-exponential factor A = 1012 s-1. The best wetting ability of methylamine compared to H2O molecules makes CH3NH2 molecules a refractory species for low coverage. Other binding energies of astrophysical relevant molecules are gathered and compared, but we could not link the chemical functional groups (amino, methyl, hydroxyl, and carbonyl) with the binding energy properties. Implications of these high binding energies are discussed.
Hydrogen in rocks: an energy source for deep microbial communities

NASA Technical Reports Server (NTRS)

Freund, Friedemann; Dickinson, J. Thomas; Cash, Michele

2002-01-01

To survive in deep subsurface environments, lithotrophic microbial communities require a sustainable energy source such as hydrogen. Though H2 can be produced when water reacts with fresh mineral surfaces and oxidizes ferrous iron, this reaction is unreliable since it depends upon the exposure of fresh rock surfaces via the episodic opening of cracks and fissures. A more reliable and potentially more voluminous H2 source exists in nominally anhydrous minerals of igneous and metamorphic rocks. Our experimental results indicate that H2 molecules can be derived from small amounts of H2O dissolved in minerals in the form of hydroxyl, OH- or O3Si-OH, whenever such minerals crystallized in an H2O-laden environment. Two types of experiments were conducted. Single crystal fracture experiments indicated that hydroxyl pairs undergo an in situ redox conversion to H2 molecules plus peroxy links, O3Si/OO\\SiO3. While the peroxy links become part of the mineral structure, the H2 molecules diffused out of the freshly fractured mineral surfaces. If such a mechanism occurred in natural settings, the entire rock column would become a volume source of H2. Crushing experiments to facilitate the outdiffusion of H2 were conducted with common crustal igneous rocks such as granite, andesite, and labradorite. At least 70 nmol of H2/g diffused out of coarsely crushed andesite, equivalent at standard pressure and temperature to 5,000 cm3 of H2/m3 of rock. In the water-saturated, biologically relevant upper portion of the rock column, the diffusion of H2 out of the minerals will be buffered by H2 saturation of the intergranular water film.
Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

NASA Astrophysics Data System (ADS)

Zhang, Huiming; Xie, Yang; Ji, Tongyu

2007-06-01

The off-resonance rotating frame technique based on the spin relaxation properties of off-resonance T1 ρ can significantly increase the sensitivity of detecting paramagnetic labeling at high magnetic fields by MRI. However, the in vivo detectable dimension for labeled cell clusters/tissues in T1 ρ-weighted images is limited by the water diffusion-exchange between mesoscopic scale compartments. An experimental investigation of the effect of water diffusion-exchange between compartments on the paramagnetic relaxation enhancement of paramagnetic agent compartment is presented for in vitro/ in vivo models. In these models, the size of paramagnetic agent compartment is comparable to the mean diffusion displacement of water molecules during the long RF pulses that are used to generate the off-resonance rotating frame. The three main objectives of this study were: (1) to qualitatively correlate the effect of water diffusion-exchange with the RF parameters of the long pulse and the rates of water diffusion, (2) to explore the effect of water diffusion-exchange on the paramagnetic relaxation enhancement in vitro, and (3) to demonstrate the paramagnetic relaxation enhancement in vivo. The in vitro models include the water permeable dialysis tubes or water permeable hollow fibers embedded in cross-linked proteins gels. The MWCO of the dialysis tubes was chosen from 0.1 to 15 kDa to control the water diffusion rate. Thin hollow fibers were chosen to provide sub-millimeter scale compartments for the paramagnetic agents. The in vivo model utilized the rat cerebral vasculatures as a paramagnetic agent compartment, and intravascular agents (Gd-DTPA) 30-BSA were administrated into the compartment via bolus injections. Both in vitro and in vivo results demonstrate that the paramagnetic relaxation enhancement is predominant in the T1 ρ-weighted image in the presence of water diffusion-exchange. The T1 ρ contrast has substantially higher sensitivity than the conventional T1 contrast in detecting paramagnetic agents, especially at low paramagnetic agent volumetric fractions, low paramagnetic agent concentrations, and low RF amplitudes. Short pulse duration, short pulse recycle delay and efficient paramagnetic relaxation can reduce the influence of water diffusion-exchange on the paramagnetic enhancement. This study paves the way for the design of off-resonance rotating experiments to detect labeled cell clusters/tissue compartments in vivo at a sub-millimeter scale.
Molecular dynamics insights into the structural and diffusive properties of ZIF-8/PDMS mixed matrix membranes in the n-butanol/water pervaporation process

NASA Astrophysics Data System (ADS)

Sun, Tao; Fang, Manquan; Wu, Zhen; Yu, Lixin; Li, Jiding

2017-04-01

Molecular dynamics (MD) simulation was used to study the structural and diffusive properties of zeolitic imidazolate framework-8 (ZIF-8)/polydimethylsiloxane (PDMS), a novel alcohol-permselective mixed matrix membrane (MMM). Simulation models of one pure PDMS membrane and three ZIF-8/PDMS MMMs with increasing loadings were successfully constructed. Non-bond energy turned out to be a strong attractive interaction between the PDMS matrix and ZIF-8 cells. The morphology and mobility of PDMS chains were characterized by mean square displacement (MSD). The fraction of free volume (FFV) of the pure membrane and MMMs was calculated and showed declining trends with increasing ZIF-8 loadings. The diffusion coefficients of n-butanol and water molecules were calculated by the Einstein relation. {D}n-\\text{butanol} first increased then decreased, while {D}{{water}} decreased with the increasing loadings. The mechanism of selective diffusion behaviour was investigated and it was found that the inner channels of ZIF-8 provided selective pathways for n-butanol. Diffusion coefficients were correlated with FFV and the results showed that the logarithm of {D}{{water}} demonstrated a good linear relation with the inverse FFV and was in agreement with the free volume theory, while {D}n-\\text{butanol} showed a significant deviation in the case of MMM-1 due to the selective diffusion channels provided by ZIF-8.
[From Brownian motion to mind imaging: diffusion MRI].

PubMed

Le Bihan, Denis

2006-11-01

The success of diffusion MRI, which was introduced in the mid 1980s is deeply rooted in the powerful concept that during their random, diffusion-driven movements water molecules probe tissue structure at a microscopic scale well beyond the usual image resolution. The observation of these movements thus provides valuable information on the structure and the geometric organization of tissues. The most successful application of diffusion MRI has been in brain ischemia, following the discovery that water diffusion drops at a very early stage of the ischemic event. Diffusion MRI provides some patients with the opportunity to receive suitable treatment at a very acute stage when brain tissue might still be salvageable. On the other hand, diffusion is modulated by the spatial orientation of large bundles of myelinated axons running in parallel through in brain white matter. This feature can be exploited to map out the orientation in space of the white matter tracks and to visualize the connections between different parts of the brain on an individual basis. Furthermore, recent data suggest that diffusion MRI may also be used to visualize rapid dynamic tissue changes, such as neuronal swelling, associated with cortical activation, offering a new and direct approach to brain functional imaging.
New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water.

PubMed

Kinoshita, Koji; Parra, Elisa; Needham, David

2017-02-15

Currently available dynamic surface tension (DST) measurement methods, such as Wilhelmy plate, droplet- or bubble-based methods, still have various experimental limitations such as the large size of the interface, convection in the solution, or a certain "dead time" at initial measurement. These limitations create inconsistencies for the kinetic analysis of surfactant adsorption/desorption, especially significant for ionic surfactants. Here, the "micropipette interfacial area-expansion method" was introduced and validated as a new DST measurement having a high enough sensitivity to detect diffusion controlled molecular adsorption at the air-water interfaces. To validate the new technique, the diffusion coefficient of 1-Octanol in water was investigated with existing models: the Ward Tordai model for the long time adsorption regime (1-100s), and the Langmuir and Frumkin adsorption isotherm models for surface excess concentration. We found that the measured diffusion coefficient of 1-Octanol, 7.2±0.8×10 -6 cm 2 /s, showed excellent agreement with the result from an alternative method, "single microdroplet catching method", to measure the diffusion coefficient from diffusion-controlled microdroplet dissolution, 7.3±0.1×10 -6 cm 2 /s. These new techniques for determining adsorption and diffusion coefficients can apply for a range of surface active molecules, especially the less-characterized ionic surfactants, and biological compounds such as lipids, peptides, and proteins. Copyright Â© 2016 Elsevier Inc. All rights reserved.
Evolution and Transport of Water in the Upper Regolith of Mars

NASA Technical Reports Server (NTRS)

Hudson, T. L.; Aharonson, O.; Schorghofer, N.; Hecht, M. H.; Bridges, N. T.; Green, J. R.

2003-01-01

Long standing theoretical predictions [1-3], as well as recent spacecraft observations [4] indicate that large quantities of ice is present in the high latitudes upper decimeters to meters of the Martian regolith. At shallower depths and warmer locations small amounts of H2O, either adsorbed or free, may be present transiently. An understanding of the evolution of water based on theoretical and experimental considerations of the processes operating at the Martian environment is required. In particular, the porosity, diffusivity, and permeability of soils and their effect on water vapor transport under Mars-like conditions have been estimated, but experimental validation of such models is lacking. Goal: Three related mechanisms may affect water transport in the upper Martian regolith. 1) diffusion along a concentration gradient under isobaric conditions, 2) diffusion along a thermal gradient, which may give rise to a concentration gradient as ice sublimes or molecules desorb from the regolith, and 3) hydraulic flow, or mass motion in response to a pressure gradient. Our combined theoretical and experimental investigation seeks to disentangle these mechanisms and determine which process(es) are dominant in the upper regolith over various timescales. A detailed one-dimensional model of the upper regolith is being created which incorporates water adsorption/ desorption, condensation, porosity, diffusivity, and permeability effects. Certain factors such as diffusivity are difficult to determine theoretically due to the wide range of intrinsic grain properties such as particle sizes, shapes, packing densities, and emergent properties such as tortuosity. An experiment is being designed which will allow us to more accurately determine diffusivity, permeability, and water desorption isotherms for regolith simulants.
Water Permeation through the Sodium-Dependent Galactose Cotransporter vSGLT

PubMed Central

Choe, Seungho; Rosenberg, John M.; Abramson, Jeff; Wright, Ernest M.; Grabe, Michael

2010-01-01

It is well accepted that cotransporters facilitate water movement by two independent mechanisms: osmotic flow through a water channel in the protein and flow driven by ion/substrate cotransport. However, the molecular mechanism of transport-linked water flow is controversial. Some researchers believe that it occurs via cotransport, in which water is pumped along with the transported cargo, while others believe that flow is osmotic in response to an increase in intracellular osmolarity. In this letter, we report the results of a 200-ns molecular dynamics simulation of the sodium-dependent galactose cotransporter vSGLT. Our simulation shows that a significant number of water molecules cross the protein through the sugar-binding site in the presence as well as the absence of galactose, and 70–80 water molecules accompany galactose as it moves from the binding site into the intracellular space. During this event, the majority of water molecules in the pathway are unable to diffuse around the galactose, resulting in water in the inner half of the transporter being pushed into the intracellular space and replaced by extracellular water. Thus, our simulation supports the notion that cotransporters act as both passive water channels and active water pumps with the transported substrate acting as a piston to rectify the motion of water. PMID:20923633
Permeability of uncharged organic molecules in reverse osmosis desalination membranes.

PubMed

Dražević, Emil; Košutić, Krešimir; Svalina, Marin; Catalano, Jacopo

2017-06-01

Reverse osmosis (RO) membranes are primarily designed for removal of salts i.e. for desalination of brackish and seawater, but they have also found applications in removal of organic molecules. While it is clear that steric exclusion is the dominant removal mechanism, the fundamental explanation for how and why the separation occurs remains elusive. Until recently there was no strong microscopic evidences elucidating the structure of the active polyamide layers of RO membranes, and thus they have been conceived as "black boxes"; or as an array of straight capillaries with a distribution of radii; or as polymers with a small amount of polymer free domains. The knowledge of diffusion and sorption coefficients is a prerequisite for understanding the intrinsic permeability of any organic solute in any polymer. At the same time, it is technically challenging to accurately measure these two fundamental parameters in very thin (20-300 nm) water-swollen active layers. In this work we have measured partition and diffusion coefficients and RO permeabilities of ten organic solutes in water-swollen active layers of two types of RO membranes, low (SWC4+) and high flux (XLE). We deduced from our results and recent microscopic studies that the solute flux of organic molecules in polyamide layer of RO membranes occurs in two domains, dense polymer (the key barrier layer) and the water filled domains. Copyright © 2017 Elsevier Ltd. All rights reserved.
Dynamics of water in sulfonated poly(phenylene) membranes

NASA Astrophysics Data System (ADS)

Osti, Naresh; Etampawala, Thusitha; Shrestha, Umesh; Perahia, Dvora; Cornelius, Christopher

2011-03-01

The dynamics of water in networks formed by highly rigid ionic polymers, sulfonated poly(phenylene) as observed by quasi elastic neutron scattering (QENS) is presented. These rigid ionic polymers have potential as effective ion exchange membranes with impact on a large number of applications from water purification to clean energy, where its rigidity distinguishes it from other ionic polymers. Its transport characteristics are affected by its rigidness as well as by direct interactions with the solvent. Our QENS studies as a function of sulfonation levels, temperature and solvent content have shown that on the time scale of the measurement, the polymers are rigid. While macroscopically all samples swell, and transport water, the water molecules appear locally rather confined. Water however remind non-frozen to subzero temperatures. The results will be discussed in view of theoretical models including continues diffusion and hopping of solvent molecules.
Kinetic analysis of an anion exchange absorbent for CO2 capture from ambient air.

PubMed

Shi, Xiaoyang; Li, Qibin; Wang, Tao; Lackner, Klaus S

2017-01-01

This study reports a preparation method of a new moisture swing sorbent for CO2 capture from air. The new sorbent components include ion exchange resin (IER) and polyvinyl chloride (PVC) as a binder. The IER can absorb CO2 when surrounding is dry and release CO2 when surrounding is wet. The manuscript presents the studies of membrane structure, kinetic model of absorption process, performance of desorption process and the diffusivity of water molecules in the CO2 absorbent. It has been proved that the kinetic performance of CO2 absorption/desorption can be improved by using thin binder and hot water treatment. The fast kinetics of P-100-90C absorbent is due to the thin PVC binder, and high diffusion rate of H2O molecules in the sample. The impressive is this new CO2 absorbent has the fastest CO2 absorption rate among all absorbents which have been reported by other up-to-date literatures.
Kinetic analysis of an anion exchange absorbent for CO2 capture from ambient air

PubMed Central

Shi, Xiaoyang; Li, Qibin; Lackner, Klaus S.

2017-01-01

This study reports a preparation method of a new moisture swing sorbent for CO2 capture from air. The new sorbent components include ion exchange resin (IER) and polyvinyl chloride (PVC) as a binder. The IER can absorb CO2 when surrounding is dry and release CO2 when surrounding is wet. The manuscript presents the studies of membrane structure, kinetic model of absorption process, performance of desorption process and the diffusivity of water molecules in the CO2 absorbent. It has been proved that the kinetic performance of CO2 absorption/desorption can be improved by using thin binder and hot water treatment. The fast kinetics of P-100-90C absorbent is due to the thin PVC binder, and high diffusion rate of H2O molecules in the sample. The impressive is this new CO2 absorbent has the fastest CO2 absorption rate among all absorbents which have been reported by other up-to-date literatures. PMID:28640914
Translational and rotational dynamics of monosaccharide solutions.

PubMed

Lelong, Gérald; Howells, W Spencer; Brady, John W; Talón, César; Price, David L; Saboungi, Marie-Louise

2009-10-01

Molecular dynamics computer simulations have been carried out on aqueous solutions of glucose at concentrations bracketing those previously measured with quasi-elastic neutron scattering (QENS), in order to investigate the motions and interactions of the sugar and water molecules. In addition, QENS measurements have been carried out on fructose solutions to determine whether the effects previously observed for glucose apply to monosaccharide solutions. The simulations indicate a dynamical analogy between higher solute concentration and lower temperature that could provide a key explanation of the bioprotective phenomena observed in many living organisms. The experimental results on fructose solutions show qualitatively similar behavior to the glucose solutions. The dynamics of the water molecules are essentially the same, while the translational diffusion of the sugar molecules is slightly faster in the fructose solutions.

Rapid Water Transport through Organic Layers on Ice.

PubMed

Kong, Xiangrui; Toubin, Céline; Habartova, Alena; Pluharova, Eva; Roeselova, Martina; Pettersson, Jan B C

2018-05-31

Processes involving atmospheric aerosol and cloud particles are affected by condensation of organic compounds that are omnipresent in the atmosphere. On ice particles, organic compounds with hydrophilic functional groups form hydrogen bonds with the ice and orient their hydrophobic groups away from the surface. The organic layer has been expected to constitute a barrier to gas uptake, but recent experimental studies suggest that the accommodation of water molecules on ice is only weakly affected by condensed short-chain alcohol layers. Here, we employ molecular dynamics simulations to study the water interactions with n-butanol covered ice at 200 K and show that the small effect of the condensed layer is due to efficient diffusion of water molecules along the surface plane while seeking appropriate sites to penetrate, followed by penetration driven by the combined attractive forces from butanol OH groups and water molecules within the ice. The water molecules that penetrate through the n-butanol layer become strongly bonded by approximately three hydrogen bonds at the butanol-ice interface. The obtained accommodation coefficient (0.81 ± 0.03) is in excellent agreement with results from previous environmental molecular beam experiments, leading to a picture where an adsorbed n-butanol layer does not alter the apparent accommodation coefficient but dramatically changes the detailed molecular dynamics and kinetics.
Hindered diffusion of high molecular weight compounds in brain extracellular microenvironment measured with integrative optical imaging.

PubMed

Nicholson, C; Tao, L

1993-12-01

This paper describes the theory of an integrative optical imaging system and its application to the analysis of the diffusion of 3-, 10-, 40-, and 70-kDa fluorescent dextran molecules in agarose gel and brain extracellular microenvironment. The method uses a precisely defined source of fluorescent molecules pressure ejected from a micropipette, and a detailed theory of the intensity contributions from out-of-focus molecules in a three-dimensional medium to a two-dimensional image. Dextrans tagged with either tetramethylrhodamine or Texas Red were ejected into 0.3% agarose gel or rat cortical slices maintained in a perfused chamber at 34 degrees C and imaged using a compound epifluorescent microscope with a 10 x water-immersion objective. About 20 images were taken at 2-10-s intervals, recorded with a cooled CCD camera, then transferred to a 486 PC for quantitative analysis. The diffusion coefficient in agarose gel, D, and the apparent diffusion coefficient, D*, in brain tissue were determined by fitting an integral expression relating the measured two-dimensional image intensity to the theoretical three-dimensional dextran concentration. The measurements in dilute agarose gel provided a reference value of D and validated the method. Values of the tortuosity, lambda = (D/D*)1/2, for the 3- and 10-kDa dextrans were 1.70 and 1.63, respectively, which were consistent with previous values derived from tetramethylammonium measurements in cortex. Tortuosities for the 40- and 70-kDa dextrans had significantly larger values of 2.16 and 2.25, respectively. This suggests that the extracellular space may have local constrictions that hinder the diffusion of molecules above a critical size that lies in the range of many neurotrophic compounds.
Diffusion of a Highly-Charged Supramolecular Assembly: Direct Observation of Ion-Association in Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

University of California, Berkeley; Lawrence Berkeley National Laboratory; Raymond, Kenneth

2007-10-22

Understanding the solution behavior of supramolecular assemblies is essential for a full understanding of the formation and chemistry of synthetic host-guest systems. While the interaction between host and guest molecules is generally the focus of mechanistic studies of host-guest complexes, the interaction of the host-guest complex with other species in solution remains largely unknown, although in principle accessible by diffusion studies. Several NMR techniques are available to monitor diffusion and have recently been reviewed. Pulsed gradient spin-echo (PGSE) NMR methods have attracted increasing interest, since they allow diffusion coefficients to be measured with high accuracy; they have been successfully usedmore » with observation of {sup 7}Li and {sup 31}P nuclei as well as with {sup 1}H NMR. We report here the direct measurement of diffusion coefficients to observe ion-association interactions by counter cations with a highly-charged supramolecular assembly. Raymond and coworkers have described the design and chemistry of a class of metal-ligand supramolecular assemblies over the past decade. The [Ga{sub 4}L{sub 6}]{sup 12-} (L = 1,5-bis(2,3-dihydroxybenzamido)naphthalene) (1) (Figure 1) assembly has garnered the most attention, with the exploration of the dynamics and mechanism of guest exchange as well as the ability of 1 to achieve either stoichiometric or catalytic reactions inside its interior cavity. Recent studies have revealed the importance of counter cations in solution on the chemistry of 1. During the mechanistic study of the C-H bond activation of aldehydes by [Cp*Ir(PMe{sub 3})(olefin){sup +} {contained_in} 1]{sup 11-} a stepwise guest dissociation mechanism with an ion-paired intermediate was proposed. Similarly, in the mechanism for the hydrolysis of iminium cations generated from the 3-aza Cope rearrangement of enammonium cations in 1, the presence of an exterior ion association was part of the kinetic model. To further substantiate the indirect kinetic evidence for such ion-paired species, we sought to explore the solution behavior of 1 by studying the diffusion of 1 with varying alkali and tetraalkyl ammonium cations. For large molecules in solution, such as synthetic supramolecular assemblies, the diffusion behavior of host and guest molecules can provide valuable information on host-guest interaction. One characteristic feature of a stable host-guest complex is that the host and guest molecules diffuse at the same rate in solution; this has been observed in a number of supramolecular systems. In order to confirm that this system was suitable for study by diffusion NMR spectroscopy, a PGSE-DOSY spectrum was acquired of [NEt{sub 4} {contained_in} 1]{sup 11-} (Figure 2), which shows that the host and guest molecules diffuse at the same rate. Quantitative analysis of the data, from monitoring the integral of host and guest resonances as a function of applied gradient strength, gave identical diffusion coefficients, confirming that the host and guest molecules diffuse together.« less
Water transport and clustering behavior in homopolymer and graft copolymer polylactide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, An; Koo, Donghun; Theryo, Grayce

2015-02-19

Polylactide is a bio-based and biodegradable polymer well-known for its renewable origins. Water sorption and clustering behavior in both a homopolymer polylactide and a graft copolymer of polylactide was studied using the quartz crystal microbalance/heat conduction calorimetry (QCM/HCC) technique. The graft copolymer, poly(1,5-cyclooctadiene-co-5-norbornene-2-methanol-graft-D,L-lactide), contained polylactide chains (95 wt.%) grafted onto a hydrophobic rubbery backbone (5 wt.%). Clustering is an important phenomenon in the study of water transport properties in polymers since the presence of water clusters can affect the water diffusivity. The HCC method using the thermal power signals and Van't Hoff's law were both employed to estimate the watermore » sorption enthalpy. Sorption enthalpy of water in both polymers was determined to be approximately -40 kJ/mol for all water activity levels. Zimm-Lundberg analysis showed that water clusters start to form at a water activity of 0.4. The engaged species induced clustering (ENSIC) model was used to curve fit sorption isotherms and showed that the affinity among water molecules is higher than that between water molecules and polymer chains. All the methods used indicate that clustering of water molecules exists in both polymers.« less
Microfiberoptic fluorescence photobleaching reveals size-dependent macromolecule diffusion in extracellular space deep in brain.

PubMed

Zador, Zsolt; Magzoub, Mazin; Jin, Songwan; Manley, Geoffrey T; Papadopoulos, Marios C; Verkman, A S

2008-03-01

Diffusion in brain extracellular space (ECS) is important for nonsynaptic intercellular communication, extracellular ionic buffering, and delivery of drugs and metabolites. We measured macromolecular diffusion in normally light-inaccessible regions of mouse brain by microfiberoptic epifluorescence photobleaching, in which a fiberoptic with a micron-size tip is introduced deep in brain tissue. In brain cortex, the diffusion of a noninteracting molecule [fluorescein isothiocyanate (FITC)-dextran, 70 kDa] was slowed 4.5 +/- 0.5-fold compared with its diffusion in water (D(o)/D), and was depth-independent down to 800 microm from the brain surface. Diffusion was significantly accelerated (D(o)/D of 2.9+/-0.3) in mice lacking the glial water channel aquaporin-4. FITC-dextran diffusion varied greatly in different regions of brain, with D(o)/D of 3.5 +/- 0.3 in hippocampus and 7.4 +/- 0.3 in thalamus. Remarkably, D(o)/D in deep brain was strongly dependent on solute size, whereas diffusion in cortex changed little with solute size. Mathematical modeling of ECS diffusion required nonuniform ECS dimensions in deep brain, which we call "heterometricity," to account for the size-dependent diffusion. Our results provide the first data on molecular diffusion in ECS deep in brain in vivo and demonstrate previously unrecognized hindrance and heterometricity for diffusion of large macromolecules in deep brain.
Numerical simulation model of hyperacute/acute stage white matter infarction.

PubMed

Sakai, Koji; Yamada, Kei; Oouchi, Hiroyuki; Nishimura, Tsunehiko

2008-01-01

Although previous studies have revealed the mechanisms of changes in diffusivity (apparent diffusion coefficient [ADC]) in acute brain infarction, changes in diffusion anisotropy (fractional anisotropy [FA]) in white matter have not been examined. We hypothesized that membrane permeability as well as axonal swelling play important roles, and we therefore constructed a simulation model using random walk simulation to replicate the diffusion of water molecules. We implemented a numerical diffusion simulation model of normal and infarcted human brains using C++ language. We constructed this 2-pool model using simple tubes aligned in a single direction. Random walk simulation diffused water. Axon diameters and membrane permeability were then altered in step-wise fashion. To estimate the effects of axonal swelling, axon diameters were changed from 6 to 10 microm. Membrane permeability was altered from 0% to 40%. Finally, both elements were combined to explain increasing FA in the hyperacute stage of white matter infarction. The simulation demonstrated that simple water shift into the intracellular space reduces ADC and increases FA, but not to the extent expected from actual human cases (ADC approximately 50%; FA approximately +20%). Similarly, membrane permeability alone was insufficient to explain this phenomenon. However, a combination of both factors successfully replicated changes in diffusivity indices. Both axonal swelling and reduced membrane permeability appear important in explaining changes in ADC and FA based on eigenvalues in hyperacute-stage white matter infarction.
Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory★

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-80329-7.
Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

PubMed

Ghysels, An; Venable, Richard M; Pastor, Richard W; Hummer, Gerhard

2017-06-13

A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied to oxygen in lipid bilayers. By a separation of variables in the Smoluchowski diffusion equation, the multidimensional diffusion is reduced to coupled one-dimensional diffusion problems that are treated by discretization. The resulting diffusivity profiles characterize the membrane transport dynamics as a function of the position across the membrane, discriminating between diffusion normal and parallel to the membrane. The methodology is first validated with neat water, neat hexadecane, and a hexadecane slab surrounded by water, the latter being a simple model for a lipid membrane. Next, a bilayer consisting of pure 1-palmitoyl 2-oleoylphosphatidylcholine (POPC), and a bilayer mimicking the lipid composition of the inner mitochondrial membrane, including cardiolipin, are investigated. We analyze the detailed time evolution of oxygen molecules, in terms of both normal diffusion through and radial diffusion inside the membrane. Diffusion is fast in the more loosely packed interleaflet region, and anisotropic, with oxygen spreading more rapidly in the membrane plane than normal to it. Visualization of the propagator shows that oxygen enters the membrane rapidly, reaching its thermodynamically favored center in about 1 ns, despite the free energy barrier at the headgroup region. Oxygen transport is quantified by computing the oxygen permeability of the membranes and the average radial diffusivity, which confirm the anisotropy of the diffusion. The position-dependent diffusion constants and free energies are used to construct compartmental models and test assumptions used in estimating permeability, including Overton's rule. In particular, a hexadecane slab surrounded by water is found to be a poor model of oxygen transport in membranes because the relevant energy barriers differ substantially.
Molecular hydrogen solvated in water – A computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Śmiechowski, Maciej, E-mail: Maciej.Smiechowski@pg.gda.pl

2015-12-28

The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electronmore » pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.« less
Capacitive Sensing of Intercalated H2O Molecules Using Graphene.

PubMed

Olson, Eric J; Ma, Rui; Sun, Tao; Ebrish, Mona A; Haratipour, Nazila; Min, Kyoungmin; Aluru, Narayana R; Koester, Steven J

2015-11-25

Understanding the interactions of ambient molecules with graphene and adjacent dielectrics is of fundamental importance for a range of graphene-based devices, particularly sensors, where such interactions could influence the operation of the device. It is well-known that water can be trapped underneath graphene and its host substrate; however, the electrical effect of water beneath graphene and the dynamics of how the interfacial water changes with different ambient conditions has not been quantified. Here, using a metal-oxide-graphene variable-capacitor (varactor) structure, we show that graphene can be used to capacitively sense the intercalation of water between graphene and HfO2 and that this process is reversible on a fast time scale. Atomic force microscopy is used to confirm the intercalation and quantify the displacement of graphene as a function of humidity. Density functional theory simulations are used to quantify the displacement of graphene induced by intercalated water and also explain the observed Dirac point shifts as being due to the combined effect of water and oxygen on the carrier concentration in the graphene. Finally, molecular dynamics simulations indicate that a likely mechanism for the intercalation involves adsorption and lateral diffusion of water molecules beneath the graphene.
Molecular dynamics study of the diffusivity of a hydrophobic drug Cucurbitacin B in pseudo-poly(ethylene oxide-b-caprolactone) micelle environments.

PubMed

Razavilar, Negin; Choi, Phillip

2014-07-08

Isobaric-isothermal molecular dynamics simulation was used to study the diffusion of a hydrophobic drug Cucurbitacin B (CuB) in pseudomicelle environments consisting of poly(ethylene oxide-b-caprolactone) (PEO-b-PCL) swollen by various amounts of water. Two PEO-b-PCL configurations, linear and branched, with the same total molecular weight were used. For the branched configuration, the block copolymer contained one linear block of PEO with the same molecular weight as that of the PEO block used in the linear configuration but with one end connecting to three PCL blocks with the same chain length, hereafter denoted PEO-b-3PCL. Regardless of the configuration, the simulation results showed that the diffusivity of CuB was insensitive to the water concentration up to ∼8 wt % while that of water decreased with an increasing water concentration. The diffusivity of CuB (10(-8) cm(2)/s) was 3 orders of magnitude lower than that of water (10(-5) cm(2)/s). This is attributed to the fact that CuB relied on the wiggling motion of the block copolymers to diffuse while water molecules diffused via a hopping mechanism. The rates at which CuB and water diffused into PEO-b-PCL were twice those in PEO-b-3PCL because the chain mobility and the degree of swelling are higher and there are fewer intermolecular hydrogen bonds in the case of PEO-b-PCL. The velocity autocorrelation functions of CuB show that the free volume holes formed by PEO-b-3PCL are more rigid than those formed by PEO-b-PCL, making CuB exhibit higher-frequency collision motion in PEO-b-3PCL than in PEO-b-PCL, and the difference in frequency is insensitive to water concentration.
Geoengineering with Charged Droplets

NASA Astrophysics Data System (ADS)

Gokturk, H.

2011-12-01

Water molecules in a droplet are held together by intermolecular forces generated by hydrogen bonding which has a bonding energy of only about 0.2 eV. One can create a more rugged droplet by using an ion as a condensation nucleus. In that case, water molecules are held together by the interaction between the ion and the dipole moments of the water molecules surrounding the ion, in addition to any hydrogen bonding. In this research, properties of such charged droplets were investigated using first principle quantum mechanical calculations. A molecule which exhibits positive electron affinity is a good candidate to serve as the ionic condensation nucleus, because addition of an electron to such a molecule creates an energetically more stable state than the neutral molecule. A good example is the oxygen molecule (O2) where energy of O2 negative (O2-) ion is lower than that of the neutral O2 by about 0.5 eV. Examples of other molecules which have positive electron affinity include ozone (O3), nitrogen dioxide (NO2) and sulfur oxides (SOx, x=1-3). Atomic models used in the calculations consisted of a negative ion of one of the molecules mentioned above surrounded by water molecules. Calculations were performed using the DFT method with B3LYP hybrid functional and Pople type basis sets with polarization and diffuse functions. Energy of interaction between O2- ion and the water molecule was found to be ~0.7 eV. This energy is an order of magnitude greater than the thermal energy of even the highest temperatures encountered in the atmosphere. Once created, charged rugged droplets can survive in hot and dry climates where they can be utilized to create humidity and precipitation. The ion which serves as the nucleus of the droplet can attract not only water molecules but also other dipolar gases in the atmosphere. Such dipolar gases include industrial pollutants, for example nitrogen dioxide (NO2) or sulfur dioxide (SO2). Energy of interaction between O2- ion and pollutant molecules was calculated to be ~0.5 eV for NO2 and ~0.9 eV for SO2. These values are comparable to that of water, hence charged droplets have the potential to serve as scavengers of pollutants in the atmosphere. The charged droplet can also interact with quadrupolar gases depending on the charge distribution of the gas. A quadrupole of interest is carbon dioxide (CO2) where oxygens are slightly negative and carbon is slightly positive in a neutral molecule. When CO2 is in the vicinity of a negative ion, the carbon atom gets attracted to the ion, whereas oxygens are repelled from it. This interaction distorts the linear geometry of CO2, turning it into a small dipole. Energy of interaction between O2- ion and CO2 was calculated to be ~0.3 eV which is smaller than those of the above mentioned dipoles, but still significantly greater than the typical thermal energy at 25 C (~0.03 eV). One can expect the diffusion of atmospheric CO2 into the droplets to be enhanced due to the charge. Hence such droplets can help capture the CO2 in the atmosphere and sequester it simply as rain. Charged droplets can be created using electrical,optical, thermal or other means. A method which utilizes solar energy will be described in the presentation.
Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

PubMed Central

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876
Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

PubMed

D'Agostino, Carmine; Gladden, Lynn F; Mantle, Mick D; Abbott, Andrew P; Ahmed, Essa I; Al-Murshedi, Azhar Y M; Harris, Robert C

2015-06-21

Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added. This indicates a clear and significant change in inter-molecular interactions. In aqueous Ethaline, the hydroxyl species of Ch(+) and HBD show a stronger interaction with water as water is added to the system. In the case of Glyceline, water has little effect on both hydroxyl proton diffusion of Ch(+) and HBD. In Reline, it is likely that water allows the formation of small amounts of ammonium hydroxide. The most surprising observation is from the self-diffusion of water, which is considerably higher that expected from a homogeneous liquid. This leads to the conclusion that Reline and Glyceline form mixtures that are inhomogeneous at a microscopic level despite the hydrophilicity of the salt and HBD. This work shows that PFG NMR is a powerful tool to elucidate both molecular dynamics and inter-molecular interactions in complex liquid mixtures, such as the aqueous DES mixtures.
The nature of water within bacterial spores: protecting life in extreme environments

NASA Astrophysics Data System (ADS)

Rice, Charles V.; Friedline, Anthony; Johnson, Karen; Zachariah, Malcolm M.; Thomas, Kieth J., III

2011-10-01

The bacterial spore is a formidable container of life, protecting the vital contents from chemical attack, antimicrobial agents, heat damage, UV light degradation, and water dehydration. The exact role of the spore components remains in dispute. Nevertheless, water molecules are important in each of these processes. The physical state of water within the bacterial spore has been investigated since the early 1930's. The water is found two states, free or bound, in two different areas, core and non-core. It is established that free water is accessible to diffuse and exchange with deuterated water and that the diffusible water can access all areas of the spore. The presence of bound water has come under recent scrutiny and has been suggested the water within the core is mobile, rather than bound, based on the analysis of deuterium relaxation rates. Using an alternate method, deuterium quadrupole-echo spectroscopy, we are able to distinguish between mobile and immobile water molecules. In the absence of rapid motion, the deuterium spectrum of D2O is dominated by a broad line, whose line shape is used as a characteristic descriptor of molecular motion. The deuterium spectrum of bacterial spores reveals three distinct features: the broad peak of immobilized water, a narrow line of water in rapid motion, and a signal of intermediate width. This third signal is assigned this peak from partially deuterated proteins with the spore in which N-H groups have undergone exchange with water deuterons to form N-D species. As a result of these observations, the nature of water within the spore requires additional explanation to understand how the spore and its water preserve life.
Macromolecule diffusion and confinement in prokaryotic cells.

PubMed

Mika, Jacek T; Poolman, Bert

2011-02-01

We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The extremely high macromolecule crowding of prokaryotes is used to rationalize the reported lower diffusion coefficients as compared to eukaryotes, and we speculate on the nature of the barriers for diffusion observed for proteins (and mRNAs) in vivo. Building on in vitro experiments and modeling studies, we evaluate the size dependence of diffusion coefficients for macromolecules in vivo, in case of both water-soluble and integral membrane proteins. We comment on the possibilities of anomalous diffusion and provide examples where the macromolecule mobility may be limiting biological processes. Copyright © 2010 Elsevier Ltd. All rights reserved.
Water of Hydration Dynamics in Minerals Gypsum and Bassanite: Ultrafast 2D IR Spectroscopy of Rocks.

PubMed

Yan, Chang; Nishida, Jun; Yuan, Rongfeng; Fayer, Michael D

2016-08-03

Water of hydration plays an important role in minerals, determining their crystal structures and physical properties. Here ultrafast nonlinear infrared (IR) techniques, two-dimensional infrared (2D IR) and polarization selective pump-probe (PSPP) spectroscopies, were used to measure the dynamics and disorder of water of hydration in two minerals, gypsum (CaSO4·2H2O) and bassanite (CaSO4·0.5H2O). 2D IR spectra revealed that water arrangement in freshly precipitated gypsum contained a small amount of inhomogeneity. Following annealing at 348 K, water molecules became highly ordered; the 2D IR spectrum became homogeneously broadened (motional narrowed). PSPP measurements observed only inertial orientational relaxation. In contrast, water in bassanite's tubular channels is dynamically disordered. 2D IR spectra showed a significant amount of inhomogeneous broadening caused by a range of water configurations. At 298 K, water dynamics cause spectral diffusion that sampled a portion of the inhomogeneous line width on the time scale of ∼30 ps, while the rest of inhomogeneity is static on the time scale of the measurements. At higher temperature, the dynamics become faster. Spectral diffusion accelerates, and a portion of the lower temperature spectral diffusion became motionally narrowed. At sufficiently high temperature, all of the dynamics that produced spectral diffusion at lower temperatures became motionally narrowed, and only homogeneous broadening and static inhomogeneity were observed. Water angular motions in bassanite exhibit temperature-dependent diffusive orientational relaxation in a restricted cone of angles. The experiments were made possible by eliminating the vast amount of scattered light produced by the granulated powder samples using phase cycling methods.
Effects of added surfactant on swelling and molecular transport in drug-loaded tablets based on hydrophobically modified poly(acrylic acid).

PubMed

Knöös, Patrik; Wahlgren, Marie; Topgaard, Daniel; Ulvenlund, Stefan; Piculell, Lennart

2014-08-14

A combination of NMR chemical shift imaging and self-diffusion experiments is shown to give a detailed molecular picture of the events that occur when tablets of hydrophobically modified poly(acrylic acid) loaded with a drug (griseofulvin) swell in water in the presence or absence of surfactant (sodium octylbenzenesulfonate). The hydrophobic substituents on the polymer bind and trap the surfactant molecules in mixed micelles, leading to a slow effective surfactant transport that occurs via a small fraction of individually dissolved surfactant molecules in the water domain. Because of the efficient binding of surfactant, the penetrating water is found to diffuse past the penetrating surfactant into the polymer matrix, pushing the surfactant front outward as the matrix swells. The added surfactant has little effect on the transport of drug because both undissolved solid drug and surfactant-solubilized drug function as reservoirs that essentially follow the polymer as it swells. However, the added surfactant nevertheless has a strong indirect effect on the release of griseofulvin, through the effect of the surfactant on the solubility and erosion of the polymer matrix. The surfactant effectively solubilizes the hydrophobically modified polymer, making it fully miscible with water, leading to a more pronounced swelling and a slower erosion of the polymer matrix.
Applying Petri nets to modeling the chemical stage of radiobiological mechanism

NASA Astrophysics Data System (ADS)

Barilla, J.; Lokajíček, M.; Pisaková, H.; Simr, P.

2015-03-01

The chemical stage represents important part of radiological mechanism as double strand breaks of DNA molecules represent main damages leading to final biological effect. These breaks are formed mainly by water radicals arising in clusters formed by densely ionizing ends of primary or secondary charged particles in neighborhood of a DNA molecule. The given effect may be significantly influenced by other species present in water, which may depend on the size and diffusion of corresponding clusters. We have already proposed a model describing the corresponding process (i.e., the combined effect of cluster diffusion and chemical reactions) running in individual radical clusters and influencing the formation probability of main damages (i.e., DSBs). Now a full number of corresponding species will be considered. With the help of Continuous Petri nets it will then be possible to follow the time evolution of corresponding species in individual clusters, which might be important especially in the case of studying the biological effect of very low-LET radiation. The results in deoxygenated water will be presented; the ratio of final and initial contents of corresponding species being in good agreement with values established experimentally.
Influence of carboxymethyl cellulose and sodium alginate on sweetness intensity of Aspartame.

PubMed

Han, Xue; Xu, Shu-Zhen; Dong, Wen-Rui; Wu, Zhai; Wang, Ren-Hai; Chen, Zhong-Xiu

2014-12-01

Sensory evaluation of Aspartame in the presence of sodium carboxymethyl cellulose (CMC-L) and sodium alginate (SA) revealed that only CMC-L showed a suppression effect, while SA did not. By using an artificial taste receptor model, we found that the presence of SA or CMC-L resulted in a decrease in association constants. Further investigation of CMC-L solution revealed that the decrease in water mobility and diffusion also contribute to the suppression effect. In the case of SA, the decreased viscosity and comparatively higher amount of free water facilitated the diffusion of sweetener, which might compensate for the decreased binding constant between Aspartame and receptor. This may suppress the impact of SA on sweetness intensity. The results suggest that exploring the binding affinity of taste molecules with the receptor, along with water mobility and diffusion in hydrocolloidal structures, provide sufficient information for understanding the mechanism behind the effect of macromolecular hydrocolloids on taste. Copyright © 2014 Elsevier Ltd. All rights reserved.

Demonstration of the AGI Universal Samplers (F.K.A. the GORE Modules) for Passive Sampling of Groundwater

DTIC Science & Technology

2014-03-27

Coefficient from Water into the Sorbent KOW Octanol-Water Partition Coefficient LF Low Flow LNAPL Light Non-aqueous Phase Liquid LTM Long-Term...Once in the vapor phase, the molecule can then diffuse through the mem- ERDC/CRREL TR-14-4 5 brane while liquid water is prevented from passing...remediation at this site was conducted in two phases. Phase I consisted of vertical contamina- tion profiling followed by the in situ injection of an
Demonstration of the AGI Universal Samplers (F.K.A. the GORE (registered trademark) Modules) for Passive Sampling of Groundwater

DTIC Science & Technology

2014-03-01

Coefficient from Water into the Sorbent KOW Octanol-Water Partition Coefficient LF Low Flow LNAPL Light Non-aqueous Phase Liquid LTM Long-Term...Once in the vapor phase, the molecule can then diffuse through the mem- ERDC/CRREL TR-14-4 5 brane while liquid water is prevented from passing...remediation at this site was conducted in two phases. Phase I consisted of vertical contamina- tion profiling followed by the in situ injection of an
Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations.

PubMed

Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf

2017-03-22

Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.
Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals.

PubMed

McDaniel, Jesse G; Yethiraj, Arun

2017-05-18

Bilayers composed of lipid or surfactant molecules are central to biological membranes and lamellar lyotropic liquid crystalline (LLC) phases. Common to these systems are phases that exhibit either ordered or disordered packing of the hydrophobic tails. In this work, we study the impact of surfactant ordering, i.e., disordered L α and ordered L β LLC phases, on the dynamics of water and sodium ions in the lamellar phases of dicarboxylate gemini surfactants. We study the different phases at identical hydration levels by changing the length of the hydrophobic tails; surfactants with shorter tails form L α phases and those with longer tails form L β phases. We find that the L α phases exhibit lower density and greater compressibility than the L β phases, with a hydration-dependent headgroup surface area. These structural differences significantly affect the relative dynamic properties of the phases, primarily the mobility of the surfactant molecules tangential to the bilayer surface, as well as the rates of water and ion diffusion. We find ∼20-50% faster water diffusion in the L α phases compared to the L β phases, with the differences most pronounced at low hydration. This coupling between water dynamics and surfactant mobility is verified using additional simulations in which the surfactant tails are frozen. Our study indicates that gemini surfactant LLCs provide an important prototypical system for characterizing properties shared with more complex biological lipid membranes.
Hydrodynamic and Nonhydrodynamic Contributions to the Bimolecular Collision Rates of Solute Molecules in Supercooled Bulk Water

PubMed Central

2015-01-01

Bimolecular collision rate constants of a model solute are measured in water at T = 259–303 K, a range encompassing both normal and supercooled water. A stable, spherical nitroxide spin probe, perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl, is studied using electron paramagnetic resonance spectroscopy (EPR), taking advantage of the fact that the rotational correlation time, τR, the mean time between successive spin exchanges within a cage, τRE, and the long-time-averaged spin exchange rate constants, Kex, of the same solute molecule may be measured independently. Thus, long- and short-time translational diffusion behavior may be inferred from Kex and τRE, respectively. In order to measure Kex, the effects of dipole–dipole interactions (DD) on the EPR spectra must be separated, yielding as a bonus the DD broadening rate constants that are related to the dephasing rate constant due to DD, Wdd. We find that both Kex and Wdd behave hydrodynamically; that is to say they vary monotonically with T/η or η/T, respectively, where η is the shear viscosity, as predicted by the Stokes–Einstein equation. The same is true of the self-diffusion of water. In contrast, τRE does not follow hydrodynamic behavior, varying rather as a linear function of the density reaching a maximum at 276 ± 2 K near where water displays a maximum density. PMID:24874024
Towards a unified model of passive drug permeation I: origins of the unstirred water layer with applications to ionic permeation.

PubMed

Ghosh, Avijit; Scott, Dennis O; Maurer, Tristan S

2014-02-14

In this work, we provide a unified theoretical framework describing how drug molecules can permeate across membranes in neutral and ionized forms for unstirred in vitro systems. The analysis provides a self-consistent basis for the origin of the unstirred water layer (UWL) within the Nernst-Planck framework in the fully unstirred limit and further provides an accounting mechanism based simply on the bulk aqueous solvent diffusion constant of the drug molecule. Our framework makes no new assumptions about the underlying physics of molecular permeation. We hold simply that Nernst-Planck is a reasonable approximation at low concentrations and all physical systems must conserve mass. The applicability of the derived framework has been examined both with respect to the effect of stirring and externally applied voltages to measured permeability. The analysis contains data for 9 compounds extracted from the literature representing a range of permeabilities and aqueous diffusion coefficients. Applicability with respect to ionized permeation is examined using literature data for the permanently charged cation, crystal violet, providing a basis for the underlying mechanism for ionized drug permeation for this molecule as being due to mobile counter-current flow. Copyright © 2013 Elsevier B.V. All rights reserved.
Water permeation through the sodium-dependent galactose cotransporter vSGLT.

PubMed

Choe, Seungho; Rosenberg, John M; Abramson, Jeff; Wright, Ernest M; Grabe, Michael

2010-10-06

It is well accepted that cotransporters facilitate water movement by two independent mechanisms: osmotic flow through a water channel in the protein and flow driven by ion/substrate cotransport. However, the molecular mechanism of transport-linked water flow is controversial. Some researchers believe that it occurs via cotransport, in which water is pumped along with the transported cargo, while others believe that flow is osmotic in response to an increase in intracellular osmolarity. In this letter, we report the results of a 200-ns molecular dynamics simulation of the sodium-dependent galactose cotransporter vSGLT. Our simulation shows that a significant number of water molecules cross the protein through the sugar-binding site in the presence as well as the absence of galactose, and 70-80 water molecules accompany galactose as it moves from the binding site into the intracellular space. During this event, the majority of water molecules in the pathway are unable to diffuse around the galactose, resulting in water in the inner half of the transporter being pushed into the intracellular space and replaced by extracellular water. Thus, our simulation supports the notion that cotransporters act as both passive water channels and active water pumps with the transported substrate acting as a piston to rectify the motion of water. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
[Lateral diffusion of saturated phosphatidylcholines in cholesterol-containing bilayers].

PubMed

Filippov, A V; Rudakova, M A; Oradd, G; Lindblom, J

2007-01-01

Lateral diffusion in oriented bilayers of saturated cholesterol-containing phosphatidylcholines, dipalmitoylphosphatidylcholine and dimyrilstoylphosphatidylcholine upon their limiting hydration has been studied by NMR with impulse gradient of magnetic field. For both systems, similar dependences of the coefficient of lateral diffusion on temperature and cholesterol concentration were observed, which agree with the phase diagram showing the presence of regions of ordered and unordered liquid-crystalline phases and a two-phase region. Under similar conditions, the coefficient of lateral diffusion for dipalmytoylphosphatidylcholine has lower values, which is in qualitative agreement with its greater molecular mass. A comparison of data for dipalmytoylphosphatidylcholine with the results obtained earlier for dipalmytoylsphyngomyelin/cholesterol under the same conditions shows, despite a similarity in phase diagrams, greater (two- to threefold) differences in the values of the coefficient of lateral diffusion and a different mode of dependence of the coefficient on cholesterol concentration. A comparison of data for dimyrilstoylphosphatidylcholine with the results obtained previously shows that the values of the coefficient of lateral diffusion and the mode of its dependence on cholesterol concentration coincide in the region of higher concentrations (more than 15 mole %) and differ in the region of lower concentrations (below 15 mole %). The discrepancies may be explained by different contents of water in the systems during the measurements. At a limiting hydration (more than 35%) of water, the coefficient of lateral diffusion decreases with increasing cholesterol concentration. If the content of water is about 25% (as a result of equilibrium hydration from vapors), the coefficient of lateral diffusion of phosphatidylcholine is probably independent of cholesterol concentration. This results from a denser packing of molecules in the bilayer at a lower water concentration, an effect that competes with the ordering effect of cholesterol.
Inclusion compounds between α-, β- and γ-cyclodextrins: iron II lactate: a theoretical and experimental study using diffusion coefficients and molecular mechanics

NASA Astrophysics Data System (ADS)

Leite, Rosiley A.; Lino, Antonio C. S.; Takahata, Yuji

2003-01-01

The inclusion compounds between iron II lactate and three different cyclodextrins (CDs) were studied by means of experimental and theoretical data. The importance of iron II in the human metabolism effort the necessity of a minimum concentration to the human life. Malnutrition is one great problem in social politics of many countries on the world. The possibility to the development of novel medicines with the iron II species stable look for an increase on the efficiency for this kind of aid. Kinetics measurements confirm the possibility to stop the oxidation reaction. It was the first indication of efficient molecular encapsulation. Diffusion coefficient measurements were carried out by Taylor-Aris diffusion technique. The decrease of diffusion coefficients measured for iron II lactate when alone and forming the inclusion complexes was obtained for all hosts molecules used. Molecular Mechanics calculations were performed to elucidate the perfect arrange of iron II lactate inside CDs cavity. No great differences were obtained to the binding energy for the different hosts. Using the software HyperChem6.03v MM+, AMBER94 and OPLS Forced Fields for iron atom in two chemical environments (a) vacuum and (b) with addition of 250 water molecules (MM+). The solvent treatment was decisive to the order of stability. This order was β-CD>γ-CD>α-CD, the same order of solubility in water. The results contained in this work confirm the possibility to protect iron II lactate against oxidation.
Detailed study of the water trimer potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fowler, J.E.; Schaefer, H.F. III

The potential energy surface of the water trimer has been studied through the use of ab initio quantum mechanical methods. Five stationary points were located, including one minimum and two transition states. All geometries were optimized at levels up to the double-[Zeta] plus polarization plus diffuse (DZP + diff) single and double excitation coupled cluster (CCSD) level of theory. CCSD single energy points were obtained for the minimum, two transition states, and the water monomer using the triple-[Zeta] plus double polarization plus diffuse (TZ2P + diff) basis at the geometries predicted by the DZP + diff CCSD method. Reported aremore » the following: geometrical parameters, total and relative energies, harmonic vibrational frequencies and infrared intensities for the minimum, and zero point vibrational energies for the minimum, two transition states, and three separated water molecules. 27 refs., 5 figs., 10 tabs.« less
Site-specific vibrational spectral signatures of water molecules in the magic H3O+(H2O)20 and Cs+(H2O)20 clusters

PubMed Central

Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; Johnson, Mark A.; Heine, Nadja; Gewinner, Sandy; Schöllkopf, Wieland; Esser, Tim K.; Fagiani, Matias R.; Knorke, Harald; Asmis, Knut R.

2014-01-01

Theoretical models of proton hydration with tens of water molecules indicate that the excess proton is embedded on the surface of clathrate-like cage structures with one or two water molecules in the interior. The evidence for these structures has been indirect, however, because the experimental spectra in the critical H-bonding region of the OH stretching vibrations have been too diffuse to provide band patterns that distinguish between candidate structures predicted theoretically. Here we exploit the slow cooling afforded by cryogenic ion trapping, along with isotopic substitution, to quench water clusters attached to the H3O+ and Cs+ ions into structures that yield well-resolved vibrational bands over the entire 215- to 3,800-cm−1 range. The magic H3O+(H2O)20 cluster yields particularly clear spectral signatures that can, with the aid of ab initio predictions, be traced to specific classes of network sites in the predicted pentagonal dodecahedron H-bonded cage with the hydronium ion residing on the surface. PMID:25489068
Site-specific vibrational spectral signatures of water molecules in the magic H 3O +(H 2O) 20 and Cs +(H 2O) 20 clusters

DOE PAGES

Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; ...

2014-12-08

Here, theoretical models of proton hydration with tens of water molecules indicate that the excess proton is embedded on the surface of clathrate-like cage structures with one or two water molecules in the interior. The evidence for these structures has been indirect, however, because the experimental spectra in the critical H-bonding region of the OH stretching vibrations have been too diffuse to provide band patterns that distinguish between candidate structures predicted theoretically. Here we exploit the slow cooling afforded by cryogenic ion trapping, along with isotopic substitution, to quench water clusters attached to the H 3O + and Cs +more » ions into structures that yield well-resolved vibrational bands over the entire 215- to 3,800-cm -1 range. The magic H 3O +(H 2O) 20 cluster yields particularly clear spectral signatures that can, with the aid of ab initio predictions, be traced to specific classes of network sites in the predicted pentagonal dodecahedron H-bonded cage with the hydronium ion residing on the surface.« less
The effects of ethanol on the size-exclusion characteristics of type I dentin collagen to adhesive resin monomers.

PubMed

Chiba, A; Zhou, J; Nakajima, M; Tan, J; Tagami, J; Scheffel, D L S; Hebling, J; Agee, K A; Breschi, L; Grégoire, G; Jang, S S; Tay, F R; Pashley, D H

2016-03-01

During dentin bonding with etch-and-rinse adhesive systems, phosphoric acid etching of mineralized dentin solubilizes the mineral crystallites and replaces them with bound and unbound water. During the infiltration phase of dentin bonding, solvated adhesive resin comonomers are supposed to replace all of the unbound collagen water and polymerize into copolymers. A recently published review suggested that dental monomers are too large to enter and displace water from tightly-packed collagen molecules. Conversely, recent work from the authors' laboratory demonstrated that HEMA and TEGDMA freely equilibrate with water-saturated dentin matrices. However, because adhesive blends are solvated in organic solvents, those solvents may remove enough free water to allow collagen molecules to come close enough to exclude adhesive monomer permeation. The present study analyzed the size-exclusion characteristics of dentin collagen, using a gel permeation-like column chromatography technique, filled with dentin powder instead of Sephadex beads as the stationary phase. The elution volumes of different sized test molecules, including adhesive resin monomers, studied in both water-saturated dentin, and again in ethanol-dehydrated dentin powder, showed that adhesive resin monomers can freely diffuse into both hydrated and dehydrated collagen molecules. Under these in vitro conditions, all free and some of the loosely-bound water seems to have been removed by ethanol. These results validate the concept that adhesive resin monomers can permeate tightly-bound water in ethanol-saturated collagen molecules during infiltration by etch-and-rinse adhesives. It has been reported that collagen molecules in dentin matrices are packed too close together to allow permeation of adhesive monomers between them. Resin infiltration, in this view, would be limited to extrafibrillar spaces. Our work suggests that monomers equilibrate with collagen water in both water and ethanol-saturated dentin matrices. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Diffusion of a Concentrated Lattice Gas in a Regular Comb Structure

NASA Astrophysics Data System (ADS)

Garcia, Paul; Wentworth, Christopher

2008-10-01

Understanding diffusion in constrained geometries is of interest in a variety of contexts as varied as mass transport in disordered solids, such as a percolation cluster, or intercellular transport of water molecules in biological tissue. In this investigation we explore diffusion in a very simple constrained geometry: a comb-like structure involving a one-dimensional backbone of lattice sites with regularly spaced teeth of fixed length. The model considered assumes a fixed concentration of diffusing particles can hop to nearest-neighbor sites only, and they do not interact with each other except that double occupancy is not allowed. The system is simulated using a Monte Carlo simulation procedure. The mean-square displacement of a tagged particle is calculated from the simulation as a function of time. The simulation shows normal diffusive behavior after a period of anomalous diffusion that increases as the tooth size increases.
Dehydration of multilamellar fatty acid membranes: Towards a computational model of the stratum corneum

NASA Astrophysics Data System (ADS)

MacDermaid, Christopher M.; DeVane, Russell H.; Klein, Michael L.; Fiorin, Giacomo

2014-12-01

The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded "droplets."
Communication: Coordinate-dependent diffusivity from single molecule trajectories

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Makarov, Dmitrii E.

2017-11-01

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.
The catalytic effect of H2O on the hydrolysis of CO32- in hydrated clusters and its implication in the humidity driven CO2 air capture.

PubMed

Xiao, Hang; Shi, Xiaoyang; Zhang, Yayun; Liao, Xiangbiao; Hao, Feng; Lackner, Klaus S; Chen, Xi

2017-10-18

The hydration of ions in nanoscale hydrated clusters is ubiquitous and essential in many physical and chemical processes. Here we show that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO 3 2- with n = 1-8 water molecules is investigated using an ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal mol -1 as the number of water molecules increases from 1 to 6. Meanwhile, the degree of hydrolysis of CO 3 2- is significantly increased compared to the bulk water solution scenario. Incomplete hydration shells facilitate the hydrolysis of CO 3 2- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO 2 air capture driven by the humidity-swing. Instead, the pore-diffusion of ions is expected to be the time-limiting step in the humidity driven CO 2 air capture. The effect of humidity on the speed of CO 2 air capture was studied by conducting a CO 2 absorption experiment using IER with a high ratio of CO 3 2- to H 2 O molecules. Our result is able to provide valuable insights into designing efficient CO 2 air-capture sorbents.
Determining anisotropic conductivity using diffusion tensor imaging data in magneto-acoustic tomography with magnetic induction

NASA Astrophysics Data System (ADS)

Ammari, Habib; Qiu, Lingyun; Santosa, Fadil; Zhang, Wenlong

2017-12-01

In this paper we present a mathematical and numerical framework for a procedure of imaging anisotropic electrical conductivity tensor by integrating magneto-acoutic tomography with data acquired from diffusion tensor imaging. Magneto-acoustic tomography with magnetic induction (MAT-MI) is a hybrid, non-invasive medical imaging technique to produce conductivity images with improved spatial resolution and accuracy. Diffusion tensor imaging (DTI) is also a non-invasive technique for characterizing the diffusion properties of water molecules in tissues. We propose a model for anisotropic conductivity in which the conductivity is proportional to the diffusion tensor. Under this assumption, we propose an optimal control approach for reconstructing the anisotropic electrical conductivity tensor. We prove convergence and Lipschitz type stability of the algorithm and present numerical examples to illustrate its accuracy and feasibility.
New insights in dehydration stress behavior of two maize hybrids using advanced distributed reactivity model (DRM). Responses to the impact of 24-epibrassinolide

PubMed Central

Janković, Bojan; Janković, Marija; Nikolić, Bogdan; Dimkić, Ivica; Lalević, Blažo; Raičević, Vera

2017-01-01

Proposed distributed reactivity model of dehydration for seedling parts of two various maize hybrids (ZP434, ZP704) was established. Dehydration stresses were induced thermally, which is also accompanied by response of hybrids to heat stress. It was found that an increased value of activation energy counterparts within radicle dehydration of ZP434, with a high concentration of 24-epibrassinolide (24-EBL) at elevated operating temperatures, probably causes activation of diffusion mechanisms in cutin network and may increases likelihood of formation of free volumes, large enough to accommodate diffusing molecule. Many small random effects were detected and can be correlated with micro-disturbing in a space filled with water caused by thermal gradients, increasing capillary phenomena, and which can induce thermo-capillary migration. The influence of seedling content of various sugars and minerals on dehydration was also examined. Estimated distributed reactivity models indicate a dependence of reactivity on structural arrangements, due to present interactions between water molecules and chemical species within the plant. PMID:28644899
New insights in dehydration stress behavior of two maize hybrids using advanced distributed reactivity model (DRM). Responses to the impact of 24-epibrassinolide.

PubMed

Waisi, Hadi; Janković, Bojan; Janković, Marija; Nikolić, Bogdan; Dimkić, Ivica; Lalević, Blažo; Raičević, Vera

2017-01-01

Proposed distributed reactivity model of dehydration for seedling parts of two various maize hybrids (ZP434, ZP704) was established. Dehydration stresses were induced thermally, which is also accompanied by response of hybrids to heat stress. It was found that an increased value of activation energy counterparts within radicle dehydration of ZP434, with a high concentration of 24-epibrassinolide (24-EBL) at elevated operating temperatures, probably causes activation of diffusion mechanisms in cutin network and may increases likelihood of formation of free volumes, large enough to accommodate diffusing molecule. Many small random effects were detected and can be correlated with micro-disturbing in a space filled with water caused by thermal gradients, increasing capillary phenomena, and which can induce thermo-capillary migration. The influence of seedling content of various sugars and minerals on dehydration was also examined. Estimated distributed reactivity models indicate a dependence of reactivity on structural arrangements, due to present interactions between water molecules and chemical species within the plant.

Spin relaxation measurements of electrostatic bias in intermolecular exploration

NASA Astrophysics Data System (ADS)

Teng, Ching-Ling; Bryant, Robert G.

2006-04-01

We utilize the paramagnetic contribution to proton spin-lattice relaxation rate constants induced by freely diffusing charged paramagnetic centers to investigate the effect of charge on the intermolecular exploration of a protein by the small molecule. The proton NMR spectrum provided 255 resolved resonances that report how the explorer molecule local concentration varies with position on the surface. The measurements integrate over local dielectric constant variations, and, in principle, provide an experimental characterization of the surface free energy sampling biases introduced by the charge distribution on the protein. The experimental results for ribonuclease A obtained using positive, neutral, and negatively charged small nitroxide radicals are qualitatively similar to those expected from electrostatic calculations. However, while systematic electrostatic trends are apparent, the three different combinations of the data sets do not yield internally consistent values for the electrostatic contribution to the intermolecular free energy. We attribute this failure to the weakness of the electrostatic sampling bias for charged nitroxides in water and local variations in effective translational diffusion constant at the water-protein interface, which enters the nuclear spin relaxation equations for the nitroxide-proton dipolar coupling.
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.
Wyman's equation and oxygen flux through the red cell.

PubMed

McCabe, Michael; Maguire, David J

2007-01-01

Wyman's equation of 1966 describes the facilitation of flux of a reversibly bound substrate such as oxygen, consequent on the translational diffusion of the binding protein (the carrier). While Wyman's equation, or some modification of it such as that by Murray 2, may provide a realistic description of the flux of oxygen through a dilute solution of haemoglobin (see also Wittenburg), it is unlikely to be the complete explanation, nor even the basis, for oxygen transport through the intact red cell. The mature erythrocyte contains approximately 350 g/l haemoglobin, and while this suggests that only 35% of the available water volume is actually occupied by the protein, the remaining 65% is unavailable for protein translational diffusion due to the mutual exclusion of the haemoglobin molecules. For this reason we have examined other possible mechanisms whereby haemoglobin may facilitate the translational diffusion of oxygen within the erythrocyte. Possible alternatives include rotational diffusion by the haemoglobins, intracellular shuffling of haemoglobins due to shape changes by the erythrocyte, and haemoglobin rotations and oxygen exchange consequent on the charge change which accompanies substration and desubstration of the haemoglobin molecule. Finally the dipole interactions are shown to generate significant intermolecular attractions between adjacent haemoglobins.
Possible influence of the Kuramoto length in a photo-catalytic water splitting reaction revealed by Poisson-Nernst-Planck equations involving ionization in a weak electrolyte

NASA Astrophysics Data System (ADS)

Suzuki, Yohichi; Seki, Kazuhiko

2018-03-01

We studied ion concentration profiles and the charge density gradient caused by electrode reactions in weak electrolytes by using the Poisson-Nernst-Planck equations without assuming charge neutrality. In weak electrolytes, only a small fraction of molecules is ionized in bulk. Ion concentration profiles depend on not only ion transport but also the ionization of molecules. We considered the ionization of molecules and ion association in weak electrolytes and obtained analytical expressions for ion densities, electrostatic potential profiles, and ion currents. We found the case that the total ion density gradient was given by the Kuramoto length which characterized the distance over which an ion diffuses before association. The charge density gradient is characterized by the Debye length for 1:1 weak electrolytes. We discuss the role of these length scales for efficient water splitting reactions using photo-electrocatalytic electrodes.
Fluorescence-correlation spectroscopy study of molecular transport within reversed-phase chromatographic particles compared to planar model surfaces.

PubMed

Cooper, Justin; Harris, Joel M

2014-12-02

Reversed-phase liquid chromatography (RPLC) is a widely used technique for molecular separations. Stationary-phase materials for RPLC generally consist of porous silica-gel particles functionalized with n-alkane ligands. Understanding motions of molecules within the interior of these particles is important for developing efficient chromatographic materials and separations. To characterize these dynamics, time-resolved spectroscopic methods (photobleach recovery, fluorescence correlation, single-molecule imaging) have been adapted to measure molecular diffusion rates, typically at n-alkane-modified planar silica surfaces, which serve as models of chromatographic interfaces. A question arising from these studies is how dynamics of molecules on a planar surface relate to motions of molecules within the interior of a porous chromatographic particle. In this paper, imaging-fluorescence-correlation spectroscopy is used to measure diffusion rates of a fluorescent probe molecule 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) within authentic RPLC porous silica particles and compared with its diffusion at a planar C18-modified surface. The results show that surface diffusion on the planar C18 substrate is much faster than the diffusion rate of the probe molecule through a chromatographic particle. Surface diffusion within porous particles, however, is governed by molecular trajectories along the tortuous contours of the interior surface of the particles. By accounting for the greater surface area that a molecule must explore to diffuse macroscopic distances through the particle, the molecular-scale diffusion rates on the two surfaces can be compared, and they are virtually identical. These results provide support for the relevance of surface-diffusion measurements made on planar model surfaces to the dynamic behavior of molecules on the internal surfaces of porous chromatographic particles.
Inferring diffusion in single live cells at the single-molecule level

PubMed Central

Robson, Alex; Burrage, Kevin; Leake, Mark C.

2013-01-01

The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single-molecule and single-cell level can add significant insight into understanding molecular architectures of diffusing molecules and the nanoscale environment in which the molecules diffuse. The tool of choice for monitoring dynamic molecular localization in live cells is fluorescence microscopy, especially so combining total internal reflection fluorescence with the use of fluorescent protein (FP) reporters in offering exceptional imaging contrast for dynamic processes in the cell membrane under relatively physiological conditions compared with competing single-molecule techniques. There exist several different complex modes of diffusion, and discriminating these from each other is challenging at the molecular level owing to underlying stochastic behaviour. Analysis is traditionally performed using mean square displacements of tracked particles; however, this generally requires more data points than is typical for single FP tracks owing to photophysical instability. Presented here is a novel approach allowing robust Bayesian ranking of diffusion processes to discriminate multiple complex modes probabilistically. It is a computational approach that biologists can use to understand single-molecule features in live cells. PMID:23267182
Surface pressure and elasticity of hydrophobin HFBII layers on the air-water interface: rheology versus structure detected by AFM imaging.

PubMed

Stanimirova, Rumyana D; Gurkov, Theodor D; Kralchevsky, Peter A; Balashev, Konstantin T; Stoyanov, Simeon D; Pelan, Eddie G

2013-05-21

Here, we combine experiments with Langmuir trough and atomic force microscopy (AFM) to investigate the reasons for the special properties of layers from the protein HFBII hydrophobin spread on the air-water interface. The hydrophobin interfacial layers possess the highest surface dilatational and shear elastic moduli among all investigated proteins. The AFM images show that the spread HFBII layers are rather inhomogeneous, (i.e., they contain voids, monolayer and multilayer domains). A continuous compression of the layer leads to filling the voids and transformation of a part of the monolayer into a trilayer. The trilayer appears in the form of large surface domains, which can be formed by folding and subduction of parts from the initial monolayer. The trilayer appears also in the form of numerous submicrometer spots, which can be obtained by forcing protein molecules out of the monolayer and their self-assembly into adjacent pimples. Such structures are formed because not only the hydrophobic parts, but also the hydrophilic parts of the HFBII molecules can adhere to each other in the water medium. If a hydrophobin layer is subjected to oscillations, its elasticity considerably increases, up to 500 mN/m, which can be explained with compaction. The relaxation of the layer's tension after expansion or compression follows the same relatively simple law, which refers to two-dimensional diffusion of protein aggregates within the layer. The characteristic diffusion time after compression is longer than after expansion, which can be explained with the impedence of diffusion in the more compact interfacial layer. The results shed light on the relation between the mesoscopic structure of hydrophobin interfacial layers and their unique mechanical properties that find applications for the production of foams and emulsions of extraordinary stability; for the immobilization of functional molecules at surfaces, and as coating agents for surface modification.
Dynamics and cluster formation in charged and uncharged Ficoll70 solutions

NASA Astrophysics Data System (ADS)

Palit, Swomitra; Yethiraj, Anand

2017-08-01

We apply pulsed-field-gradient NMR (PFG NMR) technique to measure the translational diffusion for both uncharged and charged polysaccharide (Ficoll70) in water. Analysis of the data indicates that the NMR signal attenuation above a certain packing fraction can be adequately fitted with a bi-exponential function. The self-diffusion measurements also show that the Ficoll70, an often-used compact, spherical polysucrose molecule, is itself nonideal, exhibiting signs of both softness and attractive interactions in the form of a stable suspension consisting of monomers and clusters. Further, we can quantify the fraction of monomers and clusters. This work strengthens the picture of the existence of a bound water layer within and around a porous Ficoll70 particle.
Anisotropic dynamics of water ultra-confined in macroscopically oriented channels of single-crystal beryl: A multi-frequency analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anovitz, Lawrence; Mamontov, Eugene; Ishai, Paul ben

2013-01-01

The properties of fluids can be significantly altered by the geometry of their confining environments. While there has been significant work on the properties of such confined fluids, the properties of fluids under ultraconfinement, environments where, at least in one plane, the dimensions of the confining environment are similar to that of the confined molecule, have not been investigated. This paper investigates the dynamic properties of water in beryl (Be3Al2Si6O18), the structure of which contains approximately 5-A-diam channels parallel to the c axis. Three techniques, inelastic neutron scattering, quasielastic neutron scattering, and dielectric spectroscopy, have been used to quantify thesemore » properties over a dynamic range covering approximately 16 orders of magnitude. Because beryl can be obtained in large single crystals we were able to quantify directional variations, perpendicular and parallel to the channel directions, in the dynamics of the confined fluid. These are significantly anisotropic and, somewhat counterintuitively, show that vibrations parallel to the c-axis channels are significantly more hindered than those perpendicular to the channels. The effective potential for vibrations in the c direction is harder than the potential in directions perpendicular to it. There is evidence of single-file diffusion of water molecules along the channels at higher temperatures, but below 150 K this diffusion is strongly suppressed. No such suppression, however, has been observed in the channel-perpendicular direction. Inelastic neutron scattering spectra include an intramolecular stretching O-H peak at 465 meV. As this is nearly coincident with that known for free water molecules and approximately 30 meV higher than that in liquid water or ice, this suggests that there is no hydrogen bonding constraining vibrations between the channel water and the beryl structure. However, dielectric spectroscopic measurements at higher temperatures and lower frequencies yield an activation energy for the dipole reorientation of 16.4 0.14 kJ/mol, close to the energy required to break a hydrogen bond in bulk water. This may suggest the presence of some other form of bonding between the water molecules and the structure, but the resolution of the apparent contradiction between the inelastic neutron and dielectric spectroscopic results remains uncertain.« less
Effect of polyethyleneimine modified graphene on the mechanical and water vapor barrier properties of methyl cellulose composite films.

PubMed

Liu, Hongyu; Liu, Cuiyun; Peng, Shuge; Pan, Bingli; Lu, Chang

2018-02-15

A series of novel methyl cellulose (MC) composite films were prepared using polyethyleneimine reduced graphene oxide (PEI-RGO) as an effective filler for water vapor barrier application. The as-prepared PEI-RGO/MC composites were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, tensile test and scanning electron microscopy. The experimental and theoretical results exhibited that PEI-RGO was uniformly dispersed in the MC matrix without aggregation and formed an aligned dispersion. The addition of PEI-RGO resulted in an enhanced surface hydrophobicity and a tortuous diffusion pathway for water molecules. Water vapor permeability of PEI-RGO/MC with loading of 3.0% of surface modified graphene was as low as 5.98×10 -11 gmm -2 s -1 Pa -1 . The synergistic effects of enhanced surface hydrophobicity and tortuous diffusion pathway were accounted for the improved water vapor barrier performance of the PEI-RGO/MC composite films. Copyright © 2017 Elsevier Ltd. All rights reserved.
Molecular dynamics simulations of energy dissipation and non-thermal diffusion on amorphous solid water.

PubMed

Fredon, A; Cuppen, H M

2018-02-21

Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. Especially, saturated, hydrogen-rich molecules are formed through surface chemistry where the interstellar grains act as a meeting place and absorbing energy. Here we present the results of thousands of molecular dynamics simulations to quantify the outcome of an energy dissipation process. Admolecules on top of an amorphous solid water surface have been given translational energy between 0.5 and 5 eV. Three different surface species are considered, CO 2 , H 2 O and CH 4 , spanning a range in binding energies, number of internal degrees of freedom and molecular weight. The results are compared against a previous study using a crystalline water ice surface. Possible outcomes of a dissipation process are adsorption - possibly after long-range diffusion-, desorption and desorption of a surface molecule. The three admolecules were found to bind at different locations on the surface, particularly in terms of height. Water preferably binds on top of the surface, whereas methane fills the nanopores on the surface. This has direct consequences for desorption, travelled distance, and kick-out probabilities. The admolecules are found to frequently travel several tens of angstroms before stabilizing on a binding site, allowing follow-up reactions en route. We present kick-out probabilities and we have been able to quantify the desorption probability which depends on the binding energy of the species, the translational excitation, and a factor that accounts for difference in binding site height. We provide expressions that can be incorporated in astrochemical models to predict grain surface formation and return into the gas phase of these products.
Capacity and Delay Spread in Multilayer Diffusion-Based Molecular Communication (DBMC) Channel.

PubMed

Md Mustam, Saizalmursidi; Syed-Yusof, Sharifah K; Zubair, Suleiman

2016-10-01

In nanoscale communication, diffusion-based molecular communication (DBMC) in which information is encoded into molecule patterns by a transmitter nanomachine, has emerged as a promising communication system, particularly for biomedical and healthcare applications. Although, numerous studies have been conducted to evaluate and analyze DBMC systems, investigation on DBMC system through a multilayer channel has received less attention. The aims of this paper are to formulate channel characteristics and to evaluate the performance of multilayer DBMC channel in terms of delay spread and capacity. In this paper, the propagation of molecules over an n- layer channel is assumed to follow the Brownian motion and subjected to Fick's law of diffusion. Fourier transform is used to convert time to frequency domain functions. Besides, the multilayer channel is considered as a linear and deterministic channel. For the performance evaluation, the air-water-blood plasma medium representing the simplified multilayer diffusion model in the respiratory system was chosen. It was found that a high channel capacity can be achieved with wide transmission bandwidth, short transmission distance, and high averaged transmitted power. In addition, the findings showed that channel delay spread increases as both the transmission distance, and the pulse duration increased. By setting the symbol duration greater than the pulse duration or delay spread, an inter-symbol interference problem due to previous molecules transmission can be mitigated. These findings can be used as a guide in the development and fabrication of future artificial nanocommunication and nanonetworks systems involving multilayer transmission medium.
Reduction of diffusional defocusing in hydrodynamically focused flows

DOEpatents

Affleck, Rhett L.; Demas, James N.; Goodwin, Peter M.; Keller, Richard; Wu, Ming

1998-01-01

An analyte fluid stream with first molecules having relatively low molecular weight and a corresponding high coefficient of diffusion has reduced diffusional defocusing out of an analyte fluid stream. The analyte fluid stream of first molecules is associated with second molecules of relatively high molecular weight having a relatively low coefficient of diffusion and a binding constant effective to associate with the first molecules. A focused analyte fluid stream is maintained since the combined molecular weight of the associated first and second molecules is effective to minimize diffusion of the first molecules out of the analyte fluid stream.
Reduction of diffusional defocusing in hydrodynamically focused flows

DOEpatents

Affleck, R.L.; Demas, J.N.; Goodwin, P.M.; Keller, R.; Wu, M.

1998-09-01

An analyte fluid stream with first molecules having relatively low molecular weight and a corresponding high coefficient of diffusion has reduced diffusional defocusing out of an analyte fluid stream. The analyte fluid stream of first molecules is associated with second molecules of relatively high molecular weight having a relatively low coefficient of diffusion and a binding constant effective to associate with the first molecules. A focused analyte fluid stream is maintained since the combined molecular weight of the associated first and second molecules is effective to minimize diffusion of the first molecules out of the analyte fluid stream. 6 figs.
Time-dependent gas-liquid interaction in molecular-sized nanopores.

PubMed

Sun, Yueting; Li, Penghui; Qiao, Yu; Li, Yibing

2014-10-08

Different from a bulk phase, a gas nanophase can have a significant effect on liquid motion. Herein we report a series of experimental results on molecular behaviors of water in a zeolite β of molecular-sized nanopores. If sufficient time is provided, the confined water molecules can be "locked" inside a nanopore; otherwise, gas nanophase provides a driving force for water "outflow". This is due to the difficult molecular site exchanges and the relatively slow gas-liquid diffusion in the nanoenvironment. Depending on the loading rate, the zeolite β/water system may exhibit either liquid-spring or energy-absorber characteristics.
Communication: Water on hexagonal boron nitride from diffusion Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Hamdani, Yasmine S.; Ma, Ming; Michaelides, Angelos, E-mail: angelos.michaelides@ucl.ac.uk

2015-05-14

Despite a recent flurry of experimental and simulation studies, an accurate estimate of the interaction strength of water molecules with hexagonal boron nitride is lacking. Here, we report quantum Monte Carlo results for the adsorption of a water monomer on a periodic hexagonal boron nitride sheet, which yield a water monomer interaction energy of −84 ± 5 meV. We use the results to evaluate the performance of several widely used density functional theory (DFT) exchange correlation functionals and find that they all deviate substantially. Differences in interaction energies between different adsorption sites are however better reproduced by DFT.
Simulations of water transport through carbon nanotubes: how different water models influence the conduction rate.

PubMed

Liu, L; Patey, G N

2014-11-14

The conduction rate of water through (8,8) and (9,9) carbon nanotubes at 300 K and a pressure difference of 220 MPa is investigated using molecular dynamics simulations. The TIP3P, SPC/E, and TIP4P/2005 water models are considered. The pressure-driven flow rate is found to be strongly model dependent for both nanotubes. The fastest model (TIP3P) has a flow rate that is approximately five times faster than the slowest (TIP4P/2005). It is shown that the flow rate is significantly influenced by the structure taken on by the water molecules confined in the nanotube channels. The slower models, TIP4P/2005 and SPC/E, tend to favor stacked ring arrangements, with the molecules of a ring moving together through the nanotube, in what we term a "cluster-by-cluster" conduction mode. Confined TIP3P water has a much weaker tendency to form ring structures, and those that do form are fragile and break apart under flow conditions. This creates a much faster "diffusive" conduction mode where the water molecules mainly move through the tube as individual particles, rather than as components of a larger cluster. Our results demonstrate that water models developed to describe the properties of bulk water can behave very differently in confined situations.
Multiscale Modeling of Diffusion in a Crowded Environment.

PubMed

Meinecke, Lina

2017-11-01

We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.
First-principles study of water desorption from montmorillonite surface.

PubMed

Zhang, Yao; Meng, Yingfeng; Liu, Houbin; Yang, Mingli

2016-05-01

Knowledge about water desorption is important to give a full picture of water diffusion in montmorillonites (MMT), which is a driving factor in MMT swelling. The desorption paths and energetics of water molecules from the surface of MMT with trapped Li(+), Na(+) or K(+) counterions were studied using periodic density functional theory calculations. Two paths--surface and vacuum desorption--were designed for water desorption starting from a stationary structure in which water bonds with both the counterion and the MMT surface. Surface desorption is energetically more favorable than vacuum desorption due to water-surface hydrogen bonds that help stabilize the intermediate structure of water released from the counterion. The energy barriers of water desorption are in the order of Li(+) > Na(+) > K(+), which can be attributed to the short ionic radius of Li(+), which favors strong binding with the water molecule. The temperature dependence of water adsorption and desorption rates were compared based on the computed activation energies. Our calculations reveal that the water desorption on the MMT surface has a different mechanism from water adsorption, which results from surface effects favoring stabilization of water conformers during the desorption process.
Osmosis and thermodynamics explained by solute blocking.

PubMed

Nelson, Peter Hugo

2017-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult's law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed; others can be tested experimentally or by simulation.

Osmosis and thermodynamics explained by solute blocking

PubMed Central

Nelson, Peter Hugo

2016-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult’s law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed, others can be tested experimentally or by simulation. PMID:27225298
Degradation process by effect of water molecules during negative bias temperature stress in amorphous-InGaZnO thin-film transistor

NASA Astrophysics Data System (ADS)

Lee, Yeol-Hyeong; Cho, Yong-Jung; Kim, Woo-Sic; Park, Jeong Ki; Kim, Geon Tae; Kim, Ohyun

2017-10-01

We explained how H2O degrades amorphous-InGaZnO thin-film transistors. H2O caused serious degradation only during negative bias temperature stress (NBTS). Degradation was caused by molecules that were absorbed or diffused from the outside. We suggest that degradation under NBTS is caused by the migration of hydrogen ions among oxygen vacancies. Under illumination, the soaking time t S did not affect the threshold voltage shift ΔV th. We consider that this independence occurred because illumination caused ionization from the oxygen vacancy VO state to VO 2+, which impeded hydrogen migration induced by electric field and thereby protected the device from degradation after exposure to water.
Modeling fluid diffusion in cerebral white matter with random walks in complex environments

NASA Astrophysics Data System (ADS)

Levy, Amichai; Cwilich, Gabriel; Buldyrev, Sergey V.; Weeden, Van J.

2012-02-01

Recent studies with diffusion MRI have shown new aspects of geometric order in the brain, including complex path coherence within the cerebral cortex, and organization of cerebral white matter and connectivity across multiple scales. The main assumption of these studies is that water molecules diffuse along myelin sheaths of neuron axons in the white matter and thus the anisotropy of their diffusion tensor observed by MRI can provide information about the direction of the axons connecting different parts of the brain. We model the diffusion of particles confined in the space of between the bundles of cylindrical obstacles representing fibrous structures of various orientations. We have investigated the directional properties of the diffusion, by studying the angular distribution of the end point of the random walks as a function of their length, to understand the scale over which the distribution randomizes. We will show evidence of qualitative change in the behavior of the diffusion for different volume fractions of obstacles. Comparisons with three-dimensional MRI images will be illustrated.
Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.

PubMed

Chevalier, Michael W; El-Samad, Hana

2012-08-28

Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.
Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals

DOE PAGES

McDaniel, Jesse G.; Yethiraj, Arun

2017-04-26

Bilayers composed of lipid or surfactant molecules are central to biological membranes and lamellar lyotropic liquid crystalline (LLC) phases. Common to these systems are phases that exhibit either ordered or disordered packing of the hydrophobic tails. In this work, we study the impact of surfactant ordering, i.e., disordered L α and ordered L β LLC phases, on the dynamics of water and sodium ions in the lamellar phases of dicarboxylate gemini surfactants. We study the different phases at identical hydration levels by changing the length of the hydrophobic tails; surfactants with shorter tails form L α phases and those withmore » longer tails form L β phases. We find that the L α phases exhibit lower density and greater compressibility than the L β phases, with a hydration-dependent headgroup surface area. These structural differences significantly affect the relative dynamic properties of the phases, primarily the mobility of the surfactant molecules tangential to the bilayer surface, as well as the rates of water and ion diffusion. We find ~20–50% faster water diffusion in the L α phases compared to the L β phases, with the differences most pronounced at low hydration. This coupling between water dynamics and surfactant mobility is verified using additional simulations in which the surfactant tails are frozen. Our study indicates that gemini surfactant LLCs provide an important prototypical system for characterizing properties shared with more complex biological lipid membranes.« less
Determination of the Trajectory of Ballistic Missiles Using a Dense GPS Array

NASA Astrophysics Data System (ADS)

Heki, K.; Ozeki, M.

2009-12-01

The dense array of ~1000 Global Positioning System (GPS) receivers in Japan provides useful information on atmosphere and ionosphere in terms of delays of microwaves in propagation media. Here we introduce its brand-new application, determination of the trajectories of ballistic missiles by using their electron depletion signatures in ionosphere. Booker (1961) first detected F-region ion depletion associated with a missile passage. Later, formation of an ionospheric hole by the launch of Skylab was observed, and Mendillo et al. (1975) attributed the electron depletion to the water molecules in the rocket exhaust. In Japan, ionospheric depletion after the launch of the H-IIA rocket was observed at GPS receivers in southern Japan using differences in phases between the two carrier frequencies L1 and L2 (Furuya & Heki, 2008). The so-called Taepodong-1, and -2 (the North Korean government claims that they successfully launched satellites), ballistic missiles with liquid fuel engines, were launched from Musudanri, North Korea, in August 1998, and April 2009, respectively. Their first stage engines splashed down onto the Japan Sea, and their second stage engines flew over northeastern Japan and reached the Pacific Ocean. We investigated GPS data before and after the launches, and detected that linear electron depletion areas appear in the northern part of the Japan Sea (~300 km east of the launch pad) approximately six minutes after the launch. Such electron depletion occurs as a result of exchange of positive charges between oxygen ions and water molecules, and dissociative recombination of water with electrons. The ionospheric hole rapidly grows and gradually decays as the water molecules diffuse. By comparing the numerical simulation results of ionospheric hole formation (water diffusion and chemical reaction) and the observed change in ionospheric total electron content (TEC), we conclude that the Taepodong-1 exhaust included water molecules ~0.5 percent of those in the H-IIA rocket. Taepodong-2, on the other hand, made a larger and longer-lasting hole and water molecules in its exhaust appear to be eight times as many as in Taepodong-1. This perhaps reflects improvement in thrust of the Taepodong series. We estimated the most likely trajectory of the Taepodong-2 constraining the coordinates of the launch pad and splashdown point. The missile reached the ionospheric F region in six minutes after the launch and flew above northeastern Japan about 9-10 minutes after the launch.
Nature of water and hydrogen reactions on transition metal surfaces studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tatarkhanov, Mouslim Magomedovich

Scanning Tunneling Microscopy (STM) has already been established as a tool for the investigation of simple reaction mechanisms. In this work I present results of two parallel studies using STM: first, hydrogen on Ru(0001) surface and second, water on Ru(0001) and Pd(111). In both studies initial stages of adsorption up to saturation monolayer coverage were investigated by variable temperature scanning tunneling microscopy (VT STM). The first step of the hydrogen adsorption study was the identification and characterization of the various coverage structures on clean Ru(0001). Hydrogen was found to adsorb dissociatively forming ( 3x3 )R30°, 3 domains of (2x1), (2x2)-3H and (1x1) for increasing coverages of theta=0.3 ML, 0.5 ML, 0.75 ML and 0.1 ML respectively. Some of these structures were observed to coexist at intermediate coverage values. In addition effects of impurities such as oxygen and carbon on hydrogen adsorption has been discussed. Next, near saturation coverage the interesting mechanism of how H 2 dissociates and binds to the surface of Ru(0001) has been observed. We found that the H2 dissociation takes place only on Ru sites where the metal atom is not bound to any H atom. Such active sites are formed when at least 3 H-vacancies aggregate by thermal diffusion. Sites formed by single H-vacancies (i.e. unoccupied Ru sites) or pairs of adjoining vacancies were found to be unreactive toward H2. H-vacancies were observed as single entities diffusing on the surface at 50 K and able to form transient triangular shaped aggregations where H2 molecules dissociated. It was found that the diffusion and aggregation of the H-vacancies is essential in creation of active sites where dissociative adsorption of hydrogen occurs. The first step of water studies was the initial stages of growth of water on the hexagonal surfaces of Pd(111) and Ru(0001) in the temperature range between 40 K and 130 K. In addition, DFT calculations and STM image simulations were used to validate the models. Below 130 K water dissociation does not occur at any appreciable rate and only molecular films are formed. At these temperatures the kinetics of water growth leads to structures where the molecules bind to the metal substrate through the O-lone pair while making 3 H-bonds with neighboring molecules and form clusters of hexagonal units with a honeycomb structure. This bonding geometry imposes limitations to the size of the clusters, with unsaturated H-bonds confined to the cluster periphery. It is found that growth proceeds by attachement of water molecules to the edge of the clusters by H-bonds. These molecules bind only weakly to the metal substrate and can hop around the edges. Comparison of DFT and STM image calculations with experiments shows that on Pd the edge-attached molecules form two different structures, a metastable one where the molecule is elevated by 2.7 A with respect to the cluster molecules, and another where they are elevated by only 0.4 A. On Ru only the less elevated (0.4 A higher) edge-attached molecules are observed. In next final step, water structures on Ru(0001) were studied at temperatures above 140K. STM findings were backed by x-ray absorption spectroscopy. Additional DFT calculations and STM simulations provided validation of proposed models. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H 2O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentiallymostly parallel to the surface. STM images show that the mixed H2O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H2O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripes geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.
Studies of molecular diffusion in single-supported bilayer lipid membranes at low hydration by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Miskowiec, A.; Bai, M.; Lever, M.; Taub, H.; Hansen, F. Y.; Jenkins, T.; Tyagi, M.; Neumann, D. A.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.

2011-03-01

We have extended our investigation of the quasielastic neutron scattering from single-supported bilayer lipid membranes to a sample of lower hydration using the backscattering spectrometer BASIS at the SNS of ORNL. To focus on the diffusive motion of the water, tail-deuterated DMPC membranes were deposited onto Si O2 -coated Si(100) substrates and characterized by AFM. Compared to a sample of higher hydration, the dryer sample does not have a step-like freezing transition at ~ 267 K and shows less intensity at higher temperatures of a broad Lorentzian component representing bulk-like water. However, the broad component of the ``wet'' and ``dry'' samples behaves similarly at lower temperatures. The dryer sample also shows evidence of a narrow Lorentzian component that has a different temperature dependence than that attributed to conformational changes of the alkyl tails of the lipid molecules in the wet sample. We tentatively identify this slower diffusive motion (time scale ~ 1 ns) with water more tightly bound to the membrane. Supported by NSF Grant No. DMR-0705974.
Unifying diffusion and seepage for nonlinear gas transport in multiscale porous media

NASA Astrophysics Data System (ADS)

Song, Hongqing; Wang, Yuhe; Wang, Jiulong; Li, Zhengyi

2016-09-01

We unify the diffusion and seepage process for nonlinear gas transport in multiscale porous media via a proposed new general transport equation. A coherent theoretical derivation indicates the wall-molecule and molecule-molecule collisions drive the Knudsen and collective diffusive fluxes, and constitute the system pressure across the porous media. A new terminology, nominal diffusion coefficient can summarize Knudsen and collective diffusion coefficients. Physical and numerical experiments show the support of the new formulation and provide approaches to obtain the diffusion coefficient and permeability simultaneously. This work has important implication for natural gas extraction and greenhouse gases sequestration in geological formations.
Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen.

PubMed

Sodeifian, Gholamhossein; Razmimanesh, Fariba

2018-05-10

In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug-water hydrogen bond in protein-free systems and protein-drug hydrogen bond in the systems containing protein.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohanta, Dayanidhi; Jana, Madhurima, E-mail: janam@nitrkl.ac.in

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein’s structure is almost insignificant at T1more » and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2’s native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein’s solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2’s surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein’s surface during the unfolding process.« less
Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2

NASA Astrophysics Data System (ADS)

Mohanta, Dayanidhi; Jana, Madhurima

2016-04-01

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein's structure is almost insignificant at T1 and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2's native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein's solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2's surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein's surface during the unfolding process.
Temperature Dependence of Nonelectrolyte Permeation across Red Cell Membranes

PubMed Central

Galey, W. R.; Owen, J. D.; Solomon, A. K.

1973-01-01

The temperature dependence of permeation across human red cell membranes has been determined for a series of hydrophilic and lipophilic solutes, including urea and two methyl substituted derivatives, all the straight-chain amides from formamide through valeramide and the two isomers, isobutyramide and isovaleramide. The temperature coefficient for permeation by all the hydrophilic solutes is 12 kcal mol-1 or less, whereas that for all the lipophilic solutes is 19 kcal mol-1 or greater. This difference is consonant with the view that hydrophilic molecules cross the membrane by a path different from that taken by the lipophilic ones. The thermodynamic parameters associated with lipophile permeation have been studied in detail. ΔG is negative for adsorption of lipophilic amides onto an oil-water interface, whereas it is positive for transfer of the polar head from the aqueous medium to bulk lipid solvent. Application of absolute reaction rate theory makes it possible to make a clear distinction between diffusion across the water-red cell membrane interface and diffusion within the membrane. Diffusion coefficients and apparent activation enthalpies and entropies have been computed for each process. Transfer of the polar head from the solvent into the interface is characterized by ΔG ‡ = 0 kcal mol-1 and ΔS ‡ negative, whereas both of these parameters have large positive values for diffusion within the membrane. Diffusion within the membrane is similar to what is expected for diffusion through a highly associated viscous fluid. PMID:4708405
Fish skin as a model membrane: structure and characteristics.

PubMed

Konrádsdóttir, Fífa; Loftsson, Thorsteinn; Sigfússon, Sigurdur Dadi

2009-01-01

Synthetic and cell-based membranes are frequently used during drug formulation development for the assessment of drug availability. However, most of the currently used membranes do not mimic mucosal membranes well, especially the aqueous mucous layer of the membranes. In this study we evaluated catfish (Anarichas lupus L) skin as a model membrane. Permeation of hydrocortisone, lidocaine hydrochloride, benzocaine, diethylstilbestrol, naproxen, picric acid and sodium nitrate through skin from a freshly caught catfish was determined in Franz diffusion cells. Both lipophilic and hydrophilic molecules permeate through catfish skin via hydrated channels or aqueous pores. No correlation was observed between the octanol/water partition coefficient of the permeating molecules and their permeability coefficient through the skin. Permeation through catfish skin was found to be diffusion controlled. The results suggest that permeation through the fish skin proceeds via a diffusion-controlled process, a process that is similar to drug permeation through the aqueous mucous layer of a mucosal membrane. In addition, the fish skin, with its collagen matrix structure, appears to possess similar properties to the eye sclera.
Magnetic resonance imaging of mass transport and structure inside a phototrophic biofilm.

PubMed

Ramanan, Baheerathan; Holmes, William M; Sloan, William T; Phoenix, Vernon R

2013-05-01

The aim of this study was to utilize magnetic resonance imaging (MRI) to image structural heterogeneity and mass transport inside a biofilm which was too thick for photon based imaging. MRI was used to map water diffusion and image the transport of the paramagnetically tagged macromolecule, Gd-DTPA, inside a 2.5 mm thick cyanobacterial biofilm. The structural heterogeneity of the biofilm was imaged at resolutions down to 22 × 22 μm, enabling the impact of biofilm architecture on the mass transport of both water and Gd-DTPA to be investigated. Higher density areas of the biofilm correlated with areas exhibiting lower relative water diffusion coefficients and slower transport of Gd-DTPA, highlighting the impact of biofilm structure on mass transport phenomena. This approach has potential for shedding light on heterogeneous mass transport of a range of molecular mass molecules in biofilms.
Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions.

PubMed

Chen, Pan; Terenzi, Camilla; Furó, István; Berglund, Lars A; Wohlert, Jakob

2018-05-15

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13 C NMR longitudinal relaxation times ( T 1 ) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.
Self-diffusion of protons in H{sub 2}O ice VII at high pressures: Anomaly around 10 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noguchi, Naoki, E-mail: noguchi-n@okayama-u.ac.jp; Okuchi, Takuo

2016-06-21

The self-diffusion of ice VII in the pressure range of 5.5–17 GPa and temperature range of 400–425 K was studied using micro Raman spectroscopy and a diamond anvil cell. The diffusion was monitored by observing the distribution of isotope tracers: D{sub 2}O and H{sub 2}{sup 18}O. The diffusion coefficient of hydrogen reached a maximum value around 10 GPa. It was two orders of magnitude greater at 10 GPa than at 6 GPa. Hydrogen diffusion was much faster than oxygen diffusion, which indicates that protonic diffusion is the dominant mechanism for the diffusion of hydrogen in ice VII. This mechanism ismore » in remarkable contrast to the self-diffusion in ice I{sub h} that is dominated by an interstitial mechanism for the whole water molecule. An anomaly around 10 GPa in ice VII indicates that the rate-determining process for the proton diffusion changes from the diffusion of ionic defects to the diffusion of rotational defects, which was suggested by proton conductivity measurements and molecular dynamics simulations.« less
Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.

PubMed

Gnanasekaran, Ramachandran

2017-11-08

We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg 2+ , doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication.
Origin of 1/f noise in hydration dynamics on lipid membrane surfaces

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji

2015-01-01

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes. PMID:25743377
Combination of broadband diffuse optical spectroscopy with magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Merritt, Sean Isaiah

Broadband diffuse optical spectroscopy (DOS) is an emerging optical technique used to measure absorption and scattering of bulk tissue non-invasively within the near-infrared (600--1050 nm). The ultimate aim of my advisors group is for broadband DOS to become an established medical diagnostic technique used clinically on various tissue types including breast, muscle and bone. The specific goal for my research is to use established magnetic resonance (MR) techniques for the purpose of continued development and validation of broadband DOS. The initial studies carried out were a validation of broadband DOS through a direct comparison with MRI. Both techniques are sensitive to signals produced by water and lipids in tissue. There is also sensitivity to blood flow, which MRI measures using exogenous contrast agents and broadband DOS is sensitive through measurement of total hemoglobin content (THC) and tissue oxygen saturation (StO2). These validation studies were compared initially in a rat tumor model in which both techniques were used simultaneously. A qualitative correlation was found between the MR images of water content and blood perfusion compared with the DOS water and THC values. A more quantitative comparison was made between measuring absolute water and lipid content in phantoms and in human tissue, which showed a strong correlation. The in vivo study also validated that broadband DOS was interrogating bone marrow in the tibia. The second half of this thesis is focused on developing new capabilities of broadband DOS and the MRI literature is used as a guide. When a water molecule hydrogen bonds to another molecule, the absorption spectrum in the near-infrared which is due to the vibrational overtone of the OH bond will change. The expected changes were observed in tissue and an algorithm was developed to fit for a tissue bound water parameter. Also, as tissue temperature changes, the fraction of water bound to other water molecules changes and can be used to fit for deep tissue temperature. Preliminary validation of these two techniques is carried out and there appears to be great potential for these methods.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Pooja; Ali, Sk. M., E-mail: musharaf@barc.gov.in

Water in nanotube exhibits remarkably different properties from the bulk phase, which can be exploited in various nanoconfinement based technologies. The properties of water within nanotube can be further tuned by varying the nanotube electrostatics and functionalization of nanotube ends. Here, therefore, we investigate the effect of quantum partial charges and carbon nanotube (CNT) termination in terms of associated entropic forces. An attempt has been made to correlate the entropic forces with various dynamical and structural properties. The simulated structural features are consistent with general theoretical aspects, in which the interfacial water molecules at H terminated CNT are found tomore » be distributed in a different way as compared to other CNTs. The rotational entropy components for different cases of CNTs are well corroborated by the decay time of hydrogen bond (HB) correlation functions. A part of this event has been explained in terms of orientation of water molecules in the chain, i.e., the change in direction of dipole moment of water molecules in the chain and it has been revealed that the HBs of CNT confined water molecules show long preserving correlation if their rotations inside CNT are restricted. Furthermore, the translational entropy components are rationally integrated with the differing degree of translational constraints, added by the CNTs. To the best of our information, perhaps this is the first study where the thermodynamic effects introduced by H-termination and induced dipole of CNT have been investigated. Additionally, we present a bridge relation between “translational diffusivity and configurational entropy” for water transport from bulk phase to inside CNTs.« less
Diffusion and bulk flow in phloem loading: A theoretical analysis of the polymer trap mechanism for sugar transport in plants

NASA Astrophysics Data System (ADS)

Dölger, Julia; Rademaker, Hanna; Liesche, Johannes; Schulz, Alexander; Bohr, Tomas

2014-10-01

Plants create sugar in the mesophyll cells of their leaves by photosynthesis. This sugar, mostly sucrose, has to be loaded via the bundle sheath into the phloem vascular system (the sieve elements), where it is distributed to growing parts of the plant. We analyze the feasibility of a particular loading mechanism, active symplasmic loading, also called the polymer trap mechanism, where sucrose is transformed into heavier sugars, such as raffinose and stachyose, in the intermediary-type companion cells bordering the sieve elements in the minor veins of the phloem. Keeping the heavier sugars from diffusing back requires that the plasmodesmata connecting the bundle sheath with the intermediary cell act as extremely precise filters, which are able to distinguish between molecules that differ by less than 20% in size. In our modeling, we take into account the coupled water and sugar movement across the relevant interfaces, without explicitly considering the chemical reactions transforming the sucrose into the heavier sugars. Based on the available data for plasmodesmata geometry, sugar concentrations, and flux rates, we conclude that this mechanism can in principle function, but that it requires pores of molecular sizes. Comparing with the somewhat uncertain experimental values for sugar export rates, we expect the pores to be only 5%-10% larger than the hydraulic radius of the sucrose molecules. We find that the water flow through the plasmodesmata, which has not been quantified before, contributes only 10%-20% to the sucrose flux into the intermediary cells, while the main part is transported by diffusion. On the other hand, the subsequent sugar translocation into the sieve elements would very likely be carried predominantly by bulk water flow through the plasmodesmata. Thus, in contrast to apoplasmic loaders, all the necessary water for phloem translocation would be supplied in this way with no need for additional water uptake across the plasma membranes of the phloem.
Diffusion and bulk flow in phloem loading: a theoretical analysis of the polymer trap mechanism for sugar transport in plants.

PubMed

Dölger, Julia; Rademaker, Hanna; Liesche, Johannes; Schulz, Alexander; Bohr, Tomas

2014-10-01

Plants create sugar in the mesophyll cells of their leaves by photosynthesis. This sugar, mostly sucrose, has to be loaded via the bundle sheath into the phloem vascular system (the sieve elements), where it is distributed to growing parts of the plant. We analyze the feasibility of a particular loading mechanism, active symplasmic loading, also called the polymer trap mechanism, where sucrose is transformed into heavier sugars, such as raffinose and stachyose, in the intermediary-type companion cells bordering the sieve elements in the minor veins of the phloem. Keeping the heavier sugars from diffusing back requires that the plasmodesmata connecting the bundle sheath with the intermediary cell act as extremely precise filters, which are able to distinguish between molecules that differ by less than 20% in size. In our modeling, we take into account the coupled water and sugar movement across the relevant interfaces, without explicitly considering the chemical reactions transforming the sucrose into the heavier sugars. Based on the available data for plasmodesmata geometry, sugar concentrations, and flux rates, we conclude that this mechanism can in principle function, but that it requires pores of molecular sizes. Comparing with the somewhat uncertain experimental values for sugar export rates, we expect the pores to be only 5%-10% larger than the hydraulic radius of the sucrose molecules. We find that the water flow through the plasmodesmata, which has not been quantified before, contributes only 10%-20% to the sucrose flux into the intermediary cells, while the main part is transported by diffusion. On the other hand, the subsequent sugar translocation into the sieve elements would very likely be carried predominantly by bulk water flow through the plasmodesmata. Thus, in contrast to apoplasmic loaders, all the necessary water for phloem translocation would be supplied in this way with no need for additional water uptake across the plasma membranes of the phloem.
Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

2016-09-01

Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.
Conversion of lanthanide glutarate chlorides with interstitial THF into lanthanide glutarates with unprecedented topologies

DOE PAGES

Zehnder, Ralph A.; Jenkins, James; Zeller, Matthias; ...

2017-11-26

Here, using slow diffusion methods at room temperature (RT), we obtained four isomorphous lanthanide glutarate chlorides, accommodating interstitial THF and water molecules, [Ln 2(Glut) 2Cl 2(H 2O) 8]·2H 2O·THF, with Ln = La , Ce, Pr, Nd. They assemble as 3-dimensional (3D) lanthanide (Ln) coordination polymers with LnO 10 coordination polyhedra. Their topology was elucidated to be a 4-coordinated sql net. slowly dissolve in water liberating the entrapped THF molecules and reassemble as regular Ln-glutarate hydrates when the solution is deprived of THF and water by slow evaporation. The new products crystallize as [Ln 2(Glut) 3(H 2O) 3]·5H 2O, withmore » Ln = La, Ce, Pr, and [Nd 2(Glut) 3(H 2O) 2]·3.5H 2O.« less
Conversion of lanthanide glutarate chlorides with interstitial THF into lanthanide glutarates with unprecedented topologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zehnder, Ralph A.; Jenkins, James; Zeller, Matthias

Here, using slow diffusion methods at room temperature (RT), we obtained four isomorphous lanthanide glutarate chlorides, accommodating interstitial THF and water molecules, [Ln 2(Glut) 2Cl 2(H 2O) 8]·2H 2O·THF, with Ln = La , Ce, Pr, Nd. They assemble as 3-dimensional (3D) lanthanide (Ln) coordination polymers with LnO 10 coordination polyhedra. Their topology was elucidated to be a 4-coordinated sql net. slowly dissolve in water liberating the entrapped THF molecules and reassemble as regular Ln-glutarate hydrates when the solution is deprived of THF and water by slow evaporation. The new products crystallize as [Ln 2(Glut) 3(H 2O) 3]·5H 2O, withmore » Ln = La, Ce, Pr, and [Nd 2(Glut) 3(H 2O) 2]·3.5H 2O.« less
Combined effects of the drug distribution and mucus diffusion properties of self-microemulsifying drug delivery systems on the oral absorption of fenofibrate.

PubMed

Sunazuka, Yushi; Ueda, Keisuke; Higashi, Kenjirou; Tanaka, Yusuke; Moribe, Kunikazu

2018-05-24

We present the absorption improvement mechanism of fenofibrate (FFB), a Biopharmaceutics Classification System (BCS) class II drug, from self-microemulsifying drug delivery systems (SMEDDS), centered on improving the diffusion of FFB through the unstirred water layer (UWL). Four SMEDDS formulations containing Labrafac™ lipophile WL 1349 (WL1349) or Labrafil ® M 1944CS (M1944) oils and NIKKOL HCO-40 (HCO40) or NIKKOL HCO-60 (HCO60) surfactants were prepared. Every SMEDDS formulation formed microemulsion droplets of approximately 30 nm. In vitro tests showed that the microemulsion droplets containing M1944 had relatively small FFB solubilization capacities, causing larger amounts of FFB to be dissolved in the bulk water phase, compared to the droplets containing WL1349. The diffusivity of the microemulsion droplets through the mucin solution layer was enhanced when using HCO40 compared to HCO60. The oral absorption in rats was the highest when using the SMEDDS formulation containing M1944 and HCO40. High FFB distribution in the bulk water phase and fast diffusion of microemulsion droplets through the mucus layer contributed to the efficient delivery of FFB molecules through the UWL to the epithelial cells, leading to enhanced FFB absorption. Copyright © 2018 Elsevier B.V. All rights reserved.
Modeling and Uncertainty Quantification of Vapor Sorption and Diffusion in Heterogeneous Polymers

DOE PAGES

Sun, Yunwei; Harley, Stephen J.; Glascoe, Elizabeth A.

2015-08-13

A high-fidelity model of kinetic and equilibrium sorption and diffusion is developed and exercised. The gas-diffusion model is coupled with a triple-sorption mechanism: Henry’s law absorption, Langmuir adsorption, and pooling or clustering of molecules at higher partial pressures. Sorption experiments are conducted and span a range of relative humidities (0-95%) and temperatures (30-60°C). Kinetic and equilibrium sorption properties and effective diffusivity are determined by minimizing the absolute difference between measured and modeled uptakes. Uncertainty quantification and sensitivity analysis methods are described and exercised herein to demonstrate the capability of this modeling approach. Water uptake in silica-filled and unfilled poly(dimethylsiloxane) networksmore » is investigated; however, the model is versatile enough to be used with a wide range of materials and vapors.« less
High Interfacial Barriers at Narrow Carbon Nanotube-Water Interfaces.

PubMed

Varanasi, Srinivasa Rao; Subramanian, Yashonath; Bhatia, Suresh K

2018-06-26

Water displays anomalous fast diffusion in narrow carbon nanotubes (CNTs), a behavior that has been reproduced in both experimental and simulation studies. However, little is reported on the effect of bulk water-CNT interfaces, which is critical to exploiting the fast transport of water across narrow carbon nanotubes in actual applications. Using molecular dynamics simulations, we investigate here the effect of such interfaces on the transport of water across arm-chair CNTs of different diameters. Our results demonstrate that diffusion of water is significantly retarded in narrow CNTs due to bulk regions near the pore entrance. The slowdown of dynamics can be attributed to the presence of large energy barriers at bulk water-CNT interfaces. The presence of such intense barriers at the bulk-CNT interface arises due to the entropy contrast between the bulk and confined regions, with water molecules undergoing high translational and rotational entropy gain on entering from the bulk to the CNT interior. The intensity of such energy barriers decreases with increase in CNT diameter. These results are very important for emerging technological applications of CNTs and other nanoscale materials, such as in nanofluidics, water purification, nanofiltration, and desalination, as well as for biological transport processes.
Fractal analysis of lateral movement in biomembranes.

PubMed

Gmachowski, Lech

2018-04-01

Lateral movement of a molecule in a biomembrane containing small compartments (0.23-μm diameter) and large ones (0.75 μm) is analyzed using a fractal description of its walk. The early time dependence of the mean square displacement varies from linear due to the contribution of ballistic motion. In small compartments, walking molecules do not have sufficient time or space to develop an asymptotic relation and the diffusion coefficient deduced from the experimental records is lower than that measured without restrictions. The model makes it possible to deduce the molecule step parameters, namely the step length and time, from data concerning confined and unrestricted diffusion coefficients. This is also possible using experimental results for sub-diffusive transport. The transition from normal to anomalous diffusion does not affect the molecule step parameters. The experimental literature data on molecular trajectories recorded at a high time resolution appear to confirm the modeled value of the mean free path length of DOPE for Brownian and anomalous diffusion. Although the step length and time give the proper values of diffusion coefficient, the DOPE speed calculated as their quotient is several orders of magnitude lower than the thermal speed. This is interpreted as a result of intermolecular interactions, as confirmed by lateral diffusion of other molecules in different membranes. The molecule step parameters are then utilized to analyze the problem of multiple visits in small compartments. The modeling of the diffusion exponent results in a smooth transition to normal diffusion on entering a large compartment, as observed in experiments.
Quantifying the transport properties of lipid mesophases by theoretical modelling of diffusion experiments

NASA Astrophysics Data System (ADS)

Antognini, Luca M.; Assenza, Salvatore; Speziale, Chiara; Mezzenga, Raffaele

2016-08-01

Lyotropic Liquid Crystals (LLCs) are a class of lipid-based membranes with a strong potential for drug-delivery employment. The characterization and control of their transport properties is a central issue in this regard, and has recently prompted a notable volume of research on the topic. A promising experimental approach is provided by the so-called diffusion setup, where the drug molecules diffuse from a feeding chamber filled with water to a receiving one passing through a LLC. In the present work we provide a theoretical framework for the proper description of this setup, and validate it by means of targeted experiments. Due to the inhomogeneity of the system, a rich palette of different diffusion dynamics emerges from the interplay of the different time- and lengthscales thereby present. Our work paves the way to the employment of diffusion experiments to quantitatively characterize the transport properties of LLCs, and provides the basic tools for device diffusion setups with controlled kinetic properties.
Thermodynamic Derivation of the Activation Energy for Ice Nucleation

NASA Technical Reports Server (NTRS)

Barahona, D.

2015-01-01

Cirrus clouds play a key role in the radiative and hydrological balance of the upper troposphere. Their correct representation in atmospheric models requires an understanding of the microscopic processes leading to ice nucleation. A key parameter in the theoretical description of ice nucleation is the activation energy, which controls the flux of water molecules from the bulk of the liquid to the solid during the early stages of ice formation. In most studies it is estimated by direct association with the bulk properties of water, typically viscosity and self-diffusivity. As the environment in the ice-liquid interface may differ from that of the bulk, this approach may introduce bias in calculated nucleation rates. In this work a theoretical model is proposed to describe the transfer of water molecules across the ice-liquid interface. Within this framework the activation energy naturally emerges from the combination of the energy required to break hydrogen bonds in the liquid, i.e., the bulk diffusion process, and the work dissipated from the molecular rearrangement of water molecules within the ice-liquid interface. The new expression is introduced into a generalized form of classical nucleation theory. Even though no nucleation rate measurements are used to fit any of the parameters of the theory the predicted nucleation rate is in good agreement with experimental results, even at temperature as low as 190 K, where it tends to be underestimated by most models. It is shown that the activation energy has a strong dependency on temperature and a weak dependency on water activity. Such dependencies are masked by thermodynamic effects at temperatures typical of homogeneous freezing of cloud droplets; however, they may affect the formation of ice in haze aerosol particles. The new model provides an independent estimation of the activation energy and the homogeneous ice nucleation rate, and it may help to improve the interpretation of experimental results and the development of parameterizations for cloud formation.
Quantum tunneling of oxygen atoms on very cold surfaces.

PubMed

Minissale, M; Congiu, E; Baouche, S; Chaabouni, H; Moudens, A; Dulieu, F; Accolla, M; Cazaux, S; Manicó, G; Pirronello, V

2013-08-02

Any evolving system can change state via thermal mechanisms (hopping a barrier) or via quantum tunneling. Most of the time, efficient classical mechanisms dominate at high temperatures. This is why an increase of the temperature can initiate the chemistry. We present here an experimental investigation of O-atom diffusion and reactivity on water ice. We explore the 6-25 K temperature range at submonolayer surface coverages. We derive the diffusion temperature law and observe the transition from quantum to classical diffusion. Despite the high mass of O, quantum tunneling is efficient even at 6 K. As a consequence, the solid-state astrochemistry of cold regions should be reconsidered and should include the possibility of forming larger organic molecules than previously expected.
Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene.

PubMed

Shahbabaei, Majid; Kim, Daejoong

2017-08-09

In this study, molecular dynamics (MD) simulations are used to examine the water transport properties through asymmetric hourglass-shaped pores in multilayer nanoporous graphene with a constant interlayer separation of 6 Å. The properties of the tested asymmetric hourglass-shaped pores [with the models having long cone (l 1 , -P) and short cone (l 2 , +P) entrances] are compared to a symmetric pore model. The study findings indicate that the water occupancy increases across the asymmetric pore (l 1 , -P) compared to (l 2 , +P), because of the length effect. The asymmetric pore, (l 1 , -P), yields higher flux compared to (l 2 , +P) and even the symmetric model, which can be attributed to the increase in the hydrogen bonds. In addition, the single-file water molecules across the narrowest pore diameter inside the (l 2 , +P) pore exhibit higher viscosity compared to those in the (l 1 , -P) pore because of the increase in the water layering effect. Moreover, it is found that the permeability inside the multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules before approaching the layer with the smallest pore diameter. The probability of dipole orientation exhibits wider distribution inside the (l 1 , -P) system compared to (l 2 , +P), implying an enhanced formation of hydrogen bonding of water molecules. This results in the fast flow of water molecules. The MD trajectory shows that the dipole orientation across the single-layer graphene has frequently flipped compared to the dipole orientation across the pores in multilayer graphene, which is maintained during the whole simulation time (although the dipole orientation has flipped for a few picoseconds at the beginning of the simulation). This can be attributed to the energy barrier induced by the individual layer. The diffusion coefficient of water molecules inside the (l 2 , +P) system increases with pressure difference, however, it decreases inside the (l 1 , -P) system because of the increase in the number of collisions. It was found that the velocity in the axial direction (z-direction) has a significant impact on the permeation ability of water molecules across the asymmetric nanopores examined in this study. Finally, the study results suggest that the appropriate design of an asymmetric hourglass-shaped nanopore in multilayer graphene can significantly improve the water permeation rate even compared to a symmetric structure.
Diffusion properties of molecules at the blood-brain interface: potential contributions of astrocyte endfeet to diffusion barrier functions.

PubMed

Nuriya, Mutsuo; Shinotsuka, Takanori; Yasui, Masato

2013-09-01

Molecular diffusion in the extracellular space (ECS) plays a key role in determining tissue physiology and pharmacology. The blood-brain barrier regulates the exchange of substances between the brain and the blood, but the diffusion properties of molecules at this blood-brain interface, particularly around the astrocyte endfeet, are poorly characterized. In this study, we used 2-photon microscopy and acute brain slices of mouse neocortex and directly assessed the diffusion patterns of fluorescent molecules. By observing the diffusion of unconjugated and 10-kDa dextran-conjugated Alexa Fluor 488 from the ECS of the brain parenchyma to the blood vessels, we find various degrees of diffusion barriers at the endfeet: Some allow the invasion of dye inside the endfoot network while others completely block it. Detailed analyses of the time course for dye clearance support the existence of a tight endfoot network capable of acting as a diffusion barrier. Finally, we show that this diffusion pattern collapses under pathological conditions. These data demonstrate the heterogeneous nature of molecular diffusion dynamics around the endfeet and suggest that these structures can serve as the diffusion barrier. Therefore, astrocyte endfeet may add another layer of regulation to the exchange of molecules between blood vessels and brain parenchyma.
Diffusion of small molecules into medaka embryos improved by electroporation

PubMed Central

2013-01-01

Background Diffusion of small molecules into fish embryos is essential for many experimental procedures in developmental biology and toxicology. Since we observed a weak uptake of lithium into medaka eggs we started a detailed analysis of its diffusion properties using small fluorescent molecules. Results Contrary to our expectations, not the rigid outer chorion but instead membrane systems surrounding the embryo/yolk turned out to be the limiting factor for diffusion into medaka eggs. The consequence is a bi-phasic uptake of small molecules first reaching the pervitelline space with a diffusion half-time in the range of a few minutes. This is followed by a slow second phase (half-time in the range of several hours) during which accumulation in the embryo/yolk takes place. Treatment with detergents improved the uptake, but strongly affected the internal distribution of the molecules. Testing electroporation we could establish conditions to overcome the diffusion barrier. Applying this method to lithium chloride we observed anterior truncations in medaka embryos in agreement with its proposed activation of Wnt signalling. Conclusions The diffusion of small molecules into medaka embryos is slow, caused by membrane systems underneath the chorion. These results have important implications for pharmacologic/toxicologic techniques like the fish embryo test, which therefore require extended incubation times in order to reach sufficient concentrations in the embryos. PMID:23815821
Time-dependent Gas-liquid Interaction in Molecular-sized Nanopores

PubMed Central

Sun, Yueting; Li, Penghui; Qiao, Yu; Li, Yibing

2014-01-01

Different from a bulk phase, a gas nanophase can have a significant effect on liquid motion. Herein we report a series of experimental results on molecular behaviors of water in a zeolite β of molecular-sized nanopores. If sufficient time is provided, the confined water molecules can be “locked” inside a nanopore; otherwise, gas nanophase provides a driving force for water “outflow”. This is due to the difficult molecular site exchanges and the relatively slow gas-liquid diffusion in the nanoenvironment. Depending on the loading rate, the zeolite β/water system may exhibit either liquid-spring or energy-absorber characteristics. PMID:25293525
Transport of secondary electrons and reactive species in ion tracks

NASA Astrophysics Data System (ADS)

Surdutovich, Eugene; Solov'yov, Andrey V.

2015-08-01

The transport of reactive species brought about by ions traversing tissue-like medium is analysed analytically. Secondary electrons ejected by ions are capable of ionizing other molecules; the transport of these generations of electrons is studied using the random walk approximation until these electrons remain ballistic. Then, the distribution of solvated electrons produced as a result of interaction of low-energy electrons with water molecules is obtained. The radial distribution of energy loss by ions and secondary electrons to the medium yields the initial radial dose distribution, which can be used as initial conditions for the predicted shock waves. The formation, diffusion, and chemical evolution of hydroxyl radicals in liquid water are studied as well. COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy.
NMR and molecular dynamics study of the size, shape, and composition of reverse micelles in a cetyltrimethylammonium bromide (CTAB)/n-hexane/pentanol/water microemulsion.

PubMed

Mills, Amanda J; Wilkie, John; Britton, Melanie M

2014-09-11

The size, shape, and composition of reverse micelles (RMs) in a cetyltrimethylammonium bromide (CTAB)/pentanol/n-hexane/water microemulsion were investigated using pulsed gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) measurements and molecular modeling. PGSTE data were collected at observation times (Δ) of 10, 40, and 450 ms. At long observation times, CTAB and pentanol exhibited single diffusion coefficients. However, at short (Δ ≤ 40 ms) observation times both CTAB and pentanol exhibited slow and fast diffusion coefficients. These NMR data indicate that both CTAB and pentanol molecules reside in different environments within the microemulsion and that there is exchange between regions on the millisecond time scale. Molecular dynamic simulations of the CTAB RM, in a solvent box containing n-hexane and pentanol, produced an ellipsoid shaped RM. Using structural parameters from these simulations and the Stokes-Einstein relation, the structure factor and dimensions of the reverse micelle were determined. Analysis of the composition of the interphase also showed that there was a variation in the ratio of surfactant to cosurfactant molecules depending on the curvature of the interphase.
Diffusivity Measurements of Volatile Organics in Levitated Viscous Aerosol Particles

NASA Astrophysics Data System (ADS)

Bastelberger, Sandra; Krieger, Ulrich; Luo, Beiping; Peter, Thomas

2017-04-01

Field measurements indicating that atmospheric secondary aerosol (SOA) particles can be present in a highly viscous, glassy state have spurred numerous studies addressing low water diffusivities in glassy aerosols, focusing on kinetic limitations to hygroscopic growth and the plasticizing effect of water. Less is known about diffusion limitations of organic molecules and oxidants in viscous matrices and how these might affect atmospheric chemistry and gas-particle phase partitioning of complex mixtures with constituents of different volatility. Often viscosity data has been used to infer diffusivity via the Stokes- Einstein relationship even though strong deviations from this relationship have been observed for matrices of high viscosity. In this study, we provide a quantitative estimate for the diffusivity of a volatile organic in a viscous matrix. Evaporation of single particles generated from an aqueous solution of sucrose and a small quantity of volatile tetraethylene glycol (PEG-4) is investigated in an electrodynamic balance at controlled relative humidity (RH) and temperature conditions, thereby varying the viscosity of the sucrose matrix. The evaporative loss of tetraethylene glycol as determined by Mie resonance spectroscopy is used in conjunction with a diffusion model to retrieve translational diffusion coefficients of tetraethylene glycol. The evaporation of PEG-4 shows a pronounced RH and temperature dependence and is severely depressed for RH 30% corresponding to diffusivities < 10-14 cm2/s at temperatures as high as 15 °C, implying that atmospheric volatile organic compounds (VOC) can be subject to severe diffusion limitations in glassy SOA. Comparison of the experimentally derived diffusivities with viscosity estimates for the ternary system reveals a breakdown of the Stokes-Einstein relationship.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations.

PubMed

Gruenbaum, Scott M; Pieniazek, Piotr A; Skinner, J L

2011-10-28

In a previous report, we calculated the infrared absorption spectrum and both the isotropic and anisotropic pump-probe signals for the OD stretch of isotopically dilute water in dilauroylphosphatidylcholine (DLPC) multi-bilayers as a function of the lipid hydration level. These results were then compared to recent experimental measurements and are in generally good agreement. In this paper, we will further investigate the structure and dynamics of hydration water using molecular dynamics simulations and calculations of the two-dimensional infrared and vibrational echo peak shift observables for hydration water in DLPC membranes. These observables have not yet been measured experimentally, but future comparisons may provide insight into spectral diffusion processes and hydration water heterogeneity. We find that at low hydration levels the motion of water molecules inside the lipid membrane is significantly arrested, resulting in very slow spectral diffusion. At higher hydration levels, spectral diffusion is more rapid, but still slower than in bulk water. We also investigate the effects of several common approximations on the calculation of spectroscopic observables by computing these observables within multiple levels of theory. The impact of these approximations on the resulting spectra affects our interpretation of these measurements and reveals that, for example, the cumulant approximation, which may be valid for certain systems, is not a good approximation for a highly heterogeneous environment such as hydration water in lipid multi-bilayers.
Diffusion in cementitious materials. 2: Further investigations of chloride and oxygen diffusion in well-cured OPC and OPC/30%PFA pastes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ngala, V.T.; Page, C.L.; Parrott, L.J.

1995-05-01

Steady-state diffusion of dissolved oxygen and chloride ions in hydrated OPC and OPC/30%PFA pastes, hydrated for 2 weeks at 20 C and 10 weeks at 38 C, was studied at water/binder (w/s) ratios 0.4, 0.5, 0.6 and 0.7. Total porosity and a simple measure of capillary porosity, the volume fractions of the water lost in specimens from a saturated surface dry condition to a near-constant weight at 90.7% relative humidity, were also determined. The diffusion rate of chloride ions diminished markedly, to very low values, as the capillary porosity approached zero. For a given w/s ratio or capillary porosity themore » chloride ion diffusion coefficient for OPC/30%PFA pastes was about one order of magnitude smaller than that to OPC pastes. The rate of diffusion of dissolved oxygen also diminished as the capillary porosity reduced but it was still significant as the capillary porosity approached zero. For a given capillary porosity the oxygen diffusion coefficient for OPC/30%PFA pastes was about 30% smaller than that for OPC pastes. The results support the view that chloride ion diffusion in pastes of low capillary porosity is retarded by the surface charge of the hydrated cement gel. In contrast, the hydrated cement gel is much more permeable to the similarly-sized, neutral oxygen molecule.« less
Column densities resulting from shuttle sublimator/evaporator operation. [optical density of nozzle flow containing water vapor

NASA Technical Reports Server (NTRS)

Naumann, R. J.

1973-01-01

The proposed disposal of H2O from the shuttle fuel cell operation by ejecting it in vapor form through a supersonic nozzle at the rate of 100 lb/day has been investigated from the point of view of the possible interference to astronomical experiments. If the nozzle is located at the tail and directed along the shuttle longitudinal axis, the resulting column density will be less than 10 to th 12th power molecules/sq cm at viewing angles larger than 48 deg above the longitudinal axis. The molecules in the trail will diffuse rapidly. The column density contribution from molecules expelled on the previous orbit is 1.3 x 10 to the 8th power molecules/sq cm. This contribution diminishes by the inverse square root of the number of orbits since the molecules were expelled. The molecular backscatter from atmospheric molecules is also calculated. If the plume is directed into the flight path, the column density along a perpendicular is found to be 1.5 x 10 to the 11th power molecules/sq cm. The return flux is estimated to be of the order of 10 to the 12th power molecules/sq cm/sec at the stagnation point. With reasonable care in design of experiments to protect them from the backscatter flux of water molecules, the expulsion of 100 lb/day does not appear to create an insurmountable difficulty for the shuttle experiments.
Enhanced gas absorption in the ionic liquid 1-n-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]) confined in silica slit pores: a molecular simulation study.

PubMed

Shi, Wei; Luebke, David R

2013-05-07

Two-dimensional NPxyT and isostress-osmotic (N2PxyTf1) Monte Carlo simulations were used to compute the density and gas absorption properties of the ionic liquid (IL) 1-n-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]) confined in silica slit pores (25-45 Å). Self-diffusivity values for both gas and IL were calculated from NVE molecular dynamics simulations using both smooth and atomistic potential models for silica. The simulations showed that the molar volume of [hmim][Tf2N] confined in 25-45-Å silica slit pores is 12-31% larger than that of the bulk IL at 313-573 K and 1 bar. The amounts of CO2, H2, and N2 absorbed in the confined IL are 1.1-3 times larger than those in the bulk IL because of the larger molar volume of the confined IL compared to the bulk IL. The CO2, N2, and H2 molecules are generally absorbed close to the silica wall where the IL density is very low. This arrangement causes the self-diffusivities of these gases in the confined IL to be 2-8 times larger than those in the bulk IL at 298-573 K. The solubilities of water in the confined and bulk ILs are similar, which is likely due to strong water interactions with [hmim][Tf2N] through hydrogen bonding, so that the molar volume of the confined IL plays a less important role in determining the H2O solubility. Water molecules are largely absorbed in the IL-rich region rather than close to the silica wall. The self-diffusivities of water correlate with those of the confined IL. The confined IL exhibits self-diffusivities larger than those of the bulk IL at lower temperatures, but smaller than those of the bulk IL at higher temperatures. The findings from our simulations are consistent with available experimental data for similar confined IL systems.
Energetic and dynamic analysis of transport of Na + and K + through a cyclic peptide nanotube in water and in lipid bilayers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Yeonho; Lee, Ji Hye; Hwang, Hoon

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na + and K + are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(D-Leu-Trp) 4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and lipid bilayers, and that themore » selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. Here the PMF and diffusivity profiles for Na + and K + reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na + and K + ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.« less
Energetic and dynamic analysis of transport of Na + and K + through a cyclic peptide nanotube in water and in lipid bilayers

DOE PAGES

Song, Yeonho; Lee, Ji Hye; Hwang, Hoon; ...

2016-11-04

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na + and K + are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(D-Leu-Trp) 4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and lipid bilayers, and that themore » selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. Here the PMF and diffusivity profiles for Na + and K + reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na + and K + ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.« less
Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

DOE PAGES

Diallo, S. O.; Vlcek, L.; Mamontov, E.; ...

2015-02-17

When water molecules are confined to nanoscale spacings, such as in the nanometer-size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures (~150 K), leading to a metastable liquid state with remarkable physical properties. Here we have investigated the ambient pressure diffusive dynamics of water in microporous Kynol ACF-10 (average pore size ~11.6 Å, with primarily slit-like pores) from temperature T = 280 K in its stable liquid state down to T = 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be, respectively, higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time (more » $${{\\tau}}$$) when compared to previous findings indicate that it is the width of the slit pores-not their curvature-that primarily affects the dynamics of water for pore sizes larger than 10 Å. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 Å gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer Q (Q ≤ 0.9 Å -1). At high Q, however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. Consequently, the simulations are compared to the experiments at low Q, where the two can be best reconciled. The best agreement is obtained for the diffusion parameter D associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bimodal exponential model, is used to parametrize the self-correlation function I (Q,t).« less
Following 18O uptake in scCO2–H2O mixtures with Raman spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Windisch, Charles F.; Schaef, Herbert T.; Martin, Paul F.

2012-03-01

The kinetics of 18O/16O isotopic exchange in scCO2 containing liquid water was followed with Raman spectroscopy using a specially designed high-pressure optical cell. Characteristic bands from the C16O18O and C18O2 molecules were identified in the supercritical phase and measured in the spectra as a function of time after introducing liquid H218O into scC16O2. Temporal dependence indicated the isotopic exchange was diffusion-limited in our cell for both molecules, and that the chemical reactions within the liquid phase were comparatively rapid. However, the ratio of concentrations of the 18O-labeled CO2 molecules, C18O2/C16O18O, was much higher than expected in the supercritical phase, suggestingmore » the role of an intermediate step, possibly desorption, in moderating the concentrations of these species in the liquid water phase.« less
Terahertz spectroscopic investigation of gallic acid and its monohydrate

NASA Astrophysics Data System (ADS)

Zhang, Bo; Li, Shaoping; Wang, Chenyang; Zou, Tao; Pan, Tingting; Zhang, Jianbing; Xu, Zhou; Ren, Guanhua; Zhao, Hongwei

2018-02-01

The low-frequency spectra of gallic acid (GA) and its monohydrate were investigated by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.5 to 4.5 THz. The dehydration process of GA monohydrate was monitored on-line. The kinetic mechanism of the dehydration process was analyzed depending on the THz spectral change at different temperatures. The results indicate that the diffusion of water molecule dominates the speed of the entire dehydration process. Solid-state density functional theory (DFT) calculations of the vibrational modes of both GA and its monohydrate were performed based on their crystalline structures for better interpreting the experimental THz spectra. The results demonstrate that the characterized features of GA mainly originate from the collective vibrations of molecules. And the interactions between GA and water molecules are responsible for THz fingerprint of GA monohydrate. Multi-techniques including differential scanning calorimetry and thermogravimetry (DSC-TG) and powder X-ray diffraction (PXRD) were also carried out to further investigate GA and its monohydrate.
Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

PubMed Central

Hu, Qin; Si, Xiuhua April

2018-01-01

Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high-polarity chemicals such as acrolein. PMID:29584651
The importance of size-exclusion characteristics of type I collagen in bonding to dentin matrices

PubMed Central

M, Takahashi; M, Nakajima; J, Tagami; DLS, Scheffel; RM, Carvalho; A, Mazzoni; M, Carrilho; A, Tezvergil-Mutluay; L, Breschi; L, Tjäderhane; SS, Jang; FR, Tay; KA, Agee; DH, Pashley

2013-01-01

The mineral phase of dentin is located primarily within collagen fibrils. During development, bone or dentin collagen fibrils are formed first and then water within the fibril is replaced with apatite crystallites. Mineralized collagen contains very little water. During dentin bonding, acid-etching of mineralized dentin solubilizes the mineral crystallites and replaces them with water. During the infiltration phase of dentin bonding, adhesive comonomers are supposed to replace all of the collagen water with adhesive monomers that are then polymerized into copolymers. The authors of a recently published review suggested that dental monomers were too large to enter and displace water from collagen fibrils. If that were true, the endogenous proteases bound to dentin collagen could be responsible for unimpeded collagen degradation that is responsible for the poor durability of resin-dentin bonds. The current work studied the size-exclusion characteristics of dentin collagen, using a gel-filtration-like column chromatography technique, using dentin powder instead of Sephadex. The elution volumes of test molecules, including adhesive monomers, revealed that adhesive monomers smaller than about 1000 Da can freely diffuse into collagen water, while molecules of 10,000 Da begin to be excluded, and bovine serum albumin (66,000 Da) was fully excluded. These results validate the concept that dental monomers can permeate between collagen molecules during infiltration by etch-and-rinse adhesives. PMID:23928333
Quantitative phenomenological model of the BOLD contrast mechanism

NASA Astrophysics Data System (ADS)

Dickson, John D.; Ash, Tom W. J.; Williams, Guy B.; Sukstanskii, Alexander L.; Ansorge, Richard E.; Yablonskiy, Dmitriy A.

2011-09-01

Different theoretical models of the BOLD contrast mechanism are used for many applications including BOLD quantification (qBOLD) and vessel size imaging, both in health and disease. Each model simplifies the system under consideration, making approximations about the structure of the blood vessel network and diffusion of water molecules through inhomogeneities in the magnetic field created by deoxyhemoglobin-containing blood vessels. In this study, Monte-Carlo methods are used to simulate the BOLD MR signal generated by diffusing water molecules in the presence of long, cylindrical blood vessels. Using these simulations we introduce a new, phenomenological model that is far more accurate over a range of blood oxygenation levels and blood vessel radii than existing models. This model could be used to extract physiological parameters of the blood vessel network from experimental data in BOLD-based experiments. We use our model to establish ranges of validity for the existing analytical models of Yablonskiy and Haacke, Kiselev and Posse, Sukstanskii and Yablonskiy (extended to the case of arbitrary time in the spin echo sequence) and Bauer et al. (extended to the case of randomly oriented cylinders). Although these models are shown to be accurate in the limits of diffusion under which they were derived, none of them is accurate for the whole physiological range of blood vessels radii and blood oxygenation levels. We also show the extent of systematic errors that are introduced due to the approximations of these models when used for BOLD signal quantification.
Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.

PubMed

Koh, Hye Ran; Wang, Xinlei; Myong, Sua

2016-08-01

TRBP, one of double strand RNA binding proteins (dsRBPs), is an essential cofactor of Dicer in the RNA interference pathway. Previously we reported that TRBP exhibits repetitive diffusion activity on double strand (ds)RNA in an ATP independent manner. In the TRBP-Dicer complex, the diffusion mobility of TRBP facilitates Dicer-mediated RNA cleavage. Such repetitive diffusion of dsRBPs on a nucleic acid at the nanometer scale can be appropriately captured by several single molecule detection techniques. Here, we provide a step-by-step guide to four different single molecule fluorescence assays by which the diffusion activity of dsRBPs on dsRNA can be detected. One color assay, termed protein induced fluorescence enhancement enables detection of unlabeled protein binding and diffusion on a singly labeled RNA. Two-color Fluorescence Resonance Energy Transfer (FRET) in which labeled dsRBPs is applied to labeled RNA, allows for probing the motion of protein along the RNA axis. Three color FRET reports on the diffusion movement of dsRBPs from one to the other end of RNA. The single molecule pull down assay provides an opportunity to collect dsRBPs from mammalian cells and examine the protein-RNA interaction at single molecule platform. Copyright © 2016 Elsevier Inc. All rights reserved.
Single Molecule Spectral Diffusion in a Solid Detected Via Fluorescence Spectroscopy

DTIC Science & Technology

1991-10-15

other local fields) at the position of the molecule, the spectral jumps may occur because the class II pentacene molecules are coupled to an...and identify by block number) FIELD jGROUP SUB-GROUP_ Single molecule spectroscopy Precision detection Spectral diffusion, Pentacene in p-terphenyl 19...significant increases in detection sensitivity for single pentacene molecules in crystals of p-terphenyl at low temperatures. With the increased signal to
Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers

DOE PAGES

Moskovitz, Yevgeny; Yang, Hui

2015-01-08

Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns-long) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules at a pressure range of 1 - 1000 bar and temperature of 310 Kelvin. Xenon and argon have been tested as model gases for general anesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremor at hyperbaric conditions. The analysis of stacked radial pair distributionmore » functions of DOPC headgroup atoms revealed the explicit solvation potential of gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor; while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar patterns of the order parameter for both DOPC acyl chains, which is opposite to the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the ‘critical volume’ hypothesis of anesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1 - 100 bar could be associated with the possible manifestation of neurological tremor at the atomic scale. The non-immobilizer neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing monolayers undulations rate, which indicates enhanced diffusivity, rather than atom size, as the key factor.« less
Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness.

PubMed Central

Paula, S; Volkov, A G; Van Hoek, A N; Haines, T H; Deamer, D W

1996-01-01

Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths. PMID:8770210
Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness

NASA Technical Reports Server (NTRS)

Paula, S.; Volkov, A. G.; Van Hoek, A. N.; Haines, T. H.; Deamer, D. W.

1996-01-01

Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths.
Measurement of Small Molecular Dopant F4TCNQ and C 60F 36 Diffusion in Organic Bilayer Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun; Rochester, Chris W.; Jacobs, Ian E.

2015-12-03

The diffusion of molecules through and between organic layers is a serious stability concern in organic electronic devices. In this paper, the temperature-dependent diffusion of molecular dopants through small molecule hole transport layers is observed. Specifically we investigate bilayer stacks of small molecules used for hole transport (MeO-TPD) and p-type dopants (F4TCNQ and C 60F 36) used in hole injection layers for organic light emitting diodes and hole collection electrodes for organic photovoltaics. With the use of absorbance spectroscopy, photoluminescence spectroscopy, neutron reflectometry, and near-edge X-ray absorption fine structure spectroscopy, we are able to obtain a comprehensive picture of themore » diffusion of fluorinated small molecules through MeO-TPD layers. F4TCNQ spontaneously diffuses into the MeO-TPD material even at room temperature, while C 60F 36, a much bulkier molecule, is shown to have a substantially higher morphological stability. Finally, this study highlights that the differences in size/geometry and thermal properties of small molecular dopants can have a significant impact on their diffusion in organic device architectures.« less
Permeability-diffusivity modeling vs. fractional anisotropy on white matter integrity assessment and application in schizophrenia.

PubMed

Kochunov, P; Chiappelli, J; Hong, L E

2013-01-01

Diffusion tensor imaging (DTI) assumes a single pool of anisotropically diffusing water to calculate fractional anisotropy (FA) and is commonly used to ascertain white matter (WM) deficits in schizophrenia. At higher b-values, diffusion-signal decay becomes bi-exponential, suggesting the presence of two, unrestricted and restricted, water pools. Theoretical work suggests that semi-permeable cellular membrane rather than the presence of two physical compartments is the cause. The permeability-diffusivity (PD) parameters measured from bi-exponential modeling may offer advantages, over traditional DTI-FA, in identifying WM deficits in schizophrenia. Imaging was performed in N = 26/26 patients/controls (age = 20-61 years, average age = 40.5 ± 12.6). Imaging consisted of fifteen b-shells: b = 250-3800 s/mm(2) with 30 directions/shell, covering seven slices of mid-sagittal corpus callosum (CC) at 1.7 × 1.7 × 4.6 mm. 64-direction DTI was also collected. Permeability-diffusivity-index (PDI), the ratio of restricted to unrestricted apparent diffusion coefficients, and the fraction of unrestricted compartment (Mu) were calculated for CC and cingulate gray matter (GM). FA values for CC were calculated using tract-based-spatial-statistics. Patients had significantly reduced PDI in CC (p ≅ 10(- 4)) and cingulate GM (p = 0.002), while differences in CC FA were modest (p ≅ .03). There was no group-related difference in Mu. Additional theoretical-modeling analysis suggested that reduced PDI in patients may be caused by reduced cross-membrane water molecule exchanges. PDI measurements for cerebral WM and GM yielded more robust patient-control differences than DTI-FA. Theoretical work offers an explanation that patient-control PDI differences should implicate abnormal active membrane permeability. This would implicate abnormal activities in ion-channels that use water as substrate for ion exchange, in cerebral tissues of schizophrenia patients.
Atomic scale behavior of oxygen-based radicals in water

NASA Astrophysics Data System (ADS)

Verlackt, C. C. W.; Neyts, E. C.; Bogaerts, A.

2017-03-01

Cold atmospheric pressure plasmas in and in contact with liquids represent a growing field of research for various applications. Understanding the interactions between the plasma generated species and the liquid is crucial. In this work we perform molecular dynamics (MD) simulations based on a quantum mechanical method, i.e. density-functional based tight-binding (DFTB), to examine the interactions of OH radicals and O atoms in bulk water. Our calculations reveal that the transport of OH radicals through water is not only governed by diffusion, but also by an equilibrium reaction of H-abstraction with water molecules. Furthermore, when two OH radicals encounter each other, they either form a stable cluster, or react, resulting in the formation of a new water molecule and an O atom. In addition, the O atoms form either oxywater (when in singlet configuration) or they remain stable in solution (when in triplet configuration), stressing the important role that O atoms can play in aqueous solution, and in contact with biomolecules. Our observations are in line with both experimental and ab initio results from the literature.

Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns.

PubMed

Wan, Rongzheng; Wang, Chunlei; Lei, Xiaoling; Zhou, Guoquan; Fang, Haiping

2015-11-06

Using molecular dynamics simulations, we show that the evaporation of nanoscale water on hydrophobic-hydrophilic patterned surfaces is unexpectedly faster than that on any surfaces with uniform wettability. The key to this phenomenon is that, on the patterned surface, the evaporation rate from the hydrophilic region only slightly decreases due to the correspondingly increased water thickness; meanwhile, a considerable number of water molecules evaporate from the hydrophobic region despite the lack of water film. Most of the evaporated water from the hydrophobic region originates from the hydrophilic region by diffusing across the contact lines. Further analysis shows that the evaporation rate from the hydrophobic region is approximately proportional to the total length of the contact lines.
Multi-Algorithm Particle Simulations with Spatiocyte.

PubMed

Arjunan, Satya N V; Takahashi, Koichi

2017-01-01

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .
Dynamics of gas bubble growth in a supersaturated solution with Sievert's solubility law.

PubMed

Gor, G Yu; Kuchma, A E

2009-07-21

This paper presents a theoretical description of diffusion growth of a gas bubble after its nucleation in supersaturated liquid solution. We study systems where gas molecules completely dissociate in the solvent into two parts, thus making Sievert's solubility law valid. We show that the difference between Henry's and Sievert's laws for chemical equilibrium conditions causes the difference in bubble growth dynamics. Assuming that diffusion flux is steady we obtain a differential equation on bubble radius. Bubble dynamics equation is solved analytically for the case of homogeneous nucleation of a bubble, which takes place at a significant pressure drop. We also obtain conditions of diffusion flux steadiness. The fulfillment of these conditions is studied for the case of nucleation of water vapor bubbles in magmatic melts.
Understanding molecular structure dependence of exciton diffusion in conjugated small molecules

NASA Astrophysics Data System (ADS)

Li, Zi; Zhang, Xu; Woellner, Cristiano F.; Lu, Gang

2014-04-01

First-principles simulations are carried out to understand molecular structure dependence of exciton diffusion in a series of small conjugated molecules arranged in a disordered, crystalline, and blend structure. Exciton diffusion length (LD), lifetime, and diffusivity in four diketopyrrolopyrrole derivatives are calculated and the results compare very well with experimental values. The correlation between exciton diffusion and molecular structure is examined in detail. In the disordered molecule structure, a longer backbone length leads to a shorter exciton lifetime and a higher exciton diffusivity, but it does not change LD substantially. Removal of the end alkyl chains or the extra branch on the side alkyl chains reduces LD. In the crystalline structure, exciton diffusion exhibits a strong anisotropy whose origin can be elucidated from the intermolecular transition density interaction point of view. In the blend structure, LD increases with the crystalline ratios, which are estimated and consistent with the experimental results.
Adsorption Behavior of Surfactant on Lignite Surface: A Comparative Experimental and Molecular Dynamics Simulation Study

PubMed Central

He, Meng; Zhang, Wei; Cao, Xiaoqiang; You, Xiaofang; Li, Lin

2018-01-01

Experimental and computational simulation methods are used to investigate the adsorption behavior of the surfactant nonylphenol ethoxylate (NPEO10), which contains 10 ethylene oxide groups, on the lignite surface. The adsorption of NPEO10 on lignite follow a Langmuir-type isotherm. The thermodynamic parameters of the adsorption process show that the whole process is spontaneous. X-ray photoelectron spectroscopic (XPS) analysis indicates that a significant fraction of the oxygen-containing functional groups on the lignitic surface were covered by NPEO10. Molecular dynamics (MD) simulations show that the NPEO10 molecules were found to adsorb at the water-coal interface. Moreover, polar interactions are the main effect in the adsorption process. The density distributions of coal, NPEO10, and water molecules along the Z axis show that the remaining hydrophobic portions of the surfactant extend into the solution, creating a more hydrophobic coal surface that repels water molecules. The negative interaction energy calculated from the density profiles of the head and tail groups along the three spatial directions between the surfactant and the lignitic surface suggest that the adsorption process is spontaneous. The self-diffusion coefficients show that the presence of NPEO10 causes higher water mobility by improving the hydrophobicity of lignite. PMID:29389899
Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations

NASA Astrophysics Data System (ADS)

Srivastava, Abhinav; Debnath, Ananya

2018-03-01

Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t-3/2. The asymptotic t-3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations reveal that the slow relaxation rates of interfacial waters in the vicinity of lipids are originated from the chemical confinement of concerted hydrogen bond networks. The analysis suggests that the networks in the hydration layer of membranes dynamically facilitate the water mediated lipid-lipid associations which can provide insights on the thermodynamic stability of soft interfaces relevant to biological systems in the future.
Various diffusion magnetic resonance imaging techniques for pancreatic cancer

PubMed Central

Tang, Meng-Yue; Zhang, Xiao-Ming; Chen, Tian-Wu; Huang, Xiao-Hua

2015-01-01

Pancreatic cancer is one of the most common malignant tumors and remains a treatment-refractory cancer with a poor prognosis. Currently, the diagnosis of pancreatic neoplasm depends mainly on imaging and which methods are conducive to detecting small lesions. Compared to the other techniques, magnetic resonance imaging (MRI) has irreplaceable advantages and can provide valuable information unattainable with other noninvasive or minimally invasive imaging techniques. Advances in MR hardware and pulse sequence design have particularly improved the quality and robustness of MRI of the pancreas. Diffusion MR imaging serves as one of the common functional MRI techniques and is the only technique that can be used to reflect the diffusion movement of water molecules in vivo. It is generally known that diffusion properties depend on the characterization of intrinsic features of tissue microdynamics and microstructure. With the improvement of the diffusion models, diffusion MR imaging techniques are increasingly varied, from the simplest and most commonly used technique to the more complex. In this review, the various diffusion MRI techniques for pancreatic cancer are discussed, including conventional diffusion weighted imaging (DWI), multi-b DWI based on intra-voxel incoherent motion theory, diffusion tensor imaging and diffusion kurtosis imaging. The principles, main parameters, advantages and limitations of these techniques, as well as future directions for pancreatic diffusion imaging are also discussed. PMID:26753059
The thermodynamic and hydrodynamic properties of macromolecules that influence the hydrodynamics of porous systems.

PubMed

Comper, W D

1994-06-21

The water flow across porous, semipermeable membranes associated with osmosis and filtration under a variety of conditions is analysed and compared to macromolecular diffusion across free-liquid boundaries, diffusion and sedimentation in the ultracentrifuge, and tracer diffusion of water. This study establishes that osmosis can be explained in terms of the irreversible thermodynamics of diffusion. For macromolecular osmotically active solutes in the semidilute concentration regime the water flows across semipermeable porous membranes are interpreted in terms of a rate-limiting solute-solvent exchange layer that exists on the solution side of the membrane adjacent to the membrane pore; both osmosis and filtration will be governed by these exchange layers. These exchange layers also yield unique properties of their constituent molecules in systems where there is osmotic equilibration between solutions of different solutes. This study also establishes the need to consider the internal osmotic pressure of membranes in the pressure balance associated with the flow across the membrane. The complex situation of partially permeable membranes is analysed for the simple case where there are no mechanical gradients and there is only one osmotically active solution that creates a rate-limiting exchange layer. This treatment predicts that the flow will be governed primarily by the osmotic pressure difference associated with the partitioning of the solute at the membrane-solution interface.
Biorelevant physicochemical profiling of (E)- and (Z)-resveratrol determined from isomeric mixtures.

PubMed

Orgován, Gábor; Gonda, Imre; Noszál, Béla

2017-05-10

Biorelevant, isomer-specific physicochemical parameters of resveratrol, a multifunctional component in red wines, with cardioprotective, anti-Alzheimer and several other pharmacologic activities were determined. The parameters include site-specific basicities, lipophilicities, solubilities and diffusion constants for the two geometric isomers. The protonation equilibria of (E)- and (Z)-resveratrol were monitored by 1 H NMR-pH titrations. Five closely related auxiliary compounds ((E)-pinostilbene, (Z)-pinostilbene, (E)-pterostilbene, (Z)-pterostilbene and resorcinol) were also studied. Combining the datasets, the group-specific protonation constants of resveratrol isomers were determined. The results show that (Z)-resveratrol is more basic at every protonation site than the (E)-isomer. Lipophilicities are quantified in terms of logP values and were determined by octanol/water partition experiments and quantitative NMR spectroscopy: (E)-resveratrol was found to be more lipophilic. Since the molecular geometries of the isomers differ, diffusion ordered NMR spectroscopy (DOSY) experiments were also carried out to quantify the diffusion capabilities of the isomers: (Z)-resveratrol of bent shape has a slightly higher diffusion coefficient than its extended (E) counterpart. A striking 10-fold difference of water solubility was found in favor of the (Z) isomer, due obviously to the reduced water-repellent character in the more compact molecule. This is so far the greatest recorded solubility difference between geometric isomers of any compounds. Copyright © 2016. Published by Elsevier B.V.
Simulated infrared spectra of triflic acid during proton dissociation.

PubMed

Laflamme, Patrick; Beaudoin, Alexandre; Chapaton, Thomas; Spino, Claude; Soldera, Armand

2012-05-05

Vibrational analysis of triflic acid (TfOH) at different water uptakes was conducted. This molecule mimics the sulfonate end of the Nafion side-chain. As the proton leaves the sulfonic acid group, structural changes within the Nafion side-chain take place. They are revealed by signal shifts in the infrared spectrum. Molecular modeling is used to follow structural modifications that occur during proton dissociation. To confirm the accuracy of the proposed structures, infrared spectra were computed via quantum chemical modeling based on density functional theory. The requirement to use additional diffuse functions in the basis set is discussed. Comparison between simulated infrared spectra of 1 and 2 acid molecules with different water contents and experimental data was performed. An accurate description of infrared spectra for systems containing 2 TfOH was obtained. Copyright © 2012 Wiley Periodicals, Inc.
Molecular modeling of diffusion coefficient and ionic conductivity of CO2 in aqueous ionic solutions.

PubMed

Garcia-Ratés, Miquel; de Hemptinne, Jean-Charles; Bonet Avalos, Josep; Nieto-Draghi, Carlos

2012-03-08

Mass diffusion coefficients of CO(2)/brine mixtures under thermodynamic conditions of deep saline aquifers have been investigated by molecular simulation. The objective of this work is to provide estimates of the diffusion coefficient of CO(2) in salty water to compensate the lack of experimental data on this property. We analyzed the influence of temperature, CO(2) concentration,and salinity on the diffusion coefficient, the rotational diffusion, as well as the electrical conductivity. We observe an increase of the mass diffusion coefficient with the temperature, but no clear dependence is identified with the salinity or with the CO(2) mole fraction, if the system is overall dilute. In this case, we notice an important dispersion on the values of the diffusion coefficient which impairs any conclusive statement about the effect of the gas concentration on the mobility of CO(2) molecules. Rotational relaxation times for water and CO(2) increase by decreasing temperature or increasing the salt concentration. We propose a correlation for the self-diffusion coefficient of CO(2) in terms of the rotational relaxation time which can ultimately be used to estimate the mutual diffusion coefficient of CO(2) in brine. The electrical conductivity of the CO(2)-brine mixtures was also calculated under different thermodynamic conditions. Electrical conductivity tends to increase with the temperature and salt concentration. However, we do not observe any influence of this property with the CO(2) concentration at the studied regimes. Our results give a first evaluation of the variation of the CO(2)-brine mass diffusion coefficient, rotational relaxation times, and electrical conductivity under the thermodynamic conditions typically encountered in deep saline aquifers.
Variable Temperature Infrared Spectroscopy Investigation of Benzoic Acid Interactions with Montmorillonite Clay Interlayer Water.

PubMed

Nickels, Tara M; Ingram, Audrey L; Maraoulaite, Dalia K; White, Robert L

2015-07-01

Molecular interactions between benzoic acid and cations and water contained in montmorillonite clay interlayer spaces are characterized by using variable temperature diffuse reflection infrared Fourier transform spectroscopy (VT-DRIFTS). Using sample perturbation and difference spectroscopy, infrared spectral changes resulting from removal of interlayer water and associated changes in local benzoic acid environments are identified. Difference spectra features can be correlated with changes in specific molecular vibrations that are characteristic of benzoic acid molecular orientation. Results suggest that the carboxylic acid functionality of benzoic acid interacts with interlayer cations through a bridging water molecule and that this interaction is affected by the nature of the cation present in the clay interlayer space.
Exp6-polar thermodynamics of dense supercritical water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bastea, S; Fried, L E

2007-12-13

We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar moleculesmore » and their mixtures.« less
Phase transitions of a water overlayer on charged graphene: from electromelting to electrofreezing.

PubMed

Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu

2014-05-21

We show by using molecular dynamics simulations that a water overlayer on charged graphene experiences first-order ice-to-liquid (electromelting), and then liquid-to-ice (electrofreezing) phase transitions with the increase of the charge value. Corresponding to the ice-liquid-ice transition, the variations of the order parameters indicate an order-disorder-order transition. The key to this novel phenomenon is the surface charge induced change of the orientations of water dipoles, which leads to the change of the water-water interactions from being attractive to repulsive at a critical charge value qc. To further uncover how the orientations of water dipoles influence the interaction strength between water molecules, a theoretical model considering both the Coulomb and van der Waals interactions is established. The results show that with the increase of the charge value, the interaction strength between water molecules decreases below qc, then increases above qc. These two inverse processes lead to electromelting and electrofreezing, respectively. Combining this model with the Eyring equation, the diffusion coefficient is obtained, the variation of which is in qualitative agreement with the simulation results. Our findings not only expand our knowledge of the graphene-water interface, but related analyses could also help recognize the controversial role of the surface charge or electric field in promoting phase transitions of water.
Exciton diffusion in disordered small molecules for organic photovoltaics: insights from first-principles simulations.

PubMed

Li, Z; Zhang, X; Lu, G

2014-05-07

Exciton diffusion in small molecules 3,6-bis(5-(benzofuran-2-yl)thiophen-2-yl)-2,5-bis(2-ethylhexyl)pyrrolo[3,4-c]pyrrole-1,4-dione [DPP(TBFu)2] is studied using first-principles simulations. We have examined dependence of exciton diffusion on structure disorder, temperature and exciton energy. We find that exciton diffusion length and diffusivity increase with structural order, temperature and the initial exciton energy. Compared to conjugated polymer poly(3-hexylthiophene) (P3HT), DPP(TBFu)2 small molecules exhibit a much higher exciton diffusivity, but a shorter lifetime. The exciton diffusion length in DPP(TBFu)2 is 50% longer than that in P3HT, yielding a higher exciton harvesting efficiency; the physical origin behind these differences is discussed. The time evolutions of exciton energy, electron-hole distance, and exciton localization are explored, and the widely speculated exciton diffusion mechanism is confirmed theoretically. The connection between exciton diffusion and carrier mobilities is also studied. Finally we point out the possibility to estimate exciton diffusivity by measuring carrier mobilities under AC electric fields.
Inhomogeneities in particle composition of single, levitated aerosol particles observed by Mie resonance spectroscopy

NASA Astrophysics Data System (ADS)

Krieger, Ulrich; Lienhard, Daniel; Bastelberger, Sandra; Steimer, Sarah

2014-05-01

Recent observations have indicated that organic aerosol particles in the atmosphere may exist in an amorphous semi-solid or even solid (i.e. glassy) state, e.g. [1]. The influence of highly viscous and glassy states on the timescale of aerosol particle equilibration with respect to water vapor have been investigated for some model systems of atmospheric aerosol, e.g. [2,3]. In particular, it has been shown that the kinetics of the water absorption/desorption process is controlled entirely by liquid-phase diffusion of water molecules for a highly viscous aerosol particle. A liquid phase diffusion model based on numerically solving the non-linear diffusion equation predicts strong internal gradients in water concentration when condensed phase diffusion impedes the water uptake from the gas phase [2]. Here we observe and quantify the internal concentration gradients in single, levitated, micron size aerosol particles of aqueous shikimic acid using elastic Mie resonance spectroscopy. A single, aqueous particle is levitated in an electro-dynamic balance (for details see [2]), dried for several days at room temperature, cooled to the target temperature and exposed to a rapid change in relative humidity. In addition to measuring the elastically backscattered light of a "white light" LED source and recording the full spectrum with a spectrograph as in [2], we use a tunable diode laser (TDL) to scan high resolution TE- and TM spectra. This combination allows observing various Mie resonance mode orders simultaneously. Since we perform the experiment at low temperatures and low humidities the changes in the Mie-spectra due to water uptake are sufficiently slow to resolve the kinetics. Experimental Mie resonance spectra are inverted to concentration profiles of water within the particle by applying the numerical diffusion model [2] in conjunction with Mie calculations of multilayered spheres [4]. [1] A. Virtanen et al. (2010): An amorphous solid state of biogenic secondary organic aerosol particles, Nature 467, 824-827. [2] B. Zobrist et al. (2011): Ultra-slow water diffusion in aqueous sucrose glasses, Phys. Chem. Chem. Phys. 13, 3514-3526. [3] D. L. Bones, J. P. Reid, D. M. Lienhard, and U. K. Krieger (2012): Comparing the mechanism of water condensation and evaporation in glassy aerosol, PNAS 109, 11613-11618. [4] O. Peña and U. Pal (2009): Scattering of electromagnetic radiation by a multilayered sphere, Comput. Phys. Commun. 180, 2348-2354.
Time-dependent water dynamics in hydrated uranyl fluoride

DOE PAGES

Miskowiec, Andrew J.; Anderson, Brian B.; Herwig, Kenneth W.; ...

2015-09-15

In this study, uranyl fluoride is a three-layer, hexagonal structure with significant stacking disorder in the c-direction. It supports a range of unsolved ‘thermodynamic’ hydrates with 0–2.5 water molecules per uranium atom, and perhaps more. However, the relationship between water, hydrate crystal structures, and thermodynamic results, collectively representing the chemical pathway through these hydrate structures, has not been sufficiently elucidated. We used high-resolution quasielastic neutron scattering to study the dynamics of water in partially hydrated uranyl fluoride powder over the course of 4 weeks under closed conditions. The spectra are composed of two quasielastic components: one is associated with translationalmore » diffusive motion of water that is approximately five to six times slower than bulk water, and the other is a slow (on the order of 2–300 ps), spatially bounded water motion. The translational component represents water diffusing between the weakly bonded layers in the crystal, while the bounded component may represent water trapped in subnanometre ‘pockets’ formed by the space between uranium-centred polymerisation units. Complementary neutron diffraction measurements do not show any significant structural changes, suggesting that a chemical conversion of the material does not occur in the thermodynamically isolated system on this timescale.« less
Neutron Scattering Analysis of Water's Glass Transition and Micropore Collapse in Amorphous Solid Water.

PubMed

Hill, Catherine R; Mitterdorfer, Christian; Youngs, Tristan G A; Bowron, Daniel T; Fraser, Helen J; Loerting, Thomas

2016-05-27

The question of the nature of water's glass transition has continued to be disputed over many years. Here we use slow heating scans (0.4 K min^{-1}) of compact amorphous solid water deposited at 77 K and an analysis of the accompanying changes in the small-angle neutron scattering signal, to study mesoscale changes in the ice network topology. From the data we infer the onset of rotational diffusion at 115 K, a sudden switchover from nondiffusive motion and enthalpy relaxation of the network at <121 K to diffusive motion across sample grains and sudden pore collapse at >121 K, in excellent agreement with the glass transition onset deduced from heat capacity and dielectric measurements. This indicates that water's glass transition is linked with long-range transport of water molecules on the time scale of minutes and, thus, clarifies its nature. Furthermore, the slow heating rates combined with the high crystallization resistance of the amorphous sample allow us to identify the glass transition end point at 136 K, which is well separated from the crystallization onset at 144 K-in contrast to all earlier experiments in the field.
Diffusion tensor optical coherence tomography

NASA Astrophysics Data System (ADS)

Marks, Daniel L.; Blackmon, Richard L.; Oldenburg, Amy L.

2018-01-01

In situ measurements of diffusive particle transport provide insight into tissue architecture, drug delivery, and cellular function. Analogous to diffusion-tensor magnetic resonance imaging (DT-MRI), where the anisotropic diffusion of water molecules is mapped on the millimeter scale to elucidate the fibrous structure of tissue, here we propose diffusion-tensor optical coherence tomography (DT-OCT) for measuring directional diffusivity and flow of optically scattering particles within tissue. Because DT-OCT is sensitive to the sub-resolution motion of Brownian particles as they are constrained by tissue macromolecules, it has the potential to quantify nanoporous anisotropic tissue structure at micrometer resolution as relevant to extracellular matrices, neurons, and capillaries. Here we derive the principles of DT-OCT, relating the detected optical signal from a minimum of six probe beams with the six unique diffusion tensor and three flow vector components. The optimal geometry of the probe beams is determined given a finite numerical aperture, and a high-speed hardware implementation is proposed. Finally, Monte Carlo simulations are employed to assess the ability of the proposed DT-OCT system to quantify anisotropic diffusion of nanoparticles in a collagen matrix, an extracellular constituent that is known to become highly aligned during tumor development.
Diffusion MRI and its role in neuropsychology

PubMed Central

Mueller, Bryon A; Lim, Kelvin O; Hemmy, Laura; Camchong, Jazmin

2015-01-01

Diffusion Magnetic Resonance Imaging (dMRI) is a popular method used by neuroscientists to uncover unique information about the structural connections within the brain. dMRI is a non-invasive imaging methodology in which image contrast is based on the diffusion of water molecules in tissue. While applicable to many tissues in the body, this review focuses exclusively on the use of dMRI to examine white matter in the brain. In this review, we begin with a definition of diffusion and how diffusion is measured with MRI. Next we introduce the diffusion tensor model, the predominant model used in dMRI. We then describe acquisition issues related to acquisition parameters and scanner hardware and software. Sources of artifacts are then discussed, followed by a brief review of analysis approaches. We provide an overview of the limitations of the traditional diffusion tensor model, and highlight several more sophisticated non-tensor models that better describe the complex architecture of the brain’s white matter. We then touch on reliability and validity issues of diffusion measurements. Finally, we describe examples of ways in which dMRI has been applied to studies of brain disorders and how identified alterations relate to symptomatology and cognition. PMID:26255305

Aluminum/water reactions under extreme conditions

NASA Astrophysics Data System (ADS)

Hooper, Joseph

2013-03-01

We discuss mechanisms that may control the reaction of aluminum and water under extreme conditions. We are particularly interested in the high-temperature, high-strain regime where the native oxide layer is destroyed and fresh aluminum is initially in direct contact with liquid or supercritical water. Disparate experimental data over the years have suggested rapid oxidation of aluminum is possible in such situations, but no coherent picture has emerged as to the basic oxidation mechanism or the physical processes that govern the extent of reaction. We present theoretical and computational analysis of traditional metal/water reaction mechanisms that treat diffusion through a dynamic oxide layer or reaction limited by surface kinetics. Diffusion through a fresh solid oxide layer is shown to be far too slow to have any effect on the millisecond timescale (even at high temperatures). Quantum molecular dynamics simulations of liquid Al and water surface reactions show rapid water decomposition at the interface, catalyzed by adjacent water molecules in a Grotthus-like relay mechanism. The surface reaction barriers are far too low for this to be rate-limiting in any way. With these straightforward mechanisms ruled out, we investigate two more complex possibilities for the rate-limiting factor; first, we explore the possibility that newly formed oxide remains a metastable liquid well below its freezing point, allowing for diffusion-limited reactions through the oxide shell but on a much faster timescale. The extent of reaction would then be controlled by the solidification kinetics of alumina. Second, we discuss preliminary analysis on surface erosion and turbulent mixing, which may play a prominent role during hypervelocity penetration of solid aluminum projectiles into water.
Influence of oxygen on the chemical stage of radiobiological mechanism

NASA Astrophysics Data System (ADS)

Barilla, Jiří; Lokajíček, Miloš V.; Pisaková, Hana; Simr, Pavel

2016-07-01

The simulation of the chemical stage of radiobiological mechanism may be very helpful in studying the radiobiological effect of ionizing radiation when the water radical clusters formed by the densely ionizing ends of primary or secondary charged particle may form DSBs damaging DNA molecules in living cells. It is possible to study not only the efficiency of individual radicals but also the influence of other species or radiomodifiers (mainly oxygen) being present in water medium during irradiation. The mathematical model based on Continuous Petri nets (proposed by us recently) will be described. It makes it possible to analyze two main processes running at the same time: chemical radical reactions and the diffusion of radical clusters formed during energy transfer. One may study the time change of radical concentrations due to the chemical reactions running during diffusion process. Some orientation results concerning the efficiency of individual radicals in DSB formation (in the case of Co60 radiation) will be presented; the influence of oxygen present in water medium during irradiation will be shown, too.
ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water

PubMed Central

Banerjee, D.; Bhat, S. N.; Bhat, S. V.; Leporini, D.

2009-01-01

Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, Tg = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called “no man's land” (the range 150–235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at ≈225 K. The reorientation of the probe molecules decouples from the viscosity below ≈225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes–Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974–12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360:324–328] and the fragile-to-strong dynamic cross-over at ≈228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-to-strong liquid transition in water. Nature 398:492–494]. PMID:19556546
Are leaf physiological traits related to leaf water isotopic enrichment in restinga woody species?

PubMed

Rosado, Bruno H P; De Mattos, Eduardo A; Sternberg, Leonel Da S L

2013-09-01

During plant-transpiration, water molecules having the lighter stable isotopes of oxygen and hydrogen evaporate and diffuse at a faster rate through the stomata than molecules having the heavier isotopes, which cause isotopic enrichment of leaf water. Although previous models have assumed that leaf water is well-mixed and isotopically uniform, non-uniform stomatal closure, promoting different enrichments between cells, and different pools of water within leaves, due to morpho-physiological traits, might lead to inaccuracies in isotopic models predicting leaf water enrichment. We evaluate the role of leaf morpho-physiological traits on leaf water isotopic enrichment in woody species occurring in a coastal vegetation of Brazil known as restinga. Hydrogen and oxygen stable isotope values of soil, plant stem and leaf water and leaf traits were measured in six species from restinga vegetation during a drought and a wet period. Leaf water isotopic enrichment relative to stem water was more homogeneous among species during the drought in contrast to the wet period suggesting convergent responses to deal to temporal heterogeneity in water availability. Average leaf water isotopic enrichment relative to stem water during the drought period was highly correlated with relative apoplastic water content. We discuss this observation in the context of current models of leaf water isotopic enrichment as a function of the Péclet effect. We suggest that future studies should include relative apoplastic water content in isotopic models.
Effects of Shapes of Solute Molecules on Diffusion: A Study of Dependences on Solute Size, Solvent, and Temperature.

PubMed

Chan, T C; Li, H T; Li, K Y

2015-12-24

Diffusivities of basically linear, planar, and spherical solutes at infinite dilution in various solvents are studied to unravel the effects of solute shapes on diffusion. On the basis of the relationship between the reciprocal of diffusivity and the molecular volume of solute molecules with similar shape in a given solvent at constant temperature, the diffusivities of solutes of equal molecular volume but different shapes are evaluated and the effects due to different shapes of two equal-sized solute molecules on diffusion are determined. It is found that the effects are dependent on the size of the solute pairs studied. Evidence of the dependence of the solute-shape effects on solvent properties is also demonstrated and discussed. Here, some new diffusion data of aromatic compounds in methanol at different temperatures are reported. The result for methanol in this study indicates that the effects of solute shape on diffusivity are only weakly dependent on temperature.
Analyte concentration at the tip of a nanopipette.

PubMed

Calander, Nils

2009-10-15

Concentration of molecules within the tips of nanopipettes when applying a DC voltage is herein investigated using finite-element simulations. The ion concentrations and fluxes due to diffusion, electro-migration, and electro-osmotic flow, and the electric potential are determined by the simultaneous solution of the Nernst-Planck, Poisson, and Navier-Stokes equations within the water solution containing sodium and chloride ions and negatively charged molecules. The electric potential within the pipette glass wall is at the same time determined by the Poisson equation together with appropriate boundary conditions and accounts for a field effect through the wall. Fixed negative surface charge on both the internal and external glass surfaces of the nanopipette is included together with the field effect through the glass wall to account for the electric double layer and the electro-osmosis. The inclusion of the field effect through the pipette wall is new compared to previous modeling of similar structures and is shown to be crucial for the behavior at the tip. It is demonstrated that the concentration of molecules is a consequence of ionic charge accumulation at the tip screening the electric field, thereby slowing down the electrophoretic motion of the molecules, which is further slowed down or stopped by the oppositely directed electro-osmosis. It is also shown that the trapping is very sensitive to the properties of the molecule, that is, its electrophoretic mobility and diffusion coefficient, the properties of the pipette, the ionic strength of the solution, and the applied electric field.
CO Depletion: A Microscopic Perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cazaux, S.; Martín-Doménech, R.; Caro, G. M. Muñoz

In regions where stars form, variations in density and temperature can cause gas to freeze out onto dust grains forming ice mantles, which influences the chemical composition of a cloud. The aim of this paper is to understand in detail the depletion (and desorption) of CO on (from) interstellar dust grains. Experimental simulations were performed under two different (astrophysically relevant) conditions. In parallel, Kinetic Monte Carlo simulations were used to mimic the experimental conditions. In our experiments, CO molecules accrete onto water ice at temperatures below 27 K, with a deposition rate that does not depend on the substrate temperature.more » During the warm-up phase, the desorption processes do exhibit subtle differences, indicating the presence of weakly bound CO molecules, therefore highlighting a low diffusion efficiency. IR measurements following the ice thickness during the TPD confirm that diffusion occurs at temperatures close to the desorption. Applied to astrophysical conditions, in a pre-stellar core, the binding energies of CO molecules, ranging between 300 and 850 K, depend on the conditions at which CO has been deposited. Because of this wide range of binding energies, the depletion of CO as a function of A{sub V} is much less important than initially thought. The weakly bound molecules, easily released into the gas phase through evaporation, change the balance between accretion and desorption, which result in a larger abundance of CO at high extinctions. In addition, weakly bound CO molecules are also more mobile, and this could increase the reactivity within interstellar ices.« less
Molecular Dynamics Simulations for Loading-Dependent Diffusion of CO2, SO2, CH4, and Their Binary Mixtures in ZIF-10: The Role of Hydrogen Bond.

PubMed

Li, Li; Yang, Deshuai; Fisher, Trevor R; Qiao, Qi; Yang, Zhen; Hu, Na; Chen, Xiangshu; Huang, Liangliang

2017-10-24

The loading-dependent diffusion behavior of CH 4 , CO 2 , SO 2 , and their binary mixtures in ZIF-10 has been investigated in detail by using classical molecular dynamics simulations. Our simulation results demonstrate that the self-diffusion coefficient D i of CH 4 molecules decreases sharply and monotonically with the loading while those of both CO 2 and SO 2 molecules initially display a slight increase at low uptakes and follow a slow decrease at high uptakes. Accordingly, the interaction energies between CH 4 molecules and ZIF-10 remain nearly constant regardless of the loading due to the absence of hydrogen bonds (HBs), while the interaction energies between CO 2 (or SO 2 ) and ZIF-10 decease rapidly with the loading, especially at small amounts of gas molecules. Such different loading-dependent diffusion and interaction mechanisms can be attributed to the relevant HB behavior between gas molecules and ZIF-10. At low loadings, both the number and strength of HBs between CO 2 (or SO 2 ) molecules and ZIF-10 decrease obviously as the loading increases, which is responsible for the slight increase of their diffusion coefficients. However, at high loadings, their HB strength increases with the loading. Similar loading-dependent phenomena of diffusion, interaction, and HB behavior can be observed for CH 4, CO 2 , and SO 2 binary mixtures in ZIF-10, only associated with some HB competition between CO 2 and SO 2 molecules in the case of the CO 2 /SO 2 mixture.
Arrhenius analysis of anisotropic surface self-diffusion on the prismatic facet of ice.

PubMed

Gladich, Ivan; Pfalzgraff, William; Maršálek, Ondřej; Jungwirth, Pavel; Roeselová, Martina; Neshyba, Steven

2011-11-28

We present an Arrhenius analysis of self-diffusion on the prismatic surface of ice calculated from molecular dynamics simulations. The six-site water model of Nada and van der Eerden was used in combination with a structure-based criterion for determining the number of liquid-like molecules in the quasi-liquid layer. Simulated temperatures range from 230 K-287 K, the latter being just below the melting temperature of the model, 289 K. Calculated surface diffusion coefficients agree with available experimental data to within quoted precision. Our results indicate a positive Arrhenius curvature, implying a change in the mechanism of self-diffusion from low to high temperature, with a concomitant increase in energy of activation from 29.1 kJ mol(-1) at low temperature to 53.8 kJ mol(-1) close to the melting point. In addition, we find that the surface self-diffusion is anisotropic at lower temperatures, transitioning to isotropic in the temperature range of 240-250 K. We also present a framework for self-diffusion in the quasi-liquid layer on ice that aims to explain these observations.
A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

NASA Astrophysics Data System (ADS)

Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

2007-09-01

This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it improves not only the interpretation, but also the quantification.
Handheld Diffusion Test Cells

NASA Technical Reports Server (NTRS)

2001-01-01

This photo shows the Handheld Diffusion Test Cell (HH-DTC) apparatus flown on the Space Shuttle. Similar cells (inside the plastic box) will be used in the Observable Protein Crystal Growth Apparatus (OPCGA) to be operated aboard the International Space Station (ISS). The principal investigator is Dr. Alex McPherson of the University of California, Irvine. Each individual cell comprises two sample chambers with a rotating center section that isolates the two from each other until the start of the experiment and after it is completed. The cells are made from optical-quality quartz glass to allow photography and interferometric observations. Each cell has a small light-emitting diode and lens to back-light the solution. In protein crystal growth experiments, a precipitating agent such as a salt solution is used to absorb and hold water but repel the protein molecules. This increases the concentration of protein until the molecules nucleate to form crystals. This cell is one of 96 that make up the experiment module portion of the OPCGA.
Handheld Diffusion Test Cells

NASA Technical Reports Server (NTRS)

2001-01-01

This photo shows an individual cell from the Handheld Diffusion Test Cell (HH-DTC) apparatus flown on the Space Shuttle. Similar cells will be used in the Observable Protein Crystal Growth Apparatus (OPCGA) to be operated aboard the International Space Station (ISS). The principal investigator is Dr. Alex McPherson of the University of California, Irvine. Each individual cell comprises two sample chambers with a rotating center section that isolates the two from each other until the start of the experiment and after it is completed. The cells are made from optical-quality quartz glass to allow photography and interferometric observations. Each cell has a small light-emitting diode and lens to back-light the solution. In protein crystal growth experiments, a precipitating agent such as a salt solution is used to absorb and hold water but repel the protein molecules. This increases the concentration of protein until the molecules nucleate to form crystals. This cell is one of 96 that make up the experiment module portion of the OPCGA.
Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel.

PubMed

Pomès, Régis; Roux, Benoît

2002-05-01

The conduction of protons in the hydrogen-bonded chain of water molecules (or "proton wire") embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a "hop-and-turn" or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H+) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H+ is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H+, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.
Multiple Diffusion Mechanisms Due to Nanostructuring in Crowded Environments

PubMed Central

Sanabria, Hugo; Kubota, Yoshihisa; Waxham, M. Neal

2007-01-01

One of the key questions regarding intracellular diffusion is how the environment affects molecular mobility. Mostly, intracellular diffusion has been described as hindered, and the physical reasons for this behavior are: immobile barriers, molecular crowding, and binding interactions with immobile or mobile molecules. Using results from multi-photon fluorescence correlation spectroscopy, we describe how immobile barriers and crowding agents affect translational mobility. To study the hindrance produced by immobile barriers, we used sol-gels (silica nanostructures) that consist of a continuous solid phase and aqueous phase in which fluorescently tagged molecules diffuse. In the case of molecular crowding, translational mobility was assessed in increasing concentrations of 500 kDa dextran solutions. Diffusion of fluorescent tracers in both sol-gels and dextran solutions shows clear evidence of anomalous subdiffusion. In addition, data from the autocorrelation function were analyzed using the maximum entropy method as adapted to fluorescence correlation spectroscopy data and compared with the standard model that incorporates anomalous diffusion. The maximum entropy method revealed evidence of different diffusion mechanisms that had not been revealed using the anomalous diffusion model. These mechanisms likely correspond to nanostructuring in crowded environments and to the relative dimensions of the crowding agent with respect to the tracer molecule. Analysis with the maximum entropy method also revealed information about the degree of heterogeneity in the environment as reported by the behavior of diffusive molecules. PMID:17040979
Solvation Dynamics in Different Phases of the Lyotropic Liquid Crystalline System.

PubMed

Roy, Bibhisan; Satpathi, Sagar; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

2015-09-03

Reverse hexagonal (HII) liquid crystalline material based on glycerol monooleate (GMO) is considered as a potential carrier for drugs and other important biomolecules due to its thermotropic phase change and excellent morphology. In this work, the dynamics of encapsulated water, which plays important role in stabilization and formation of reverse hexagonal mesophase, has been investigated by time dependent Stokes shift method using Coumarin-343 as a solvation probe. The formation of the reverse hexagonal mesophase (HII) and transformation to the L2 phase have been monitored using small-angle X-ray scattering and polarized light microscopy experiments. REES studies suggest the existence of different polar regions in both HII and L2 systems. The solvation dynamics study inside the reverse hexagonal (HII) phase reveals the existence of two different types of water molecules exhibiting dynamics on a 120-900 ps time scale. The estimated diffusion coefficients of both types of water molecules obtained from the observed dynamics are in good agreement with the measured diffusion coefficient collected from the NMR study. The calculated activation energy is found to be 2.05 kcal/mol, which is associated with coupled rotational-translational water relaxation dynamics upon the transition from "bound" to "quasi-free" state. The observed ∼2 ns faster dynamics of the L2 phase compared to the HII phase may be associated with both the phase transformation as well as thermotropic effect on the relaxation process. Microviscosities calculated from time-resolved anisotropy studies infer that the interface is almost ∼22 times higher viscous than the central part of the cylinder. Overall, our results reveal the unique dynamical features of water inside the cylinder of reverse hexagonal and inverse micellar phases.
Understanding and controlling regime switching in molecular diffusion

NASA Astrophysics Data System (ADS)

Hallerberg, S.; de Wijn, A. S.

2014-12-01

Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to either long jumps or sticks. Furthermore, by changing the prevalence of these predictors with an outside influence, the diffusion of the molecule can be controlled. The approach presented in this proof of concept study is very generic and can be applied to larger and more complex molecules. Additionally, the predictor variables can be chosen in a general way so as to be accessible in experiments, making the method feasible for control of diffusion in applications. Our results also demonstrate that data-mining techniques can be used to investigate the phase-space structure of high-dimensional nonlinear dynamical systems.
Lithium Polymer Electrolytes Based On PMMA / PEG And Penetrant Diffusion In Kraton Penta-Block Ionomer

NASA Astrophysics Data System (ADS)

Meng, Yan

The study of diffusion in polymeric material is critical to many research fields and applications, such as polymer morphology, protective coatings (paints and varnishes), separation membranes, transport phenomena, polymer electrolytes, polymer melt, and controlled release of drugs from polymer carriers [1-9]. However, it is still a challenge to understand, predict and control the diffusion of molecules and ions of different sizes in polymers [2]. This work studied the medium to long range diffusion of species (i.e., ions and molecules) in solid polymer electrolytes based on poly(ethylene glycol)/poly(methyl methacrylate) (PEG/PMMA) for Li-based batteries, and polymeric permselective membranes via pulsed-field gradient NMR and a.c. impedance. Over the past decades polymer electrolytes have attracted much attention because of their promising technological application as an ion-conducting medium in solid-state batteries, fuel cells, electrochromic displays, and chemical sensors [10, 11]. However, despite numerous studies related to ionic transport in these electrolytes the understanding of the migration mechanism is still far from being complete, and progress in the field remains largely empirical [10, 12-15]. Among various candidates for solid polymer electrolyte (SPE) material, the miscible polymer pair, poly(ethylene oxide)/poly(methyl methacrylate) (PEO/PMMA), is an attractive one, because there is a huge difference in mobility between PEO and PMMA in their blends, and PEO chains remain exceptionally mobile in the blend even at temperature below the glass transition temperature of the blend [ 16]. Thus the mechanical strength and dimensional stability is maintained by PMMA component, while the chain motions or rearrangements of the PEO component virtually contribute to the ion transport [17]. The current work prepared two types of SPE based on poly(ethylene glycol) (PEG) /PMMA (40/60 by weight) for Li-based batteries: lithium bis(trifluoromethylsulfonylimide) (LiN(SO2CF3)2, LiTFSI) doped SPE and single-ion SPE. PEG, which is the very low molecular weight version of PEO, was used instead of PLO due to PEG's advantages of being noncrystalline, higher mobility, and having relatively high ionic conductivity when doped with alkali metal salts [18]. The medium to long range diffusion of species (i.e., ions and molecules) were studied via pulsed-field gradient NMR and a.c. impedance, along with other properties. For the LiTFSI doped system, the samples are named with their F0 to Li ratios. The order of diffusivity of ions is 16:1> 24:1> 8:1, while the order of a.c. conductivity is 24:1 > 16:1> 8:1. The largest diffusion 7Li coefficient is 1.4 x 108 cm 2/s in 16:1 at 77°C , and the largest a.c. conductivity is 1.43x 10-5S/cm for 24:1 at 68°C. The discrepancy between the diffusivity order and conductivity order is attributed to the formation of neutral contact ion pairs by a substantial fraction of ions in 16:1 . As the salt concentration is increased as 24:1→16:1→8:1, there is the transition of mostly free ions (i.e., 24:1)→free ions+contact ion pairs (i.e.. 16:1)→free ions+contact ion pairs+higher aggregates (i.e., 8:1). For the single-ion system, ion pairing of lithium PMMA ionomer is a serious problem due to the relatively low acidity of its corresponding acid and the low dielectric constant of the solvent (i.e. PEG). The Li+ diffusivity is fair (on the order of 10-8 cm2/s at 65°C, 77°C, and 89°C), but the fraction of free Li+ is only 1-2%. This severely limits the resulting a.c. conductivity, which is 2.72x 10-7 S/cm for 40P600 at 81°C. The second project involves studying the transport properties of a sulfonated pentablock copolymer, poly(para-methylstyrene)--b-hydrogenated polybutadiene-b-polystyrene-bhydrogenated polybutadiene - b-poly(para-methylstyrene) with polystyrene sulfonated in the midblock(PMS-HPB-sS-HPB-PMS), as pemrselective membranes for protective clothing, with high permeability to water and low permeability to hazardous organic chemicals. In addition, this work also contributes to study of polymer electrolyte membrane for fuel cell systems, because water transport in polymer electrolyte membranes (PEMs) has a profound effect on the performance of a fuel cell, yet is surprisingly the least studied property of PEMs[19]. The self-diffusion coefficients of different penetrant molecules, i.e., water, dimethyl methylphosphonate (DMMP), and ethanol in the said ionomer were accurately measured with PFG NMR as functions of temperature and concentration of solvents. Water exhibited self-diffusion coefficients two orders of magnitude higher than DMMP, while ethanol lies in between. Their effective volume to surface ratios of domains where diffusion took place were determined. The volume to surface ratios of water and DMMP are quite different, suggesting they may have different local geometry of the pores they reside in, while the V p/Seff ratios for water and ethanol are similar, thereby suggesting similar local environments of these solvents in the ionomer.
Structure and dynamics of reverse micelles containing supercooled water investigated by neutron scattering

NASA Astrophysics Data System (ADS)

Spehr, Tinka; Frick, Bernhard; Grillo, Isabelle; Falus, Peter; Müller, Martin; Stühn, Bernd

2009-03-01

We present a detailed neutron scattering study of the structure, shape fluctuations, and translational diffusion of microemulsion droplets at low temperatures. We investigate the ternary microemulsion D2O , AOT [bis(2-ethyl-hexyl) sulfosuccinate], and toluene-d8 (or heptane-d16) which forms spherical water droplets surrounded by a monolayer of AOT dispersed in oil around room temperature. At T=290K , varying the molar ratio ω of water to AOT between 3 and 12, we find using small angle neutron scattering water core radii Rc between 7 and 18Å , respectively. We characterize the structure at low temperatures down to T=220K . Upon cooling the droplet structure is maintained and Rc stays roughly constant down to temperatures where the confined water is deeply supercooled. At an ω -dependent temperature Ts we observe for all compositions a shrinking of the droplets, which depends on the initial droplet size: the smaller the initial radii, the lower the Ts is. At the lowest investigated temperature T=220K we find an ω -independent remaining water core corresponding to a number of about 2 water molecules per AOT molecule. Neutron spin-echo spectroscopy is used to monitor shape fluctuations and translational diffusion for one microemulsion ( ω=8 , Rw=12Å ) from T=300K down to temperatures below the corresponding shrinking temperature Ts . Thereby we determine the bending elasticity to be κ=0.3kBT over the whole investigated temperature range where the droplets are stable. From these results we cannot establish a link between surfactant membrane elasticity and low temperature structural instability of the droplets. Moreover, our results show that reverse AOT micelles are an excellent tool for the study of soft confined water over a broad range of confining sizes and temperatures down to the supercooled state.
Alteration of bentonite when contacted with supercritical CO2

NASA Astrophysics Data System (ADS)

Jinseok, K.; Jo, H. Y.; Yun, S. T.

2014-12-01

Deep saline formations overlaid by impermeable caprocks with a high sealing capacity are attractive CO2 storage reservoirs. Shales, which consist of mainly clay minerals, are potential caprocks for the CO2 storage reservoirs. The properties of clay minerals in shales may affect the sealing capacity of shales. In this study, changes in clay minerals' properties when contacted with supercritical (SC) CO2 at various conditions were investigated. Bentonite, whichis composed of primarily montmorillonite, was used as the clay material in this study. Batch reactor tests on wet bentonite samples in the presence of SC CO2 with or without aqueous phases were conducted at high pressure (12 MPa) and moderate temperature (50 oC) conditions for a week. Results show that the bentonite samples obtained from the tests with SC CO2 had less change in porosity than those obtained from the tests without SC CO2 (vacuum-drying) at a given reaction time, indicating that the bentonite samples dried in the presence of SC CO2 maintained their structure. These results suggest that CO2 molecules can diffuse into interlayer of montmorillonite, which is a primary mineral of bentonite, and form a single CO2 molecule layer or double CO2 molecule layers. The CO2 molecules can displace water molecules in the interlayer, resulting in maintaining the interlayer spacing when dehydration occurs. Noticeable changes in reacted bentonite samples obtained from the tests with an aqueous phase (NaCl, CaCl2, or sea water) are decreases in the fraction of plagioclase and pyrite and formation of carbonate minerals (i.e., calcite and dolomite) and halite. In addition, no significant exchanges of Na or Ca on the exchangeable complex of the montmorillonite in the presence of SC CO2 occurred, resulting in no significant changes in the swelling capacity of bentonite samples after reacting with SC CO2 in the presence of aqueous phases. These results might be attributed by the CO2 molecule layer, which prevents diffusion of ions into the interlayer.
Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

NASA Astrophysics Data System (ADS)

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2016-09-01

A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

Molecular Dynamics Simulation of Amorphous Hydroxypropylmethylcellulose and Its Mixtures With Felodipine and Water.

PubMed

Xiang, Tian-Xiang; Anderson, Bradley D

2017-03-01

Understanding drug-polymer molecular interactions, their miscibility, supersaturation potential, and the effects of water uptake may be invaluable for selecting amorphous polymer dispersions that can maximize the oral bioavailability of poorly water-soluble drugs. Molecular dynamics simulations were performed using a model for hydroxypropylmethylcellulose (HPMC) resembling the substitution patterns found experimentally. HPMC at low and high water contents (0.9%-23.0% wt/wt) and mixtures with a hydrophobic drug, felodipine (FEL), were constructed. T g values and densities after ∼30 ns aging at 298 K were close to published results. Except for hydrogen bonds (HBs) between the 5-O- and a 3-OH group in a neighboring repeat unit, HPMC oxygen atoms have a low HB probability (p < 0.1) perhaps due to shielding by surrounding substituents. Water molecules tend to be isolated at low water content while clusters were prevalent at ≥10.7% water. The Flory-Huggins FEL-HPMC interaction parameter (-0.20 ± 0.07) predicts complete miscibility at all HPMC compositions, in agreement with experiments. However, HBs between the FEL-N-H and HPMC favoring miscibility are disrupted with increasing water. Apparent diffusion coefficients versus water content were generated for water and FEL and a theory for the non-Einsteinian nature of water diffusion is proposed. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.
Self-diffusion in periodic porous media: a comparison of numerical simulation and eigenvalue methods.

PubMed

Schwartz, L M; Bergman, D J; Dunn, K J; Mitra, P P

1996-01-01

Random walk computer simulations are an important tool in understanding magnetic resonance measurements in porous media. In this paper we focus on the description of pulsed field gradient spin echo (PGSE) experiments that measure the probability, P(R,t), that a diffusing water molecule will travel a distance R in a time t. Because PGSE simulations are often limited by statistical considerations, we will see that valuable insight can be gained by working with simple periodic geometries and comparing simulation data to the results of exact eigenvalue expansions. In this connection, our attention will be focused on (1) the wavevector, k, and time dependent magnetization, M(k, t); and (2) the normalized probability, Ps(delta R, t), that a diffusing particle will return to within delta R of the origin after time t.
Microimaging of transient guest profiles to monitor mass transfer in nanoporous materials

NASA Astrophysics Data System (ADS)

Kärger, Jörg; Binder, Tomas; Chmelik, Christian; Hibbe, Florian; Krautscheid, Harald; Krishna, Rajamani; Weitkamp, Jens

2014-04-01

The intense interactions of guest molecules with the pore walls of nanoporous materials is the subject of continued fundamental research. Stimulated by their thermal energy, the guest molecules in these materials are subject to a continuous, irregular motion, referred to as diffusion. Diffusion, which is omnipresent in nature, influences the efficacy of nanoporous materials in reaction and separation processes. The recently introduced techniques of microimaging by interference and infrared microscopy provide us with a wealth of information on diffusion, hitherto inaccessible from commonly used techniques. Examples include the determination of surface barriers and the sticking coefficient's analogue, namely the probability that, on colliding with the particle surface, a molecule may continue its diffusion path into the interior. Microimaging is further seen to open new vistas in multicomponent guest diffusion (including the detection of a reversal in the preferred diffusion pathways), in guest-induced phase transitions in nanoporous materials and in matching the results of diffusion studies under equilibrium and non-equilibrium conditions.
Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling

DOE PAGES

Lv, Chao; Aitchison, Erick W.; Wu, Dongsheng; ...

2015-06-29

Hydrogen sulfide (H 2S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H 2S and its structural analogue, water (H 2O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. Here, as revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is,more » the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H 2S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. Lastly, this study not only explains why H 2S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes.« less
Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.

PubMed

Lv, Chao; Aitchison, Erick W; Wu, Dongsheng; Zheng, Lianqing; Cheng, Xiaolin; Yang, Wei

2016-03-05

Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
Nitrogen diffusion in hafnia and the impact of nitridation on oxygen and hydrogen diffusion: A first-principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sathiyanarayanan, Rajesh, E-mail: rajessat@in.ibm.com, E-mail: rajesh.sathiyanarayanan@gmail.com; Pandey, R. K.; Murali, K. V. R. M.

2015-01-21

Using first-principles simulations, we have computed incorporation energies and diffusion barriers of ammonia, the nitrogen molecule and atomic nitrogen in monoclinic hafnia (m-HfO{sub 2}). Our calculations show that ammonia is likely to dissociate into an NH{sub 2} molecular unit, whereas the nitrogen molecule remains as a molecule either in the interstitial space or at an oxygen lattice site. The lowest energy pathway for the diffusion of atomic nitrogen interstitials consists of the hopping of the nitrogen interstitial between neighboring three-coordinated lattice oxygen atoms that share a single Hf atom, and the barrier for such hops is determined by a switchingmore » mechanism. The substitutional nitrogen atom shows a preference for diffusion through the doubly positive oxygen vacancy-mediated mechanism. Furthermore, we have investigated the impact of nitrogen atoms on the diffusion barriers of oxygen and hydrogen interstitials in m-HfO{sub 2}. Our results show that nitrogen incorporation has a significant impact on the barriers for oxygen and hydrogen diffusion: nitrogen atoms attract oxygen and hydrogen interstitials diffusing in the vicinity, thereby slowing down (reducing) their diffusion (diffusion length)« less
Imaging fluorescence-correlation spectroscopy for measuring fast surface diffusion at liquid/solid interfaces.

PubMed

Cooper, Justin T; Harris, Joel M

2014-08-05

The development of techniques to probe interfacial molecular transport is important for understanding and optimizing surface-based analytical methods including surface-enhanced spectroscopies, biological assays, and chemical separations. Single-molecule-fluorescence imaging and tracking has been used to measure lateral diffusion rates of fluorescent molecules at surfaces, but the technique is limited to the study of slower diffusion, where molecules must remain relatively stationary during acquisition of an image in order to build up sufficient intensity in a spot to detect and localize the molecule. Although faster time resolution can be achieved by fluorescence-correlation spectroscopy (FCS), where intensity fluctuations in a small spot are related to the motions of molecules on the surface, long-lived adsorption events arising from surface inhomogeneity can overwhelm the correlation measurement and mask the surface diffusion of the moving population. Here, we exploit a combination of these two techniques, imaging-FCS, for measurement of fast interfacial transport at a model chromatographic surface. This is accomplished by rapid imaging of the surface using an electron-multiplied-charged-coupled-device (CCD) camera, while limiting the acquisition to a small area on the camera to allow fast framing rates. The total intensity from the sampled region is autocorrelated to determine surface diffusion rates of molecules with millisecond time resolution. The technique allows electronic control over the acquisition region, which can be used to avoid strong adsorption sites and thus minimize their contribution to the measured autocorrelation decay and to vary the acquisition area to resolve surface diffusion from adsorption and desorption kinetics. As proof of concept, imaging-FCS was used to measure surface diffusion rates, interfacial populations, and adsorption-desorption rates of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine (DiI) on planar C18- and C1-modified surfaces.
Pseudolatex preparation using a novel emulsion-diffusion process involving direct displacement of partially water-miscible solvents by distillation.

PubMed

Quintanar-Guerrero, D; Allémann, E; Fessi, H; Doelker, E

1999-10-25

Pseudolatexes were obtained by a new process based on an emulsification-diffusion technique involving partially water-miscible solvents. The preparation method consisted of emulsifying an organic solution of polymer (saturated with water) in an aqueous solution of a stabilizing agent (saturated with solvent) using conventional stirrers, followed by direct solvent distillation. The technique relies on the rapid displacement of the solvent from the internal into the external phase which thereby provokes polymer aggregation. Nanoparticle formation is believed to occur because rapid solvent diffusion produces regions of local supersaturation near the interface, and nanoparticles are formed due to the ensuing interfacial phase transformations and polymer aggregation that occur in these interfacial domains. Using this method, it was possible to prepare pseudolatexes of biodegradable and non-biodegradable polymers such as poly(D,L-lactic acid) and poly(epsilon-caprolactone), Eudragit E, cellulose acetate phthalate, cellulose acetate trimellitate using ethyl acetate or 2-butanone as partially water-miscible solvents and poly(vinyl alcohol) or poloxamer 407 as stabilizing agent. A transition from nano- to microparticles was observed at high polymer concentrations. At concentrations above 30% w/v of Eudragit E in ethyl acetate or cellulose acetate phthalate in 2-butanone only microparticles were obtained. This behaviour was attributed to decreased transport of polymer molecules into the aqueous phase.
On the vanishing of the t-term in the short-time expansion of the diffusion coefficient for oscillating gradients in diffusion NMR

NASA Astrophysics Data System (ADS)

Laun, Frederik B.; Demberg, Kerstin; Nagel, Armin M.; Uder, Micheal; Kuder, Tristan A.

2017-11-01

Nuclear magnetic resonance (NMR) diffusion measurements can be used to probe porous structures or biological tissues by means of the random motion of water molecules. The short-time expansion of the diffusion coefficient in powers of sqrt(t), where t is the diffusion time related to the duration of the diffusion-weighting magnetic field gradient profile, is universally connected to structural parameters of the boundaries restricting the diffusive motion. The sqrt(t)-term is proportional to the surface to volume ratio. The t-term is related to permeability and curvature. The short time expansion can be measured with two approaches in NMR-based diffusion experiments: First, by the use of diffusion encodings of short total duration and, second, by application of oscillating gradients of long total duration. For oscillating gradients, the inverse of the oscillation frequency becomes the relevant time scale. The purpose of this manuscript is to show that the oscillating gradient approach is blind to the t-term. On the one hand, this prevents fitting of permeability and curvature measures from this term. On the other hand, the t-term does not bias the determination of the sqrt(t)-term in experiments.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.

Hierarchical mesoporous zeolites exhibit higher catalytic activities and longer lifetime compared to the traditional microporous zeolites due to improved diffusivity of substrate molecules and their enhanced access to the zeolite active sites. Understanding diffusion of biomass pyrolysis vapors and their upgraded products in such materials is fundamentally important during catalytic fast pyrolysis (CFP) of lignocellulosic biomass, since diffusion makes major contribution to determine shape selectivity and product distribution. However, diffusivities of biomass relevant species in hierarchical mesoporous zeolites are poorly characterized, primarily due to the limitations of the available experimental technology. In this work, molecular dynamics (MD) simulations are utilizedmore » to investigate the diffusivities of several selected coke precursor molecules, benzene, naphthalene, and anthracene, in hierarchical mesoporous H-ZSM-5 zeolite. The effects of temperature and size of mesopores on the diffusivity of the chosen model compounds are examined. The simulation results demonstrate that diffusion within the microspores as well as on the external surface of mesoporous H-ZSM-5 dominates only at low temperature. At pyrolysis relevant temperatures, mass transfer is essentially conducted via diffusion along the mesopores. Additionally, the results illustrate the heuristic diffusion model, such as the extensively used Knudsen diffusion, overestimates the diffusion of bulky molecules in the mesopores, thus making MD simulation a powerful and compulsory approach to explore diffusion in zeolites.« less
Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering

NASA Astrophysics Data System (ADS)

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G.; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V.; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F.

2016-01-01

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth’s deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å-1 corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.
Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering.

PubMed

Foglia, Fabrizia; Hazael, Rachael; Simeoni, Giovanna G; Appavou, Marie-Sousai; Moulin, Martine; Haertlein, Michael; Trevor Forsyth, V; Seydel, Tilo; Daniel, Isabelle; Meersman, Filip; McMillan, Paul F

2016-01-07

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth's deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å(-1) corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.
Paleotemperatures derived from the EPICA Dome-C core based on isotopic diffusion in the firn pack.

NASA Astrophysics Data System (ADS)

Gkinis, V.; Johnsen, S. J.; Vinther, B.; Sheldon, S.; Ritz, C.; Masson-Delmotte, V.

2009-04-01

Water isotope ratios as measured from ice core samples have been used as a proxy for past temperatures. Based i.a. on a Rayleigh fractionation process they record the cloud temperature during snow formation. However, changes in the temperature and humidity of the vapor source can also affect the isotopic signal of the polar precipitation, thus inducing isotopic artifacts. Furthermore, for the case of the Antarctic ice cap, temperature inversions frequently occur during snow formation. As a result, the cloud temperature as recorded by the water isotopes can differ significantly from the temperature at the surface. After the deposition of snow and until pore close off, a diffusive process occurs in the pore space of the firn pack, mixing water vapor from different layers and smoothing the isotopic profiles. The smoothing depends only on the resulting diffusion length. This process is temperature dependent and it presents a slightly different rate between the two isotopic species of water, H218O and HD16O. This is because the fractionation factors as defined for these two isotopic species have a different dependence on temperature. In this study we present a temperature reconstruction based on the different diffusion rates of H218O and HD16O water molecules in firn. The advantage of such an approach is that the temperatures estimated represent the actual conditions in the firn stack. As a result, we can surpass the artifacts that can possibly disrupt the use of the classical technique. We will present temperature estimations as extracted from two high resolution (2.5 cm) data sets, from the EPICA Dome C deep core focused on the Holoene Climatic Optimum and the Last Glacial Maximum and compare them with results obtained with the classical slope method as well as constrains imposed by the measured temperature profile. We will also address the problems of spectral power estimation for determining the diffusion lengths.
An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

PubMed

Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

2016-03-14

Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.
Time scale of random sequential adsorption.

PubMed

Erban, Radek; Chapman, S Jonathan

2007-04-01

A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) The kinetics of the chemical reaction between adsorbing molecules and the surface and (ii) geometrical constraints on the surface made by molecules which are already adsorbed. The process (i) is modeled in a diffusion-driven context, i.e., the conditional probability of adsorbing a molecule provided that the molecule hits the surface is related to the macroscopic surface reaction rate. The geometrical constraint (ii) is modeled using random sequential adsorption (RSA), which is the sequential addition of molecules at random positions on a surface; one attempt to attach a molecule is made per one RSA simulation time step. By coupling RSA with the diffusion of molecules in the solution above the surface the RSA simulation time step is related to the real physical time. The method is illustrated on a model of chemisorption of reactive polymers to a virus surface.
Conserved linear dynamics of single-molecule Brownian motion.

PubMed

Serag, Maged F; Habuchi, Satoshi

2017-06-06

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.
Conserved linear dynamics of single-molecule Brownian motion

PubMed Central

Serag, Maged F.; Habuchi, Satoshi

2017-01-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance. PMID:28585925
Conserved linear dynamics of single-molecule Brownian motion

NASA Astrophysics Data System (ADS)

Serag, Maged F.; Habuchi, Satoshi

2017-06-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.
Clogging in micromachined Joule-Thomson coolers: Mechanism and preventive measures

NASA Astrophysics Data System (ADS)

Cao, H. S.; Vanapalli, S.; Holland, H. J.; Vermeer, C. H.; ter Brake, H. J. M.

2013-07-01

Micromachined Joule-Thomson coolers can be used for cooling small electronic devices. However, a critical issue for long-term operation of these microcoolers is the clogging caused by the deposition of water that is present as impurity in the working fluid. We present a model that describes the deposition process considering diffusion and kinetics of water molecules. In addition, the deposition and sublimation process was imaged, and the experimental observation fits well to the modeling predictions. By changing the temperature profile along the microcooler, the operating time of the microcooler under test at 105 K extends from 11 to 52 h.
Humidity-insensitive water evaporation from molecular complex fluids.

PubMed

Salmon, Jean-Baptiste; Doumenc, Frédéric; Guerrier, Béatrice

2017-09-01

We investigated theoretically water evaporation from concentrated supramolecular mixtures, such as solutions of polymers or amphiphilic molecules, using numerical resolutions of a one-dimensional model based on mass transport equations. Solvent evaporation leads to the formation of a concentrated solute layer at the drying interface, which slows down evaporation in a long-time-scale regime. In this regime, often referred to as the falling rate period, evaporation is dominated by diffusive mass transport within the solution, as already known. However, we demonstrate that, in this regime, the rate of evaporation does not also depend on the ambient humidity for many molecular complex fluids. Using analytical solutions in some limiting cases, we first demonstrate that a sharp decrease of the water chemical activity at high solute concentration leads to evaporation rates which depend weakly on the humidity, as the solute concentration at the drying interface slightly depends on the humidity. However, we also show that a strong decrease of the mutual diffusion coefficient of the solution enhances considerably this effect, leading to nearly independent evaporation rates over a wide range of humidity. The decrease of the mutual diffusion coefficient indeed induces strong concentration gradients at the drying interface, which shield the concentration profiles from humidity variations, except in a very thin region close to the drying interface.

Effects of hypotonic stress and ouabain on the apparent diffusion coefficient of water at cellular and tissue levels in Aplysia.

PubMed

Jelescu, Ileana Ozana; Ciobanu, Luisa; Geffroy, Françoise; Marquet, Pierre; Le Bihan, Denis

2014-03-01

There is evidence that physiological or pathological cell swelling is associated with a decrease of the apparent diffusion coefficient (ADC) of water in tissues, as measured with MRI. However the mechanism remains unclear. Magnetic resonance microscopy, performed on small tissue samples, has the potential to distinguish effects occurring at cellular and tissue levels. A three-dimensional diffusion prepared fast imaging with steady-state free precession sequence for MR microscopy was implemented on a 17.2 T imaging system and used to investigate the effect of two biological challenges known to cause cell swelling, exposure to a hypotonic solution or to ouabain, on Aplysia nervous tissue. The ADC was measured inside isolated neuronal soma and in the region of cell bodies of the buccal ganglia. Both challenges resulted in an ADC increase inside isolated neuronal soma (+31 ± 24% and +30 ± 11%, respectively) and an ADC decrease at tissue level in the buccal ganglia (-12 ± 5% and -18 ± 8%, respectively). A scenario involving a layer of water molecules bound to the inflating cell membrane surface is proposed to reconcile this apparent discrepancy. Copyright © 2014 John Wiley & Sons, Ltd.
Automated optimization of water-water interaction parameters for a coarse-grained model.

PubMed

Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

2014-02-13

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.
Effect of metal ion intercalation on the structure of MXene and water dynamics on its internal surfaces

DOE PAGES

Osti, Naresh C.; Naguib, Michael; Ostadhossein, Alireza; ...

2016-03-24

MXenes are a recently discovered class of 2D materials with an excellent potential for energy storage applications. Because MXene surfaces are hydrophilic and attractive interaction forces between the layers are relatively weak, water molecules can spontaneously intercalate at ambient humidity and significantly influence the key properties of this 2D material. Using complementary X-ray and neutron scattering techniques, we demonstrate that intercalation with potassium cations significantly improves structural homogeneity and water stability in MXenes. Furthermore, in agreement with molecular dynamics simulations, intercalated potassium ions reduce the water self-diffusion coefficient by 2 orders of magnitude, suggesting greater stability of hydrated MXene againstmore » changing environmental conditions.« less
Dynamical mechanism of antifreeze proteins to prevent ice growth

NASA Astrophysics Data System (ADS)

Kutschan, B.; Morawetz, K.; Thoms, S.

2014-08-01

The fascinating ability of algae, insects, and fishes to survive at temperatures below normal freezing is realized by antifreeze proteins (AFPs). These are surface-active molecules and interact with the diffusive water-ice interface thus preventing complete solidification. We propose a dynamical mechanism on how these proteins inhibit the freezing of water. We apply a Ginzburg-Landau-type approach to describe the phase separation in the two-component system (ice, AFP). The free-energy density involves two fields: one for the ice phase with a low AFP concentration and one for liquid water with a high AFP concentration. The time evolution of the ice reveals microstructures resulting from phase separation in the presence of AFPs. We observed a faster clustering of pre-ice structure connected to a locking of grain size by the action of AFP, which is an essentially dynamical process. The adsorption of additional water molecules is inhibited and the further growth of ice grains stopped. The interfacial energy between ice and water is lowered allowing the AFPs to form smaller critical ice nuclei. Similar to a hysteresis in magnetic materials we observe a thermodynamic hysteresis leading to a nonlinear density dependence of the freezing point depression in agreement with the experiments.
Coarse-grained model of nanoscale segregation, water diffusion, and proton transport in Nafion membranes

NASA Astrophysics Data System (ADS)

Vishnyakov, Aleksey; Mao, Runfang; Lee, Ming-Tsung; Neimark, Alexander V.

2018-01-01

We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation. The simulation results qualitatively, and in many respects quantitatively, predict the specifics of nanoscale segregation in the hydrated Nafion membrane into hydrophobic and hydrophilic subphases, water diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from a collection of isolated water clusters to a 3D network of pores filled with water embedded in the hydrophobic matrix. The segregated morphology is characterized in terms of the pore size distribution with the average size growing with hydration from ˜1 to ˜4 nm. Comparison of the predicted water diffusivity with the experimental data taken from different sources shows good agreement at high and moderate hydration and substantial deviation at low hydration, around and below the percolation threshold. This discrepancy is attributed to the dynamic percolation effects of formation and rupture of merging bridges between the water clusters, which become progressively important at low hydration, when the coarse-grained model is unable to mimic the fine structure of water network that includes singe molecule bridges. Selected simulations of water diffusion are performed for the alkali metal substituted membrane which demonstrate the effects of the counter-ions on membrane self-assembly and transport. The hydration dependence of the proton diffusivity reproduces semi-qualitatively the trend of the diverse experimental data, showing a sharp decrease around the percolation threshold. Overall, the proposed model opens up an opportunity to study self-assembly and water and proton transport in polyelectrolytes using computationally efficient DPD simulations, and, with further refinement, it may become a practical tool for theory informed design and optimization of perm-selective and ion-conducting membranes with improved properties.
Physical Chemical Controls of Methane and other Hydrocarbon gases in Outer Solar System Water-Ice Systems

NASA Astrophysics Data System (ADS)

Osegovic, J. P.; Max, M. D.

2012-12-01

Saturn's moon Enceladus appear to have liquid water under its thin icy surface that has venting water and complex hydrocarbons. Jupiter's moon Europa is locked under a very thick layer of surface ice. Because Saturn's moon Titan contains abundant hydrocarbon gasses and liquids and both Saturn and Jupiter contain abundant hydrocarbon gases, it is likely that Europa also may have significant quantities of hydrocarbon gases in their water-ice systems. Both of these moons have the potential for life. We have begun to explore the impact that gas hydrate, which is a crystalline material composed of water and gas molecules, has on the availability of liquid water on a planet's surface: what conditions need to be present to initiate hydrate formation from a primordial selection of gases, salts, and water, how isolated hydrate systems evolve under the condition of mass transfer from ex-hydrate stability conditions to pro-hydrate stability conditions, the timespan of conditions that hydrate formation can host liquid solutions in an otherwise cooling regime; and the impact that additional chemistry, such as primitive chemosynthesis, may have on the sequestered hydrocarbon gases in hydrate. The analog for gas hydrate on these moons is the Permafrost hydrate system of Earth. Gas hydrate and water ice are stable in a compound cryosphere with ice extending downward from cold surface conditions to about the 273 K isotherm. Hydrate, depending on the mixture of gases in it, is stable from some depth below the surface to some isotherm that could be considerably in excess of 273 K. Salinity may strongly affect stability conditions. In order to estimate the thickness of the gas hydrate stability zone and its effect on 'planetary' heat flow, we model heat production as a function of mass flow. Variables are gravity, ice thickness, temperature of the surrounding medium (space, ice, and water), the thickness of the "ocean", the and the thermophysical properties of the gas being transferred. The model is constrained by the molecular diffusion rate of gas approaching the hydrate phase boundary. The heat produced or consumed by the hydrate system will affect the ice system and phase boundary. Fick's law can be used to model steady state diffusion. Flux is related to the diffusivity of the component and as a function of concentration and the distance over which the reactions take place. Initial model calculations indicate that in some cases, methane (ΔH = -56 kJ/mol for small molecules (CH4, N2, CO2, H2S) may affect the water-ice energy balance sufficiently to contribute to the maintenance of a deep ocean below ice. The effect of the presence of higher density hydrocarbons (ΔH = -72 kJ/mol for ethane and -126 kJ/mol for propane) accentuate the thermal transfer effect but may diffuse too slowly to be a thermal forcing agent in the hydrate system.
Volatilization of benzene and eight alkyl-substituted benzene compounds from water

USGS Publications Warehouse

Rathbun, R.E.; Tai, D.Y.

1988-01-01

Predicting the fate of organic compounds in streams and rivers often requires knowledge of the volatilization characteristics of the compounds. The reference-substance concept, involving laboratory-determined ratios of the liquid-film coefficients for volatilization of the organic compounds to the liquid-film coefficient for oxygen absorption, is used to predict liquid-film coefficients for streams and rivers. In the absence of experimental data, two procedures have been used for estimating these liquid-film coefficient ratios. These procedures, based on the molecular-diffusion coefficient and on the molecular weight, have been widely used but never extensively evaluated. Liquid-film coefficients for the volatilization of benzene and eight alkyl-substituted benzene compounds (toluene through n-octylbenzene) from water were measured in a constant-temperature, stirred water bath. Liquid-film coefficients for oxygen absorption were measured simultaneously. A range of water mixing conditions was used with a water temperature of 298.2 K. The ratios of the liquid-film coefficients for volatilization to the liquid-film coefficient for oxygen absorption for all of the organic compounds were independent of mixing conditions in the water. Experimental ratios ranged from 0.606 for benzene to 0.357 for n-octylbenzene. The molecular-diffusion-coefficient procedure accurately predicted the ratios for ethylbenzene through n-pentylbenzene with a power dependence of 0.566 on the molecular-diffusion coefficient, in agreement with published values. Predicted ratios for benzene and toluene were slightly larger than the experimental ratios. These differences were attributed to possible interactions between the molecules of these compounds and the water molecules and to benzene-benzene interactions that form dimers. Because these interactions also are likely to occur in natural waters, it was concluded that the experimental ratios are more correct than the predicted ratios for application purposes in the reference-substance concept. Predicted ratios for n-hexylbenzene, n-heptylbenzene, and n-octylbenzene were larger than the experimental ratios. These differences were attributed to a sorption-desorption process between these compounds and the surfaces of the constant-temperature water bath. Other experimental problems associated with preparing water solutions of these slightly soluble compounds also may have contributed to the differences. Because these processes are not part of the true volatilization process, it was concluded that the predicted ratios for these three compounds are probably more correct than the experimental ratios for application purposes in the reference-substance concept. Any model of the fate of these compounds in streams and rivers would have to include terms accounting for sorption processes, however. The molecular-weight procedure accurately predicted the ratios for ethylbenzene through n-pentylbenzene, but only if the power dependence on the molecular weight was decreased from the commonly used -0.500 to -0.427. Deviations for the low- and high-molecular-weight compounds were similar to those observed for the molecular-diffusion-coefficient procedure.
Whole-body diffusion kurtosis imaging: initial experience on non-Gaussian diffusion in various organs.

PubMed

Filli, Lukas; Wurnig, Moritz; Nanz, Daniel; Luechinger, Roger; Kenkel, David; Boss, Andreas

2014-12-01

Diffusion kurtosis imaging (DKI) is based on a non-Gaussian diffusion model that should inherently better account for restricted water diffusion within the complex microstructure of most tissues than the conventional diffusion-weighted imaging (DWI), which presumes Gaussian distributed water molecule displacement probability. The aim of this investigation was to test the technical feasibility of in vivo whole-body DKI, probe for organ-specific differences, and compare whole-body DKI and DWI results. Eight healthy subjects underwent whole-body DWI on a clinical 3.0 T magnetic resonance imaging system. Echo-planar images in the axial orientation were acquired at b-values of 0, 150, 300, 500, and 800 mm²/s. Parametrical whole-body maps of the diffusion coefficient (D), the kurtosis (K), and the traditional apparent diffusion coefficient (ADC) were generated. Goodness of fit was compared between DKI and DWI fits using the sums of squared residuals. Data groups were tested for significant differences of the mean by paired Student t tests. Good-quality parametrical whole-body maps of D, K, and ADC could be computed. Compared with ADC values, D values were significantly higher in the cerebral gray matter (by 30%) and white matter (27%), renal cortex (23%) and medulla (21%), spleen (101%), as well as erector spinae muscle (34%) (each P value <0.001). No significant differences between D and ADC were found in the cerebrospinal fluid (P = 0.08) and in the liver (P = 0.13). Curves of DKI fitted the measurement points significantly better than DWI curves did in most organs. Whole-body DKI is technically feasible and may reflect tissue microstructure more meaningfully than whole-body DWI.
Diffusion of aromatic hydrocarbons in hierarchical mesoporous H-ZSM-5 zeolite

DOE PAGES

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; ...

2018-02-08

Hierarchical mesoporous zeolites exhibit higher catalytic activities and longer lifetime compared to the traditional microporous zeolites due to improved diffusivity of substrate molecules and their enhanced access to the zeolite active sites. Understanding diffusion of biomass pyrolysis vapors and their upgraded products in such materials is fundamentally important during catalytic fast pyrolysis (CFP) of lignocellulosic biomass, since diffusion makes major contribution to determine shape selectivity and product distribution. However, diffusivities of biomass relevant species in hierarchical mesoporous zeolites are poorly characterized, primarily due to the limitations of the available experimental technology. In this work, molecular dynamics (MD) simulations are utilizedmore » to investigate the diffusivities of several selected coke precursor molecules, benzene, naphthalene, and anthracene, in hierarchical mesoporous H-ZSM-5 zeolite. The effects of temperature and size of mesopores on the diffusivity of the chosen model compounds are examined. The simulation results demonstrate that diffusion within the microspores as well as on the external surface of mesoporous H-ZSM-5 dominates only at low temperature. At pyrolysis relevant temperatures, mass transfer is essentially conducted via diffusion along the mesopores. Additionally, the results illustrate the heuristic diffusion model, such as the extensively used Knudsen diffusion, overestimates the diffusion of bulky molecules in the mesopores, thus making MD simulation a powerful and compulsory approach to explore diffusion in zeolites.« less
Single-Molecule Detection in Micron-Sized Capillaries

NASA Astrophysics Data System (ADS)

Ball, David A.; Shen, Guoqing; Davis, Lloyd M.

2004-11-01

The detection of individual molecules in solution by laser-induced fluorescence is becoming an increasingly important tool for biophysics research and biotechnology applications. In a typical single-molecule detection (SMD) experiment, diffusion is the dominant mode of transport of fluorophores through the focused laser beam. In order to more rapidly process a large number of slowly diffusing bio-molecules for applications in pharmaceutical drug discovery, a flow can be introduced within a capillary. If the flow speed is sufficient, bio-molecules will be carried through the probe volume significantly faster than by diffusion alone. Here we discuss SMD near the tip of, and in, such micron-sized capillaries, with a high numerical-aperture microscope objective used for confocal-epi-illumination along the axis of the capillary. Problems such as molecular adsorption to the glass are also addressed.
Random walk on a leash: a simple single-molecule diffusion model for surface-tethered redox molecules with flexible linkers.

PubMed

Huang, Kuan-Chun; White, Ryan J

2013-08-28

We develop a random walk model to simulate the Brownian motion and the electrochemical response of a single molecule confined to an electrode surface via a flexible molecular tether. We use our simple model, which requires no prior knowledge of the physics of the molecular tether, to predict and better understand the voltammetric response of surface-confined redox molecules when motion of the redox molecule becomes important. The single molecule is confined to a hemispherical volume with a maximum radius determined by the flexible molecular tether (5-20 nm) and is allowed to undergo true three-dimensional diffusion. Distance- and potential-dependent electron transfer probabilities are evaluated throughout the simulations to generate cyclic voltammograms of the model system. We find that at sufficiently slow cyclic voltammetric scan rates the electrochemical reaction behaves like an adsorbed redox molecule with no mass transfer limitation; thus, the peak current is proportional to the scan rate. Conversely, at faster scan rates the diffusional motion of the molecule limits the simulated peak current, which exhibits a linear dependence on the square root of the scan rate. The switch between these two limiting regimes occurs when the diffusion layer thickness, (2Dt)(1/2), is ~10 times the tether length. Finally, we find that our model predicts the voltammetric behavior of a redox-active methylene blue tethered to an electrode surface via short flexible single-stranded, polythymine DNAs, allowing the estimation of diffusion coefficients for the end-tethered molecule.
Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

2018-03-01

We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.
Characterization of the organic ligand shell of semiconductor quantum dots by fluorescence quenching experiments.

PubMed

Boldt, Klaus; Jander, Sebastian; Hoppe, Kathrin; Weller, Horst

2011-10-25

We present the characterization of the organic ligand shell of CdSe/Cd(x)Zn(1-x)S/ZnS nanoparticles by means of fluorescence quenching experiments. Both electron scavengers and acceptors for resonance energy transfer were employed as probes. Different quenching behavior for short and long chain thiol ligands in water was found. It could be shown that poly(ethylene oxide) (PEO)-capping of the particles comprises a densely packed inner shell and a loosely packed outer shell in which ions and small molecules diffuse unhindered. A quantitative uptake of quencher molecules into the PEO shell was observed, through which the particle volume including the ligand sphere could be determined.
Transport dynamics -- one particle at a time

NASA Astrophysics Data System (ADS)

Granick, Steve

2010-03-01

By watching particles and molecules diffuse, one-by-one, the full displacement probability distribution can be measured, enabling one to see experimentally how, how fast, and with what fidelity to classical assumptions, particles and molecules diffuse through complex environments. This allows us to measuring the confining tube potential through which thin actin filaments reptate, and also some of the amazing differences in diffusion rate between colloidal particles and phospholipid vesicles of the same size. Pervasively, we find that Brownian diffusion can be non-Gaussian.
Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics

PubMed Central

2018-01-01

Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard–Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell–Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer (J. Phys. Chem. B, 2004, 108, 15873−15879). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard–Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell–Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell–Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations. PMID:29664633
Computer Simulations of Small Molecules in Membranes: Insights from Computer Simulations into the Interactions of Small Molecules with Lipid Bilayers

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; New, Michael H.; Schweighofer, Karl; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

Two of Ernest Overton's lasting contributions to biology are the Meyer-Overton relationship between the potency of an anesthetic and its solubility in oil, and the Overton rule which relates the permeability of a membrane to the oil-water partition coefficient of the permeating molecule. A growing body of experimental evidence, however, cannot be reconciled with these theories. In particular, the molecular nature of membranes, unknown to Overton, needs to be included in any description of these phenomena. Computer simulations are ideally suited for providing atomic-level information about the behavior of small molecules in membranes. The authors discuss simulation studies relevant to Overton's ideas. Through simulations it was found that anesthetics tend to concentrate at interfaces and their anesthetic potency correlates better with solubility at the water-membrane interface than with solubility in oil. Simulation studies of membrane permeation revealed the anisotropic nature of the membranes, as evidenced, for example, by the highly nonuniform distribution of free volume in the bilayer. This, in turn, influences the diffusion rates of solutes, which increase with the depth in the membrane. Small solutes tend to move by hopping between voids in the bilayer, and this hopping motion may be responsible for the deviation from the Overton rule of the permeation rates of these molecules.
Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F(1)-ATPase.

PubMed

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-19

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F(1), which is a component of F(o)F(1) adenosine triphosphate synthase. We discuss the energetic properties of F(1) and identify a high energy barrier of the rotary potential to be 20k(B)T, with the condition that the adenosine diphosphates are tightly bound to the F(1) catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.
Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F1-ATPase

NASA Astrophysics Data System (ADS)

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-01

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F1 , which is a component of Fo F1 adenosine triphosphate synthase. We discuss the energetic properties of F1 and identify a high energy barrier of the rotary potential to be 20 kBT , with the condition that the adenosine diphosphates are tightly bound to the F1 catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.
Characterization of water molecular state in in-vivo thick tissues using diffuse optical spectroscopic imaging

NASA Astrophysics Data System (ADS)

Chung, So Hyun

Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. A bound water index (BWI) was developed that quantifies the spectral shift and shape changes observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopic imaging (DOSI). DOSI quantitatively measures light absorption and scattering spectra in cm-deep tissues and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOSI to MRI and a conductivity cell using bound water phantoms. Non-invasive BWI measurements of malignant and normal tissues in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p<0.0001) compared to normal tissues. BWI showed potential as a prognostic index based on high correlations with tumor grade and size. An algorithm for absolute temperature measurements in deep tissues was developed based on resolving opposing effects of water vibrational frequency shifts due to macromolecular binding. DOSI measures absolute temperature with a difference of 1.1+/-0.91°C from a thermistor. Deep tissue temperature measured in forearms during cold-stress was consistent with previously reported invasively-measured deep tissue temperature. Finally, the BWI was compared to Apparent Diffusion Coefficient (ADC) of diffusion weighted MRI in 9 breast cancer patients. The BWI and ADC correlated (R=0.8, p=<0.01) and both parameters decreased with increasing bulk water content in cancer tissues. Although BWI and ADC are positively correlated in vivo, BWI appears to be more sensitive to free water in the extracellular matrix while ADC reflects increased tumor cellularity. The relationship between ADC, BWI and bulk water concentration suggests that both parameters have potential for assessing tumor histopathological grade. My results confirm the importance of water as a critical tissue component that can potentially provide unique insight into the molecular pathophysiology of cancer.
Radical-induced chemistry from VUV photolysis of interstellar ice analogues containing formaldehyde

NASA Astrophysics Data System (ADS)

Butscher, Teddy; Duvernay, Fabrice; Danger, Grégoire; Chiavassa, Thierry

2016-09-01

Surface processes and radical chemistry within interstellar ices are increasingly suspected to play an important role in the formation of complex organic molecules (COMs) observed in several astrophysical regions and cometary environments. We present new laboratory experiments on the low-temperature solid state formation of complex organic molecules - glycolaldehyde, ethylene glycol, and polyoxymethylene - through radical-induced reactivity from VUV photolysis of formaldehyde in water-free and water-dominated ices. Radical reactivity and endogenous formation of COMs were monitored in situ via infrared spectroscopy in the solid state and post photolysis with temperature programmed desorption (TPD) using a quadripole mass spectrometer. We show the ability of free radicals to be stored when formed at low temperature in water-dominated ices, and to react with other radicals or on double bonds of unsaturated molecules when the temperature increases. It experimentally confirms the role of thermal diffusion in radical reactivity. We propose a new pathway for formaldehyde polymerisation induced by HCO radicals that might explain some observations made by the Ptolemy instrument on board the Rosetta lander Philae. In addition, our results seem to indicate that H-atom additions on H2CO proceed preferentially through CH2OH intermediate radicals rather than the CH3O radical.

Diffuse X-ray scattering from benzil, C(14)H(10)O(2): analysis via automatic refinement of a Monte Carlo model.

PubMed

Welberry, T R; Goossens, D J; Edwards, A J; David, W I

2001-01-01

A recently developed method for fitting a Monte Carlo computer-simulation model to observed single-crystal diffuse X-ray scattering has been used to study the diffuse scattering in benzil, diphenylethanedione, C(6)H(5)-CO-CO-C(6)H(5). A model involving 13 parameters consisting of 11 intermolecular force constants, a single intramolecular torsional force constant and a local Debye-Waller factor was refined to give an agreement factor, R = [summation operator omega(Delta I)(2)/summation operator omega I(obs)(2)](1/2), of 14.5% for 101,324 data points. The model was purely thermal in nature. The analysis has shown that the diffuse lines, which feature so prominently in the observed diffraction patterns, are due to strong longitudinal displacement correlations. These are transmitted from molecule to molecule via a network of contacts involving hydrogen bonding of an O atom on one molecule and the para H atom of the phenyl ring of a neighbouring molecule. The analysis also allowed the determination of a torsional force constant for rotations about the single bonds in the molecule. This is the first diffuse scattering study in which measurement of such internal molecular torsion forces has been attempted.
Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

DOE PAGES

Zarzycki, Piotr; Gilbert, Benjamin

2016-04-27

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short-and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without externalmore » water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.« less
Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

PubMed Central

Zarzycki, Piotr; Gilbert, Benjamin

2016-01-01

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species. PMID:27118164
Radial inhomogeneities in particle composition of single, levitated aerosol particles observed by Mie resonance spectroscopy (Invited)

NASA Astrophysics Data System (ADS)

Krieger, U. K.; Steimer, S.; Lienhard, D.; Bastelberger, S.

2013-12-01

Recent observations have indicated that organic aerosol particles in the atmosphere may exist in an amorphous semi-solid or even solid (i.e. glassy) state, e.g. [1]. The influence of highly viscous and glassy states on the timescale of aerosol particle equilibration with respect to water vapor have been investigated for some model systems of atmospheric aerosol, e.g. [2,3]. In particular, it has been shown that the kinetics of the water absorption/desorption process is controlled entirely by liquid-phase diffusion of water molecules for a highly viscous aerosol particle. A liquid phase diffusion model based on numerically solving the non-linear diffusion equation predicts strong internal gradients in water concentration when condensed phase diffusion impedes the water uptake from the gas phase [2]. Here we observe and quantify the internal concentration gradients in single, levitated, micron size aerosol particles of aqueous MBTCA (3-methyl-1,2,3-Butanetricarboxylic acid) and shikimic acid using elastic Mie resonance spectroscopy. A single, aqueous particle is levitated in an electro-dynamic balance (for details see [2]), dried for several days at room temperature, cooled to the target temperature and exposed to a rapid change in relative humidity. In addition to measuring the elastically backscattered light of a 'white light ' LED source and recording the full spectrum with a spectrograph as in [2], we use a tunable diode laser (TDL) to scan high resolution TE- and TM spectra. This combination allows observing various Mie resonance mode orders simultaneously. Since we perform the experiment at low temperatures and low humidities the changes in the Mie-spectra due to water uptake are sufficiently slow to resolve the kinetics. Experimental Mie resonance spectra are inverted to concentration profiles of water within the particle by applying the numerical diffusion model [2] in conjunction with Mie calculations of multilayered spheres [4]. Potential implications for gas to particle partitioning and heterogeneous chemistry are discussed. [1] A. Virtanen et al. (2010): An amorphous solid state of biogenic secondary organic aerosol particles, Nature 467, 824-827. [2] B. Zobrist et al. (2011): Ultra-slow water diffusion in aqueous sucrose glasses, Phys. Chem. Chem. Phys. 13, 3514-3526. [3] D. L. Bones, J. P. Reid, D. M. Lienhard, and U. K. Krieger (2012): Comparing the mechanism of water condensation and evaporation in glassy aerosol, PNAS 109, 11613-11618. [4] O. Peña and U. Pal (2009): Scattering of electromagnetic radiation by a multilayered sphere, Comput. Phys. Commun. 180, 2348-2354.
Chirality Differentiation by Diffusion in Chiral Nematic Liquid Crystals

NASA Astrophysics Data System (ADS)

Jiang, Jinghua; Yang, Deng-Ke

2017-01-01

Chirality is of great importance in the living world. It helps differentiate biochemical reactions such as those that take place during digestion. It may also help differentiate physical processes such as diffusion. Aiming to study the latter effect, we investigate the diffusion of guest chiral molecules in chiral nematic (cholesteric) liquid-crystal hosts. We discover that the diffusion dramatically depends on the handedness of the guest and host molecules and the chiral differentiation is greatly enhanced by the proper alignment of the liquid-crystal host. The diffusion of a guest chiral molecule in a chiral host with the same handedness is much faster than in a chiral host with opposite handedness. We also observe that the differentiation of chirality depends on the diffusion direction with respect to the twisting direction (helical axis). These results might be important in understanding effects of chirality on physical processes that take place in biological organisms. In addition, this effect could be utilized for enantiomer separation.
Observation of Spectral Diffusion in Crystals Using Single Impurity Molecules

DTIC Science & Technology

1990-10-31

from 12pentacene photophysical parameters including intersystem crossing . Apparently (and not surprisingly), the local pentacene environment this... pentacene molecules inp-terphenyl, both stable as well as spectrally diffusing single molecules can be observed. 20 DISTRIBUTION/AVAILABILITY OF ABSTRACT 121...with ultrathin sublimed crystals have removed this obstacle. For the case of pentacene impurities in crystals of p-terphenyl, we observe two radically
Coupling of the hydration water dynamics and the internal dynamics of actin detected by quasielastic neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujiwara, Satoru, E-mail: fujiwara.satoru@jaea.go.jp; Plazanet, Marie; Oda, Toshiro

2013-02-15

Highlights: ► Quasielastic neutron scattering spectra of F-actin and G-actin were measured. ► Analysis of the samples in D{sub 2}O and H{sub 2}O provided the spectra of hydration water. ► The first layer hydration water around F-actin is less mobile than around G-actin. ► This difference in hydration water is in concert with the internal dynamics of actin. ► Water outside the first layer behaves bulk-like but influenced by the first layer. -- Abstract: In order to characterize dynamics of water molecules around F-actin and G-actin, quasielastic neutron scattering experiments were performed on powder samples of F-actin and G-actin, hydratedmore » either with D{sub 2}O or H{sub 2}O, at hydration ratios of 0.4 and 1.0. By combined analysis of the quasielastic neutron scattering spectra, the parameter values characterizing the dynamics of the water molecules in the first hydration layer and those of the water molecules outside of the first layer were obtained. The translational diffusion coefficients (D{sub T}) of the hydration water in the first layer were found to be 1.2 × 10{sup −5} cm{sup 2}/s and 1.7 × 10{sup −5} cm{sup 2}/s for F-actin and G-actin, respectively, while that for bulk water was 2.8 × 10{sup −5} cm{sup 2}/s. The residence times were 6.6 ps and 5.0 ps for F-actin and G-actin, respectively, while that for bulk water was 0.62 ps. These differences between F-actin and G-actin, indicating that the hydration water around G-actin is more mobile than that around F-actin, are in concert with the results of the internal dynamics of F-actin and G-actin, showing that G-actin fluctuates more rapidly than F-actin. This implies that the dynamics of the hydration water is coupled to the internal dynamics of the actin molecules. The D{sub T} values of the water molecules outside of the first hydration layer were found to be similar to that of bulk water though the residence times are strongly affected by the first hydration layer. This supports the recent observation on intracellular water that shows bulk-like behavior.« less
Hyper alginate gel microbead formation by molecular diffusion at the hydrogel/droplet interface.

PubMed

Hirama, Hirotada; Kambe, Taisuke; Aketagawa, Kyouhei; Ota, Taku; Moriguchi, Hiroyuki; Torii, Toru

2013-01-15

We report a simple method for forming monodispersed, uniformly shaped gel microbeads with precisely controlled sizes. The basis of our method is the placement of monodispersed sodium alginate droplets, formed by a microfluidic device, on an agarose slab gel containing a high-osmotic-pressure gelation agent (CaCl(2) aq.): (1) the droplets are cross-linked (gelated) due to the diffusion of the gelation agent from the agarose slab gel to the sodium alginate droplets and (2) the droplets simultaneously shrink to a fraction of their original size (<100 μm in diameter) due to the diffusion of water molecules from the sodium alginate droplets to the agarose slab gel. We verified the mass transfer mechanism between the droplet and the agarose slab gel. This method circumvents the limitations of gel microbead formation, such as the need to prepare microchannels of various sizes, microchannel clogging, and the deformation of the produced gel microbeads.
The Controversial Role of Inter-diffusion in Glass Alteration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gin, Stephane; Neill, Lindsay; Fournier, M.

2016-11-15

Current kinetic models for nuclear waste glasses (e.g. GM2001, GRAAL) are based on a set of mechanisms that have been generally agreed upon within the international waste glass community. These mechanisms are: hydration of the glass, ion exchange reactions (the two processes are referred as inter-diffusion), hydrolysis of the silicate network, and condensation/precipitation of partly or completely hydrolyzed species that produces a porous and amorphous layer and crystalline phases on surface of the altered glass. Recently, a new idea with origins in the mineral dissolution community has been proposed that excludes inter-diffusion process as a potential rate-limiting mechanism. To understandmore » how the so-called interfacial dissolution/precipitation model can change the current understanding of glass behavior, a key experiment used to account for this model was replicated to further revisit the interpretation. This experiment was performed at 50°C, with SON68 glass, in static mode, deionized water and S/V ratio of 10 m-1 for 6 months. It turn out that glass alters in an intermediate kinetic regime between the forward and the residual rate. According to previous and new solid characterizations, it is concluded that neither a simple inter-diffusion model nor the interfacial dissolution precipitation model can account for the observed elemental profiles within the alteration layer. More generally, far and close-to-saturation conditions must be distinguished and literature provides evidences that inter-diffusion takes place in slightly acidic conditions and far from saturation. However, closer to saturation, when a sufficiently dense layer is formed, a new approach is proposed requiring a full description of chemical reactions taking place within the alteration layer and involving water molecules as it is thought that water accessibility to the pristine glass is the rate-limiting process.« less
Wet model of Saturn's ionosphere: Water from the rings

NASA Technical Reports Server (NTRS)

Connerney, J. E. P.; Waite, J. H.

1984-01-01

Current theoretical models of Saturn's ionosphere are difficult to reconcile with the ionospheric electron density profiles obtained from the Pioneer and Voyager radio occultation observations and the large diurnal variation of maximum ionospheric electron density deduced from studies of Saturn lightning discharges. A model of Saturn's ionosphere is proposed in which water plays a major role as a minor constituent present by virtue of downward diffusion from an external source. This model of the Saturn ionosphere is a classical 'F2' type layer resulting from the photodissociative production of H(+) from H2 and rapid chemical loss due to a series of charge exchange reactions with water. A planet-wide influx of about 4x10 to the 7th power molecules/sec/sq cm of water from the rings is consistent with the observed ionospheric electron densities and estimates of influx due to micrometeoride bombardment of the rings. An enhanced influx of water occurs at latitudes (-38 deg, +44 deg) magnetically connected to the inner edge of Saturn's B ring which results from an electromagnetic erosion process contributing substantially to the (local) upper atmosphere water content. Present day influx at these latitudes is possibly as large as 2x10 to the 9th power molecules/sec/sq cm.
Organization and mobility of water in amorphous and crystalline trehalose

NASA Astrophysics Data System (ADS)

Kilburn, Duncan; Townrow, Sam; Meunier, Vincent; Richardson, Robert; Alam, Ashraf; Ubbink, Job

2006-08-01

The disaccharide trehalose is accumulated by microorganisms, such as yeasts, and multicellular organisms, such as tardigrades, when conditions of extreme drought occur. In this way these organisms can withstand dehydration through the formation of an intracellular carbohydrate glass, which, with its high viscosity and hydrogen-bonding interactions, stabilizes and protects the integrity of complex biological structures and molecules. This property of trehalose can also be harnessed in the stabilization of liposomes, proteins and in the preservation of red blood cells, but the underlying mechanism of bioprotection is not yet fully understood. Here we use positron annihilation lifetime spectroscopy to probe the free volume of trehalose matrices; specifically, we develop a molecular picture of the organization and mobility of water in both amorphous and crystalline states. Whereas in amorphous matrices, water increases the average intermolecular hole size, in the crystalline dihydrate it is organized as a confined one-dimensional fluid in channels of fixed diameter that allow activated diffusion of water in and out of the crystallites. We present direct real-time evidence of water molecules unloading reversibly from these channels, thereby acting as both a sink and a source of water in low-moisture systems. We postulate that this behaviour may provide the overall stability required to keep organisms viable through dehydration conditions.
Resolving Fast, Confined Diffusion in Bacteria with Image Correlation Spectroscopy.

PubMed

Rowland, David J; Tuson, Hannah H; Biteen, Julie S

2016-05-24

By following single fluorescent molecules in a microscope, single-particle tracking (SPT) can measure diffusion and binding on the nanometer and millisecond scales. Still, although SPT can at its limits characterize the fastest biomolecules as they interact with subcellular environments, this measurement may require advanced illumination techniques such as stroboscopic illumination. Here, we address the challenge of measuring fast subcellular motion by instead analyzing single-molecule data with spatiotemporal image correlation spectroscopy (STICS) with a focus on measurements of confined motion. Our SPT and STICS analysis of simulations of the fast diffusion of confined molecules shows that image blur affects both STICS and SPT, and we find biased diffusion rate measurements for STICS analysis in the limits of fast diffusion and tight confinement due to fitting STICS correlation functions to a Gaussian approximation. However, we determine that with STICS, it is possible to correctly interpret the motion that blurs single-molecule images without advanced illumination techniques or fast cameras. In particular, we present a method to overcome the bias due to image blur by properly estimating the width of the correlation function by directly calculating the correlation function variance instead of using the typical Gaussian fitting procedure. Our simulation results are validated by applying the STICS method to experimental measurements of fast, confined motion: we measure the diffusion of cytosolic mMaple3 in living Escherichia coli cells at 25 frames/s under continuous illumination to illustrate the utility of STICS in an experimental parameter regime for which in-frame motion prevents SPT and tight confinement of fast diffusion precludes stroboscopic illumination. Overall, our application of STICS to freely diffusing cytosolic protein in small cells extends the utility of single-molecule experiments to the regime of fast confined diffusion without requiring advanced microscopy techniques. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Trapping gases in metal-organic frameworks with a selective surface molecular barrier layer

DOE PAGES

Tan, Kui; Zuluaga, Sebastian; Fuentes, Erika; ...

2016-12-13

The main challenge for gas storage and separation in nanoporous materials is that many molecules of interest adsorb too weakly to be effectively retained. Instead of synthetically modifying the internal surface structure of the entire bulk—as is typically done to enhance adsorption—here we show that post exposure of a prototypical porous metal-organic framework to ethylenediamine can effectively retain a variety of weakly adsorbing molecules (for example, CO, CO 2, SO 2, C 2H 4, NO) inside the materials by forming a monolayer-thick cap at the external surface of microcrystals. Furthermore, this capping mechanism, based on hydrogen bonding as explained bymore » ab initio modelling, opens the door for potential selectivity. For example, water molecules are shown to disrupt the hydrogen-bonded amine network and diffuse through the cap without hindrance and fully displace/release the retained small molecules out of the metal-organic framework at room temperature. Lastly, these findings may provide alternative strategies for gas storage, delivery and separation.« less
Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.
Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Derek D.; Greenfield, Michael L., E-mail: greenfield@egr.uri.edu

2014-01-21

The dynamics properties of a new “next generation” model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxationmore » rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ∼42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.« less
Interactions between water and 1-butyl-1-methylpyrrolidinium ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fadeeva, Tatiana A.; DeVine, Jessalyn A.; Castner, Edward W., E-mail: ed.castner@rutgers.edu

2015-08-14

We report experimental results on the diffusivity of water in two ionic liquids obtained using the pulsed-gradient spin-echo NMR method. Both ionic liquids have the same cation, 1-butyl-1-methylpyrrolidinium, but different trifluoromethyl-containing anions. One has a strongly hydrophobic anion, bis(trifluoromethylsulfonyl)amide, while the second has a hydrophilic anion, trifluoromethylsulfonate. Transport of water in these ionic liquids is much faster than would be predicted from hydrodynamic laws, indicating that the neutral water molecules experience a very different friction than the anions and cations at the molecular level. Temperature-dependent viscosities, conductivities, and densities are reported as a function of water concentration to further analyzemore » the properties of the ionic liquid-water mixtures. These results on the properties of water in ionic liquids should be of interest to researchers in diverse areas ranging from separations, solubilizing biomass and energy technologies.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Lv, Chao; Aitchison, Erick W.; Wu, Dongsheng

Hydrogen sulfide (H 2S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H 2S and its structural analogue, water (H 2O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. Here, as revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is,more » the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H 2S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. Lastly, this study not only explains why H 2S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes.« less
Catalytic combustion of styrene over copper based catalyst: inhibitory effect of water vapor.

PubMed

Pan, Hongyan; Xu, Mingyao; Li, Zhong; Huang, Sisi; He, Chun

2009-07-01

The effects of water vapor on the activity of the copper based catalysts with different supports such as CuO/gamma-Al2O3, CuO/SiO2 and CuO/TiO2 for styrene combustion were investigated. The catalytic activity of the catalysts was tested in the absence of and presence of water vapor and the catalysts were characterized. Temperature programmed desorption (TPD) experiments and diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) measurements were conducted in order to estimate and explain the water effects. Results showed that the existence of water vapor had a significant negative effect on the catalytic activity of these copper based catalysts due to the competition adsorption of water molecule. DRIFTS studies showed that the catalyst CuO/gamma-Al2O3 had the strongest adsorption of water, while the catalyst CuO/TiO2 had the weakest adsorption of water. H2O-TPD studies also indicated that the order of desorption activation energies of water vapor on the catalysts or the strength of interactions of water molecules with the surfaces of the catalysts was CuO/gamma-Al2O3>CuO/SiO2>CuO/TiO2. As a consequence of that, the CuO/TiO2 exhibited the better durability to water vapor, while CuO/gamma-Al2O3 had the poorest durability to water vapor among these three catalysts.
Effects of Orientation and Anisometry of Magnetic Resonance Imaging Acquisitions on Diffusion Tensor Imaging and Structural Connectomes.

PubMed

Tudela, Raúl; Muñoz-Moreno, Emma; López-Gil, Xavier; Soria, Guadalupe

2017-01-01

Diffusion-weighted imaging (DWI) quantifies water molecule diffusion within tissues and is becoming an increasingly used technique. However, it is very challenging as correct quantification depends on many different factors, ranging from acquisition parameters to a long pipeline of image processing. In this work, we investigated the influence of voxel geometry on diffusion analysis, comparing different acquisition orientations as well as isometric and anisometric voxels. Diffusion-weighted images of one rat brain were acquired with four different voxel geometries (one isometric and three anisometric in different directions) and three different encoding orientations (coronal, axial and sagittal). Diffusion tensor scalar measurements, tractography and the brain structural connectome were analyzed for each of the 12 acquisitions. The acquisition direction with respect to the main magnetic field orientation affected the diffusion results. When the acquisition slice-encoding direction was not aligned with the main magnetic field, there were more artifacts and a lower signal-to-noise ratio that led to less anisotropic tensors (lower fractional anisotropic values), producing poorer quality results. The use of anisometric voxels generated statistically significant differences in the values of diffusion metrics in specific regions. It also elicited differences in tract reconstruction and in different graph metric values describing the brain networks. Our results highlight the importance of taking into account the geometric aspects of acquisitions, especially when comparing diffusion data acquired using different geometries.
Evaporation enhancement in soils: a critical review

NASA Astrophysics Data System (ADS)

Rutten, Martine; van de Giesen, Nick

2015-04-01

Temperature gradients in the top layer of the soil are, especially during the daytime, steeper than would be expected if thermal conduction was the primary heat transfer mechanism. Evaporation seems to have significant influence on the soil heat budget. Only part of the surface soil heat flux is conducted downwards, increasing the soil temperatures, and part is used for evaporation, acting as a sink to the soil heat budget. For moist soils, the evaporation is limited by the transport of water molecules to the surface. The classical view is that water vapor is transported from the evaporation front to the surface by diffusion. Diffusion is mixing due to the random movement of molecules resulting in flattening concentration gradients. In soil, the diffusive vapor flux and the resulting latent heat flux are generally small. We found that transport enhancement is necessary in order to sustain vapor fluxes that are large enough to sustain latent heat fluxes, as well as being large enough to explain the observed temperature gradients. Enhancement of vapor diffusion is a known phenomenon, subject to debate on the explanations of underlying mechanism. In an extensive literature review on vapor enhancement in soils, the plausibility of various mechanisms was assessed. We reviewed mechanisms based on (combinations of) diffusive, viscous, buoyant, capillary and external pressure forces including: thermodiffusion, dispersion, Stefan's flow, Knudsen diffusion, liquid island effect, hydraulic lift, free convection, double diffusive convection and forced convection. The analysis of the order of magnitude of the mechanisms based on first principles clearly distinguished between plausible and implausible mechanisms. Thermodiffusion, Stefan's flow, Knudsen effects, liquid islands do not significantly contribute to enhanced evaporation. Double diffusive convection seemed unlikely due to lack of experimental evidence, but could not be completely excluded from the list of potential mechanisms. Hydraulic lift, the mechanism that small capillaries lift liquid water to the surface where it evaporates, does significantly contribute to enhanced evaporation from soils, also from dryer soils. The experimental evidence for and the theoretical underpinnings of this mechanism are convincing. However, we sought mechanisms that both explain enhanced evaporation and steep temperature gradients in the soil during the daytime. These often observed gradients consist of a sharp decrease of temperature with a depth up to the depth of the evaporation front. Hydraulic lift cannot explain this because the evaporation front is located at the surface. One remaining mechanism is forced convection due to atmospheric pressure fluctuations, also referred to as wind pumping. Wind pumping causes displacement and flow velocities too small for significant convective and too small for significant dispersive transport, when steady state dispersion formulations are used. However, experiments do indicate significant dispersive transport that can be explained by dispersion under unsteady flow conditions. Forced convection due to pressure fluctuations seems to be the only mechanism that can explain both enhanced evaporation and the steep temperature gradients.

Classification of Dynamical Diffusion States in Single Molecule Tracking Microscopy

PubMed Central

Bosch, Peter J.; Kanger, Johannes S.; Subramaniam, Vinod

2014-01-01

Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins. PMID:25099798
Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes.

PubMed

Hernandez-Perez, Ruth; García-Cordero, José L; Escobar, Juan V

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.
Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes

NASA Astrophysics Data System (ADS)

Hernandez-Perez, Ruth; García-Cordero, José L.; Escobar, Juan V.

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.
Molecular dimensions and surface diffusion assisted mechanically robust slippery perfluoropolyether impregnated mesoporous alumina interfaces

NASA Astrophysics Data System (ADS)

Rowthu, Sriharitha; Balic, Edin E.; Hoffmann, Patrik

2017-12-01

Accomplishing mechanically robust omniphobic surfaces is a long-existing challenge, and can potentially find applications in bioengineering, tribology and paint industries. Slippery liquid impregnated mesoporous α-Al2O3 interfaces are achieved with water, alkanes, water based and oil based high viscosity acrylic paints. Incredibly high abrasion-resistance (wear coefficients ≤10-8 mm3 N-1 m-1) and ultra-low friction coefficients (≥0.025) are attained, attributing to the hard alumina matrix and continuous replenishment of perfluoropolyether aided by capillarity and surface diffusion processes. A variety of impregnating liquids employed suggest that large molecules, faster surface diffusion and lowest evaporation rate generate the rare combination of high wear-resistance and omniphobicity. It is noteworthy that these novel liquid impregnated Al2O3 composites exhibit outstanding load bearing capacity up to 350 MPa; three orders of magnitude higher than achievable by the state of the art omniphobic surfaces. Further, our developed thermodynamic calculations suggest that the relative thermodynamic stability of liquid impregnated composites is linearly proportional to the spreading coefficient (S) of the impregnating liquid with the matrix material and is an important tool for the selection of an appropriate matrix material for a given liquid.
Calixarene cleansing formulation for uranium skin contamination.

PubMed

Phan, Guillaume; Semili, Naïma; Bouvier-Capely, Céline; Landon, Géraldine; Mekhloufi, Ghozlene; Huang, Nicolas; Rebière, François; Agarande, Michelle; Fattal, Elias

2013-10-01

An oil-in-water cleansing emulsion containing calixarene molecule, an actinide specific chelating agent, was formulated in order to improve the decontamination of uranium from the skin. Commonly commercialized cosmetic ingredients such as surfactants, mineral oil, or viscosifying agents were used in preparing the calixarene emulsion. The formulation was characterized in terms of size and apparent viscosity measurements and then was tested for its ability to limit uranyl ion permeation through excoriated pig-ear skin explants in 24-h penetration studies. Calixarene emulsion effectiveness was compared with two other reference treatments consisting of DTPA and EHBP solutions. Application of calixarene emulsion induced the highest decontamination effect with an 87% decrease in uranium diffusion flux. By contrast, EHBP and DTPA solutions only allowed a 50% and 55% reduction of uranium permeation, respectively, and had the same effect as a simple dilution of the contamination by pure water. Uranium diffusion decrease was attributed to uranyl ion-specific chelation by calixarene within the formulation, since no significant effect was obtained after application of the same emulsion without calixarene. Thus, calixarene cleansing emulsion could be considered as a promising treatment in case of accidental contamination of the skin by highly diffusible uranium compounds.
How amide hydrogens exchange in native proteins.

PubMed

Persson, Filip; Halle, Bertil

2015-08-18

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.
How amide hydrogens exchange in native proteins

PubMed Central

Persson, Filip; Halle, Bertil

2015-01-01

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754
Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

NASA Astrophysics Data System (ADS)

Varfolomeeva, Vera V.; Terentev, Alexey V.

2018-01-01

Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.
Influence of molecular shape, conformability, net surface charge, and tissue interaction on transscleral macromolecular diffusion.

PubMed

Srikantha, Nishanthan; Mourad, Fatma; Suhling, Klaus; Elsaid, Naba; Levitt, James; Chung, Pei Hua; Somavarapu, Satyanarayana; Jackson, Timothy L

2012-09-01

The purpose of this study was to investigate the influence of molecular shape, conformability, net surface charge and tissue interaction on transscleral diffusion. Unfixed, porcine sclera was clamped in an Ussing chamber. Fluorophore-labelled neutral albumin, neutral dextran, or neutral ficoll were placed in one hemi-chamber and the rate of transscleral diffusion was measured over 24 h using a spectrophotometer. Experiments were repeated using dextrans and ficoll with positive or negative net surface charges. Fluorescence recovery after photobleaching (FRAP) was undertaken to compare transscleral diffusion with diffusion through a solution. All molecules were 70 kDa. With FRAP, the diffusion coefficient (D) of neutral molecules was highest for albumin, followed by ficoll, then dextran (p < 0.0001). Positive dextrans diffused fastest, followed by negative, then neutral dextrans (p = 0.0004). Neutral ficoll diffused the fastest, followed by positive then negative ficoll (p = 0.5865). For the neutral molecules, transscleral D was highest for albumin, followed by dextran, then ficoll (p < 0.0001). D was highest for negative ficoll, followed by neutral, then positive ficoll (p < 0.0001). By contrast, D was highest for positive dextran, followed by neutral, then negative dextran (p = 0.0021). In conclusion, diffusion in free solution does not predict transscleral diffusion and the molecular-tissue interaction is important. Molecular size, shape, and charge may all markedly influence transscleral diffusion, as may conformability to a lesser degree, but their effects may be diametrically opposed in different molecules, and their influence on diffusion is more complex than previously thought. Each variable cannot be considered in isolation, and the interplay of all these variables needs to be tested, when selecting or designing drugs for transscleral delivery. Copyright © 2012 Elsevier Ltd. All rights reserved.
Hydraulic fracturing in cells and tissues: fracking meets cell biology.

PubMed

Arroyo, Marino; Trepat, Xavier

2017-02-01

The animal body is largely made of water. A small fraction of body water is freely flowing in blood and lymph, but most of it is trapped in hydrogels such as the extracellular matrix (ECM), the cytoskeleton, and chromatin. Besides providing a medium for biological molecules to diffuse, water trapped in hydrogels plays a fundamental mechanical role. This role is well captured by the theory of poroelasticity, which explains how any deformation applied to a hydrogel causes pressure gradients and water flows, much like compressing a sponge squeezes water out of it. Here we review recent evidence that poroelastic pressures and flows can fracture essential biological barriers such as the nuclear envelope, the cellular cortex, and epithelial layers. This type of fracture is known in engineering literature as hydraulic fracturing or 'fracking'. Copyright © 2016 Elsevier Ltd. All rights reserved.
CO Diffusion and Desorption Kinetics in CO2 Ices

NASA Astrophysics Data System (ADS)

Cooke, Ilsa R.; Öberg, Karin I.; Fayolle, Edith C.; Peeler, Zoe; Bergner, Jennifer B.

2018-01-01

The diffusion of species in icy dust grain mantles is a fundamental process that shapes the chemistry of interstellar regions; yet, measurements of diffusion in interstellar ice analogs are scarce. Here we present measurements of CO diffusion into CO2 ice at low temperatures (T = 11–23 K) using CO2 longitudinal optical phonon modes to monitor the level of mixing of initially layered ices. We model the diffusion kinetics using Fick’s second law and find that the temperature-dependent diffusion coefficients are well fit by an Arrhenius equation, giving a diffusion barrier of 300 ± 40 K. The low barrier along with the diffusion kinetics through isotopically labeled layers suggest that CO diffuses through CO2 along pore surfaces rather than through bulk diffusion. In complementary experiments, we measure the desorption energy of CO from CO2 ices deposited at 11–50 K by temperature programmed desorption and find that the desorption barrier ranges from 1240 ± 90 K to 1410 ± 70 K depending on the CO2 deposition temperature and resultant ice porosity. The measured CO–CO2 desorption barriers demonstrate that CO binds equally well to CO2 and H2O ices when both are compact. The CO–CO2 diffusion–desorption barrier ratio ranges from 0.21 to 0.24 dependent on the binding environment during diffusion. The diffusion–desorption ratio is consistent with the above hypothesis that the observed diffusion is a surface process and adds to previous experimental evidence on diffusion in water ice that suggests surface diffusion is important to the mobility of molecules within interstellar ices.
Surface transport mechanisms in molecular glasses probed by the exposure of nano-particles

NASA Astrophysics Data System (ADS)

Ruan, Shigang; Musumeci, Daniele; Zhang, Wei; Gujral, Ankit; Ediger, M. D.; Yu, Lian

2017-05-01

For a glass-forming liquid, the mechanism by which its surface contour evolves can change from bulk viscous flow at high temperatures to surface diffusion at low temperatures. We show that this mechanistic change can be conveniently detected by the exposure of nano-particles native in the material. Despite its high chemical purity, the often-studied molecular glass indomethacin contains low-concentration particles approximately 100 nm in size and 0.3% in volume fraction. Similar particles are present in polystyrene, another often-used model. In the surface-diffusion regime, particles are gradually exposed in regions vacated by host molecules, for example, the peak of a surface grating and the depletion zone near a surface crystal. In the viscous-flow regime, particle exposure is not observed. The surface contour around an exposed particle widens over time in a self-similar manner as 3 (Bt)1/4, where B is a surface mobility constant and the same constant obtained by surface grating decay. This work suggests that in a binary system composed of slow- and fast-diffusing molecules, slow-diffusing molecules can be stranded in surface regions vacated by fast-diffusing molecules, effectively leading to phase separation.
Interstellar Ice Chemistry: From Water to Complex Organics

NASA Astrophysics Data System (ADS)

Oberg, Karin I.; Fayolle, E.; Linnartz, H.; van Dishoeck, E.; Fillion, J.; Bertin, M.

2013-06-01

Molecular cloud cores, protostellar envelopes and protoplanetary disk midplanes are all characterized by freeze-out of atoms and molecules (other than H and H2) onto interstellar dust grains. On the grain surface, atom addition reactions, especially hydrogenation, are efficient and H2O forms readily from O, CH3OH from CO etc. The result is an icy mantle typically dominated by H2O, but also rich in CO2, CO, NH3, CH3OH and CH4. These ices are further processed through interactions with radiation, electrons and energetic particles. Because of the efficiency of the freeze-out process, and the complex chemistry that succeeds it, these icy grain mantles constitute a major reservoir of volatiles during star formation and are also the source of much of the chemical evolution observed in star forming regions. Laboratory experiments allow us to explore how molecules and radicals desorb, dissociate, diffuse and react in ices when exposed to different sources of energy. Changes in ice composition and structure is constrained using infrared spectroscopy and mass spectrometry. By comparing ice desorption, segregation, and chemistry efficiencies under different experimental conditions, we can characterize the basic ice processes, e.g. diffusion of different species, that underpin the observable changes in ice composition and structure. This information can then be used to predict the interstellar ice chemical evolution. I will review some of the key laboratory discoveries on ice chemistry during the past few years and how they have been used to predict and interpret astronomical observations of ice bands and gas-phase molecules associated with ice evaporation. These include measurements of thermal diffusion in and evaporation from ice mixtures, non-thermal diffusion efficiencies (including the recent results on frequency resolved UV photodesorption), and the expected temperature dependencies of the complex ice chemistry regulated by radical formation and diffusion. Based on these examples I will argue that the combination of laboratory experiments and observations is crucial to formulate and to test hypotheses on key processes that regulate the interstellar ice chemistry.
Optimized Unlike-Pair Interactions for Water-Carbon Dioxide Mixtures described by the SPC/E and EPM2 Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlcek, Lukas; Chialvo, Ariel A; Cole, David

The unlike- pair interaction parameters for the SPC/E- EPM2 models have been optimized to reproduce the mutual solubility of water and carbon dioxide at the conditions of liquid- supercritical fluid phase equilibria. An efficient global optimization of the parameters is achieved through an implementation of the coupling parameter approach, adapted to phase equilibria calculations in the Gibbs ensemble, that explicitly corrects for the over- polarization of the SPC/E water molecule in the non- polar CO2 environments. The resulting H2O- CO2 force field reproduces accurately the available experimental solubilities at the two fluid phases in equilibria as well as the correspondingmore » species tracer diffusion coefficients.« less
Modeling solute clustering in the diffusion layer around a growing crystal.

PubMed

Shiau, Lie-Ding; Lu, Yung-Fang

2009-03-07

The mechanism of crystal growth from solution is often thought to consist of a mass transfer diffusion step followed by a surface reaction step. Solute molecules might form clusters in the diffusion step before incorporating into the crystal lattice. A model is proposed in this work to simulate the evolution of the cluster size distribution due to the simultaneous aggregation and breakage of solute molecules in the diffusion layer around a growing crystal in the stirred solution. The crystallization of KAl(SO(4))(2)12H(2)O from aqueous solution is studied to illustrate the effect of supersaturation and diffusion layer thickness on the number-average degree of clustering and the size distribution of solute clusters in the diffusion layer.
Diffusion and Clustering of Carbon Dioxide on Non-porous Amorphous Solid Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Jiao; Emtiaz, Shahnewaj M.; Vidali, Gianfranco

2017-03-01

Observations by ISO and Spitzer toward young stellar objects showed that CO{sub 2} segregates in the icy mantles covering dust grains. Thermal processing of the ice mixture was proposed as being responsible for the segregation. Although several laboratories studied thermally induced segregation, a satisfying quantification is still missing. We propose that the diffusion of CO{sub 2} along pores inside water ice is the key to quantify segregation. We combined Temperature Programmed Desorption and Reflection Absorption InfraRed Spectroscopy to study how CO{sub 2} molecules interact on a non-porous amorphous solid water (np-ASW) surface. We found that CO{sub 2} diffuses significantly onmore » an np-ASW surface above 65 K and clusters are formed at well below one monolayer. A simple rate equation simulation finds that the diffusion energy barrier of CO{sub 2} on np-ASW is 2150 ± 50 K, assuming a diffusion pre-exponential factor of 10{sup 12} s{sup −1}. This energy should also apply to the diffusion of CO{sub 2} on the wall of pores. The binding energy of CO{sub 2} from CO{sub 2} clusters and CO{sub 2} from H{sub 2}O ice has been found to be 2415 ± 20 K and 2250 ± 20 K, respectively, assuming the same prefactor for desorption. CO{sub 2}–CO{sub 2} interaction is stronger than CO{sub 2}–H{sub 2}O interaction, in agreement with the experimental finding that CO{sub 2} does not wet the np-ASW surface. For comparison, we carried out similar experiments with CO on np-ASW, and found that the CO–CO interaction is always weaker than CO–H{sub 2}O. As a result, CO wets the np-ASW surface. This study should be of help to uncover the thermal history of CO{sub 2} on the icy mantles of dust grains.« less
Application of Paramagnetically Tagged Molecules for Magnetic Resonance Imaging of Biofilm Mass Transport Processes▿

PubMed Central

Ramanan, B.; Holmes, W. M.; Sloan, W. T.; Phoenix, V. R.

2010-01-01

Molecules become readily visible by magnetic resonance imaging (MRI) when labeled with a paramagnetic tag. Consequently, MRI can be used to image their transport through porous media. In this study, we demonstrated that this method could be applied to image mass transport processes in biofilms. The transport of a complex of gadolinium and diethylenetriamine pentaacetic acid (Gd-DTPA), a commercially available paramagnetic molecule, was imaged both in agar (as a homogeneous test system) and in a phototrophic biofilm. The images collected were T1 weighted, where T1 is an MRI property of the biofilm and is dependent on Gd-DTPA concentration. A calibration protocol was applied to convert T1 parameter maps into concentration maps, thus revealing the spatially resolved concentrations of this tracer at different time intervals. Comparing the data obtained from the agar experiment with data from a one-dimensional diffusion model revealed that transport of Gd-DTPA in agar was purely via diffusion, with a diffusion coefficient of 7.2 × 10−10 m2 s−1. In contrast, comparison of data from the phototrophic biofilm experiment with data from a two-dimensional diffusion model revealed that transport of Gd-DTPA inside the biofilm was by both diffusion and advection, equivalent to a diffusion coefficient of 1.04 × 10−9 m2 s−1. This technology can be used to further explore mass transport processes in biofilms, either by using the wide range of commercially available paramagnetically tagged molecules and nanoparticles or by using bespoke tagged molecules. PMID:20435773
SPECIAL ISSUE DEVOTED TO THE 80TH BIRTHDAY OF S.A. AKHMANOV: Transient coherent anti-Stokes Raman scattering spectroscopy as a tool for measuring the diffusion coefficient and size of gas molecules

NASA Astrophysics Data System (ADS)

Nikitin, Sergei Yu

2009-07-01

Formulas are derived for evaluating the diffusion coefficient and size of gas molecules from transient coherent anti-Stokes Raman scattering measurements. Numerical estimates are presented for hydrogen.
Kinetics of the initial steps of G protein-coupled receptor-mediated cellular signaling revealed by single-molecule imaging.

PubMed

Lill, Yoriko; Martinez, Karen L; Lill, Markus A; Meyer, Bruno H; Vogel, Horst; Hecht, Bert

2005-08-12

We report on an in vivo single-molecule study of the signaling kinetics of G protein-coupled receptors (GPCR) performed using the neurokinin 1 receptor (NK1R) as a representative member. The NK1R signaling cascade is triggered by the specific binding of a fluorescently labeled agonist, substance P (SP). The diffusion of single receptor-ligand complexes in plasma membrane of living HEK 293 cells is imaged using fast single-molecule wide-field fluorescence microscopy at 100 ms time resolution. Diffusion trajectories are obtained which show intra- and intertrace heterogeneity in the diffusion mode. To investigate universal patterns in the diffusion trajectories we take the ligand-binding event as the common starting point. This synchronization allows us to observe changes in the character of the ligand-receptor-complex diffusion. Specifically, we find that the diffusion of ligand-receptor complexes is slowed down significantly and becomes more constrained as a function of time during the first 1000 ms. The decelerated and more constrained diffusion is attributed to an increasing interaction of the GPCR with cellular structures after the ligand-receptor complex is formed.
Optical measurement of transverse molecular diffusion in a microchannel.

PubMed Central

Kamholz, A E; Schilling, E A; Yager, P

2001-01-01

Quantitative analysis of molecular diffusion is a necessity for the efficient design of most microfluidic devices as well as an important biophysical method in its own right. This study demonstrates the rapid measurement of diffusion coefficients of large and small molecules in a microfluidic device, the T-sensor, by means of conventional epifluorescence microscopy. Data were collected by monitoring the transverse flux of analyte from a sample stream into a second stream flowing alongside it. As indicated by the low Reynolds numbers of the system (< 1), flow is laminar, and molecular transport between streams occurs only by diffusion. Quantitative determinations were made by fitting data with predictions of a one-dimensional model. Analysis was made of the flow development and its effect on the distribution of diffusing analyte using a three-dimensional modeling software package. Diffusion coefficients were measured for four fluorescently labeled molecules: fluorescein-biotin, insulin, ovalbumin, and streptavidin. The resulting values differed from accepted results by an average of 2.4%. Microfluidic system parameters can be selected to achieve accurate diffusion coefficient measurements and to optimize other microfluidic devices that rely on precise transverse transport of molecules. PMID:11259309

Fluorescence correlation spectroscopy diffusion laws to probe the submicron cell membrane organization.

PubMed

Wawrezinieck, Laure; Rigneault, Hervé; Marguet, Didier; Lenne, Pierre-François

2005-12-01

To probe the complexity of the cell membrane organization and dynamics, it is important to obtain simple physical observables from experiments on live cells. Here we show that fluorescence correlation spectroscopy (FCS) measurements at different spatial scales enable distinguishing between different submicron confinement models. By plotting the diffusion time versus the transverse area of the confocal volume, we introduce the so-called FCS diffusion law, which is the key concept throughout this article. First, we report experimental FCS diffusion laws for two membrane constituents, which are respectively a putative raft marker and a cytoskeleton-hindered transmembrane protein. We find that these two constituents exhibit very distinct behaviors. To understand these results, we propose different models, which account for the diffusion of molecules either in a membrane comprising isolated microdomains or in a meshwork. By simulating FCS experiments for these two types of organization, we obtain FCS diffusion laws in agreement with our experimental observations. We also demonstrate that simple observables derived from these FCS diffusion laws are strongly related to confinement parameters such as the partition of molecules in microdomains and the average confinement time of molecules in a microdomain or a single mesh of a meshwork.
Room temperature ionic liquids interacting with bio-molecules: an overview of experimental and computational studies

NASA Astrophysics Data System (ADS)

Benedetto, Antonio; Ballone, Pietro

2016-03-01

We briefly review experimental and computational studies of room temperature ionic liquids (RTILs) interacting with important classes of biomolecules, including phospholipids, peptides and proteins, nucleic acids and carbohydrates. Most of these studies have been driven by the interest for RTILs applications as solvents. Thus, available experimental data cover primarily thermodynamic properties such as the reciprocal solubility of RTILs and bio-molecules, as well as phase boundaries. Less extensive data are also available on transport properties such as diffusion and viscosity of homogeneous binary (RTILs/biomolecules) and ternary (RTIL/biomolecules/water) solutions. Most of the structural information at the atomistic level, of interest especially for biochemical, pharmaceutical and nanotechnology applications, has been made available by molecular dynamics simulations. Major exceptions to this statement are represented by the results from NMR and circular dichroism spectroscopy, by selected neutron and X-ray scattering data, and by recent neutron reflectometry measurements on lipid bilayers on surfaces, hydrated by water-RTIL solutions. A final section of our paper summarizes new developments in the field of RTILs based on amino acids, that combine in themselves the two main aspects of our discussion, i.e. ionic liquids and bio-molecules.
Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

2016-11-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume. This work is funded by NSF under Grant DMS-1222550.
Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.
Water transport by Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS). The dependence of substrate size studied at high resolution

PubMed Central

Zeuthen*, Thomas; Belhage, Bo; Zeuthen, Emil

2006-01-01

The relation between substrate and water transport was studied in Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS) expressed in Xenopus oocytes. The water transport was monitored from changes in oocyte volume at a resolution of 20 pl, more than one order of magnitude better than previous investigations. The rate of cotransport was monitored as the clamp current obtained from two-electrode voltage clamp. The high resolution data demonstrated a fixed ratio between the turn-over of the cotransporter and the rate of water transport. This applied to experiments in which the rate of cotransport was changed by isosmotic application of substrate, by rapid changes in clamp voltage, or by poisoning. Transport of larger substrates gave rise to less water transport. For the rabbit SGLT1, 378 ± 20 (n = 18 oocytes) water molecules were cotransported along with the 2 Na+ ions and the glucose-analogue α-MDG (MW 194); using the larger sugar arbutin (MW 272) this number was reduced by a factor of at least 0.86 ± 0.03 (15). For the human SGLT1 the respective numbers were 234 ± 12 (18) and 0.85 ± 0.8 (7). For NIS, 253 ± 16 (12) water molecules were cotransported for each 2 Na+ and 1 thiocyanate (SCN−, MW 58), with I− as anion (MW 127) only 162 ± 11 (19) water molecules were cotransported. The effect of substrate size suggests a molecular mechanism for water cotransport and is opposite to what would be expected from unstirred layer effects. Data were analysed by a model which combined cotransport and osmosis at the membrane with diffusion in the cytoplasm. The combination of high resolution measurements and precise modelling showed that water transport across the membrane can be explained by cotransport of water in the membrane proteins and that intracellular unstirred layers effects are minute. PMID:16322051
Asymmetric osmotic water permeation through a vesicle membrane

NASA Astrophysics Data System (ADS)

Su, Jiaye; Zhao, Yunzhen; Fang, Chang; Shi, Yue

2017-05-01

Understanding the water permeation through a cell membrane is of primary importance for biological activities and a key step to capture its shape transformation in salt solution. In this work, we reveal the dynamical behaviors of osmotically driven transport of water molecules across a vesicle membrane by molecular dynamics simulations. Of particular interest is that the water transport in and out of vesicles is highly distinguishable given the osmotic force are the same, suggesting an asymmetric osmotic transportation. This asymmetric phenomenon exists in a broad range of parameter space such as the salt concentration, temperature, and vesicle size and can be ascribed to the similar asymmetric potential energy of lipid-ion, lipid-water, lipid-solution, lipid-lipid, and the lipid-lipid energy fluctuation. Specifically, the water flux has a linear increase with the salt concentration, similar to the prediction by Nernst-Planck equation or Fick's first law. Furthermore, due to the Arrhenius relation between the membrane permeability and temperature, the water flux also exhibits excellent Arrhenius dependence on the temperature. Meanwhile, the water flux shows a linear increase with the vesicle surface area since the flux amount across a unit membrane area should be a constant. Finally, we also present the anonymous diffusion behaviors for the vesicle itself, where transitions from normal diffusion at short times to subdiffusion at long times are identified. Our results provide significant new physical insights for the osmotic water permeation through a vesicle membrane and are helpful for future experimental studies.
Biomimetic air sampling for detection of low concentrations of molecules and bioagents : LDRD 52744 final report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, Robert Clark

2003-12-01

Present methods of air sampling for low concentrations of chemicals like explosives and bioagents involve noisy and power hungry collectors with mechanical parts for moving large volumes of air. However there are biological systems that are capable of detecting very low concentrations of molecules with no mechanical moving parts. An example is the silkworm moth antenna which is a highly branched structure where each of 100 branches contains about 200 sensory 'hairs' which have dimensions of 2 microns wide by 100 microns long. The hairs contain about 3000 pores which is where the gas phase molecules enter the aqueous (lymph)more » phase for detection. Simulations of diffusion of molecules indicate that this 'forest' of hairs is 'designed' to maximize the extraction of the vapor phase molecules. Since typical molecules lose about 4 decades in diffusion constant upon entering the liquid phase, it is important to allow air diffusion to bring the molecule as close to the 'sensor' as possible. The moth acts on concentrations as low as 1000 molecules per cubic cm. (one part in 1e16). A 3-D collection system of these dimensions could be fabricated by micromachining techniques available at Sandia. This LDRD addresses the issues involved with extracting molecules from air onto micromachined structures and then delivering those molecules to microsensors for detection.« less
Improving receiver performance of diffusive molecular communication with enzymes.

PubMed

Noel, Adam; Cheung, Karen C; Schober, Robert

2014-03-01

This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules and then degrade them so that they cannot interfere with future transmissions. A lower bound expression on the expected number of molecules measured at the receiver is derived. A simple binary receiver detection scheme is proposed where the number of observed molecules is sampled at the time when the maximum number of molecules is expected. Insight is also provided into the selection of an appropriate bit interval. The expected bit error probability is derived as a function of the current and all previously transmitted bits. Simulation results show the accuracy of the bit error probability expression and the improvement in communication performance by having active enzymes present.
Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes.

PubMed

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi

2015-07-07

Classical molecular dynamics simulations have been performed to investigate the dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes (CPNTs) with various radii, i.e., 8×(WL¯)n=3,4,5/POPE. The results show that ethanol molecules spontaneously fill the octa- and deca-CPNTs, but not the hexa-CPNT. In the octa-CPNT, ethanol molecules are trapped at individual gaps with their carbon skeletons perpendicular to the tube axis and hydroxyl groups towards the tube wall, forming a broken single-file chain. As the channel radius increases, ethanol molecules inside the deca-CPNT tend to form a tubular layer and the hydroxyl groups mainly stretch towards the tube axis. Computations of diffusion coefficients indicate that ethanol molecules in the octa-CPNT nearly lost their diffusion abilities, while those in the deca-CPNT diffuse as 4.5 times as in a (8, 8) carbon nanotube with a similar tube diameter. The osmotic and diffusion permeabilities (pf and pd, respectively) of the octa- and deca-CPNTs transporting ethanol were deduced for the first time. The distributions of the gauche and trans conformers of ethanol molecules in two CPNTs are quite similar, both with approximately 57% gauche conformers. The non-bonded interactions of channel ethanol with a CPNT wall and surrounding ethanol were explored. The potential of mean force elucidates the mechanism underlying the transporting characteristics of channel ethanol in a transmembrane CPNT.
Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

PubMed

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. © 2011 American Chemical Society
An adsorption diffusion model for removal of para-chlorophenol by activated carbon derived from bituminous coal.

PubMed

Sze, M F F; McKay, G

2010-05-01

Batch adsorption experiments were carried out to study the adsorptive removal and diffusion mechanism of para-chlorophenol (p-CP) onto Calgon Filtrasorb 400 (F400) activated carbon. The external mass transfer resistance is negligible in the adsorption process carried out under different conditions in batch operation. Intraparticle diffusion model plots were used to correlate the batch p-CP adsorption data; three distinct linear sections were obtained for every batch operation. The textural properties of F400 activated carbon showed that it has a large portion of supermicropores, which is comparable to the size of the p-CP molecules. Due to the stronger interactions between p-CP molecules and F400 micropores, p-CP molecules predominantly diffused and occupied active sites in micropore region by hopping mechanism, and eventually followed by a slow filling of mesopores and micropores. This hypothesis is proven by the excellent agreement of the intraparticle diffusion model plots and the textural properties of F400 activated carbon. Copyright 2009 Elsevier Ltd. All rights reserved.
PCNA appears in two populations of slow and fast diffusion with a constant ratio throughout S-phase in replicating mammalian cells.

PubMed

Zessin, Patrick J M; Sporbert, Anje; Heilemann, Mike

2016-01-13

DNA replication is a fundamental cellular process that precedes cell division. Proliferating cell nuclear antigen (PCNA) is a central scaffold protein that orchestrates DNA replication by recruiting many factors essential for the replication machinery. We studied the mobility of PCNA in live mammalian cells using single-particle tracking in combination with photoactivated-localization microscopy (sptPALM) and found two populations. The first population which is only present in cells with active DNA replication, showed slow diffusion and was found to be located in replication foci. The second population showed fast diffusion, and represents the nucleoplasmic pool of unbound PCNA not involved in DNA replication. The ratio of these two populations remained constant throughout different stages of S-phase. A fraction of molecules in both populations showed spatially constrained mobility. We determined an exploration radius of ~100 nm for 13% of the slow-diffusing PCNA molecules, and of ~600 nm for 46% of the fast-diffusing PCNA molecules.
Modeling the interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube

NASA Technical Reports Server (NTRS)

Jaffe, Richard L.; Walther, Jens H.; Zimmerli, Urs; Koumoutsakos, Petros

2004-01-01

It has been observed that a carbon nanotube (CNT) AFM tip coated with ethylene diamine (EDA) penetrates the liquid water-air interface more easily than an uncoated nanotube tip. The EDA coating remains intact through repeated cycles of dipping and removal. In order to understand the physical basis for this observation, we use ab initio quantum chemistry calculations to study the EDA-CNT-water interaction and to parameterize a force field describing this system. Molecular dynamics (MD) simulations are carried out for EDA-water mixtures and an EDA-coated carbon nanotube immmed in water. These simulations are similar to our earlier MD study that characterized the CNT-water interface. The attractive CNT-EDA and CNT-water interactions arise primarily from van der Waals forces, and the EDA-EDA, EDA-water and water-water interactions are mainly due to hydrogen bond formation. The binding energ of single EDA molecule to the nanotube is nearly three times larger than the corresponding value found for water (4.3 versus 1.5 kcal mol, respectively). The EDA molecules readily stick to and diffuse along the CNT surface. As a resulf mixing of the EDA and water films does not occur on the timescale of the MD simulations. The EDA film reduces the hydrophobicity of the nanotube surface and acts like a prototypical surfactant in stabilizing the suspension of carbon nanotubes in water. For this presentation, we use the MD simulations to determine how the presence of the carbon nanotube surface perturbs the properties of EDA-water mixtures.
A deeper insight into an intriguing acetonitrile-water binary mixture: synergistic effect, dynamic Stokes shift, fluorescence correlation spectroscopy, and NMR studies.

PubMed

Koley, Somnath; Ghosh, Subhadip

2016-11-30

An insight study reveals the strong synergistic solvation behaviours from reporter dye molecules within the acetonitrile (ACN)-water (WT) binary mixture. Synergism of a binary mixture refers to some unique changes of the physical and thermodynamic properties of the solvent mixture, originating from the interactions among its cosolvents, which are absent within the pure cosolvents. Synergistic solvation of a binary mixture is likely to be fundamental for greater stabilization of an excited state solute dipole; at least to some extent greater as compared to one stabilized by any of its cosolvents alone. A dynamic Stokes shift due to the solvation of an excited dipole in the ACN-WT binary mixture is found to be highly relevant to the ground state physical properties of the solute molecule (polarity, hydrophilicity, acidity, etc.). Largely different solvation times in the ACN-WT mixture are observed from different dye molecules with widely varying polarities. However, earlier study shows that dye molecules, irrespective of their varying polarities, exhibit very similar solvation times within a pure solvent (J. Phys. Chem. B, 2014, 118, 7577-7785). On further study with fluorescence correlation spectroscopy (FCS) we observed that, unlike the translational diffusion coefficient (D t ) of a dye molecule within a pure solvent, which remains the same irrespective of the location of the dye molecule inside the solvent, a broad distribution among the D t values of a dye molecule is obtained from different locations within the ACN-WT binary mixture. Lastly our 1 H NMR study in the ACN-WT binary mixture shows the existence of strong hydrogen bond interactions among the cosolvents in the ACN-WT mixture.
Dynamic Asphaltene-Stearic Acid Competition at the Oil-Water Interface.

PubMed

Sauerer, Bastian; Stukan, Mikhail; Buiting, Jan; Abdallah, Wael; Andersen, Simon

2018-05-15

Interfacial tension (IFT) is one of the major parameters which govern the fluid flow in oil production and recovery. This paper investigates the interfacial activity of different natural surfactants found in crude oil. The main objective was to better understand the competition between carboxylic acids and asphaltenes on toluene/water interfaces. Dynamic IFT was measured for water-in-oil pendant drops contrary to most studies using oil-in-water drops. Stearic acid (SA) was used as model compound for surface-active carboxylic acids in crude. The influence of concentration of these species on dynamic IFT between model oil and deionized water was examined. The acid concentrations were of realistic values (total acid number 0.1 to 2 mg KOH/g oil) while asphaltene concentrations were low and set between 10 and 100 ppm. In mixtures, the initial surface pressure was entirely determined by the SA content while asphaltenes showed a slow initial diffusion to the interface followed by increased adsorption at longer times. The final surface pressure was higher for asphaltenes compared to SA, but for binaries, the final surface pressure was always lower than the sum of the individuals. At high SA concentration, surface pressures of mixtures were dominated entirely by the SA, although, Langmuir isotherm analysis shows that asphaltenes bind to the interface 200-250 times stronger than SA. The surface area/molecule for both SA and asphaltenes were found to be larger than the values reported in recent literature. Various approaches to dynamic surface adsorption were tested, showing that apparent diffusivity of asphaltenes is very low, in agreement with other works. Hence, the adsorption is apparently under barrier control. A possible hypothesis is that at the initial phase of the experiment and at lower concentration of asphaltenes, the interface is occupied by stearic acid molecules forming a dense layer of hydrocarbon chains that may repel the asphaltenes.
Diffusion modulation of DNA by toehold exchange

NASA Astrophysics Data System (ADS)

Rodjanapanyakul, Thanapop; Takabatake, Fumi; Abe, Keita; Kawamata, Ibuki; Nomura, Shinichiro M.; Murata, Satoshi

2018-05-01

We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.
Lateral diffusion in model membranes is independent of the size of the hydrophobic region of molecules.

PubMed Central

Balcom, B J; Petersen, N O

1993-01-01

We have systematically investigated the probe size and shape dependence of lateral diffusion in model dimyristoyl phosphatidylcholine membranes. Linear hydrophobic polymers, which differ in length by an order of magnitude, were used to explore the effect on the lateral diffusion coefficient of hydrodynamic restrictions in the bilayer interior. The polymers employed are isoprenoid alcohols--citronellol, solanesol, and dolichol. Tracer lateral diffusion coefficients were measured by fluorescence photobleaching recovery. Despite the large difference in lengths, the nitrobenzoxadiazole labelled alcohols all diffuse at the rate of lipid self-diffusion (5.0 x 10(-12) m2 s-1, 29 degrees C) in the liquid crystal phase. Companion measurements in isotropic polymer solution, in gel phase lipid membranes and with nonpolar fluorescent polyaromatic hydrocarbons, show a marked dependence of the lateral diffusion coefficient on the probe molecule size. Our results in the liquid crystal phase are in accord with free area theory which asserts that lateral diffusion in the membrane is restricted by the surface-free area. Probe molecules which are significantly longer than the host phospholipid, seven times longer in the case of dolichol, are still restricted in their lateral motion by the surface properties of the bilayer in the liquid crystal phase. Fluorescence quenching experiments indicate that the nitrobenzoxadiazole label does not reside at the aqueous interface, although it must reside in close proximity according to the diffusion measurements. PMID:8218892
Evaluation of Proteins' Rotational Diffusion Coefficients from Simulations of Their Free Brownian Motion in Volume-Occupied Environments.

PubMed

Długosz, Maciej; Antosiewicz, Jan M

2014-01-14

We have investigated the rotational dynamics of hen egg white lysozyme in monodisperse aqueous solutions of concentrations up to 250 mg/mL, using a rigid-body Brownian dynamics method that accurately accounts for anisotropies of diffusing objects. We have examined the validity of the free diffusion concept in the analysis of computer simulations of volume-occupied molecular solutions. We have found that, when as the only intermolecular interaction, the excluded volume effect is considered, rotational diffusion of molecules adheres to the free diffusion model. Further, we present a method based on the exact (in the case of the free diffusion) analytic forms of autocorrelation functions of particular vectors rigidly attached to diffusing objects, which allows one to obtain from results of molecular simulations the three principal rotational diffusion coefficients characterizing rotational Brownian motion of an arbitrarily shaped rigid particle for an arbitrary concentration of crowders. We have applied this approach to trajectories resulting from Brownian dynamics simulations of hen egg white lysozyme solutions. We show that the apparent anisotropy of proteins' rotational motions increases with an increasing degree of crowding. Finally, we demonstrate that even if the hydrodynamic anisotropy of molecules is neglected and molecules are simulated using their average translational and rotational diffusion coefficients, excluded volume effects still lead to their anisotropic rotational dynamics.
Nanopipette Delivery of Individual Molecules to Cellular Compartments for Single-Molecule Fluorescence Tracking

PubMed Central

Bruckbauer, Andreas; James, Peter; Zhou, Dejian; Yoon, Ji Won; Excell, David; Korchev, Yuri; Jones, Roy; Klenerman, David

2007-01-01

We have developed a new method, using a nanopipette, for controlled voltage-driven delivery of individual fluorescently labeled probe molecules to the plasma membrane which we used for single-molecule fluorescence tracking (SMT). The advantages of the method are 1), application of the probe to predefined regions on the membrane; 2), release of only one or a few molecules onto the cell surface; 3), when combined with total internal reflection fluorescence microscopy, very low background due to unbound molecules; and 4), the ability to first optimize the experiment and then repeat it on the same cell. We validated the method by performing an SMT study of the diffusion of individual membrane glycoproteins labeled with Atto 647-wheat germ agglutin in different surface domains of boar spermatozoa. We found little deviation from Brownian diffusion with a mean diffusion coefficient of 0.79 ± 0.04 μm2/s in the acrosomal region and 0.10 ± 0.02 μm2/s in the postacrosomal region; this difference probably reflects different membrane structures. We also showed that we can analyze diffusional properties of different subregions of the cell membrane and probe for the presence of diffusion barriers. It should be straightforward to extend this new method to other probes and cells, and it can be used as a new tool to investigate the cell membrane. PMID:17631532
Analyses of Disruption of Cerebral White Matter Integrity in Schizophrenia with MR Diffusion Tensor Fiber Tracking Method

NASA Astrophysics Data System (ADS)

Yamamoto, Utako; Kobayashi, Tetsuo; Kito, Shinsuke; Koga, Yoshihiko

We have analyzed cerebral white matter using magnetic resonance diffusion tensor imaging (MR-DTI) to measure the diffusion anisotropy of water molecules. The goal of this study is the quantitative evaluation of schizophrenia. Diffusion tensor images are acquired for patients with schizophrenia and healthy comparison subjects, group-matched for age, sex, and handedness. Fiber tracking is performed on the superior longitudinal fasciculus for the comparison between the patient and comparison groups. We have analysed and compared the cross-sectional area on the starting coronal plane and the mean and standard deviation of the fractional anisotropy and the apparent diffusion coefficient along fibers in the right and left hemispheres. In the right hemisphere, the cross-sectional areas in patient group are significantly smaller than those in the comparison group. Furthermore, in the comparison group, the cross-sectional areas in the right hemisphere are significantly larger than those in the left hemisphere, whereas there is no significant difference in the patient group. These results suggest that we may evaluate the disruption in white matter integrity in schizophrenic patients quantitatively by comparing the cross-sectional area of the superior longitudinal fasciculus in the right and left hemispheres.

Hyper-mobility of water around actin filaments revealed using pulse-field gradient spin-echo {sup 1}H NMR and fluorescence spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wazawa, Tetsuichi; CREST, JST, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012; Sagawa, Takashi

2011-01-28

Research highlights: {yields} Translationally hyper-mobile water has been detected around actin filaments. {yields} Translationally hyper-mobile water is formed upon polymerization of actin. {yields} Low water viscosity was found around F-actin using fluorescence anisotropy. {yields} Formation of hyper-mobile water may explain endothermic actin polymerization. -- Abstract: This paper reports that water molecules around F-actin, a polymerized form of actin, are more mobile than those around G-actin or in bulk water. A measurement using pulse-field gradient spin-echo {sup 1}H NMR showed that the self-diffusion coefficient of water in aqueous F-actin solution increased with actin concentration by {approx}5%, whereas that in G-actin solutionmore » was close to that of pure water. This indicates that an F-actin/water interaction is responsible for the high self-diffusion of water. The local viscosity around actin was also investigated by fluorescence measurements of Cy3, a fluorescent dye, conjugated to Cys 374 of actin. The steady-state fluorescence anisotropy of Cy3 attached to F-actin was 0.270, which was lower than that for G-actin, 0.334. Taking into account the fluorescence lifetimes of the Cy3 bound to actin, their rotational correlation times were estimated to be 3.8 and 9.1 ns for F- and G-actin, respectively. This indicates that Cy3 bound to F-actin rotates more freely than that bound to G-actin, and therefore the local water viscosity is lower around F-actin than around G-actin.« less
Anomalous Extracellular Diffusion in Rat Cerebellum

PubMed Central

Xiao, Fanrong; Hrabe, Jan; Hrabetova, Sabina

2015-01-01

Extracellular space (ECS) is a major channel transporting biologically active molecules and drugs in the brain. Diffusion-mediated transport of these substances is hindered by the ECS structure but the microscopic basis of this hindrance is not fully understood. One hypothesis proposes that the hindrance originates in large part from the presence of dead-space (DS) microdomains that can transiently retain diffusing molecules. Because previous theoretical and modeling work reported an initial period of anomalous diffusion in similar environments, we expected that brain regions densely populated by DS microdomains would exhibit anomalous extracellular diffusion. Specifically, we targeted granular layers (GL) of rat and turtle cerebella that are populated with large and geometrically complex glomeruli. The integrative optical imaging (IOI) method was employed to evaluate diffusion of fluorophore-labeled dextran (MW 3000) in GL, and the IOI data analysis was adapted to quantify the anomalous diffusion exponent dw from the IOI records. Diffusion was significantly anomalous in rat GL, where dw reached 4.8. In the geometrically simpler turtle GL, dw was elevated but not robustly anomalous (dw = 2.6). The experimental work was complemented by numerical Monte Carlo simulations of anomalous ECS diffusion in several three-dimensional tissue models containing glomeruli-like structures. It demonstrated that both the duration of transiently anomalous diffusion and the anomalous exponent depend on the size of model glomeruli and the degree of their wrapping. In conclusion, we have found anomalous extracellular diffusion in the GL of rat cerebellum. This finding lends support to the DS microdomain hypothesis. Transiently anomalous diffusion also has a profound effect on the spatiotemporal distribution of molecules released into the ECS, especially at diffusion distances on the order of a few cell diameters, speeding up short-range diffusion-mediated signals in less permeable structures. PMID:25954895
An approach to the research on ion and water properties in the interphase between the plasma membrane and bulk extracellular solution.

PubMed

Hibino, Hiroshi; Takai, Madoka; Noguchi, Hidenori; Sawamura, Seishiro; Takahashi, Yasufumi; Sakai, Hideki; Shiku, Hitoshi

2017-07-01

In vivo, cells are immersed in an extracellular solution that contains a variety of bioactive substances including ions and water. Classical electrophysiological analyses of epithelial cells in the stomach and small intestine have revealed that within a distance of several hundred micrometers above their apical plasma membrane, lies an extracellular layer that shows ion concentration gradients undetectable in the bulk phase. This "unstirred layer", which contains stagnant solutes, may also exist between the bulk extracellular solution and membranes of other cells in an organism and may show different properties. On the other hand, an earlier study using a bacterial planar membrane indicated that H + released from a transporter migrates in the horizontal direction along the membrane surface much faster than it diffuses vertically toward the extracellular space. This result implies that between the membrane surface and unstirred layer, there is a "nanointerface" that has unique ionic dynamics. Advanced technologies have revealed that the nanointerface on artificial membranes possibly harbors a highly ordered assembly of water molecules. In general, hydrogen bonds are involved in formation of the ordered water structure and can mediate rapid transfer of H + between neighboring molecules. This description may match the phenomenon on the bacterial membrane. A recent study has suggested that water molecules in the nanointerface regulate the gating of K + channels. Here, the region comprising the unstirred layer and nanointerface is defined as the interphase between the plasma membrane and bulk extracellular solution (iMES). This article briefly describes the physicochemical properties of ions and water in the iMES and their physiological significance. We also describe the methodologies that are currently used or will be applicable to the interphase research.
Multicomponent Diffusion of Penetrant Mixtures in Rubbery Polymers: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Bringuier, Stefan; Varady, Mark; Knox, Craig; Cabalo, Jerry; Pearl, Thomas; Mantooth, Brent

The importance of understanding transport of chemical species across liquid-solid boundaries is of particular interest in the decontamination of harmful chemicals absorbed within polymeric materials. To characterize processes associated with liquid-phase extraction of absorbed species from polymers, it is necessary to determine an appropriate physical description of species transport in multicomponent systems. The Maxwell-Stefan (M-S) formulation is a rigorous description of mass transport in multicomponent solutions, in which, mutual diffusivities determine the degree of relative motion between interacting molecules in response to a chemical potential gradient. The work presented focuses on the determination of M-S diffusivities from molecular dynamics (MD) simulations of nerve agent O-ethyl S-[2(diisopropylamino)ethyl] methylphosphonothioate (VX), water, and methanol mixtures within a poly(dimethylsiloxane) matrix. We investigate the composition dependence of M-S diffusivities and compare the results to values predicted using empirical relations for binary and ternary mixtures. Finally, we highlight the pertinent differences in molecular mechanisms associated with species transport and employ non-equilibrium MD to probe transport across the mixture-polymer interface.
Histological evidence for drug diffusion across the cerebral meninges into the underlying neocortex in rats.

PubMed

Ludvig, Nandor; Sheffield, Lynette G; Tang, Hai M; Baptiste, Shirn L; Devinsky, Orrin; Kuzniecky, Ruben I

2008-01-10

Transmeningeal pharmacotherapy has been proposed to treat neurological disorders with localized pathology, such as intractable focal epilepsy. As a step toward understanding the diffusion and intracortical spread of transmeningeally delivered drugs, the present study used histological methods to determine the extent to which a marker compound, N-methyl-D-aspartate (NMDA), can diffuse into the neocortex through the meninges. Rats were implanted with bilateral parietal cortical epidural cups filled with 50 mM NMDA on the right side and artificial cerebrospinal fluid (ACSF) in the contralateral side. After 24 h, the histological effects of these treatments were evaluated using cresyl violet (Nissl) staining. The epidural NMDA exposure caused neuronal loss that in most animals extended from the pial surface through layer V. The area indicated by this neuronal loss was localized to the neocortical region underlying the epidural cup. These results suggest that NMDA-like, water soluble, small molecules can diffuse through the subdural/subarachnoid space into the underlying neocortex and spread in a limited fashion, close to the meningeal penetration site.
A simple and effective solution to the constrained QM/MM simulations

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.
Application of pulsed-gradient Fourier transform nuclear magnetic resonance to the study of self-diffusion of phospholipid vesicles.

PubMed

McDonald, G G; Vanderkooi, J M

1975-05-20

A pulsed-gradient Fourier transform nuclear magnetic resonance (NMR) technique was appplied to the study of diffusion of phospholipid vesicles. The diffusion coefficient of dimyristoyllecithin vesicles (DML) in a D2O-phospahte buffer at 37 degrees is D = 1.9 TIMES 10(-6) cm2/sec. In a solution made viscous by DNA addition, the diffusion coefficient of DML vesicles was 3.5 times 10(-7) cm2/sec. These values compare favorably with the diffusion rate for liposomes as determined by ultracentrifugation and by Stokes law calculation. The data suggest that DML diffusion is controlled primarily by whole liposome migration as opposed to movement of individual molecules within the liposome, liposome rotation, or fast exchange between lecithin molecules in solution and in vesicles.
Theory of Transport of Long Polymer Molecules through Carbon Nanotube Channels

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Srivastava, Deepak

2003-01-01

A theory of transport of long chain polymer molecules through carbon nanotube (CNT) channels is developed using Fokker-Planck equation and direct molecular dynamics (MD) simulations. The mean transport or translocation time tau is found to depend on the chemical potential energy, entropy and diffusion coefficient. A power law dependence tau approx. N(sup 2)is found where N is number of monomers in a molecule. For 10(exp 5)-unit long polyethylene molecules, tau is estimated to be approx. 1micro-s. The diffusion coefficient of long polymer molecules inside CNTs, like that of short ones, are found to be few orders of magnitude larger than in ordinary silicate based zeolite systems.
Simulation of Changes in Diffusion Related to Different Pathologies at Cellular Level After Traumatic Brain Injury

PubMed Central

Lin, Mu; He, Hongjian; Schifitto, Giovanni; Zhong, Jianhui

2016-01-01

Purpose The goal of the current study was to investigate tissue pathology at the cellular level in traumatic brain injury (TBI) as revealed by Monte Carlo simulation of diffusion tensor imaging (DTI)-derived parameters and elucidate the possible sources of conflicting findings of DTI abnormalities as reported in the TBI literature. Methods A model with three compartments separated by permeable membranes was employed to represent the diffusion environment of water molecules in brain white matter. The dynamic diffusion process was simulated with a Monte Carlo method using adjustable parameters of intra-axonal diffusivity, axon separation, glial cell volume fraction, and myelin sheath permeability. The effects of tissue pathology on DTI parameters were investigated by adjusting the parameters of the model corresponding to different stages of brain injury. Results The results suggest that the model is appropriate and the DTI-derived parameters simulate the predominant cellular pathology after TBI. Our results further indicate that when edema is not prevalent, axial and radial diffusivity have better sensitivity to axonal injury and demyelination than other DTI parameters. Conclusion DTI is a promising biomarker to detect and stage tissue injury after TBI. The observed inconsistencies among previous studies are likely due to scanning at different stages of tissue injury after TBI. PMID:26256558
DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarman, Sten, E-mail: sarman@ownit.nu; Wang, Yong-Lei; Laaksonen, Aatto

The self-diffusion coefficients of nematic phases of various model systems consisting of regular convex calamitic and discotic ellipsoids and non-convex bodies such as bent-core molecules and soft ellipsoid strings have been obtained as functions of the shear rate in a shear flow. Then the self-diffusion coefficient is a second rank tensor with three different diagonal components and two off-diagonal components. These coefficients were found to be determined by a combination of two mechanisms, which previously have been found to govern the self-diffusion of shearing isotropic liquids, namely, (i) shear alignment enhancing the diffusion in the direction parallel to the streamlinesmore » and hindering the diffusion in the perpendicular directions and (ii) the distortion of the shell structure in the liquid whereby a molecule more readily can escape from a surrounding shell of nearest neighbors, so that the mobility increases in every direction. Thus, the diffusion parallel to the streamlines always increases with the shear rate since these mechanisms cooperate in this direction. In the perpendicular directions, these mechanisms counteract each other so that the behaviour becomes less regular. In the case of the nematic phases of the calamitic and discotic ellipsoids and of the bent core molecules, mechanism (ii) prevails so that the diffusion coefficients increase. However, the diffusion coefficients of the soft ellipsoid strings decrease in the direction of the velocity gradient because the broadsides of these molecules are oriented perpendicularly to this direction due the shear alignment (i). The cross coupling coefficient relating a gradient of tracer particles in the direction of the velocity gradient and their flow in the direction of the streamlines is negative and rather large, whereas the other coupling coefficient relating a gradient in the direction of the streamlines and a flow in the direction of the velocity gradient is very small.« less
Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.
String-like collective motion and diffusion in the interfacial region of ice

NASA Astrophysics Data System (ADS)

Wang, Xinyi; Tong, Xuhang; Zhang, Hao; Douglas, Jack F.

2017-11-01

We investigate collective molecular motion and the self-diffusion coefficient Ds of water molecules in the mobile interfacial layer of the secondary prismatic plane (11 2 ¯ 0 ) of hexagonal ice by molecular dynamics simulation based on the TIP4P/2005 water potential and a metrology of collective motion drawn from the field of glass-forming liquids. The width ξ of the mobile interfacial layer varies from a monolayer to a few nm as the temperature is increased towards the melting temperature Tm, in accordance with recent simulations and many experimental studies, although different experimental methods have differed in their precise estimates of the thickness of this layer. We also find that the dynamics within this mobile interfacial ice layer is "dynamically heterogeneous" in a fashion that has many features in common with glass-forming liquids and the interfacial dynamics of crystalline Ni over the same reduced temperature range, 2/3 < T/Tm < 1. In addition to exhibiting non-Gaussian diffusive transport, decoupling between mass diffusion and the structural relaxation time, and stretched exponential relaxation, we find string-like collective molecular exchange motion in the interfacial zone within the ice interfacial layer and colored noise fluctuations in the mean square molecular atomic displacement 〈u2〉 after a "caging time" of 1 ps, i.e., the Debye-Waller factor. However, while the heterogeneous dynamics of ice is clearly similar in many ways to molecular and colloidal glass-forming materials, we find distinct trends between the diffusion coefficient activation energy Ea for diffusion Ds and the interfacial width ξ from the scale of collective string-like motion L than those found in glass-forming liquids.
Jump rates for surface diffusion of large molecules from first principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen

2015-04-21

We apply a recently developed stochastic model for the surface diffusion of large molecules to calculate jump rates for 9,10-dithioanthracene on a Cu(111) surface. The necessary input parameters for the stochastic model are calculated from first principles using density functional theory (DFT). We find that the inclusion of van der Waals corrections to the DFT energies is critical to obtain good agreement with experimental results for the adsorption geometry and energy barrier for diffusion. The predictions for jump rates in our model are in excellent agreement with measured values and show a marked improvement over transition state theory (TST). Wemore » find that the jump rate prefactor is reduced by an order of magnitude from the TST estimate due to frictional damping resulting from energy exchange with surface phonons, as well as a rotational mode of the diffusing molecule.« less
Simulation of stochastic diffusion via first exit times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lötstedt, Per, E-mail: perl@it.uu.se; Meinecke, Lina, E-mail: lina.meinecke@it.uu.se

2015-11-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a methodmore » based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions.« less
Simulation of stochastic diffusion via first exit times

PubMed Central

Lötstedt, Per; Meinecke, Lina

2015-01-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a method based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions. PMID:26600600
Benchmark of ReaxFF force field for subcritical and supercritical water.

PubMed

Manzano, Hegoi; Zhang, Weiwei; Raju, Muralikrishna; Dolado, Jorge S; López-Arbeloa, Iñigo; van Duin, Adri C T

2018-06-21

Water in the subcritical and supercritical states has remarkable properties that make it an excellent solvent for oxidation of hazardous chemicals, waste separation, and green synthesis. Molecular simulations are a valuable complement to experiments in order to understand and improve the relevant sub- and super-critical reaction mechanisms. Since water molecules under these conditions can act not only as a solvent but also as a reactant, dissociative force fields are especially interesting to investigate these processes. In this work, we evaluate the capacity of the ReaxFF force field to reproduce the microstructure, hydrogen bonding, dielectric constant, diffusion, and proton transfer of sub- and super-critical water. Our results indicate that ReaxFF is able to simulate water properties in these states in very good quantitative agreement with the existing experimental data, with the exception of the static dielectric constant that is reproduced only qualitatively.
Quantum fluctuations increase the self-diffusive motion of para-hydrogen in narrow carbon nanotubes.

PubMed

Kowalczyk, Piotr; Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester

2011-05-28

Quantum fluctuations significantly increase the self-diffusive motion of para-hydrogen adsorbed in narrow carbon nanotubes at 30 K comparing to its classical counterpart. Rigorous Feynman's path integral calculations reveal that self-diffusive motion of para-hydrogen in a narrow (6,6) carbon nanotube at 30 K and pore densities below ∼29 mmol cm(-3) is one order of magnitude faster than the classical counterpart. We find that the zero-point energy and tunneling significantly smoothed out the free energy landscape of para-hydrogen molecules adsorbed in a narrow (6,6) carbon nanotube. This promotes a delocalization of the confined para-hydrogen at 30 K (i.e., population of unclassical paths due to quantum effects). Contrary the self-diffusive motion of classical para-hydrogen molecules in a narrow (6,6) carbon nanotube at 30 K is very slow. This is because classical para-hydrogen molecules undergo highly correlated movement when their collision diameter approached the carbon nanotube size (i.e., anomalous diffusion in quasi-one dimensional pores). On the basis of current results we predict that narrow single-walled carbon nanotubes are promising nanoporous molecular sieves being able to separate para-hydrogen molecules from mixtures of classical particles at cryogenic temperatures. This journal is © the Owner Societies 2011
Macro and micro analysis of small molecule diffusion in amorphous polymers

NASA Astrophysics Data System (ADS)

Putta, Santosh Krishna

In this study, both macroscopic and microscopic numerical techniques have been explored, to model and understand the diffusion behavior of small molecules in amorphous polymers, which very often do not follow the classical Fickian law. It was attempted to understand the influence of various aspects of the molecular structure of a polymer on its macroscopic diffusion behavior. At the macroscopic level, a hybrid finite-element/finite-difference model is developed to implement the coupled diffusion and deformation constitutive equations. A viscoelasticity theory, combined with time-freevolume superposition is used to model the deformation processes. A freevolume-based model is used to model the diffusion processes. The freevolume in the polymer is used as a coupling factor between the deformation and the diffusion processes. The model is shown to qualitatively describe some of the typical non-Fickian diffusion behavior in polymers. However, it does not directly involve the microstructure of a polymer. Further, some of the input parameters to the model are difficult to obtain experimentally. A numerical microscopic approach is therefore adopted to study the molecular structure of polymers. A molecular mechanics and dynamics technique combined with a modified Rotational Isomeric State (RIS) approach, is followed to generate the molecular structure for two types of polycarbonates, and, two types of polyacrylates, starting only with their chemical structures. A new efficient 3-D algorithm for Delaunay Tessellation is developed, and, then applied to discretize the molecular structure into Delaunay Tetrahedra. By using the dicretized molecular structure, size, shape, and, connectivity of free-spaces for small molecule diffusion in the above mentioned polymers, are then studied in relation to their diffusion properties. The influence of polymer and side chain flexibility, and diffusant-diffusant and diffusant-polymer molecular interactions, is also discussed with respect to the diffusion properties.
Concentration profiles of actin-binding molecules in lamellipodia

NASA Astrophysics Data System (ADS)

Falcke, Martin

2016-04-01

Motile cells form lamellipodia in the direction of motion, which are flat membrane protrusions containing an actin filament network. The network flows rearward relative to the leading edge of the lamellipodium due to actin polymerization at the front. Thus, actin binding molecules are subject to transport towards the rear of the cell in the bound state and diffuse freely in the unbound state. We analyze this reaction-diffusion-advection process with respect to the concentration profiles of these species and provide an analytic approximation for them. Network flow may cause a depletion zone of actin binding molecules close to the leading edge. The existence of such zone depends on the free molecule concentration in the cell body, on the ratio of the diffusion length to the distance bound molecules travel rearward with the flow before dissociating, and the ratio of the diffusion length to the width of the region with network flow and actin binding. Our calculations suggest the existence of depletion zones for the F-actin cross-linkers filamin and α-actinin in fish keratocytes (and other cell types), which is in line with the small elastic moduli of the F-actin network close to the leading edge found in measurements of the force motile cells are able to exert.
Extensive database of liquid phase diffusion coefficients of some frequently used test molecules in reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography.

PubMed

Song, Huiying; Vanderheyden, Yoachim; Adams, Erwin; Desmet, Gert; Cabooter, Deirdre

2016-07-15

Diffusion plays an important role in all aspects of band broadening in chromatography. An accurate knowledge of molecular diffusion coefficients in different mobile phases is therefore crucial in fundamental column performance studies. Correlations available in literature, such as the Wilke-Chang equation, can provide good approximations of molecular diffusion under reversed-phase conditions. However, these correlations have been demonstrated to be less accurate for mobile phases containing a large percentage of acetonitrile, as is the case in hydrophilic interaction liquid chromatography. A database of experimentally measured molecular diffusion coefficients of some 45 polar and apolar compounds that are frequently used as test molecules under hydrophilic interaction liquid chromatography and reversed-phase conditions is therefore presented. Special attention is given to diffusion coefficients of polar compounds obtained in large percentages of acetonitrile (>90%). The effect of the buffer concentration (5-10mM ammonium acetate) on the obtained diffusion coefficients is investigated and is demonstrated to mainly influence the molecular diffusion of charged molecules. Diffusion coefficients are measured using the Taylor-Aris method and hence deduced from the peak broadening of a solute when flowing through a long open tube. The validity of the set-up employed for the measurement of the diffusion coefficients is demonstrated by ruling out the occurrence of longitudinal diffusion, secondary flow interactions and extra-column effects, while it is also shown that radial equilibration in the 15m long capillary is effective. Copyright © 2016 Elsevier B.V. All rights reserved.

First principles study of the atomic layer deposition of alumina by TMA-H2O-process.

PubMed

Weckman, Timo; Laasonen, Kari

2015-07-14

Atomic layer deposition (ALD) is a coating technology used to produce highly uniform thin films. Aluminiumoxide, Al2O3, is mainly deposited using trimethylaluminium (TMA) and water as precursors and is the most studied ALD-process to date. However, only few theoretical studies have been reported in the literature. The surface reaction mechanisms and energetics previously reported focus on a gibbsite-like surface model but a more realistic description of the surface can be achieved when the hydroxylation of the surface is taken into account using dissociatively adsorbed water molecules. The adsorbed water changes the structure of the surface and reaction energetics change considerably when compared to previously studied surface model. Here we have studied the TMA-H2O process using density functional theory on a hydroxylated alumina surface and reproduced the previous results for comparison. Mechanisms and energetics during both the TMA and the subsequent water pulse are presented. TMA is found to adsorb exothermically onto the surface. The reaction barriers for the ligand-exchange reactions between the TMA and the surface hydroxyl groups were found to be much lower compared to previously presented results. TMA dissociation on the surface is predicted to saturate at monomethylaluminium. Barriers for proton diffusion between surface sites are observed to be low. TMA adsorption was also found to be cooperative with the formation of methyl bridges between the adsorbants. The water pulse was studied using single water molecules reacting with the DMA and MMA surface species. Barriers for these reactions were found to reasonable in the process conditions. However, stabilizing interactions amongst water molecules were found to lower the reaction barriers and the dynamical nature of water is predicted to be of importance. It is expected that these calculations can only set an upper limit for the barriers during the water pulse.
Membrane electrode assembly fabricated with the combination of Pt/C and hollow shell structured-Pt-SiO2@ZrO2 sphere for self-humidifying proton exchange membrane fuel cell

NASA Astrophysics Data System (ADS)

Ko, Y. D.; Yang, H. N.; Züttel, Andreas; Kim, S. D.; Kim, W. J.

2017-11-01

The Pt-supported hollow structured Pt-HZrO2 with the shell thickness of 27 nm is successfully synthesized. The water retention ability of Pt-HZrO2 is significantly enhanced compared with that of SiO2@ZrO2 due to the hydrophilic hollow structured HZrO2with high BET surface area. Pt-C and Pt-HZrO2 are combined with different weight fractions to prepare the double catalyst electrode (DCE). The membrane electrode assembly with the DCE is fabricated and applied to both anode and cathode or anode side only. The water flooding and thus rapid voltage drop is affected by the presence/or absence of the DCE at the cathode side. The cell test and visual experiment suggests that the Pt-HZrO2 layer adsorb the water molecules generated by the oxygen reduction reaction (ORR), preventing the water flooding. The power generation under RH 0% strongly suggests the back-diffusion of water molecules generated by the ORR. The flow rate to the cathode significantly affects the water flooding and cell performance. Higher flow rate to the cathode is advantageous to expel the water generated by the ORR, thus preventing water flooding and enhancing the cell performance. Therefore, the weight fraction of Pt-C to Pt-HZrO2 and the flow rate to the cathode should be well balanced.
Novel surface diffusion characteristics for a robust pentacene derivative on Au(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Miller, Ryan A.; Larson, Amanda; Pohl, Karsten

2017-06-01

Molecular dynamics simulations have been performed in both the ab initio and classical mechanics frameworks of 5,6,7-trithiapentacene-13-one (TTPO) molecules on flat Au(1 1 1) surfaces. Results show new surface diffusion characteristics including a strong preference for the molecule to align its long axis parallel to the sixfold Au(1 1 1) symmetry directions and subsequently diffuse along these close-packed directions, and a calculated activation energy for diffusion of 0.142 eV, about four times larger than that for pure pentacene on Au. The temperature-dependent diffusion coefficients were calculated to help quantify the molecular mobility during the experimentally observed process of forming self-assembled monolayers on gold electrodes.
Anisotropy of the water-carbon interaction: molecular simulations of water in low-diameter carbon nanotubes.

PubMed

Pérez-Hernández, Guillermo; Schmidt, Burkhard

2013-04-14

Effective Lennard-Jones models for the water-carbon interaction are derived from existing high-level ab initio calculations of water adsorbed on graphene models. The resulting potential energy well (εCO + 2εCH ≈ 1 kJ mol(-1)) is deeper than most of the previously used values in the literature on water in carbon nanotubes (CNTs). Moreover, a substantial anisotropy of the water-carbon interaction (εCO ≈ 2εCH) is obtained, which is neglected in most of the literature. We systematically investigate the effect of this anisotropy on structure and dynamics of TIP5P water confined in narrow, single-walled CNTs by means of molecular dynamics simulations for T = 300 K. While for isotropic models water usually forms one-dimensional, ordered chains inside (6,6) CNTs, we find frequent chain ruptures in simulations with medium to strongly anisotropic potentials. Here, the water molecules tend to form denser clusters displaying a liquid-like behaviour, allowing for self-diffusion along the CNT axis, in contrast to all previous simulations employing spherical (εCH = 0) interaction models. For (7,7) CNTs we observe structures close to trigonal, helical ice nanotubes which exhibit a non-monotonous dependence on the anisotropy of the water-carbon interaction. Both for vanishing and for large values of εCH we find increased fluctuations leading to a more liquid-like behaviour, with enhanced axial diffusion. In contrast, structure and dynamics of water inside (8,8) CNTs are found to be almost independent of the anisotropy of the underlying potential, which is attributed to the higher stability of the non-helical fivefold water prisms. We predict this situation to also prevail for larger CNTs, as the influence of the water-water interaction dominates over that of the water-carbon interaction.
Adenosine triphosphate diffusion through poly(ethylene glycol) diacrylate hydrogels can be tuned by cross-link density as measured by PFG-NMR

NASA Astrophysics Data System (ADS)

Majer, Günter; Southan, Alexander

2017-06-01

The diffusion of small molecules through hydrogels is of great importance for many applications. Especially in biological contexts, the diffusion of nutrients through hydrogel networks defines whether cells can survive inside the hydrogel or not. In this contribution, hydrogels based on poly(ethylene glycol) diacrylate with mesh sizes ranging from ξ = 1.1 to 12.9 nm are prepared using polymers with number-average molecular weights between Mn = 700 and 8000 g/mol. Precise measurements of diffusion coefficients D of adenosine triphosphate (ATP), an important energy carrier in biological systems, in these hydrogels are performed by pulsed field gradient nuclear magnetic resonance. Depending on the mesh size, ξ, and on the polymer volume fraction of the hydrogel after swelling, ϕ, it is possible to tune the relative ATP diffusion coefficient D/D0 in the hydrogels to values between 0.14 and 0.77 compared to the ATP diffusion coefficient D0 in water. The diffusion coefficients of ATP in these hydrogels are compared with predictions of various mathematical expressions developed under different model assumptions. The experimental data are found to be in good agreement with the predictions of a modified obstruction model or the free volume theory in combination with the sieving behavior of the polymer chains. No reasonable agreement was found with the pure hydrodynamic model.
Exploring Drug Diffusion through a Membrane: A Physical Chemistry Experiment for Health and Life Sciences Undergraduate Students

ERIC Educational Resources Information Center

Ribeiro, Isabel A. C.; Faustino, Ce´lia M. C.; Guedes, Rita C.; Alfaia, Anto´nio J. I.; Ribeiro, Maria H. L.

2015-01-01

The transport of molecules across biological membranes are critical for most cellular processes. Membrane permeability is also a key determinant for drug absorption, distribution, and elimination. Diffusion, that is, the migration of matter down a concentration gradient, is a simple mechanism by which both endogenous and drug molecules can enter…
Loading and release mechanisms of a biocide in polystyrene-block-poly(acrylic acid) block copolymer micelles.

PubMed

Vyhnalkova, Renata; Eisenberg, Adi; van de Ven, Theo G M

2008-07-24

The kinetics of loading of polystyrene197-block-poly(acrylic acid)47 (PS197-b-PAA47) micelles, suspended in water, with thiocyanomethylthiobenzothiazole biocide and its subsequent release were investigated. Loading of the micelles was found to be a two-step process. First, the surface of the PS core of the micelles is saturated with biocide, with a rate determined by the transfer of solid biocide to micelles during transient micelle-biocide contacts. Next, the biocide penetrates as a front into the micelles, lowering the Tg in the process (non-Fickian case II diffusion). The slow rate of release is governed by the height of the energy barrier that a biocide molecule must overcome to pass from PS into water, resulting in a uniform biocide concentration within the micelle, until Tg is increased to the point that diffusion inside the micelles becomes very slow. Maximum loading of biocide into micelles is approximately 30% (w/w) and is achieved in 1 h. From partition experiments, it can be concluded that the biocide has a similar preference for polystyrene as for ethylbenzene over water, implying that the maximum loading is governed by thermodynamics.
A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

PubMed

Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

2016-10-07

In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO 4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.
Molecular Diffusion in Plasma Membranes of Primary Lymphocytes Measured by Fluorescence Correlation Spectroscopy.

PubMed

Staaf, Elina; Bagawath-Singh, Sunitha; Johansson, Sofia

2017-02-01

Fluorescence correlation spectroscopy (FCS) is a powerful technique for studying the diffusion of molecules within biological membranes with high spatial and temporal resolution. FCS can quantify the molecular concentration and diffusion coefficient of fluorescently labeled molecules in the cell membrane. This technique has the ability to explore the molecular diffusion characteristics of molecules in the plasma membrane of immune cells in steady state (i.e., without processes affecting the result during the actual measurement time). FCS is suitable for studying the diffusion of proteins that are expressed at levels typical for most endogenous proteins. Here, a straightforward and robust method to determine the diffusion rate of cell membrane proteins on primary lymphocytes is demonstrated. An effective way to perform measurements on antibody-stained live cells and commonly occurring observations after acquisition are described. The recent advancements in the development of photo-stable fluorescent dyes can be utilized by conjugating the antibodies of interest to appropriate dyes that do not bleach extensively during the measurements. Additionally, this allows for the detection of slowly diffusing entities, which is a common feature of proteins expressed in cell membranes. The analysis procedure to extract molecular concentration and diffusion parameters from the generated autocorrelation curves is highlighted. In summary, a basic protocol for FCS measurements is provided; it can be followed by immunologists with an understanding of confocal microscopy but with no other previous experience of techniques for measuring dynamic parameters, such as molecular diffusion rates.
Controlling molecular condensation/diffusion of copper phthalocyanine by local electric field induced with scanning tunneling microscope tip

NASA Astrophysics Data System (ADS)

Nagaoka, Katsumi; Yaginuma, Shin; Nakayama, Tomonobu

2018-02-01

We have discovered the condensation/diffusion phenomena of copper phthalocyanine (CuPc) molecules controlled with a pulsed electric field induced by the scanning tunneling microscope tip. This behavior is not explained by the conventional induced dipole model. In order to understand the mechanism, we have measured the electronic structure of the molecule by tunneling spectroscopy and also performed theoretical calculations on molecular orbitals. These data clearly indicate that the molecule is positively charged owing to charge transfer to the substrate, and that hydrogen bonding exists between CuPc molecules, which makes the molecular island stable.
The frequency-dependent response of single aerosol particles to vapour phase oscillations and its application in measuring diffusion coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, Thomas C.; Davies, James F.; Wilson, Kevin R.

A new method for measuring diffusion in the condensed phase of single aerosol particles is proposed and demonstrated. The technique is based on the frequency-dependent response of a binary particle to oscillations in the vapour phase of one of its chemical components. Here, we discuss how this physical situation allows for what would typically be a non-linear boundary value problem to be approximately reduced to a linear boundary value problem. For the case of aqueous aerosol particles, we investigate the accuracy of the closed-form analytical solution to this linear problem through a comparison with the numerical solution of the fullmore » problem. Then, using experimentally measured whispering gallery modes to track the frequency-dependent response of aqueous particles to relative humidity oscillations, we determine diffusion coefficients as a function of water activity. The measured diffusion coefficients are compared to previously reported values found using the two common experiments: (i) the analysis of the sorption/desorption of water from a particle after a step-wise change to the surrounding relative humidity and (ii) the isotopic exchange of water between a particle and the vapour phase. The technique presented here has two main strengths: first, when compared to the sorption/desorption experiment, it does not require the numerical evaluation of a boundary value problem during the fitting process as a closed-form expression is available. Second, when compared to the isotope exchange experiment, it does not require the use of labeled molecules. Therefore, the frequency-dependent experiment retains the advantages of these two commonly used methods but does not suffer from their drawbacks.« less
The frequency-dependent response of single aerosol particles to vapour phase oscillations and its application in measuring diffusion coefficients

DOE PAGES

Preston, Thomas C.; Davies, James F.; Wilson, Kevin R.

2017-01-13

A new method for measuring diffusion in the condensed phase of single aerosol particles is proposed and demonstrated. The technique is based on the frequency-dependent response of a binary particle to oscillations in the vapour phase of one of its chemical components. Here, we discuss how this physical situation allows for what would typically be a non-linear boundary value problem to be approximately reduced to a linear boundary value problem. For the case of aqueous aerosol particles, we investigate the accuracy of the closed-form analytical solution to this linear problem through a comparison with the numerical solution of the fullmore » problem. Then, using experimentally measured whispering gallery modes to track the frequency-dependent response of aqueous particles to relative humidity oscillations, we determine diffusion coefficients as a function of water activity. The measured diffusion coefficients are compared to previously reported values found using the two common experiments: (i) the analysis of the sorption/desorption of water from a particle after a step-wise change to the surrounding relative humidity and (ii) the isotopic exchange of water between a particle and the vapour phase. The technique presented here has two main strengths: first, when compared to the sorption/desorption experiment, it does not require the numerical evaluation of a boundary value problem during the fitting process as a closed-form expression is available. Second, when compared to the isotope exchange experiment, it does not require the use of labeled molecules. Therefore, the frequency-dependent experiment retains the advantages of these two commonly used methods but does not suffer from their drawbacks.« less
Transient dichroism in photoreceptor membranes indicates that stable oligomers of rhodopsin do not form during excitation.

PubMed Central

Downer, N W; Cone, R A

1985-01-01

If a photoexcited rhodopsin molecule initiates the formation of rhodopsin oligomers during the process of visual excitation, the rate of rotational diffusion of the rhodopsin molecules involved should change markedly. Using microsecond-flash photometry, we have observed the rotational diffusion of rhodopsin throughout the time period of visual excitation and found that no detectable change occurs in its rotational diffusion rate. Partial chemical cross-linking of the retina yields oligomers of rhodopsin and causes a significant decrease in the rotational diffusion rate of rhodopsin even when as little as 20% of rhodopsin is dimeric. Moreover, the pattern of oligomers formed by cross-linking, taken together with the magnitude of decreases in rotational diffusion rate accompanying the cross-linking reaction, suggests that rhodopsin is a monomer in the dark-adapted state. The experiments reported here show that photoexcited rhodopsin molecules do not irreversibly associate with unbleached neighbors during the time course of the receptor response. Hence, it is not likely that stable oligomers of rhodopsin trigger the excitation of the photoreceptor cell. Images FIGURE 1 PMID:3919778
Self-diffusion in the non-Newtonian regime of shearing liquid crystal model systems based on the Gay-Berne potential

NASA Astrophysics Data System (ADS)

Sarman, Sten; Wang, Yong-Lei; Laaksonen, Aatto

2016-02-01

The self-diffusion coefficients of nematic phases of various model systems consisting of regular convex calamitic and discotic ellipsoids and non-convex bodies such as bent-core molecules and soft ellipsoid strings have been obtained as functions of the shear rate in a shear flow. Then the self-diffusion coefficient is a second rank tensor with three different diagonal components and two off-diagonal components. These coefficients were found to be determined by a combination of two mechanisms, which previously have been found to govern the self-diffusion of shearing isotropic liquids, namely, (i) shear alignment enhancing the diffusion in the direction parallel to the streamlines and hindering the diffusion in the perpendicular directions and (ii) the distortion of the shell structure in the liquid whereby a molecule more readily can escape from a surrounding shell of nearest neighbors, so that the mobility increases in every direction. Thus, the diffusion parallel to the streamlines always increases with the shear rate since these mechanisms cooperate in this direction. In the perpendicular directions, these mechanisms counteract each other so that the behaviour becomes less regular. In the case of the nematic phases of the calamitic and discotic ellipsoids and of the bent core molecules, mechanism (ii) prevails so that the diffusion coefficients increase. However, the diffusion coefficients of the soft ellipsoid strings decrease in the direction of the velocity gradient because the broadsides of these molecules are oriented perpendicularly to this direction due the shear alignment (i). The cross coupling coefficient relating a gradient of tracer particles in the direction of the velocity gradient and their flow in the direction of the streamlines is negative and rather large, whereas the other coupling coefficient relating a gradient in the direction of the streamlines and a flow in the direction of the velocity gradient is very small.
Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine Fluorophore into a Phospholipid Bilayer: Complementary Use of Fluorescence Quenching Studies and Molecular Dynamics Simulations

PubMed Central

Kyrychenko, Alexander; Sevriukov, Igor Yu.; Syzova, Zoya A.; Ladokhin, Alexey S.; Doroshenko, Andrey O.

2014-01-01

Successful use of fluorescence sensing in elucidating the biophysical properties of lipid membranes requires knowledge of the distribution and location of an emitting molecule in the bilayer. We report here that 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane. Comparing the fluorescence behavior of BBP in a wide variety of solvents with those in phospholipid vesicles, we suggest that the hydrogen bonding interactions between a BBP fluorophore and water molecules play a crucial role in the observed “light switch effect”. Therefore, the loss of water-induced fluorescence quenching inside a membrane are thought to be due to deep penetration of BBP into the hydrophobic, water-free region of a bilayer. Characterized by strong quenching by transition metal ions in solution, BBP also demonstrated significant shielding from the action of the quencher in the presence of phospholipid vesicles. We used the increase in fluorescence intensity, measured upon titration of probe molecules with lipid vesicles, to estimate the partition constant and the Gibbs free energy (ΔG) of transfer of BBP from aqueous buffer into a membrane. Partitioning BBP revealed strongly favorable ΔG, which depends only slightly on the lipid composition of a bilayer, varying in a range from -6.5 to -7.0 kcal/mol. To elucidate the binding interactions of the probe with a membrane on the molecular level, a distribution and favorable location of BBP in a POPC bilayer were modeled via atomistic molecular dynamics (MD) simulations using two different approaches: (i) free, diffusion-driven partitioning of the probe molecules into a bilayer and (ii) constrained umbrella sampling of a penetration profile of the dye molecule across a bilayer. Both of these MD approaches agreed with regard to the preferred location of a BBP fluorophore within the interfacial region of a bilayer, located between the hydrocarbon acyl tails and the initial portion of the lipid headgroups. MD simulations also revealed restricted permeability of water molecules into this region of a POPC bilayer, determining the strong fluorescence enhancement observed experimentally for the membrane-partitioned form of BBP. PMID:21211898
Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

PubMed

Cooper, Justin T; Peterson, Eric M; Harris, Joel M

2013-10-01

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.
Texturing formulations for uranium skin decontamination.

PubMed

Belhomme-Henry, Corinne; Phan, Guillaume; Huang, Nicolas; Bouvier, Céline; Rebière, François; Agarande, Michelle; Fattal, Elias

2014-09-01

Since no specific treatment exists in case of cutaneous contamination by radionuclides such as uranium, a nanoemulsion comprising calixarene molecules, known for their good chelation properties, was previously designed. However, this fluid topical form may be not suitable for optimal application on the skin or wounds. To develop a texturing pharmaceutical form for the treatment of wounded skins contaminated by uranium. The formulations consisted in oil-in-water (O/W) nanoemulsions, loaded with calixarene molecules. The external phase of the initial liquid nanoemulsion was modified with a combination of thermosensitive gelifying polymers: Poloxamer and HydroxyPropylMethylcellulose (HPMC) or methylcellulose (MC). These new formulations were characterized then tested by ex vivo experiments on Franz cells to prevent uranyl ions diffusion through excoriated pig ear skin explants. Despite strong changes in rheological properties, the physico-chemical characteristics of the new nanoemulsions, such as the size and the zeta potential as well as macroscopic aspect were preserved. In addition, on wounded skin, diffusion of uranyl ions, measured by ICP-MS, was limited to less than 5% for both HPMC and MC nanoemulsions. These results demonstrated that a hybrid formulation of nanoemulsion in hydrogel is efficient to treat uranium skin contamination.
Model of transient drug diffusion across cornea.

PubMed

Zhang, Wensheng; Prausnitz, Mark R; Edwards, Aurélie

2004-09-30

A mathematical model of solute transient diffusion across the cornea to the anterior chamber of the eye was developed for topical drug delivery. Solute bioavailability was predicted given solute molecular radius and octanol-to-water distribution coefficient (Phi), ocular membrane ultrastructural parameters, tear fluid hydrodynamics, as well as solute distribution volume (Vd) and clearance rate (Cla) in the anterior chamber. The results suggest that drug bioavailability is primarily determined by solute lipophilicity. In human eyes, bioavailability is predicted to range between 1% and 5% for lipophilic molecules (Phi>1), and to be less than 0.5% for hydrophilic molecules (Phi<0.01). The simulations indicate that the distribution coefficient that maximizes bioavailability is on the order of 10. It was also found that the maximum solute concentration in the anterior chamber (Cmax) and the time needed to reach Cmax significantly depend on Phi, Vd, and Cla. Consistent with experimental findings, model predictions suggest that drug bioavailability can be increased by lowering the conjunctival-to-corneal permeability ratio and reducing precorneal solute drainage. Because of its mechanistic basis, this model will be useful to predict drug transport kinetics and bioavailability for new compounds and in diseased eyes.
Characterization of thin film CO2 ice through the infrared ν1 + ν3 combination mode

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-01-01

Carbon dioxide is abundant in ice mantles of dust grains; some is found in the pure crystalline form as inferred from the double peak splitting of the bending profile at about 650 cm-1. To study how CO2 segregates into the pure form from water-rich mixtures of ice mantles and how it then crystallizes, we used Reflection Absorption InfraRed Spectroscopy to study the structural change of pure CO2 ice as a function of both ice thickness and temperature. We found that the ν1 + ν3 combination mode absorption profile at 3708 cm-1 provides an excellent probe to quantify the degree of crystallinity in CO2 ice. We also found that between 20 and 30 K, there is an ordering transition that we attribute to reorientation of CO2 molecules, while the diffusion of CO2 becomes significant at much higher temperatures. In the formation of pure crystalline CO2 in interstellar medium ices, the rate limiting process is the diffusion/segregation of CO2 molecules in the ice instead of the phase transition from amorphous to crystalline after clusters/islands of CO2 are formed.
Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

1995-01-01

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

How Water’s Properties Are Encoded in Its Molecular Structure and Energies

PubMed Central

2017-01-01

How are water’s material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth’s living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies—water’s solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions—hydroxide and protons—diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water’s molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water’s orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties. PMID:28949513
Nanomechanical measurements of ionic effect on nanoconfined water

NASA Astrophysics Data System (ADS)

Kramkowski, Edward; Khan, Shah; Hoffmann, Peter

2015-03-01

The behavior of liquid molecules confined to nanometer-scale spaces is a topic of particular interest to a variety of fields. From lab-on-a-chip medical device manufacturers to petroleum engineers involved in oil recovery, a wide range of researchers could benefit from a better understanding of the mechanics of nanoconfined liquids. Previous research has shown that above a critical strain rate, a confined liquid exhibits a solid-like response that oscillates with a period roughly equal to the molecular diameter of the liquid being observed. This indicates that when a liquid is compressed at a rate faster than the molecules can diffuse in bulk out from between the confining surfaces, it dynamically solidifies into an anisotropic layered liquid. In order to better understand the influence that the confining surfaces have on this behavior, we have been observing how the addition of different classes of ions at varying concentrations to a pure water sample either enhance or suppress the natural tendency of the water to order. The work indicates that an ion's effect on the liquid's structure is commensurate with its classification according to the Hofmeister series, with the amount of deviation from the pure behavior governed by the ionic concentration.
Water diffusion in silicate glasses: the effect of glass structure

NASA Astrophysics Data System (ADS)

Kuroda, M.; Tachibana, S.

2016-12-01

Water diffusion in silicate melts (glasses) is one of the main controlling factors of magmatism in a volcanic system. Water diffusivity in silicate glasses depends on its own concentration. However, the mechanism causing those dependences has not been fully understood yet. In order to construct a general model for water diffusion in various silicate glasses, we performed water diffusion experiments in silica glass and proposed a new water diffusion model [Kuroda et al., 2015]. In the model, water diffusivity is controlled by the concentration of both main diffusion species (i.e. molecular water) and diffusion pathways, which are determined by the concentrations of hydroxyl groups and network modifier cations. The model well explains the water diffusivity in various silicate glasses from silica glass to basalt glass. However, pre-exponential factors of water diffusivity in various glasses show five orders of magnitude variations although the pre-exponential factor should ideally represent the jump frequency and the jump distance of molecular water and show a much smaller variation. Here, we attribute the large variation of pre-exponential factors to a glass structure dependence of activation energy for molecular water diffusion. It has been known that the activation energy depends on the water concentration [Nowak and Behrens, 1997]. The concentration of hydroxyls, which cut Si-O-Si network in the glass structure, increases with water concentration, resulting in lowering the activation energy for water diffusion probably due to more fragmented structure. Network modifier cations are likely to play the same role as water. With taking the effect of glass structure into account, we found that the variation of pre-exponential factors of water diffusivity in silicate glasses can be much smaller than the five orders of magnitude, implying that the diffusion of molecular water in silicate glasses is controlled by the same atomic process.
Studies of the Terrestrial Molecular Oxygen and Carbon Cycles in Sand Dune Gases and in Biosphere 2.

NASA Astrophysics Data System (ADS)

Severinghaus, Jeffrey Peck

Molecular oxygen in the atmosphere is coupled tightly to the terrestrial carbon cycle by the processes of photosynthesis, respiration, and burning. This dissertation examines different aspects of this coupling in four chapters. Chapter 1 explores the feasibility of using air from sand dunes to reconstruct atmospheric O_2 composition centuries ago. Such a record would reveal changes in the mass of the terrestrial biosphere, after correction for known fossil fuel combustion, and constrain the fate of anthropogenic CO_2. Test drilling in sand dunes shows that sand dunes do contain old air, as shown by the concentrations of chlorofluorocarbons and ^{85}Kr. Diffusion is shown to dominate mixing rather than advection. However, biological respiration in dunes corrupts the signal, and isotopic analysis of O_2 and N _2 shows that fractionation of the gases precludes use of sand dunes as archives. Chapter 2 further explores this fractionation, revealing a previously unknown "water vapor flux fractionation" process. A flux of water vapor out of the moist dune into the dry desert air sweeps out the other gases, forcing them to diffuse back into the dune. The heavy isotopes of N_2 and O_2 diffuse more slowly, creating a steady state depletion of heavy isotopes in the dune interior. Molecular diffusion theory and a laboratory simulation of the effect agree well with the observations. Additional fractionation of the dune air occurs via thermal diffusion and gravitational settling, and it is predicted that soil gases in general will enjoy all three effects. Chapter 3 examines the cause of a mysterious drop in O _2 concentrations in the closed ecosystem of Biosphere 2, located near Tucson, Arizona. The organic -rich soil manufactured for the experiment is shown to be the culprit, with CO_2 produced by bacterial respiration of the organic matter reacting with the extensive concrete surfaces inside. Chapter 4 examines the O_2:C stoichiometry of terrestrial soil respiration and photosynthesis, in the context of using atmospheric O_2 measurements to constrain the size of the "missing sink" of CO_2. Direct measurements of soil respiration and biomatter elemental abundance suggest a value of 1.1 +/- 0.05 oxygen molecules per CO_2 molecule.
Water in Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Fayer, Michael

2014-03-01

Room temperature ionic liquids (or RTILs, salts with a melting point below 25 °C) have become a subject of intense study over the last several decades. Currently, RTIL application research includes synthesis, batteries, solar cells, crystallization, drug delivery, and optics. RTILs are often composed of an inorganic anion paired with an asymmetric organic cation which contains one or more pendant alkyl chains. The asymmetry of the cation frustrates crystallization, causing the salt's melting point to drop significantly. In general, RTILs are very hygroscopic, and therefore, it is of interest to examine the influence of water on RTIL structure and dynamics. In addition, in contrast to normal aqueous salt solutions, which crystallize at low water concentration, in an RTIL it is possible to examine isolated water molecules interacting with ions but not with other water molecules. Here, optical heterodyne-detected optical Kerr effect (OHD-OKE) measurements of orientational relaxation on a series of 1-alkyl-3-methylimidazolium tetrafluoroborate RTILs as a function of chain length and water concentration are presented. The addition of water to the longer alkyl chain RTILs causes the emergence of a long time bi-exponential orientational anisotropy decay. Such decays have not been seen previously in OHD-OKE experiments on any type of liquid and are analyzed here using a wobbling-in-a-cone model. The orientational relaxation is not hydrodynamic, with the slowest relaxation component becoming slower as the viscosity decreases for the longest chain, highest water content samples. The dynamics of isolated D2O molecules in 1-butyl-3-methylimidazolium hexafluorophosphate (BmImPF6) were examined using two dimensional infrared (2D IR) vibrational echo spectroscopy. Spectral diffusion and incoherent and coherent transfer of excitation between the symmetric and antisymmetric modes are examined. The coherent transfer experiments are used to address the nature of inhomogeneous broadening by observing ~ 100 fs time scale oscillations in the shape of the 2D IR spectra.
Effects of Water on Structure and Dynamics of Trehalose Glasses at Low Water Contents and its Relationship to Preservation Outcomes

NASA Astrophysics Data System (ADS)

Weng, Lindong; Ziaei, Shima; Elliott, Gloria D.

2016-07-01

Dry preservation of biologics in sugar glasses is regarded as a promising alternative to conventional cryopreservation. Evidence from various studies has suggested that there is a critical range of water content beyond which the viability of preserved biologics can be greatly compromised. In this study the viability of T-cells was determined as a function of end water content after microwave-assisted drying in trehalose solutions. Hydrogen-bonding and clustering phenomena in trehalose solutions of the same moisture content were also evaluated using molecular dynamics simulation. Post-rehydration viability decreased dramatically within the range of 0.1-1 gH2O/gdw. Molecular modeling revealed that as the water content approached 0.1 gH2O/gdw the matrix formed a large interconnected trehalose skeleton with a minimal number of bound water molecules scattered in the bulk. The diffusion coefficients of trehalose oxygen atoms most distant from the glycosidic linkage fluctuated around 7.5 × 10-14 m2/s within the range of 0.02-0.1 gH2O/gdw and increased again to ~1.13 × 10-13 m2/s at 0.01 gH2O/gdw and below due to the loss of water in the free volume between trehalose molecules. These insights can guide the optimal selection of final moisture contents to advance dry preservation methods.
Effects of Water on Structure and Dynamics of Trehalose Glasses at Low Water Contents and its Relationship to Preservation Outcomes.

PubMed

Weng, Lindong; Ziaei, Shima; Elliott, Gloria D

2016-07-08

Dry preservation of biologics in sugar glasses is regarded as a promising alternative to conventional cryopreservation. Evidence from various studies has suggested that there is a critical range of water content beyond which the viability of preserved biologics can be greatly compromised. In this study the viability of T-cells was determined as a function of end water content after microwave-assisted drying in trehalose solutions. Hydrogen-bonding and clustering phenomena in trehalose solutions of the same moisture content were also evaluated using molecular dynamics simulation. Post-rehydration viability decreased dramatically within the range of 0.1-1 gH2O/gdw. Molecular modeling revealed that as the water content approached 0.1 gH2O/gdw the matrix formed a large interconnected trehalose skeleton with a minimal number of bound water molecules scattered in the bulk. The diffusion coefficients of trehalose oxygen atoms most distant from the glycosidic linkage fluctuated around 7.5 × 10(-14) m(2)/s within the range of 0.02-0.1 gH2O/gdw and increased again to ~1.13 × 10(-13) m(2)/s at 0.01 gH2O/gdw and below due to the loss of water in the free volume between trehalose molecules. These insights can guide the optimal selection of final moisture contents to advance dry preservation methods.
Enzyme microheterogeneous hydration and stabilization in supercritical carbon dioxide.

PubMed

Silveira, Rodrigo L; Martínez, Julian; Skaf, Munir S; Martínez, Leandro

2012-05-17

Supercritical carbon dioxide is a promising green-chemistry solvent for many enzyme-catalyzed chemical reactions, yet the striking stability of some enzymes in such unconventional environments is not well understood. Here, we investigate the stabilization of the Candida antarctica Lipase B (CALB) in supercritical carbon dioxide-water biphasic systems using molecular dynamics simulations. The preservation of the enzyme structure and optimal activity depend on the presence of small amounts of water in the supercritical dispersing medium. When the protein is at least partially hydrated, water molecules bind to specific sites on the enzyme surface and prevent carbon dioxide from penetrating its catalytic core. Strikingly, water and supercritical carbon dioxide cover the protein surface quite heterogeneously. In the first solvation layer, the hydrophilic residues at the surface of the protein are able to pin down patches of water, whereas carbon dioxide solvates preferentially hydrophobic surface residues. In the outer solvation shells, water molecules tend to cluster predominantly on top of the larger water patches of the first solvation layer instead of spreading evenly around the remainder of the protein surface. For CALB, this exposes the substrate-binding region of the enzyme to carbon dioxide, possibly facilitating diffusion of nonpolar substrates into the catalytic funnel. Therefore, by means of microheterogeneous solvation, enhanced accessibility of hydrophobic substrates to the active site can be achieved, while preserving the functional structure of the enzyme. Our results provide a molecular picture on the nature of the stability of proteins in nonaqueous media.
CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Enhancement of water permeation across nanochannels by partial charges mimicked from biological channels

NASA Astrophysics Data System (ADS)

Gong, Xiao-Jing; Fang, Hai-Ping

2008-07-01

In biological water channel aquaporins (AQPs), it is believed that the bipolar orientation of the single-file water molecules inside the channel blocks proton permeation but not water transport. In this paper, the water permeation and particularly the water-selective behaviour across a single-walled carbon nanotube (SWNT) with two partial charges adjacent to the wall of the SWNT are studied by molecular dynamics simulations, in which the distance between the two partial charges is varied from 0.14 nm to 0.5 nm and the charges each have a quantity of 0.5 e. The two partial charges are used to mimic the charge distribution of the conserved non-pseudoautosomal (NPA) (asparagine/proline/alanine) regions in AQPs. Compared with across the nanochannel in a system with one +1 e charge, the water permeation across the nanochannel is greatly enhanced in a system with two +0.5 e charges when charges are close to the nanotube, i.e. the two partial charges permit more rapid water diffusion and maintain better bipolar order along the water file when the distance between the two charges and the wall of SWNT is smaller than about 0.05 nm. The bipolar orientation of the single-file water molecules is crucial for the exclusion of proton transfer. These findings may serve as guidelines for the future nanodevices by using charges to transport water and have biological implications because membrane water channels share a similar single-file water chain and positive charged region at centre and provide an insight into why two residues are necessitated in the central region of water channel protein.
Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

PubMed

Elsaesser, Thomas

2009-09-15

Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH stretching mode with low-frequency hydrogen-bonding modes leads to additional progressions and coherent low-frequency hydrogen-bond motions in the subpicosecond time domain. In water, the 2D spectra reveal ultrafast spectral diffusion on a sub-100 fs time scale caused by the ultrafast structural fluctuations of the strongly coupled hydrogen-bond network. Librational motions play a key role for the ultrafast loss of structural memory. Spectral diffusion rates are enhanced by resonant transfer of OH stretching quanta between water molecules, typically occurring on a 100 fs time scale. In DNA oligomers, femtosecond nonlinear vibrational spectroscopy resolves NH and OH stretching bands in the highly congested infrared spectra of these molecules, which contain alternating adenine-thymine pairs. Studies at different levels of hydration reveal the spectral signatures of water molecules directly interacting with the phosphate groups of DNA and of a second water species forming a fluctuating environment around the DNA oligomers. We expect that the application of 2D infrared spectroscopy in an extended spectral range will reveal the intrinsic coupling between water and specific functional units of DNA.
A laboratory study of magnesium-tetrabenz-porphyrin - Lack of agreement with diffuse interstellar bands

NASA Technical Reports Server (NTRS)

Donn, B.; Khanna, R. K.

1980-01-01

The visible and infrared spectra and thermal behavior of the bis-pyridal-magnesium-tetrabenz-porphyrin molecule proposed as the carrier of the diffuse interstellar bands were measured. Of the six band coincidences reported by Johnson (1977), only one, 4430 A, occurs in these experiments. This coincidence requires a special environment, not likely to occur in interstellar space but the infrared spectrum does not support Johnson's vibrational scheme. These spectroscopic and thermal measurements contradict the hypothesis that this molecule causes the diffuse bands.
Influence of Hydrogen Sulfide Exposure on the Transport and Structural Properties of the Metal–Organic Framework ZIF-8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, Akshita; Tymi?ska, Nina; Zhu, Guanghui

In this paper, the interaction between hydrogen sulfide and ZIF-8 was studied via structural characterizations and guest molecule diffusion measurements. It was found that hydrogen sulfide reacts with the ZIF-8 external particle surface to form a surface barrier that excludes the uptake of larger molecules (ethanol) and slows down the uptake of smaller molecules (carbon dioxide). Nonetheless, bulk transport properties were unaltered, as supported by pulsed field gradient nuclear magnetic resonance studies. Dispersion-corrected density functional theory calculations revealed that H 2S is consumed by reactions occurring at the ZIF external surface. These reactions result in water and defect formation, bothmore » of which were found to be exothermic and independent of both crystallographic facets ({001} and {110}) and surface termination. Finally, we concluded that these surface reactions lead to structural and chemical changes to the ZIF-8 external surface that generate surface barriers to molecular transport.« less
Influence of Hydrogen Sulfide Exposure on the Transport and Structural Properties of the Metal–Organic Framework ZIF-8

DOE PAGES

Dutta, Akshita; Tymi?ska, Nina; Zhu, Guanghui; ...

2018-03-09

In this paper, the interaction between hydrogen sulfide and ZIF-8 was studied via structural characterizations and guest molecule diffusion measurements. It was found that hydrogen sulfide reacts with the ZIF-8 external particle surface to form a surface barrier that excludes the uptake of larger molecules (ethanol) and slows down the uptake of smaller molecules (carbon dioxide). Nonetheless, bulk transport properties were unaltered, as supported by pulsed field gradient nuclear magnetic resonance studies. Dispersion-corrected density functional theory calculations revealed that H 2S is consumed by reactions occurring at the ZIF external surface. These reactions result in water and defect formation, bothmore » of which were found to be exothermic and independent of both crystallographic facets ({001} and {110}) and surface termination. Finally, we concluded that these surface reactions lead to structural and chemical changes to the ZIF-8 external surface that generate surface barriers to molecular transport.« less
Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less
Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.
Molecular dynamics of lipid bilayers studied by incoherent quasi-elastic neutron scattering

NASA Astrophysics Data System (ADS)

König, S.; Pfeiffer, W.; Bayerl, T.; Richter, D.; Sackmann, E.

1992-08-01

Molecular motions in highly oriented multilayers of dipalmitoylphosphatidylcholine were studied as a function of temperature and hydration using incoherent quasi-elastic neutron scattering (QENS). The short range diffusive motions of the lipid molecules and the chain/headgroup dynamics were evaluated : 1) by measurement of the dependence of the elastic incoherent structure factor (EISF), the line-width Γ and the dynamic structure factors on the scattering vector Q for two orientations of the sample. The orientations were chosen such that the scattering vecto Q was either predominantly perpendicular or parallel to the membrane normal ; 2) by comparing data from protonated and chain deuterated lipids and 3) by the use of instruments of different energy resolution (i.e. time-of-flight and backscattering spectrometers exploring time regimes of 10^{-13} s to 10^{-11} s and 10^{-11} s to 10^{-9} s respectively). In the fluid phase the time-of-flight spectra revealed a restricted isotropic in-plane and out-of-plane diffusion of the hydrocarbon chain and headgroup protons. The mean displacements range from ≈ 0.6 Å for methylene protons near the glycerol backbone to 7 Å for protons near the chain ends. These values are obtained for a water content of 23 wt%. The values are somewhat increased at 30wt% of water. Measurements of the temperature variation of the EISF and the line-width Γ revealed a remarkably high degree of chain dynamics in the gel (L{β '})-phase. The total elastic intensity as observed with the backscattering instrument showed that L{α}-L{β '}-phase transition is only well expressed at Q-values around 1 Å^{-1}, while the number and mobility of the chain defects characterized at Q≈ 2 Å^{-1} (possibly gtg-kinks) increase continuously between 2 °C and 70 °C. In the time regime explored by the backscattering instrument, motions of the whole lipid molecules are also seen. It was interpreted in terms of a superposition of local in-plane and out-of-plane diffusion and lateral diffusional jumps between adjacent sites as predicted by the free volume model. For a sample containing 12 wt% of water at 60 °C the diffusion coefficient for the out-of-plane motion is D^{allel}=6× 10^{-6} cm2/s with an amplitude of 2.25 Å. In-plane the diffusion coefficients range from D_{min}^{perp}=1.5× 10^{-7} cm2/s to D_{max}^{perp}=6× 10^{-6} cm2/s. The lateral diffusion coefficient is D_lat=9.7× 10^{-8} cm2/s in reasonable agreement with FRAP measurements. The strong increase of the lateral mobility with increasing water content yielded an exponential law for the variation of the diffusion coefficient with excess area per lipid (i.e. hydration) in agreement with the free volume model. The out-of-plane motion is characterized by an amplitude of about 0.5 Å in the time-of-flight time regime and of 2-3 Å in the backscattering time regime. The origin of this discrepancy could be the thermally excited membrane undulations since their relaxation times of ≈ 3× 10^{-9} s (obtained in a separate spin-echo study) agree roughly with the reciprocal line-width of 2.5× 10^{-9} s for the backscattering instrument at Qto 0. The time-of-flight result of 0.5 Å can be attributed to a dynamic surface roughness.
Two-dimensional wetting: the role of atomic steps on the nucleation of thin water films on BaF2(111) at ambient conditions.

PubMed

Cardellach, M; Verdaguer, A; Santiso, J; Fraxedas, J

2010-06-21

The interaction of water with freshly cleaved BaF(2)(111) surfaces at ambient conditions (room temperature and under controlled humidity) has been studied using scanning force microscopy in different operation modes. The images strongly suggest a high surface diffusion of water molecules on the surface indicated by the accumulation of water at step edges forming two-dimensional bilayered structures. Steps running along the 110 crystallographic directions show a high degree of hydrophilicity, as evidenced by small step-film contact angles, while steps running along other directions exhibiting a higher degree of kinks surprisingly behave in a quite opposite way. Our results prove that morphological defects such as steps can be crucial in improving two-dimensional monolayer wetting and stabilization of multilayer grown on surfaces that show good lattice mismatch with hexagonal ice.
[Effects of several low-molecular-weight organic acids on the release kinetic of endosulfan from red soil].

PubMed

Zhao, Zhen-hua; Wu, Yu; Jiang, Xin; Xia, Li-ling; Ni, Li-xiao

2009-10-15

The kinetic release behaviors of a-endosulfan from red soil with three kinds of low-molecular-weight organic acids (LMWOA: oxalate, tartrate and citrate) solution and water leaching were investigated by kinetic device designed by ourselves and batch method. The results show that: the release percentage of endosulfan from red soil by tartrate and citrate solution (10 mmol/L) can increase by 7%-18% more than that by distilled water and oxalate solution, especially for tartrate solution. There is no significant difference between distilled water and oxalate solution for the release percentage of endosulfan (p > 0.05). There are two stages of quick and slow for the release of endosulfan from red soil, and the leaching speed is quicker especially for the initial 200 mL leaching solution. When using distilled water or oxalate solution as leaching solution, the best equations that described the kinetic release behavior of endosulfan from red soil were parabola diffuse equation and double constant equation, and weren't the apparent first dynamics equation that represented the simple surface diffusion mechanism. The kinetic release behavior of endosulfan in tartrate or citrate leaching system can be described by Elovich equation (R2 > 0.99, p < 0.0001), it implied that the simple surface diffusion mechanism is not the primary factor that effected the release of endosulfan, which three-dimensional molecule structure is complex, from red soil in aqueous phase leaching systems, and it maybe related to the outward diffuse mechanism from soil particle, activation and deactivation function of soil particles surface, the dissolution of soil mineral surface and structure change of inherent organic matter that coating onto the soil mineral surface induced by LMW organic acid. It suggested that the tartrate and citrate induced the complication of the release mechanisms of the pesticides from red soil.
Mechanisms of the Diffusion of Nonpolar Substances in a Hydrophilic Ionic Liquid

NASA Astrophysics Data System (ADS)

Atamas', N. A.

2018-01-01

The structural-dynamic features of ionic liquid-nonpolar substance systems are studied by means of molecular dynamics using Frenkel's fundamental theory of a liquid and the phonon theory of the thermodynamics of a liquid, in combination with the DL_POLY_4.05 software package. Argon, methane, and benzene molecules serve as the dissolved substances. Model concepts are proposed and analyzed to describe the diffusion of molecules of a dissolved substance in an ionic liquid. It is shown that an increase in the mass of the molecules of a dissolved nonpolar substance correlates with their mobility in a hydrophilic ionic liquid (IL). This determines the diffusion of the components of dmim+/Cl- IL solutions and is responsible for the anomalous behavior of the solubility of nonpolar substances in them.
A New View of the Bacterial Cytosol Environment

PubMed Central

Cossins, Benjamin P.; Jacobson, Matthew P.; Guallar, Victor

2011-01-01

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend ∼80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often associate with proteins. Mg2+ ions were prominent in NIMS and almost absent free in solution. Κ+ is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution. PMID:21695225

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