The controlled formation and cleavage of an intramolecular d8-d8 Pt-Pt interaction in a dinuclear cycloplatinated molecular "pivot-hinge".

PubMed

Koo, Chi-Kin; Wong, Ka-Leung; Lau, Kai-Cheung; Wong, Wai-Yeung; Lam, Michael Hon-Wah

2009-08-03

The bis(diphenylphosphino)methane (dppm)-bridged dinuclear cycloplatinated complex {[Pt(L)](2)(mu-dppm)}(2+) (Pt(2)dppm; HL: 2-phenyl-6-(1H-pyrazol-3-yl)-pyridine) demonstrates interesting reversible "pivot-hinge"-like intramolecular motions in response to the protonation/deprotonation of L. In its protonated "closed" configuration, the two platinum(II) centers are held in position by intramolecular d(8)-d(8) Pt-Pt interaction. In its deprotonated "open" configuration, such Pt-Pt interaction is cleaved. To further understand the mechanism behind this hingelike motion, an analogous dinuclear cycloplatinated complex, {[Pt(L)](2)(mu-dchpm)}(2+) (Pt(2)dchpm) with bis(dicyclohexylphosphino)methane (dchpm) as the bridging ligand, was synthesized. From its protonation/deprotonation responses, it was revealed that aromatic pi-pi interactions between the phenyl moieties of the mu-dppm and the deprotonated pyrazolyl rings of L was essential to the reversible cleavage of the intramolecular Pt-Pt interaction in Pt(2)dppm. In the case of Pt(2)dchpm, spectroscopic and spectrofluorometric titrations as well as X-ray crystallography indicated that the distance between the two platinum(II) centers shrank upon deprotonation, thus causing a redshift in its room-temperature triplet metal-metal-to-ligand charge-transfer emission from 614 to 625 nm. Ab initio calculations revealed the presence of intramolecular hydrogen bonding between the deprotonated and negatively charged 1-pyrazolyl-N moiety and the methylene CH and phenyl C-H of the mu-dppm. The "open" configuration of the deprotonated Pt(2)dppm was estimated to be 19 kcal mol(-1) more stable than its alternative "closed" configuration. On the other hand, the open configuration of the deprotonated Pt(2)dchpm was 6 kcal mol(-1) less stable than its alternative closed configuration.

Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

NASA Astrophysics Data System (ADS)

Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

2015-01-01

SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the ‘binder clip-like’ motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

PubMed

Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

2015-06-01

Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.

Motion immune diffusion imaging using augmented MUSE (AMUSE) for high-resolution multi-shot EPI

PubMed Central

Guhaniyogi, Shayan; Chu, Mei-Lan; Chang, Hing-Chiu; Song, Allen W.; Chen, Nan-kuei

2015-01-01

Purpose To develop new techniques for reducing the effects of microscopic and macroscopic patient motion in diffusion imaging acquired with high-resolution multi-shot EPI. Theory The previously reported Multiplexed Sensitivity Encoding (MUSE) algorithm is extended to account for macroscopic pixel misregistrations as well as motion-induced phase errors in a technique called Augmented MUSE (AMUSE). Furthermore, to obtain more accurate quantitative DTI measures in the presence of subject motion, we also account for the altered diffusion encoding among shots arising from macroscopic motion. Methods MUSE and AMUSE were evaluated on simulated and in vivo motion-corrupted multi-shot diffusion data. Evaluations were made both on the resulting imaging quality and estimated diffusion tensor metrics. Results AMUSE was found to reduce image blurring resulting from macroscopic subject motion compared to MUSE, but yielded inaccurate tensor estimations when neglecting the altered diffusion encoding. Including the altered diffusion encoding in AMUSE produced better estimations of diffusion tensors. Conclusion The use of AMUSE allows for improved image quality and diffusion tensor accuracy in the presence of macroscopic subject motion during multi-shot diffusion imaging. These techniques should facilitate future high-resolution diffusion imaging. PMID:25762216

Detailed characterization of mechanical properties and molecular mobility within dry seed glasses: relevance to the physiology of dry biological systems.

PubMed

Ballesteros, Daniel; Walters, Christina

2011-11-01

Slow movement of molecules in glassy matrices controls the kinetics of chemical and physical reactions in dry seeds. Variation in physiological activity among seeds suggests that there are differences in mobility among seed glasses. Testing this hypothesis is difficult because few tools are available to measure molecular mobility within dry seeds. Here, motional properties within dry pea cotyledons were assessed using dynamic mechanical analysis. The technique detected several molecular relaxations between -80 and +80°C and gave a more detailed description of water content-temperature effects on molecular motion than previously understood from studies of glass formation in seeds at glass transition (Tg). Diffusive movement is delimited by the α relaxation, which appears to be analogous to Tg. β and γ relaxations were also detected at temperatures lower than α relaxations, clearly demonstrating intramolecular motion within the glassy matrix of the pea cotyledon. Glass transitions, or the mechanical counterpart α relaxation, appear to be less relevant to seed aging during dry storage than previously thought. On the other hand, β relaxation occurs at temperature and moisture conditions typically used for seed storage and has established importance for physical aging of synthetic polymer glasses. Our data show that the nature and extent of molecular motion varies considerably with moisture and temperature, and that the hydrated conditions used for accelerated aging experiments and ultra-dry conditions sometimes recommended for seed storage give greater molecular mobility than more standard seed storage practices. We believe characterization of molecular mobility is critical for evaluating how dry seeds respond to the environment and persist through time. Published 2011. This article is a US Government work and is in the public domain in the USA.

Intramolecular Dynamics within the N-Cap-SH3-SH2 Regulatory Unit of the c-Abl Tyrosine Kinase Reveal Targeting to the Cellular Membrane*♦

PubMed Central

de Oliveira, Guilherme A. P.; Pereira, Elen G.; Ferretti, Giulia D. S.; Valente, Ana Paula; Cordeiro, Yraima; Silva, Jerson L.

2013-01-01

c-Abl is a key regulator of cell signaling and is under strict control via intramolecular interactions. In this study, we address changes in the intramolecular dynamics coupling within the c-Abl regulatory unit by presenting its N-terminal segment (N-Cap) with an alternative function in the cell as c-Abl becomes activated. Using small angle x-ray scattering, nuclear magnetic resonance, and confocal microscopy, we demonstrate that the N-Cap and the Src homology (SH) 3 domain acquire μs-ms motions upon N-Cap association with the SH2-L domain, revealing a stabilizing synergy between these segments. The N-Cap-myristoyl tether likely triggers the protein to anchor to the membrane because of these flip-flop dynamics, which occur in the μs-ms time range. This segment not only presents the myristate during c-Abl inhibition but may also trigger protein localization inside the cell in a functional and stability-dependent mechanism that is lost in Bcr-Abl+ cells, which underlie chronic myeloid leukemia. This loss of intramolecular dynamics and binding to the cellular membrane is a potential therapeutic target. PMID:23928308

Intramolecular dynamics within the N-Cap-SH3-SH2 regulatory unit of the c-Abl tyrosine kinase reveal targeting to the cellular membrane.

PubMed

de Oliveira, Guilherme A P; Pereira, Elen G; Ferretti, Giulia D S; Valente, Ana Paula; Cordeiro, Yraima; Silva, Jerson L

2013-09-27

c-Abl is a key regulator of cell signaling and is under strict control via intramolecular interactions. In this study, we address changes in the intramolecular dynamics coupling within the c-Abl regulatory unit by presenting its N-terminal segment (N-Cap) with an alternative function in the cell as c-Abl becomes activated. Using small angle x-ray scattering, nuclear magnetic resonance, and confocal microscopy, we demonstrate that the N-Cap and the Src homology (SH) 3 domain acquire μs-ms motions upon N-Cap association with the SH2-L domain, revealing a stabilizing synergy between these segments. The N-Cap-myristoyl tether likely triggers the protein to anchor to the membrane because of these flip-flop dynamics, which occur in the μs-ms time range. This segment not only presents the myristate during c-Abl inhibition but may also trigger protein localization inside the cell in a functional and stability-dependent mechanism that is lost in Bcr-Abl(+) cells, which underlie chronic myeloid leukemia. This loss of intramolecular dynamics and binding to the cellular membrane is a potential therapeutic target.

Excited-state dynamics of the medicinal pigment curcumin in a hydrogel.

PubMed

Harada, Takaaki; Lincoln, Stephen F; Kee, Tak W

2016-10-12

Curcumin is a yellow polyphenol with multiple medicinal effects. These effects, however, are limited due to its poor aqueous stability and solubility. A hydrogel of 3% octadecyl randomly substituted polyacrylate (PAAC18) has been shown to provide high aqueous stability for curcumin under physiological conditions, offering a route for photodynamic therapy. In this study, the excited-state photophysics of curcumin in the PAAC18 hydrogel is investigated using a combination of femtosecond transient absorption and fluorescence upconversion spectroscopy. The transient absorption results reveal a multiexponential decay in the excited-state kinetics with fast (1 ps & 15 ps) and slow (110 ps & ≈5 ns) components. The fast decay component exhibits a deuterium isotope effect with D 2 O in the hydrogel, indicating that the 15 ps decay component is attributable to excited-state intramolecular hydrogen atom transfer of curcumin in the PAAC18 hydrogel. In addition, solvent reorganisation of excited-state curcumin is investigated using multiwavelength femtosecond fluorescence upconversion spectroscopy. The results show that the dominant solvation response (τ = 0.08 ps) is a fast inertial motion owing to the presence of bulk-like water in the vicinity of the hydrophobic octadecyl substituents of the PAAC18 hydrogel. The results also show an additional response with longer time constants of 1 and 6 ps, which is attributable to translational diffusion of confined water molecules in the three-dimensional, cross-linking network of the octadecyl substituents of PAAC18. Overall, we show that excited-state intramolecular hydrogen atom transfer and solvent reorganisation are major photophysical events for curcumin in the PAAC18 hydrogel.

Self-referenced coherent diffraction x-ray movie of Ångstrom- and femtosecond-scale atomic motion

DOE PAGES

Glownia, J. M.; Natan, A.; Cryan, J. P.; ...

2016-10-03

Time-resolved femtosecond x-ray diffraction patterns from laser-excited molecular iodine are used to create a movie of intramolecular motion with a temporal and spatial resolution of 30 fs and 0.3 Å. This high fidelity is due to interference between the nonstationary excitation and the stationary initial charge distribution. The initial state is used as the local oscillator for heterodyne amplification of the excited charge distribution to retrieve real-space movies of atomic motion on ångstrom and femtosecond scales. This x-ray interference has not been employed to image internal motion in molecules before. In conclusion, coherent vibrational motion and dispersion, dissociation, and rotationalmore » dephasing are all clearly visible in the data, thereby demonstrating the stunning sensitivity of heterodyne methods.« less

Ultrafast inter- and intramolecular vibrational energy transfer between molecules at interfaces studied by time- and polarization-resolved SFG spectroscopy.

PubMed

Yamamoto, Susumu; Ghosh, Avishek; Nienhuys, Han-Kwang; Bonn, Mischa

2010-10-28

We present experimental results on femtosecond time-resolved surface vibrational spectroscopy aimed at elucidating the sub-picosecond reorientational dynamics of surface molecules. The approach, which relies on polarization- and time-resolved surface sum frequency generation (SFG), provides a general means to monitor interfacial reorientational dynamics through vibrations inherent in surface molecules in their electronic ground state. The technique requires an anisotropic vibrational excitation of surface molecules using orthogonally polarized infrared excitation light. The decay of the resulting anisotropy is followed in real-time. We employ the technique to reveal the reorientational dynamics of vibrational transition dipoles of long-chain primary alcohols on the water surface, and of water molecules at the water-air interface. The results demonstrate that, in addition to reorientational motion of specific molecules or molecular groups at the interface, inter- and intramolecular energy transfer processes can serve to scramble the initial anisotropy very efficiently. In the two exemplary cases demonstrated here, energy transfer occurs much faster than reorientational motion of interfacial molecules. This has important implications for the interpretation of static SFG spectra. Finally, we suggest experimental schemes and strategies to decouple effects resulting from energy transfer from those associated with surface molecular motion.

An approximate classical unimolecular reaction rate theory

NASA Astrophysics Data System (ADS)

Zhao, Meishan; Rice, Stuart A.

1992-05-01

We describe a classical theory of unimolecular reaction rate which is derived from the analysis of Davis and Gray by use of simplifying approximations. These approximations concern the calculation of the locations of, and the fluxes of phase points across, the bottlenecks to fragmentation and to intramolecular energy transfer. The bottleneck to fragment separation is represented as a vibration-rotation state dependent separatrix, which approximation is similar to but extends and improves the approximations for the separatrix introduced by Gray, Rice, and Davis and by Zhao and Rice. The novel feature in our analysis is the representation of the bottlenecks to intramolecular energy transfer as dividing surfaces in phase space; the locations of these dividing surfaces are determined by the same conditions as locate the remnants of robust tori with frequency ratios related to the golden mean (in a two degree of freedom system these are the cantori). The flux of phase points across each dividing surface is calculated with an analytic representation instead of a stroboscopic mapping. The rate of unimolecular reaction is identified with the net rate at which phase points escape from the region of quasiperiodic bounded motion to the region of free fragment motion by consecutively crossing the dividing surfaces for intramolecular energy exchange and the separatrix. This new theory generates predictions of the rates of predissociation of the van der Waals molecules HeI2, NeI2 and ArI2 which are in very good agreement with available experimental data.

String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

NASA Astrophysics Data System (ADS)

Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

2018-03-01

Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.

A spin echo sequence with a single-sided bipolar diffusion gradient pulse to obtain snapshot diffusion weighted images in moving media

NASA Astrophysics Data System (ADS)

Freidlin, R. Z.; Kakareka, J. W.; Pohida, T. J.; Komlosh, M. E.; Basser, P. J.

2012-08-01

In vivo MRI data can be corrupted by motion. Motion artifacts are particularly troublesome in Diffusion Weighted MRI (DWI), since the MR signal attenuation due to Brownian motion can be much less than the signal loss due to dephasing from other types of complex tissue motion, which can significantly degrade the estimation of self-diffusion coefficients, diffusion tensors, etc. This paper describes a snapshot DWI sequence, which utilizes a novel single-sided bipolar diffusion sensitizing gradient pulse within a spin echo sequence. The proposed method shortens the diffusion time by applying a single refocused bipolar diffusion gradient on one side of a refocusing RF pulse, instead of a set of diffusion sensitizing gradients, separated by a refocusing RF pulse, while reducing the impact of magnetic field inhomogeneity by using a spin echo sequence. A novel MRI phantom that can exhibit a range of complex motions was designed to demonstrate the robustness of the proposed DWI sequence.

Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.

PubMed

Ryu, Kyoung-Seok; Tugarinov, Vitali; Clore, G Marius

2014-10-15

The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by (15)Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5-1 s) is many orders of magnitude larger than the calculated transfer time (1-100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.

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.

QTAIM and Stress Tensor Characterization of Intramolecular Interactions Along Dynamics Trajectories of a Light-Driven Rotary Molecular Motor.

PubMed

Wang, Lingling; Huan, Guo; Momen, Roya; Azizi, Alireza; Xu, Tianlv; Kirk, Steven R; Filatov, Michael; Jenkins, Samantha

2017-06-29

A quantum theory of atoms in molecules (QTAIM) and stress tensor analysis was applied to analyze intramolecular interactions influencing the photoisomerization dynamics of a light-driven rotary molecular motor. For selected nonadiabatic molecular dynamics trajectories characterized by markedly different S 1 state lifetimes, the electron densities were obtained using the ensemble density functional theory method. The analysis revealed that torsional motion of the molecular motor blades from the Franck-Condon point to the S 1 energy minimum and the S 1 /S 0 conical intersection is controlled by two factors: greater numbers of intramolecular bonds before the hop-time and unusually strongly coupled bonds between the atoms of the rotor and the stator blades. This results in the effective stalling of the progress along the torsional path for an extended period of time. This finding suggests a possibility of chemical tuning of the speed of photoisomerization of molecular motors and related molecular switches by reshaping their molecular backbones to decrease or increase the degree of coupling and numbers of intramolecular bond critical points as revealed by the QTAIM/stress tensor analysis of the electron density. Additionally, the stress tensor scalar and vector analysis was found to provide new methods to follow the trajectories, and from this, new insight was gained into the behavior of the S 1 state in the vicinity of the conical intersection.

Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes

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

Zhang, Feng; Tominaga, Keisuke, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp; Hayashi, Michitoshi, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp

2014-05-07

The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D{sup *} have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. Themore » relationship between the experimentally obtained IS and the IS obtained by PBE-D{sup *} simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D{sup *} data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D{sup *} produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D{sup *}.« less

Apparent diffusive motion of centrin foci in living cells: implications for diffusion-based motion in centriole duplication

NASA Astrophysics Data System (ADS)

Rafelski, Susanne M.; Keller, Lani C.; Alberts, Jonathan B.; Marshall, Wallace F.

2011-04-01

The degree to which diffusion contributes to positioning cellular structures is an open question. Here we investigate the question of whether diffusive motion of centrin granules would allow them to interact with the mother centriole. The role of centrin granules in centriole duplication remains unclear, but some proposed functions of these granules, for example, in providing pre-assembled centriole subunits, or by acting as unstable 'pre-centrioles' that need to be captured by the mother centriole (La Terra et al 2005 J. Cell Biol. 168 713-22), require the centrin foci to reach the mother. To test whether diffusive motion could permit such interactions in the necessary time scale, we measured the motion of centrin-containing foci in living human U2OS cells. We found that these centrin foci display apparently diffusive undirected motion. Using the apparent diffusion constant obtained from these measurements, we calculated the time scale required for diffusion to capture by the mother centrioles and found that it would greatly exceed the time available in the cell cycle. We conclude that mechanisms invoking centrin foci capture by the mother, whether as a pre-centriole or as a source of components to support later assembly, would require a form of directed motility of centrin foci that has not yet been observed.

Investigation of structure-property relationships in systematic series of novel polymers

NASA Technical Reports Server (NTRS)

Gillham, J. K.

1976-01-01

Solid state transitions in polymeric materials was associated with the onset of sub-molecular motions of the polymer chains. Although these were considered to be intramolecular in general, the local environment of the polymer molecule exerts a strong influence through, for example, the effects of crystallinity, polarity and diluents. The manner of specimen preparation and previous history also affect transitions. The transitions are considered to arise when sufficient free volume is available to permit the occurrence of these side chain and backbone reorientations. The glass transition is the principal transition of amorphous polymeric materials and is associated with the onset of long range segmental motion of the polymer backbone. The various types of shorter range motion occurring below the glass transition have been catalogued.

Anomalous diffusion of brain metabolites evidenced by diffusion-weighted magnetic resonance spectroscopy in vivo

PubMed Central

Marchadour, Charlotte; Brouillet, Emmanuel; Hantraye, Philippe; Lebon, Vincent; Valette, Julien

2012-01-01

Translational displacement of molecules within cells is a key process in cellular biology. Molecular motion potentially depends on many factors, including active transport, cytosol viscosity and molecular crowding, tortuosity resulting from cytoskeleton and organelles, and restriction barriers. However, the relative contribution of these factors to molecular motion in the cytoplasm remains poorly understood. In this work, we designed an original diffusion-weighted magnetic resonance spectroscopy strategy to probe molecular motion at subcellular scales in vivo. This led to the first observation of anomalous diffusion, that is, dependence of the apparent diffusion coefficient (ADC) on the diffusion time, for endogenous intracellular metabolites in the brain. The observed increase of the ADC at short diffusion time yields evidence that metabolite motion is characteristic of hindered random diffusion rather than active transport, for time scales up to the dozen milliseconds. Armed with this knowledge, data modeling based on geometrically constrained diffusion was performed. Results suggest that metabolite diffusion occurs in a low-viscosity cytosol hindered by ∼2-μm structures, which is consistent with known intracellular organization. PMID:22929443

Motion Artifact Reduction in Pediatric Diffusion Tensor Imaging Using Fast Prospective Correction

PubMed Central

Alhamud, A.; Taylor, Paul A.; Laughton, Barbara; van der Kouwe, André J.W.; Meintjes, Ernesta M.

2014-01-01

Purpose To evaluate the patterns of head motion in scans of young children and to examine the influence of corrective techniques, both qualitatively and quantitatively. We investigate changes that both retrospective (with and without diffusion table reorientation) and prospective (implemented with a short navigator sequence) motion correction induce in the resulting diffusion tensor measures. Materials and Methods Eighteen pediatric subjects (aged 5–6 years) were scanned using 1) a twice-refocused, 2D diffusion pulse sequence, 2) a prospectively motion-corrected, navigated diffusion sequence with reacquisition of a maximum of five corrupted diffusion volumes, and 3) a T1-weighted structural image. Mean fractional anisotropy (FA) values in white and gray matter regions, as well as tractography in the brainstem and projection fibers, were evaluated to assess differences arising from retrospective (via FLIRT in FSL) and prospective motion correction. In addition to human scans, a stationary phantom was also used for further evaluation. Results In several white and gray matter regions retrospective correction led to significantly (P < 0.05) reduced FA means and altered distributions compared to the navigated sequence. Spurious tractographic changes in the retrospectively corrected data were also observed in subject data, as well as in phantom and simulated data. Conclusion Due to the heterogeneity of brain structures and the comparatively low resolution (~2 mm) of diffusion data using 2D single shot sequencing, retrospective motion correction is susceptible to distortion from partial voluming. These changes often negatively bias diffusion tensor imaging parameters. Prospective motion correction was shown to produce smaller changes. PMID:24935904

Motion artifact reduction in pediatric diffusion tensor imaging using fast prospective correction.

PubMed

Alhamud, A; Taylor, Paul A; Laughton, Barbara; van der Kouwe, André J W; Meintjes, Ernesta M

2015-05-01

To evaluate the patterns of head motion in scans of young children and to examine the influence of corrective techniques, both qualitatively and quantitatively. We investigate changes that both retrospective (with and without diffusion table reorientation) and prospective (implemented with a short navigator sequence) motion correction induce in the resulting diffusion tensor measures. Eighteen pediatric subjects (aged 5-6 years) were scanned using 1) a twice-refocused, 2D diffusion pulse sequence, 2) a prospectively motion-corrected, navigated diffusion sequence with reacquisition of a maximum of five corrupted diffusion volumes, and 3) a T1 -weighted structural image. Mean fractional anisotropy (FA) values in white and gray matter regions, as well as tractography in the brainstem and projection fibers, were evaluated to assess differences arising from retrospective (via FLIRT in FSL) and prospective motion correction. In addition to human scans, a stationary phantom was also used for further evaluation. In several white and gray matter regions retrospective correction led to significantly (P < 0.05) reduced FA means and altered distributions compared to the navigated sequence. Spurious tractographic changes in the retrospectively corrected data were also observed in subject data, as well as in phantom and simulated data. Due to the heterogeneity of brain structures and the comparatively low resolution (∼2 mm) of diffusion data using 2D single shot sequencing, retrospective motion correction is susceptible to distortion from partial voluming. These changes often negatively bias diffusion tensor imaging parameters. Prospective motion correction was shown to produce smaller changes. © 2014 Wiley Periodicals, Inc.

Ratchet effect for nanoparticle transport in hair follicles.

PubMed

Radtke, Matthias; Patzelt, Alexa; Knorr, Fanny; Lademann, Jürgen; Netz, Roland R

2017-07-01

The motion of a single rigid nanoparticle inside a hair follicle is investigated by means of Brownian dynamics simulations. The cuticular hair structure is modeled as a periodic asymmetric ratchet-shaped surface. Induced by oscillating radial hair motion we find directed nanoparticle transport into the hair follicle with maximal velocity at a specific optimal frequency and an optimal particle size. We observe flow reversal when switching from radial to axial oscillatory hair motion. We also study the diffusion behavior and find strongly enhanced diffusion for axial motion with a diffusivity significantly larger than for free diffusion. Copyright © 2016 Elsevier B.V. All rights reserved.

Higher-Order Motion-Compensation for In Vivo Cardiac Diffusion Tensor Imaging in Rats

PubMed Central

Welsh, Christopher L.; DiBella, Edward V. R.; Hsu, Edward W.

2015-01-01

Motion of the heart has complicated in vivo applications of cardiac diffusion MRI and diffusion tensor imaging (DTI), especially in small animals such as rats where ultra-high-performance gradient sets are currently not available. Even with velocity compensation via, for example, bipolar encoding pulses, the variable shot-to-shot residual motion-induced spin phase can still give rise to pronounced artifacts. This study presents diffusion-encoding schemes that are designed to compensate for higher-order motion components, including acceleration and jerk, which also have the desirable practical features of minimal TEs and high achievable b-values. The effectiveness of these schemes was verified numerically on a realistic beating heart phantom, and demonstrated empirically with in vivo cardiac diffusion MRI in rats. Compensation for acceleration, and lower motion components, was found to be both necessary and sufficient for obtaining diffusion-weighted images of acceptable quality and SNR, which yielded the first in vivo cardiac DTI demonstrated in the rat. These findings suggest that compensation for higher order motion, particularly acceleration, can be an effective alternative solution to high-performance gradient hardware for improving in vivo cardiac DTI. PMID:25775486

Non-translational Molecular Diffusive Motion on Two Different Time Scales in Alkane Nanoparticles

NASA Astrophysics Data System (ADS)

Wang, S.-K.; Bai, M.; Taub, H.; Mamontov, E.; Herwig, K. W.; Hansen, F. Y.; Copley, J. R. D.; Jenkins, T.; Tyagi, M.; Volkmann, U. G.

2009-03-01

Using quasielastic neutron scattering, we have investigated molecular diffusive motion in n-C32H66 nanoparticles whose structure and phase transitions have been studied previously.^2 The spectra reveal non-translational (dispersionless) diffusive motion occurring simultaneously on time scales of ˜1 ns and ˜40 ps. The onset of the faster motion occurs in the crystalline phase at least 15 K below the melting point and is tentatively identified with rotation about the long molecular axis. Similarly, we suggest that the slower motion involves molecular conformational changes whose onset appears to coincide with the abrupt transition to the bulk rotator phase about 3 K below melting. These two types of diffusive motion bear a strong resemblance to those observed previously in C24 monolayers adsorbed on a graphite surface.^3 ^2M. Bai et al., Europhys. Lett. 79, 26003 (2007). ^3F. Y. Hansen et al., Phys. Rev. Lett. 92, 046103 (2004)].

Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver

2017-02-01

Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

Nanoparticle Motion in Entangled Melts of Linear and Nonconcatenated Ring Polymers

PubMed Central

2017-01-01

The motion of nanoparticles (NPs) in entangled melts of linear polymers and nonconcatenated ring polymers are compared by large-scale molecular dynamics simulations. The comparison provides a paradigm for the effects of polymer architecture on the dynamical coupling between NPs and polymers in nanocomposites. Strongly suppressed motion of NPs with diameter d larger than the entanglement spacing a is observed in a melt of linear polymers before the onset of Fickian NP diffusion. This strong suppression of NP motion occurs progressively as d exceeds a and is related to the hopping diffusion of NPs in the entanglement network. In contrast to the NP motion in linear polymers, the motion of NPs with d > a in ring polymers is not as strongly suppressed prior to Fickian diffusion. The diffusion coefficient D decreases with increasing d much slower in entangled rings than in entangled linear chains. NP motion in entangled nonconcatenated ring polymers is understood through a scaling analysis of the coupling between NP motion and the self-similar entangled dynamics of ring polymers. PMID:28392603

Effects of motion and b-matrix correction for high resolution DTI with short-axis PROPELLER-EPI

PubMed Central

Aksoy, Murat; Skare, Stefan; Holdsworth, Samantha; Bammer, Roland

2010-01-01

Short-axis PROPELLER-EPI (SAP-EPI) has been proven to be very effective in providing high-resolution diffusion-weighted and diffusion tensor data. The self-navigation capabilities of SAP-EPI allow one to correct for motion, phase errors, and geometric distortion. However, in the presence of patient motion, the change in the effective diffusion-encoding direction (i.e. the b-matrix) between successive PROPELLER ‘blades’ can decrease the accuracy of the estimated diffusion tensors, which might result in erroneous reconstruction of white matter tracts in the brain. In this study, we investigate the effects of alterations in the b-matrix as a result of patient motion on the example of SAP-EPI DTI and eliminate these effects by incorporating our novel single-step non-linear diffusion tensor estimation scheme into the SAP-EPI post-processing procedure. Our simulations and in-vivo studies showed that, in the presence of patient motion, correcting the b-matrix is necessary in order to get more accurate diffusion tensor and white matter pathway reconstructions. PMID:20222149

Anomalous versus Slowed-Down Brownian Diffusion in the Ligand-Binding Equilibrium

PubMed Central

Soula, Hédi; Caré, Bertrand; Beslon, Guillaume; Berry, Hugues

2013-01-01

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes. PMID:24209851

Nanoparticle Motion in Entangled Melts of Linear and Nonconcatenated Ring Polymers [Nanoparticle Motion in Entangled Melts of Non-Concatenated Ring Polymers].

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

Ge, Ting; Kalathi, Jagannathan T.; Halverson, Jonathan D.

The motion of nanoparticles (NPs) in entangled melts of linear polymers and non-concatenated ring polymers are compared by large-scale molecular dynamics simulations. The comparison provides a paradigm for the effects of polymer architecture on the dynamical coupling between NPs and polymers in nanocomposites. Strongly suppressed motion of NPs with diameter d larger than the entanglement spacing a is observed in a melt of linear polymers before the onset of Fickian NP diffusion. This strong suppression of NP motion occurs progressively as d exceeds a, and is related to the hopping diffusion of NPs in the entanglement network. In contrast tomore » the NP motion in linear polymers, the motion of NPs with d > a in ring polymers is not as strongly suppressed prior to Fickian diffusion. The diffusion coefficient D decreases with increasing d much slower in entangled rings than in entangled linear chains. NP motion in entangled non-concatenated ring polymers is understood through a scaling analysis of the coupling between NP motion and the self-similar entangled dynamics of ring polymers.« less

Nanoparticle Motion in Entangled Melts of Linear and Nonconcatenated Ring Polymers [Nanoparticle Motion in Entangled Melts of Non-Concatenated Ring Polymers].

DOE PAGES

Ge, Ting; Kalathi, Jagannathan T.; Halverson, Jonathan D.; ...

2017-02-13

The motion of nanoparticles (NPs) in entangled melts of linear polymers and non-concatenated ring polymers are compared by large-scale molecular dynamics simulations. The comparison provides a paradigm for the effects of polymer architecture on the dynamical coupling between NPs and polymers in nanocomposites. Strongly suppressed motion of NPs with diameter d larger than the entanglement spacing a is observed in a melt of linear polymers before the onset of Fickian NP diffusion. This strong suppression of NP motion occurs progressively as d exceeds a, and is related to the hopping diffusion of NPs in the entanglement network. In contrast tomore » the NP motion in linear polymers, the motion of NPs with d > a in ring polymers is not as strongly suppressed prior to Fickian diffusion. The diffusion coefficient D decreases with increasing d much slower in entangled rings than in entangled linear chains. NP motion in entangled non-concatenated ring polymers is understood through a scaling analysis of the coupling between NP motion and the self-similar entangled dynamics of ring polymers.« less

Transport of Internetwork Magnetic Flux Elements in the Solar Photosphere

NASA Astrophysics Data System (ADS)

Agrawal, Piyush; Rast, Mark P.; Gošić, Milan; Bellot Rubio, Luis R.; Rempel, Matthias

2018-02-01

The motions of small-scale magnetic flux elements in the solar photosphere can provide some measure of the Lagrangian properties of the convective flow. Measurements of these motions have been critical in estimating the turbulent diffusion coefficient in flux-transport dynamo models and in determining the Alfvén wave excitation spectrum for coronal heating models. We examine the motions of internetwork flux elements in Hinode/Narrowband Filter Imager magnetograms and study the scaling of their mean squared displacement and the shape of their displacement probability distribution as a function of time. We find that the mean squared displacement scales super-diffusively with a slope of about 1.48. Super-diffusive scaling has been observed in other studies for temporal increments as small as 5 s, increments over which ballistic scaling would be expected. Using high-cadence MURaM simulations, we show that the observed super-diffusive scaling at short increments is a consequence of random changes in barycenter positions due to flux evolution. We also find that for long temporal increments, beyond granular lifetimes, the observed displacement distribution deviates from that expected for a diffusive process, evolving from Rayleigh to Gaussian. This change in distribution can be modeled analytically by accounting for supergranular advection along with granular motions. These results complicate the interpretation of magnetic element motions as strictly advective or diffusive on short and long timescales and suggest that measurements of magnetic element motions must be used with caution in turbulent diffusion or wave excitation models. We propose that passive tracer motions in measured photospheric flows may yield more robust transport statistics.

Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences.

PubMed

Jez, Joseph M; Noel, Joseph P

2002-01-11

Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of bicyclic chalcones into tricyclic (S)-flavanones. The activity of CHI is essential for the biosynthesis of flavanone precursors of floral pigments and phenylpropanoid plant defense compounds. We have examined the spontaneous and CHI-catalyzed cyclization reactions of 4,2',4',6'-tetrahydroxychalcone, 4,2',4'-trihydroxychalcone, 2',4'-dihydroxychalcone, and 4,2'-dihydroxychalcone into the corresponding flavanones. The pH dependence of flavanone formation indicates that both the non-enzymatic and enzymatic reactions first require the bulk phase ionization of the substrate 2'-hydroxyl group and subsequently on the reactivity of the newly formed 2'-oxyanion during C-ring formation. Solvent viscosity experiments demonstrate that at pH 7.5 the CHI-catalyzed cyclization reactions of 4,2',4',6'-tetrahydroxychalcone, 4,2',4'-trihydroxychalcone, and 2',4'-dihydroxychalcone are approximately 90% diffusion-controlled, whereas cyclization of 4,2'-dihydroxychalcone is limited by a chemical step that likely reflects the higher pK(a) of the 2'-hydroxyl group. At pH 6.0, the reactions with 4,2',4',6'-tetrahydroxychalcone and 4,2',4'-trihydroxychalcone are approximately 50% diffusion-limited, whereas the reactions of both dihydroxychalcones are limited by chemical steps. Comparisons of the 2.1-2.3 A resolution crystal structures of CHI complexed with the products 7,4'-dihydroxyflavanone, 7-hydroxyflavanone, and 4'-hydroxyflavanone show that the 7-hydroxyflavanones all share a common binding mode, whereas 4'-hydroxyflavanone binds in an altered orientation at the active site. Our functional and structural studies support the proposal that CHI accelerates the stereochemically defined intramolecular cyclization of chalcones into biologically active (2S)-flavanones by selectively binding an ionized chalcone in a conformation conducive to ring closure in a diffusion-controlled reaction.

Unidirectional rotary motion in a molecular system

NASA Astrophysics Data System (ADS)

Kelly, T. Ross; de Silva, Harshani; Silva, Richard A.

1999-09-01

The conversion of energy into controlled motion plays an important role in both man-made devices and biological systems. The principles of operation of conventional motors are well established, but the molecular processes used by `biological motors' such as muscle fibres, flagella and cilia to convert chemical energy into co-ordinated movement remain poorly understood. Although `brownian ratchets' are known to permit thermally activated motion in one direction only, the concept of channelling random thermal energy into controlled motion has not yet been extended to the molecular level. Here we describe a molecule that uses chemical energy to activate and bias a thermally induced isomerization reaction, and thereby achieve unidirectional intramolecular rotary motion. The motion consists of a 120° rotation around a single bond connecting a three-bladed subunit to the bulky remainder of the molecule, and unidirectional motion is achieved by reversibly introducing a tether between the two units to energetically favour one of the two possible rotation directions. Although our system does not achieve continuous and fast rotation, the design principles that we have used may prove relevant for a better understanding of biological and synthetic molecular motors producing unidirectional rotary motion.

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium.

PubMed

Soula, Hédi; Caré, Bertrand; Beslon, Guillaume; Berry, Hugues

2013-11-05

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Localized diffusive motion on two different time scales in solid alkane nanoparticles

NASA Astrophysics Data System (ADS)

Wang, S.-K.; Mamontov, E.; Bai, M.; Hansen, F. Y.; Taub, H.; Copley, J. R. D.; García Sakai, V.; Gasparovic, G.; Jenkins, T.; Tyagi, M.; Herwig, K. W.; Neumann, D. A.; Montfrooij, W.; Volkmann, U. G.

2010-09-01

High-energy-resolution quasielastic neutron scattering on three complementary spectrometers has been used to investigate molecular diffusive motion in solid nano- to bulk-sized particles of the alkane n-C32H66. The crystalline-to-plastic and plastic-to-fluid phase transition temperatures are observed to decrease as the particle size decreases. In all samples, localized molecular diffusive motion in the plastic phase occurs on two different time scales: a "fast" motion corresponding to uniaxial rotation about the long molecular axis; and a "slow" motion attributed to conformational changes of the molecule. Contrary to the conventional interpretation in bulk alkanes, the fast uniaxial rotation begins in the low-temperature crystalline phase.

Brownian motion of boomerang colloidal particles.

PubMed

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V; Sun, Kai; Wei, Qi-Huo

2013-10-18

We investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

Brownian Motion of Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V.; Sun, Kai; Wei, Qi-Huo

2013-10-01

We investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

Magnetic Resonance Relaxometry at Low and Ultra low Fields.

PubMed

Volegov, P; Flynn, M; Kraus, R; Magnelind, P; Matlashov, A; Nath, P; Owens, T; Sandin, H; Savukov, I; Schultz, L; Urbaitis, A; Zotev, V; Espy, M

2010-01-01

Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) are ubiquitous tools in science and medicine. NMR provides powerful probes of local and macromolecular chemical structure and dynamics. Recently it has become possible and practical to perform MR at very low fields (from 1 μT to 1 mT), the so-called ultra-low field (ULF) regime. Pulsed pre-polarizing fields greatly enhance the signal strength and allow flexibility in signal acquisition sequences. Improvements in SQUID sensor technology allow ultra-sensitive detection in a pulsed field environment.In this regime the proton Larmor frequencies (1 Hz - 100 kHz) of ULF MR overlap (on a time scale of 10 μs to 100 ms) with "slow" molecular dynamic processes such as diffusion, intra-molecular motion, chemical reactions, and biological processes such as protein folding, catalysis and ligand binding. The frequency dependence of relaxation at ultra-low fields may provide a probe for biomolecular dynamics on the millisecond timescale (protein folding and aggregation, conformational motions of enzymes, binding and structural fluctuations of coupled domains in allosteric mechanisms) relevant to host-pathogen interactions, biofuels, and biomediation. Also this resonance-enhanced coupling at ULF can greatly enhance contrast in medical applications of ULF-MRI resulting in better diagnostic techniques.We have developed a number of instruments and techniques to study relaxation vs. frequency at the ULF regime. Details of the techniques and results are presented.Ultra-low field methods are already being applied at LANL in brain imaging, and detection of liquid explosives at airports. However, the potential power of ultra-low field MR remains to be fully exploited.

Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core

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

Hong, Liang; Cheng, Xiaolin; Glass, Dennis C.

2012-06-05

The effect of surface hydration water on internal protein motion is of fundamental interest in molecular biophysics. Here, by decomposing the picosecond to nanosecond atomic motion in molecular dynamics simulations of lysozyme at different hydration levels into three components localized single-well diffusion, methyl group rotation, and nonmethyl jumps we show that the effect of surface hydration is mainly to increase the volume of the localized single-well diffusion. As a result, these diffusive motions are coupled in such a way that the hydration effect propagates from the protein surface into the dry core.

Wind-Tunnel Modeling of Flow Diffusion over an Urban Complex.

DTIC Science & Technology

URBAN AREAS, *ATMOSPHERIC MOTION, *AIR POLLUTION, ATMOSPHERIC MOTION, WIND TUNNEL MODELS, HEAT, DIFFUSION , TURBULENT BOUNDARY LAYER, WIND, SKIN FRICTION, MATHEMATICAL MODELS, URBAN PLANNING, INDIANA.

Vibration-rotation-tunneling spectroscopy of the van der Waals Bond: A new look at intermolecular forces

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

Cohen, R.C.; Saykally, R.J.

Measurements of the low-frequency van der Waals vibrations in weakly bound complexes by high-resolution laser spectroscopy provide a means to probe intermolecular forces at unprecedented levels of detail and precision. Several new methods are presently being used to record vibration/rotation-tunneling (VRT) transitions associated with the motions of the weak bonds in van der Waals clusters. The most direct measurements are those probing only the van der Waals modes themselves, which occur at far-infrared wavelengths. This article presents a review of the information on both intramolecular forces and intramolecular dynamics that has been obtained from far-infrared VRT spectra of 18 complexesmore » during the past several years. Some rotationally resolved measurements of van der Waals modes observed in combination with electronic or vibrational excitation are also discussed. 185 refs., 15 figs., 1 tab.« less

Spurious group differences due to head motion in a diffusion MRI study

PubMed Central

Yendiki, Anastasia; Koldewyn, Kami; Kakunoori, Sita; Kanwisher, Nancy; Fischl, Bruce

2014-01-01

Diffusion-weighted MRI (DW-MRI) has become a popular imaging modality for probing the microstructural properties of white matter and comparing them between populations in vivo. However, the contrast in DW-MRI arises from the microscopic random motion of water molecules in brain tissues, which makes it particularly sensitive to macroscopic head motion. Although this has been known since the introduction of DW-MRI, most studies that use this modality for group comparisons do not report measures of head motion for each group and rely on registration-based correction methods that cannot eliminate the full effects of head motion on the DW-MRI contrast. In this work we use data from children with autism and typically developing children to investigate the effects of head motion on differences in anisotropy and diffusivity measures between groups. We show that group differences in head motion can induce group differences in DW-MRI measures, and that this is the case even when comparing groups that include control subjects only, where no anisotropy or diffusivity differences are expected. We also show that such effects can be more prominent in some white-matter pathways than others, and that they can be ameliorated by including motion as a nuisance regressor in the analyses. Our results demonstrate the importance of taking head motion into account in any population study where one group might exhibit more head motion than the other. PMID:24269273

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

Dubey, P., E-mail: purushd@barc.gov.in; Sharma, V. K.; Mitra, S.

Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. Here we report dynamics of cetyltrimethylammonium bromide (CTAB) in HAp composite, prepared by co-precipitation method, as studied by quasielastic neutron scattering (QENS) technique. It is found that the observed dynamics involved two time scales associated with fast torsional motion and segmental motion of the CTAB monomers. In addition to segmental motion of the hydrogen atoms, few undergo torsional motion as well. Torsional dynamics was described by a 2-fold jump diffusion model. The segmental dynamics of CTAB has been described assumimg the hydrogen atomsmore » undergoing diffusion inside a sphere of confined volume. While the diffusivity is found to increase with temperature, the spherical volumes within which the hydrogen atoms are undergoing diffusion remain almost unchanged.« less

Diffusion-advection within dynamic biological gaps driven by structural motion

NASA Astrophysics Data System (ADS)

Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

2018-04-01

To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

Apparent diffusion coefficient measurement in a moving phantom simulating linear respiratory motion.

PubMed

Kwee, Thomas C; Takahara, Taro; Muro, Isao; Van Cauteren, Marc; Imai, Yutaka; Nievelstein, Rutger A J; Mali, Willem P T M; Luijten, Peter R

2010-10-01

The aim of this study was to examine the effect of simulated linear respiratory motion on apparent diffusion coefficient (ADC) measurements. Six rectangular test tubes (14 × 92 mm) filled with either water, tomato ketchup, or mayonnaise were positioned in a box containing agarose gel. This box was connected to a double-acting pneumatic cylinder, capable of inducing periodic linear motion in the long-axis direction of the magnetic bore (23-mm stroke). Diffusion-weighted magnetic resonance imaging was performed for both the static and moving phantoms, and ADC measurements were made in the six test tubes in both situations. In the three test tubes whose long axes were parallel to the direction of motion, ADCs agreed well between the moving and static phantom situations. However, in two test tubes that were filled with fluids that had a considerably lower diffusion coefficient than the surrounding agarose gel, and whose long axes were perpendicular to the direction of motion, the ADCs agreed poorly between the moving and static phantom situations. ADC measurements of large homogeneous structures are not affected by linear respiratory motion. However, ADC measurements of inhomogeneous or small structures are affected by linear respiratory motion due to partial volume effects.

Anisotropic polarization π -molecular skeleton coupled dynamics in proton-displacive organic ferroelectrics

NASA Astrophysics Data System (ADS)

Fujioka, J.; Horiuchi, S.; Kida, N.; Shimano, R.; Tokura, Y.

2009-09-01

We have investigated the polarization π -molecular skeleton coupled dynamics for the proton-displacive organic ferroelectrics, cocrystal of phenazine with the 2,5-dihalo-3,6-dihydroxy-p-benzoquinones by measurements of the terahertz/infrared spectroscopy. In the course of the ferroelectric-to-paraelectric transition, the ferroelectric soft phonon mode originating from the intermolecular dynamical displacement is observed in the imaginary part of dielectric spectra γ2 , when the electric field of the light (E) is parallel to the spontaneous polarization (P) . The soft phonon mode is isolated from the intramolecular vibrational mode and hence the intramolecular skeleton dynamics is almost decoupled from the polarization fluctuation. In the spectra for E parallel to the hydrogen-bonded supramolecular chain, by contrast, the vibrational mode mainly originating from the oxygen atom motion within the π -molecular plane is anomalously blurred and amalgamated into the polarization relaxation mode concomitantly with the dynamical proton disorder. This indicates that the dynamical disorder of the intramolecular skeleton structure, specifically that of oxygen atom, is strongly enhanced by the proton fluctuation and is significantly coupled to the polarization fluctuation along the hydrogen-bonded supramolecular chain. The results are discussed in terms of the proton-mediated anisotropic polarization π -molecular skeleton interaction, which characterizes these emerging proton-displacive ferroelectrics.

Brownian Motion of Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Wei, Qi-Huo; Konya, Andrew; Wang, Feng; Selinger, Jonathan V.; Sun, Kai; Chakrabarty, Ayan

2014-03-01

We present experimental and theoretical studies on the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short-time faster to long-time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to the superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

Expansion and internal friction in unfolded protein chain.

PubMed

Yasin, U Mahammad; Sashi, Pulikallu; Bhuyan, Abani K

2013-10-10

Similarities in global properties of homopolymers and unfolded proteins provide approaches to mechanistic description of protein folding. Here, hydrodynamic properties and relaxation rates of the unfolded state of carbonmonoxide-liganded cytochrome c (cyt-CO) have been measured using nuclear magnetic resonance and laser photolysis methods. Hydrodynamic radius of the unfolded chain gradually increases as the solvent turns increasingly better, consistent with theory. Curiously, however, the rate of intrachain contact formation also increases with an increasing denaturant concentration, which, by Szabo, Schulten, and Schulten theory for the rate of intramolecular contact formation in a Gaussian polymer, indicates growing intramolecular diffusion. It is argued that diminishing nonbonded atom interactions with increasing denaturant reduces internal friction and, thus, increases the rate of polypeptide relaxation. Qualitative scaling of the extent of unfolding with nonbonded repulsions allows for description of internal friction by a phenomenological model. The degree of nonbonded atom interactions largely determines the extent of internal friction.

Active Teaching of Diffusion through History of Science, Computer Animation and Role Playing

ERIC Educational Resources Information Center

Krajsek, Simona Strgulc; Vilhar, Barbara

2010-01-01

We developed and tested a lesson plan for active teaching of diffusion in secondary schools (grades 10-13), which stimulates understanding of the thermal (Brownian) motion of particles as the principle underlying diffusion. During the lesson, students actively explore the Brownian motion through microscope observations of irregularly moving small…

Measurement of Rapid Protein Diffusion in the Cytoplasm by Photo-Converted Intensity Profile Expansion.

PubMed

Gura Sadovsky, Rotem; Brielle, Shlomi; Kaganovich, Daniel; England, Jeremy L

2017-03-14

The fluorescence microscopy methods presently used to characterize protein motion in cells infer protein motion from indirect observables, rather than measuring protein motion directly. Operationalizing these methods requires expertise that can constitute a barrier to their broad utilization. Here, we have developed PIPE (photo-converted intensity profile expansion) to directly measure the motion of tagged proteins and quantify it using an effective diffusion coefficient. PIPE works by pulsing photo-convertible fluorescent proteins, generating a peaked fluorescence signal at the pulsed region, and analyzing the spatial expansion of the signal. We demonstrate PIPE's success in measuring accurate diffusion coefficients in silico and in vitro and compare effective diffusion coefficients of native cellular proteins and free fluorophores in vivo. We apply PIPE to measure diffusion anomality in the cell and use it to distinguish free fluorophores from native cellular proteins. PIPE's direct measurement and ease of use make it appealing for cell biologists. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Coiled to diffuse: Brownian motion of a helical bacterium.

PubMed

Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

2012-09-11

We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

Brain white matter microstructure is associated with susceptibility to motion-induced nausea.

PubMed

Napadow, V; Sheehan, J; Kim, J; Dassatti, A; Thurler, A H; Surjanhata, B; Vangel, M; Makris, N; Schaechter, J D; Kuo, B

2013-05-01

Nausea is associated with significant morbidity, and there is a wide range in the propensity of individuals to experience nausea. The neural basis of the heterogeneity in nausea susceptibility is poorly understood. Our previous functional magnetic resonance imaging (fMRI) study in healthy adults showed that a visual motion stimulus caused activation in the right MT+/V5 area, and that increased sensation of nausea due to this stimulus was associated with increased activation in the right anterior insula. For the current study, we hypothesized that individual differences in visual motion-induced nausea are due to microstructural differences in the inferior fronto-occipital fasciculus (IFOF), the white matter tract connecting the right visual motion processing area (MT+/V5) and right anterior insula. To test this hypothesis, we acquired diffusion tensor imaging data from 30 healthy adults who were subsequently dichotomized into high and low nausea susceptibility groups based on the Motion Sickness Susceptibility Scale. We quantified diffusion along the IFOF for each subject based on axial diffusivity (AD); radial diffusivity (RD), mean diffusivity (MD) and fractional anisotropy (FA), and evaluated between-group differences in these diffusion metrics. Subjects with high susceptibility to nausea rated significantly (P < 0.001) higher nausea intensity to visual motion stimuli and had significantly (P < 0.05) lower AD and MD along the right IFOF compared to subjects with low susceptibility to nausea. This result suggests that differences in white matter microstructure within tracts connecting visual motion and nausea-processing brain areas may contribute to nausea susceptibility or may have resulted from an increased history of nausea episodes. © 2013 Blackwell Publishing Ltd.

Proteins as micro viscosimeters: Brownian motion revisited.

PubMed

Lavalette, Daniel; Hink, Mark A; Tourbez, Martine; Tétreau, Catherine; Visser, Antonie J

2006-08-01

Translational and rotational diffusion coefficients of proteins in solution strongly deviate from the Stokes-Einstein laws when the ambient viscosity is induced by macromolecular co-solutes rather than by a solvent of negligible size as was assumed by A. Einstein one century ago for deriving the laws of Brownian motion and diffusion. Rotational and translational motions experience different micro viscosities and both become a function of the size ratio of protein and macromolecular co-solute. Possible consequences upon fluorescence spectroscopy observations of diffusing proteins within living cells are discussed.

Characteristic power spectrum of diffusive interface dynamics in the two-dimensional Ising model

NASA Astrophysics Data System (ADS)

Masumoto, Yusuke; Takesue, Shinji

2018-05-01

We investigate properties of the diffusive motion of an interface in the two-dimensional Ising model in equilibrium or nonequilibrium situations. We focused on the relation between the power spectrum of a time sequence of spins and diffusive motion of an interface which was already clarified in one-dimensional systems with a nonequilibrium phase transition like the asymmetric simple exclusion process. It is clarified that the interface motion is a diffusion process with a drift force toward the higher-temperature side when the system is in contact with heat reservoirs at different temperatures and heat transfers through the system. Effects of the width of the interface are also discussed.

Direct measurement of the ballistic motion of a freely floating colloid in Newtonian and viscoelastic fluids.

PubMed

Hammond, Andrew P; Corwin, Eric I

2017-10-01

A thermal colloid suspended in a liquid will transition from a short-time ballistic motion to a long-time diffusive motion. However, the transition between ballistic and diffusive motion is highly dependent on the properties and structure of the particular liquid. We directly observe a free floating tracer particle's ballistic motion and its transition to the long-time regime in both a Newtonian fluid and a viscoelastic Maxwell fluid. We examine the motion of the free particle in a Newtonian fluid and demonstrate a high degree of agreement with the accepted Clercx-Schram model for motion in a dense fluid. Measurements of the functional form of the ballistic-to-diffusive transition provide direct measurements of the temperature, viscosity, and tracer radius. We likewise measure the motion in a viscoelastic Maxwell fluid and find a significant disagreement between the theoretical asymptotic behavior and our measured values of the microscopic properties of the fluid. We observe a greatly increased effective mass for a freely moving particle and a decreased plateau modulus.

Classification and Segmentation of Nanoparticle Diffusion Trajectories in Cellular Micro Environments

PubMed Central

Kroll, Alexandra; Haramagatti, Chandrashekara R.; Lipinski, Hans-Gerd; Wiemann, Martin

2017-01-01

Darkfield and confocal laser scanning microscopy both allow for a simultaneous observation of live cells and single nanoparticles. Accordingly, a characterization of nanoparticle uptake and intracellular mobility appears possible within living cells. Single particle tracking allows to measure the size of a diffusing particle close to a cell. However, within the more complex system of a cell’s cytoplasm normal, confined or anomalous diffusion together with directed motion may occur. In this work we present a method to automatically classify and segment single trajectories into their respective motion types. Single trajectories were found to contain more than one motion type. We have trained a random forest with 9 different features. The average error over all motion types for synthetic trajectories was 7.2%. The software was successfully applied to trajectories of positive controls for normal- and constrained diffusion. Trajectories captured by nanoparticle tracking analysis served as positive control for normal diffusion. Nanoparticles inserted into a diblock copolymer membrane was used to generate constrained diffusion. Finally we segmented trajectories of diffusing (nano-)particles in V79 cells captured with both darkfield- and confocal laser scanning microscopy. The software called “TraJClassifier” is freely available as ImageJ/Fiji plugin via https://git.io/v6uz2. PMID:28107406

Rotation driven translational diffusion of polyatomic ions in water: A novel mechanism for breakdown of Stokes-Einstein relation

NASA Astrophysics Data System (ADS)

Banerjee, Puja; Yashonath, Subramanian; Bagchi, Biman

2017-04-01

While most of the existing theoretical and simulation studies have focused on simple, spherical, halide and alkali ions, many chemically, biologically, and industrially relevant electrolytes involve complex non-spherical polyatomic ions like nitrate, chlorate, and sulfate to name only a few. Interestingly, some polyatomic ions in spite of being larger in size show anomalously high diffusivity and therefore cause a breakdown of the venerable Stokes-Einstein (S-E) relation between the size and diffusivity. Here we report a detailed analysis of the dynamics of anions in aqueous potassium nitrate (KNO3) and aqueous potassium acetate (CH3COOK) solutions. The two ions, nitrate (-NO3) and acetate (CH3-CO2 ), with their similar size show a large difference in diffusivity values. We present evidence that the translational motion of these polyatomic ions is coupled to the rotational motion of the ion. We show that unlike the acetate ion, nitrate ion with a symmetric charge distribution among all periphery oxygen atoms shows a faster rotational motion with large amplitude rotational jumps which enhances its translational motion due to translational-rotational coupling. By creating a family of modified-charge model systems, we have analysed the rotational motion of asymmetric polyatomic ions and the contribution of it to the translational motion. These model systems help clarifying and establishing the relative contribution of rotational motion in enhancing the diffusivity of the nitrate ion over the value predicted by the S-E relation and also over the other polyatomic ions having asymmetric charge distribution like the acetate ion. In the latter case, reduced rotational motion results in lower diffusivity values than those with symmetric charge distribution. We propose translational-rotational coupling as a general mechanism of the breakdown of the S-E relation in the case of polyatomic ions.

Rotation driven translational diffusion of polyatomic ions in water: A novel mechanism for breakdown of Stokes-Einstein relation.

PubMed

Banerjee, Puja; Yashonath, Subramanian; Bagchi, Biman

2017-04-28

While most of the existing theoretical and simulation studies have focused on simple, spherical, halide and alkali ions, many chemically, biologically, and industrially relevant electrolytes involve complex non-spherical polyatomic ions like nitrate, chlorate, and sulfate to name only a few. Interestingly, some polyatomic ions in spite of being larger in size show anomalously high diffusivity and therefore cause a breakdown of the venerable Stokes-Einstein (S-E) relation between the size and diffusivity. Here we report a detailed analysis of the dynamics of anions in aqueous potassium nitrate (KNO 3 ) and aqueous potassium acetate (CH 3 COOK) solutions. The two ions, nitrate (NO3-) and acetate (CH 3 CO2-), with their similar size show a large difference in diffusivity values. We present evidence that the translational motion of these polyatomic ions is coupled to the rotational motion of the ion. We show that unlike the acetate ion, nitrate ion with a symmetric charge distribution among all periphery oxygen atoms shows a faster rotational motion with large amplitude rotational jumps which enhances its translational motion due to translational-rotational coupling. By creating a family of modified-charge model systems, we have analysed the rotational motion of asymmetric polyatomic ions and the contribution of it to the translational motion. These model systems help clarifying and establishing the relative contribution of rotational motion in enhancing the diffusivity of the nitrate ion over the value predicted by the S-E relation and also over the other polyatomic ions having asymmetric charge distribution like the acetate ion. In the latter case, reduced rotational motion results in lower diffusivity values than those with symmetric charge distribution. We propose translational-rotational coupling as a general mechanism of the breakdown of the S-E relation in the case of polyatomic ions.

Femtosecond dynamics of a non-steroidal anti-inflammatory drug (piroxicam) in solution: The involvement of twisting motion

NASA Astrophysics Data System (ADS)

Gil, Michał; Douhal, Abderrazzak

2008-06-01

In this contribution, we report on fast and ultrafast dynamics of a non-steroidal anti-inflammatory drug, piroxicam (PX), in methyl acetate (MAC) and triacetin (TAC), two solvents of different viscosities. The enol form of PX undergoes a femtosecond (shorter than 100 fs) electronically excited state intramolecular proton-transfer reaction to produce keto tautomers. These structures exhibit an internal twisting motion to generate keto rotamers in ˜2-5 ps, a time being longer in TAC. The transient absorption/emission spectrum is very broad indicating that the potential-energy surface at the electronically excited state is very flat, and reflecting the involvement of several coordinates along which the wavepacket of the fs-produced structures evolve.

A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

PubMed Central

Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

2014-01-01

This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

PubMed

Yagasaki, Takuma; Saito, Shinji

2009-09-15

Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is elucidated by introducing the "translation-free" molecular dynamics simulation. The isotropic pump-probe signal and the polarization anisotropy decay show fast transfer of the librational energy to the surrounding water molecules, followed by relaxation to the hot ground state. These theoretical methods do not require frequently used assumptions and can thus be called ab initio methods; together with multidimensional nonlinear spectroscopies, they provide powerful methods for examining the inter- and intramolecular details of water dynamics.

Diffusion in the presence of a local attracting factor: Theory and interdisciplinary applications.

PubMed

Veermäe, Hardi; Patriarca, Marco

2017-06-01

In many complex diffusion processes the drift of random walkers is not caused by an external force, as in the case of Brownian motion, but by local variations of fitness perceived by the random walkers. In this paper, a simple but general framework is presented that describes such a type of random motion and may be of relevance in different problems, such as opinion dynamics, cultural spreading, and animal movement. To this aim, we study the problem of a random walker in d dimensions moving in the presence of a local heterogeneous attracting factor expressed in terms of an assigned position-dependent "attractiveness function." At variance with standard Brownian motion, the attractiveness function introduced here regulates both the advection and diffusion of the random walker, thus providing testable predictions for a specific form of fluctuation-relations. We discuss the relation between the drift-diffusion equation based on the attractiveness function and that describing standard Brownian motion, and we provide some explicit examples illustrating its relevance in different fields, such as animal movement, chemotactic diffusion, and social dynamics.

Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion.

PubMed

Jeon, Jae-Hyung; Chechkin, Aleksei V; Metzler, Ralf

2014-08-14

Anomalous diffusion is frequently described by scaled Brownian motion (SBM), a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is 〈x(2)(t)〉 ≃ 2K(t)t with K(t) ≃ t(α-1) for 0 < α < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion, for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely, we demonstrate that under confinement, the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments, in particular, under confinement inside cellular compartments or when optical tweezers tracking methods are used.

Diffusion in the presence of a local attracting factor: Theory and interdisciplinary applications

NASA Astrophysics Data System (ADS)

Veermäe, Hardi; Patriarca, Marco

2017-06-01

In many complex diffusion processes the drift of random walkers is not caused by an external force, as in the case of Brownian motion, but by local variations of fitness perceived by the random walkers. In this paper, a simple but general framework is presented that describes such a type of random motion and may be of relevance in different problems, such as opinion dynamics, cultural spreading, and animal movement. To this aim, we study the problem of a random walker in d dimensions moving in the presence of a local heterogeneous attracting factor expressed in terms of an assigned position-dependent "attractiveness function." At variance with standard Brownian motion, the attractiveness function introduced here regulates both the advection and diffusion of the random walker, thus providing testable predictions for a specific form of fluctuation-relations. We discuss the relation between the drift-diffusion equation based on the attractiveness function and that describing standard Brownian motion, and we provide some explicit examples illustrating its relevance in different fields, such as animal movement, chemotactic diffusion, and social dynamics.

Constrained diffusion or immobile fraction on cell surfaces: a new interpretation.

PubMed Central

Feder, T J; Brust-Mascher, I; Slattery, J P; Baird, B; Webb, W W

1996-01-01

Protein lateral mobility in cell membranes is generally measured using fluorescence photobleaching recovery (FPR). Since the development of this technique, the data have been interpreted by assuming free Brownian diffusion of cell surface receptors in two dimensions, an interpretation that requires that a subset of the diffusing species remains immobile. The origin of this so-called immobile fraction remains a mystery. In FPR, the motions of thousands of particles are inherently averaged, inevitably masking the details of individual motions. Recently, tracking of individual cell surface receptors has identified several distinct types of motion (Gross and Webb, 1988; Ghosh and Webb, 1988, 1990, 1994; Kusumi et al. 1993; Qian et al. 1991; Slattery, 1995), thereby calling into question the classical interpretation of FPR data as free Brownian motion of a limited mobile fraction. We have measured the motion of fluorescently labeled immunoglobulin E complexed to high affinity receptors (Fc epsilon RI) on rat basophilic leukemia cells using both single particle tracking and FPR. As in previous studies, our tracking results show that individual receptors may diffuse freely, or may exhibit restricted, time-dependent (anomalous) diffusion. Accordingly, we have analyzed FPR data by a new model to take this varied motion into account, and we show that the immobile fraction may be due to particles moving with the anomalous subdiffusion associated with restricted lateral mobility. Anomalous subdiffusion denotes random molecular motion in which the mean square displacements grow as a power law in time with a fractional positive exponent less than one. These findings call for a new model of cell membrane structure. PMID:8744314

Mathematics of thermal diffusion in an exponential temperature field

NASA Astrophysics Data System (ADS)

Zhang, Yaqi; Bai, Wenyu; Diebold, Gerald J.

2018-04-01

The Ludwig-Soret effect, also known as thermal diffusion, refers to the separation of gas, liquid, or solid mixtures in a temperature gradient. The motion of the components of the mixture is governed by a nonlinear, partial differential equation for the density fractions. Here solutions to the nonlinear differential equation for a binary mixture are discussed for an externally imposed, exponential temperature field. The equation of motion for the separation without the effects of mass diffusion is reduced to a Hamiltonian pair from which spatial distributions of the components of the mixture are found. Analytical calculations with boundary effects included show shock formation. The results of numerical calculations of the equation of motion that include both thermal and mass diffusion are given.

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.

Thermal drift is enough to drive a single microtubule along its axis even in the absence of motor proteins.

PubMed Central

Nakata, T; Sato-Yoshitake, R; Okada, Y; Noda, Y; Hirokawa, N

1993-01-01

One-dimensional diffusion of microtubules (MTs), a back-and-forth motion of MTs due to thermal diffusion, was reported in dynein motility assay. The interaction between MTs and dynein that allows such motion was implicated in its importance in the force generating cycle of dynein ATPase cycle. However, it was not known whether the phenomenon is special to motor proteins. Here we show two independent examples of one-dimensional diffusion of MTs in the absence of motor proteins. Dynamin, a MT-activated GTPase, causes a nucleotide dependent back-and-forth movement of single MT up to 1 micron along the longitudinal axes, although the MT never showed unidirectional consistent movement. Quantitative analysis of the motion and its nucleotide condition indicates that the motion is due to a thermal driven diffusion, restricted to one dimension, under the weak interaction between MT and dynamin. However, specific protein-protein interaction is not essential for the motion, because similar back-and-forth movement of MT was achieved on coverslips coated with only 0.8% methylcellulose. Both cases demonstrate that thermal diffusion could provide a considerable sliding of MTs only if MTs are restricted on the surface appropriately. Images FIGURE 1 FIGURE 2 FIGURE 3 PMID:7906153

Self-diffusion in dense granular shear flows.

PubMed

Utter, Brian; Behringer, R P

2004-03-01

Diffusivity is a key quantity in describing velocity fluctuations in granular materials. These fluctuations are the basis of many thermodynamic and hydrodynamic models which aim to provide a statistical description of granular systems. We present experimental results on diffusivity in dense, granular shear flows in a two-dimensional Couette geometry. We find that self-diffusivities D are proportional to the local shear rate gamma; with diffusivities along the direction of the mean flow approximately twice as large as those in the perpendicular direction. The magnitude of the diffusivity is D approximately gamma;a(2), where a is the particle radius. However, the gradient in shear rate, coupling to the mean flow, and strong drag at the moving boundary lead to particle displacements that can appear subdiffusive or superdiffusive. In particular, diffusion appears to be superdiffusive along the mean flow direction due to Taylor dispersion effects and subdiffusive along the perpendicular direction due to the gradient in shear rate. The anisotropic force network leads to an additional anisotropy in the diffusivity that is a property of dense systems and has no obvious analog in rapid flows. Specifically, the diffusivity is suppressed along the direction of the strong force network. A simple random walk simulation reproduces the key features of the data, such as the apparent superdiffusive and subdiffusive behavior arising from the mean velocity field, confirming the underlying diffusive motion. The additional anisotropy is not observed in the simulation since the strong force network is not included. Examples of correlated motion, such as transient vortices, and Lévy flights are also observed. Although correlated motion creates velocity fields which are qualitatively different from collisional Brownian motion and can introduce nondiffusive effects, on average the system appears simply diffusive.

Numerical simulations of motion-insensitive diffusion imaging based on the distant dipolar field effects.

PubMed

Lin, Tao; Sun, Huijun; Chen, Zhong; You, Rongyi; Zhong, Jianhui

2007-12-01

Diffusion weighting in MRI is commonly achieved with the pulsed-gradient spin-echo (PGSE) method. When combined with spin-warping image formation, this method often results in ghosts due to the sample's macroscopic motion. It has been shown experimentally (Kennedy and Zhong, MRM 2004;52:1-6) that these motion artifacts can be effectively eliminated by the distant dipolar field (DDF) method, which relies on the refocusing of spatially modulated transverse magnetization by the DDF within the sample itself. In this report, diffusion-weighted images (DWIs) using both DDF and PGSE methods in the presence of macroscopic sample motion were simulated. Numerical simulation results quantify the dependence of signals in DWI on several key motion parameters and demonstrate that the DDF DWIs are much less sensitive to macroscopic sample motion than the traditional PGSE DWIs. The results also show that the dipolar correlation distance (d(c)) can alter contrast in DDF DWIs. The simulated results are in good agreement with the experimental results reported previously.

Motion-induced phase error estimation and correction in 3D diffusion tensor imaging.

PubMed

Van, Anh T; Hernando, Diego; Sutton, Bradley P

2011-11-01

A multishot data acquisition strategy is one way to mitigate B0 distortion and T2∗ blurring for high-resolution diffusion-weighted magnetic resonance imaging experiments. However, different object motions that take place during different shots cause phase inconsistencies in the data, leading to significant image artifacts. This work proposes a maximum likelihood estimation and k-space correction of motion-induced phase errors in 3D multishot diffusion tensor imaging. The proposed error estimation is robust, unbiased, and approaches the Cramer-Rao lower bound. For rigid body motion, the proposed correction effectively removes motion-induced phase errors regardless of the k-space trajectory used and gives comparable performance to the more computationally expensive 3D iterative nonlinear phase error correction method. The method has been extended to handle multichannel data collected using phased-array coils. Simulation and in vivo data are shown to demonstrate the performance of the method.

Nuclear quadrupole resonance lineshape analysis for different motional models: Stochastic Liouville approach

NASA Astrophysics Data System (ADS)

Kruk, D.; Earle, K. A.; Mielczarek, A.; Kubica, A.; Milewska, A.; Moscicki, J.

2011-12-01

A general theory of lineshapes in nuclear quadrupole resonance (NQR), based on the stochastic Liouville equation, is presented. The description is valid for arbitrary motional conditions (particularly beyond the valid range of perturbation approaches) and interaction strengths. It can be applied to the computation of NQR spectra for any spin quantum number and for any applied magnetic field. The treatment presented here is an adaptation of the "Swedish slow motion theory," [T. Nilsson and J. Kowalewski, J. Magn. Reson. 146, 345 (2000), 10.1006/jmre.2000.2125] originally formulated for paramagnetic systems, to NQR spectral analysis. The description is formulated for simple (Brownian) diffusion, free diffusion, and jump diffusion models. The two latter models account for molecular cooperativity effects in dense systems (such as liquids of high viscosity or molecular glasses). The sensitivity of NQR slow motion spectra to the mechanism of the motional processes modulating the nuclear quadrupole interaction is discussed.

A Huygens principle for diffusion and anomalous diffusion in spatially extended systems

PubMed Central

Gottwald, Georg A.; Melbourne, Ian

2013-01-01

We present a universal view on diffusive behavior in chaotic spatially extended systems for anisotropic and isotropic media. For anisotropic systems, strong chaos leads to diffusive behavior (Brownian motion with drift) and weak chaos leads to superdiffusive behavior (Lévy processes with drift). For isotropic systems, the drift term vanishes and strong chaos again leads to Brownian motion. We establish the existence of a nonlinear Huygens principle for weakly chaotic systems in isotropic media whereby the dynamics behaves diffusively in even space dimension and exhibits superdiffusive behavior in odd space dimensions. PMID:23653481

The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2014-09-01

We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion.

PubMed

Bodrova, Anna S; Chechkin, Aleksei V; Cherstvy, Andrey G; Safdari, Hadiseh; Sokolov, Igor M; Metzler, Ralf

2016-07-27

It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases.

Brownian motion of arbitrarily shaped particles in two dimensions.

PubMed

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V; Sun, Kai; Wei, Qi-Huo

2014-11-25

We implement microfabricated boomerang particles with unequal arm lengths as a model for nonsymmetric particles and study their Brownian motion in a quasi-two-dimensional geometry by using high-precision single-particle motion tracking. We show that because of the coupling between translation and rotation, the mean squared displacements of a single asymmetric boomerang particle exhibit a nonlinear crossover from short-time faster to long-time slower diffusion, and the mean displacements for fixed initial orientation are nonzero and saturate out at long times. The measured anisotropic diffusion coefficients versus the tracking point position indicate that there exists one unique point, i.e., the center of hydrodynamic stress (CoH), at which all coupled diffusion coefficients vanish. This implies that in contrast to motion in three dimensions where the CoH exists only for high-symmetry particles, the CoH always exists for Brownian motion in two dimensions. We develop an analytical model based on Langevin theory to explain the experimental results and show that among the six anisotropic diffusion coefficients only five are independent because the translation-translation coupling originates from the translation-rotation coupling. Finally, we classify the behavior of two-dimensional Brownian motion of arbitrarily shaped particles into four groups based on the particle shape symmetry group and discussed potential applications of the CoH in simplifying understanding of the circular motions of microswimmers.

The effects of bound state motion on macromolecular diffusion

NASA Astrophysics Data System (ADS)

Hough, Loren; Stefferson, Michael; Norris, Samantha; Maguire, Laura; Vernerey, Franck; Betterton, Meredith

The diffusion of macromolecules is modified in crowded environments by both inert obstacles and interaction sites. Molecules are generally slowed in their movement inducing transient anomalous subdiffusion. Obstacles also modify the kinetics and equilibrium behavior of interaction between mobile proteins. In some biophysical contexts, bound molecules can still experience mobility, for example transcription factors sliding along DNA, membrane proteins with some entry and diffusion within lipid domains, or proteins that can enter into non-membrane bound compartments such as the nucleolus. We used lattice and continuum models to study the diffusive behavior of tracer particles which bind to obstacles and can diffuse within them. We show that binding significantly alters the motion of tracers. The type and degree of motion while bound is a key determinant of the tracer mobility. Our work has implications for protein-protein movement and interactions within living cells, including those involving intrinsically disordered proteins.

Real-space analysis of diffusion behavior and activation energy of individual monatomic ions in a liquid.

PubMed

Miyata, Tomohiro; Uesugi, Fumihiko; Mizoguchi, Teruyasu

2017-12-01

Investigation of the local dynamic behavior of atoms and molecules in liquids is crucial for revealing the origin of macroscopic liquid properties. Therefore, direct imaging of single atoms to understand their motions in liquids is desirable. Ionic liquids have been studied for various applications, in which they are used as electrolytes or solvents. However, atomic-scale diffusion and relaxation processes in ionic liquids have never been observed experimentally. We directly observe the motion of individual monatomic ions in an ionic liquid using scanning transmission electron microscopy (STEM) and reveal that the ions diffuse by a cage-jump mechanism. Moreover, we estimate the diffusion coefficient and activation energy for the diffusive jumps from the STEM images, which connect the atomic-scale dynamics to macroscopic liquid properties. Our method is the only available means to observe the motion, reactions, and energy barriers of atoms/molecules in liquids.

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.

O'Connell's process as a vicious Brownian motion.

PubMed

Katori, Makoto

2011-12-01

Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of the quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.

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.

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

PubMed Central

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

2015-01-01

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

DOE PAGES

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; ...

2015-03-02

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

Understanding the Origins of Dipolar Couplings and Correlated Motion in the Vibrational Spectrum of Water.

PubMed

Heyden, Matthias; Sun, Jian; Forbert, Harald; Mathias, Gerald; Havenith, Martina; Marx, Dominik

2012-08-16

The combination of vibrational spectroscopy and molecular dynamics simulations provides a powerful tool to obtain insights into the molecular details of water structure and dynamics in the bulk and in aqueous solutions. Applying newly developed approaches to analyze correlations of charge currents, molecular dipole fluctuations, and vibrational motion in real and k-space, we compare results from nonpolarizable water models, widely used in biomolecular modeling, to ab initio molecular dynamics. For the first time, we unfold the infrared response of bulk water into contributions from correlated fluctuations in the three-dimensional, anisotropic environment of an average water molecule, from the OH-stretching region down to the THz regime. Our findings show that the absence of electronic polarizability in the force field model not only results in differences in dipolar couplings and infrared absorption but also induces artifacts into the correlated vibrational motion between hydrogen-bonded water molecules, specifically at the intramolecular bending frequency. Consequently, vibrational motion is partially ill-described with implications for the accuracy of non-self-consistent, a posteriori methods to add polarizability.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

PubMed

Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C

2014-12-16

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

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

A Diffusion Approximation Based on Renewal Processes with Applications to Strongly Biased Run-Tumble Motion.

PubMed

Thygesen, Uffe Høgsbro

2016-03-01

We consider organisms which use a renewal strategy such as run-tumble when moving in space, for example to perform chemotaxis in chemical gradients. We derive a diffusion approximation for the motion, applying a central limit theorem due to Anscombe for renewal-reward processes; this theorem has not previously been applied in this context. Our results extend previous work, which has established the mean drift but not the diffusivity. For a classical model of tumble rates applied to chemotaxis, we find that the resulting chemotactic drift saturates to the swimming velocity of the organism when the chemical gradients grow increasingly steep. The dispersal becomes anisotropic in steep gradients, with larger dispersal across the gradient than along the gradient. In contrast to one-dimensional settings, strong bias increases dispersal. We next include Brownian rotation in the model and find that, in limit of high chemotactic sensitivity, the chemotactic drift is 64% of the swimming velocity, independent of the magnitude of the Brownian rotation. We finally derive characteristic timescales of the motion that can be used to assess whether the diffusion limit is justified in a given situation. The proposed technique for obtaining diffusion approximations is conceptually and computationally simple, and applicable also when statistics of the motion is obtained empirically or through Monte Carlo simulation of the motion.

Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2014-05-01

Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.

Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Fuson, Michael M.

2017-01-01

Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

Measuring nanoparticle diffusion in an ABELtrap

NASA Astrophysics Data System (ADS)

Dienerowitz, M.; Dienerowitz, F.; Börsch, M.

2018-03-01

Monitoring the Brownian motion of individual nanoscopic objects is key to investigate their transport properties and interactions with their close environment. Most techniques rely on transient diffusion through a detection volume or immobilisation, which restrict observation times or motility. We measure the diffusion coefficient and surface charge of individual nanoparticles and DNA molecules in an anti-Brownian electrokinetic trap (ABELtrap). This instrument is an active feedback trap confining the Brownian motion of a nanoparticle to the detection site by applying an electric field based on the particle’s current position. We simulate the Brownian motion of nanospheres in our sample geometry, including wall effects, due to partial confinement in the third dimension. The theoretically predicted values are in excellent agreement with our diffusion measurements in the ABELtrap. We also demonstrate the ABELtrap’s ability to measure varying sizes of DNA origami structures during denaturation.

Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion

PubMed Central

Bodrova, Anna S.; Chechkin, Aleksei V.; Cherstvy, Andrey G.; Safdari, Hadiseh; Sokolov, Igor M.; Metzler, Ralf

2016-01-01

It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases. PMID:27462008

Infinite densities for Lévy walks.

PubMed

Rebenshtok, A; Denisov, S; Hänggi, P; Barkai, E

2014-12-01

Motion of particles in many systems exhibits a mixture between periods of random diffusive-like events and ballistic-like motion. In many cases, such systems exhibit strong anomalous diffusion, where low-order moments 〈|x(t)|(q)〉 with q below a critical value q(c) exhibit diffusive scaling while for q>q(c) a ballistic scaling emerges. The mixed dynamics constitutes a theoretical challenge since it does not fall into a unique category of motion, e.g., the known diffusion equations and central limit theorems fail to describe both aspects. In this paper we resolve this problem by resorting to the concept of infinite density. Using the widely applicable Lévy walk model, we find a general expression for the corresponding non-normalized density which is fully determined by the particles velocity distribution, the anomalous diffusion exponent α, and the diffusion coefficient K(α). We explain how infinite densities play a central role in the description of dynamics of a large class of physical processes and discuss how they can be evaluated from experimental or numerical data.

Ionic-Electronic Ambipolar Transport in Metal Halide Perovskites: Can Electronic Conductivity Limit Ionic Diffusion?

PubMed

Kerner, Ross A; Rand, Barry P

2018-01-04

Ambipolar transport describes the nonequilibrium, coupled motion of positively and negatively charged particles to ensure that internal electric fields remain small. It is commonly invoked in the semiconductor community where the motion of excess electrons and holes drift and diffuse together. However, the concept of ambipolar transport is not limited to semiconductor physics. Materials scientists working on ion conducting ceramics understand ambipolar transport dictates the coupled diffusion of ions and the rate is limited by the ion with the lowest diffusion coefficient. In this Perspective, we review a third application of ambipolar transport relevant to mixed ionic-electronic conducting materials for which the motion of ions is expected to be coupled to electronic carriers. In this unique situation, the ambipolar diffusion model has been successful at explaining the photoenhanced diffusion of metal ions in chalcogenide glasses and other properties of materials. Recent examples of photoenhanced phenomena in metal halide perovskites are discussed and indicate that mixed ionic-electronic ambipolar transport is similarly important for a deep understanding of these emerging materials.

Chaotic ion motion in magnetosonic plasma waves

NASA Technical Reports Server (NTRS)

Varvoglis, H.

1984-01-01

The motion of test ions in a magnetosonic plasma wave is considered, and the 'stochasticity threshold' of the wave's amplitude for the onset of chaotic motion is estimated. It is shown that for wave amplitudes above the stochasticity threshold, the evolution of an ion distribution can be described by a diffusion equation with a diffusion coefficient D approximately equal to 1/v. Possible applications of this process to ion acceleration in flares and ion beam thermalization are discussed.

Correlated Protein Motion Measurements of Dihydrofolate Reductase Crystals

NASA Astrophysics Data System (ADS)

Xu, Mengyang; Niessen, Katherine; Pace, James; Cody, Vivian; Markelz, Andrea

2014-03-01

We report the first direct measurements of the long range structural vibrational modes in dihydrofolate reductase (DHFR). DHFR is a universal housekeeping enzyme that catalyzes the reduction of 7,8-dihydrofolate to 5,6,7,8-tetra-hydrofolate, with the aid of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH). This crucial enzymatic role as the target for anti-cancer [methotrexate (MTX)], and other clinically useful drugs, has made DHFR a long-standing target of enzymological studies. The terahertz (THz) frequency range (5-100 cm-1), corresponds to global correlated protein motions. In our lab we have developed Crystal Anisotropy Terahertz Microscopy (CATM), which directly measures these large scale intra-molecular protein vibrations, by removing the relaxational background of the solvent and residue side chain librational motions. We demonstrate narrowband features in the anisotropic absorbance for mouse DHFR with the ligand binding of NADPH and MTX single crystals as well as Escherichia coli DHFR with the ligand binding of NADPH and MTX single crystals. This work is supported by NSF grant MRI2 grant DBI2959989.

A model of oscillatory transport in granular soils, with application to barometric pumping and earth tides.

PubMed

Neeper, D A

2001-04-01

A simple algebraic model is proposed to estimate the transport of a volatile or soluble chemical caused by oscillatory flow of fluid in a porous medium. The model is applied to the barometric pumping of vapors in the vadose zone, and to the transport of dissolved species by earth tides in an aquifer. In the model, the fluid moves sinusoidally with time in the porosity of the soil. The chemical concentration in the mobile fluid is considered to equilibrate with the concentration in the surrounding matrix according to a characteristic time governed by diffusion, sorption, or other rate processes. The model provides a closed form solution, to which barometric pressure data are applied in an example of pore gas motion in the vadose zone. The model predicts that the additional diffusivity due barometric pumping in an unfractured vadose zone would be comparable to the diffusivity in stagnant pore gas if the equilibration time is 1 day or longer. Water motion due to the M2 lunar tide is examined as an example of oscillatory transport in an aquifer. It is shown that the tidal motion of the water in an aquifer might significantly increase the vertical diffusivity of dissolved species when compared to diffusion in an absolutely stagnant aquifer, but the hydrodynamic dispersivity due to tidal motion or gravitational flow would probably exceed the diffusivity due to oscillatory advection.

O'Connell's process as a vicious Brownian motion

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

Katori, Makoto

Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of themore » quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.« less

Use of the temporal median and trimmed mean mitigates effects of respiratory motion in multiple-acquisition abdominal diffusion imaging

NASA Astrophysics Data System (ADS)

Jerome, N. P.; Orton, M. R.; d'Arcy, J. A.; Feiweier, T.; Tunariu, N.; Koh, D.-M.; Leach, M. O.; Collins, D. J.

2015-01-01

Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, where averaging of successive samples at different parts of the respiratory cycle, performed in the scanner, manifests the motion as blurring of tissue boundaries and structural features and can introduce bias into calculated diffusion metrics. Storing multiple averages separately allows processing using metrics other than the mean; in this prospective volunteer study, median and trimmed mean values of signal intensity for each voxel over repeated averages and diffusion-weighting directions are shown to give images with sharper tissue boundaries and structural features for moving tissues, while not compromising non-moving structures. Expert visual scoring of derived diffusion maps is significantly higher for the median than for the mean, with modest improvement from the trimmed mean. Diffusion metrics derived from mono- and bi-exponential diffusion models are comparable for non-moving structures, demonstrating a lack of introduced bias from using the median. The use of the median is a simple and computationally inexpensive alternative to complex and expensive registration algorithms, requiring only additional data storage (and no additional scanning time) while returning visually superior images that will facilitate the appropriate placement of regions-of-interest when analysing abdominal diffusion-weighted magnetic resonance images, for assessment of disease characteristics and treatment response.

Use of the temporal median and trimmed mean mitigates effects of respiratory motion in multiple-acquisition abdominal diffusion imaging.

PubMed

Jerome, N P; Orton, M R; d'Arcy, J A; Feiweier, T; Tunariu, N; Koh, D-M; Leach, M O; Collins, D J

2015-01-21

Respiratory motion commonly confounds abdominal diffusion-weighted magnetic resonance imaging, where averaging of successive samples at different parts of the respiratory cycle, performed in the scanner, manifests the motion as blurring of tissue boundaries and structural features and can introduce bias into calculated diffusion metrics. Storing multiple averages separately allows processing using metrics other than the mean; in this prospective volunteer study, median and trimmed mean values of signal intensity for each voxel over repeated averages and diffusion-weighting directions are shown to give images with sharper tissue boundaries and structural features for moving tissues, while not compromising non-moving structures. Expert visual scoring of derived diffusion maps is significantly higher for the median than for the mean, with modest improvement from the trimmed mean. Diffusion metrics derived from mono- and bi-exponential diffusion models are comparable for non-moving structures, demonstrating a lack of introduced bias from using the median. The use of the median is a simple and computationally inexpensive alternative to complex and expensive registration algorithms, requiring only additional data storage (and no additional scanning time) while returning visually superior images that will facilitate the appropriate placement of regions-of-interest when analysing abdominal diffusion-weighted magnetic resonance images, for assessment of disease characteristics and treatment response.

An unusual slowdown of fast diffusion in a room temperature

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

Chathoth,; Mamontov, Eugene; Fulvio, Pasquale F

2013-01-01

Using quasielastic neutron scattering in the temperature range from 290 to 350 K, we show that the diffusive motions in a room temperature ionic liquid [H2NC(dma)2][BETI] become faster for a fraction of cations when the liquid is confined in a mesoporous carbon. This applies to both the localized and long-range translational diffusive motions of the highly mobile cations, although the former exhibit an unusual trend of slowing-down as the temperature is increased, until the localized diffusivity is reduced to the bulk ionic liquid value at a temperature of 350 K.

Diffusion in different models of active Brownian motion

NASA Astrophysics Data System (ADS)

Lindner, B.; Nicola, E. M.

2008-04-01

Active Brownian particles (ABP) have served as phenomenological models of self-propelled motion in biology. We study the effective diffusion coefficient of two one-dimensional ABP models (simplified depot model and Rayleigh-Helmholtz model) differing in their nonlinear friction functions. Depending on the choice of the friction function the diffusion coefficient does or does not attain a minimum as a function of noise intensity. We furthermore discuss the case of an additional bias breaking the left-right symmetry of the system. We show that this bias induces a drift and that it generally reduces the diffusion coefficient. For a finite range of values of the bias, both models can exhibit a maximum in the diffusion coefficient vs. noise intensity.

Diffusing diffusivity: Rotational diffusion in two and three dimensions

NASA Astrophysics Data System (ADS)

Jain, Rohit; Sebastian, K. L.

2017-06-01

We consider the problem of calculating the probability distribution function (pdf) of angular displacement for rotational diffusion in a crowded, rearranging medium. We use the diffusing diffusivity model and following our previous work on translational diffusion [R. Jain and K. L. Sebastian, J. Phys. Chem. B 120, 3988 (2016)], we show that the problem can be reduced to that of calculating the survival probability of a particle undergoing Brownian motion, in the presence of a sink. We use the approach to calculate the pdf for the rotational motion in two and three dimensions. We also propose new dimensionless, time dependent parameters, αr o t ,2 D and αr o t ,3 D, which can be used to analyze the experimental/simulation data to find the extent of deviation from the normal behavior, i.e., constant diffusivity, and obtain explicit analytical expressions for them, within our model.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; ...

2014-12-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

PubMed Central

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

2014-01-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions. PMID:25453071

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.

Fast internal dynamics in alcohol dehydrogenase

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

Monkenbusch, M.; Stadler, A., E-mail: a.stadler@fz-juelich.de; Biehl, R.

2015-08-21

Large-scale domain motions in alcohol dehydrogenase (ADH) have been observed previously by neutron spin-echo spectroscopy (NSE). We have extended the investigation on the dynamics of ADH in solution by using high-resolution neutron time-of-flight (TOF) and neutron backscattering (BS) spectroscopy in the incoherent scattering range. The observed hydrogen dynamics were interpreted in terms of three mobility classes, which allowed a simultaneous description of the measured TOF and BS spectra. In addition to the slow global protein diffusion and domain motions observed by NSE, a fast internal process could be identified. Around one third of the protons in ADH participate in themore » fast localized diffusive motion. The diffusion coefficient of the fast internal motions is around two third of the value of the surrounding D{sub 2}O solvent. It is tempting to associate the fast internal process with solvent exposed amino acid residues with dangling side chains.« less

Simulation of gas diffusion and sorption in nanoceramic semiconductors

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

1999-05-01

Gas diffusion and sorption in nanoceramic semiconductors are studied using atomistic simulation techniques and numerical results are presented for a variety of sorbate-sorbent systems. SnO2, BaTiO3, CuO, and MgO substrates are built on the computer using lattice constants and atomic parameters that have been either measured or computed by ab initio methods. The Universal force field is employed here for the description of both intramolecular and nonbonded interactions for various gas sorbates, including CH4, CO, CO2, and O2, pure and in binary mixtures. Mean residence times are determined by molecular dynamics computations, whereas the Henry constant and the isosteric heat of adsorption are estimated by a Monte Carlo technique. The effects of surface hydroxylation on the diffusion and sorption characteristics are quantified and discussed in view of their significance in practical gas sensing applications. The importance of fast diffusion on the response time of the sensitive layer and of the sorption efficiency on the overall sensitivity as well as the potential synergy of the two phenomena are discussed.

Femtosecond dynamics in ionic structures of a heart medicine

NASA Astrophysics Data System (ADS)

Gil, M.; Douhal, A.

2006-12-01

Femtosecond studies of ionic structures of milrinone - a medicine used to help the heart to recuperate its life - in acidic and alkaline water solutions show that the intramolecular charge transfer in the cation and in the anion happen in 550 fs and ˜1.2 ps, respectively. These times are longer than 100 fs, observed in the keto (inotropic) form. The transients also show a 2-3 ps component, assigned to cooling and twisting motion in the produced states. The result might be used for a better understanding of other functional molecules.

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

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.

Simultaneous MR elastography and diffusion acquisitions: diffusion-MRE (dMRE).

PubMed

Yin, Ziying; Magin, Richard L; Klatt, Dieter

2014-05-01

To present a new technique for concurrent MR elastography (MRE) and diffusion MRI: diffusion-MRE (dMRE). In dMRE, shear wave motion and MR signal decay due to diffusion are encoded into the phase and magnitude components of the MR signal by using a pair of bipolar gradients for both motion-sensitization and diffusion encoding. The pulse sequence timing is adjusted so that the bipolar gradients are sensitive to both coherent and incoherent intravoxel motions. The shape, number, and duration of the gradient lobes can be adjusted to provide flexibility and encoding efficiency. In this proof-of-concept study, dMRE was validated using a tissue phantom composed of a gel bead embedded in a hydrated mixture of agarose and gelatin. The apparent diffusion coefficient (ADC) and shear stiffness measured using dMRE were compared with results obtained from separate, conventional spin-echo (SE) diffusion and SE-MRE acquisitions. The averaged ADC values (n = 3) for selected ROIs in the beads were (1.75 ± 0.16) μm(2) /ms and (1.74 ± 0.16) μm(2) /ms for SE-diffusion and dMRE methods, respectively. The corresponding shear stiffness values in the beads were (2.45 ± 0.23) kPa and (2.42 ± 0.20) kPa. Simultaneous MRE and diffusion acquisition is feasible and can be implemented with no observable interference between the two methods. Copyright © 2014 Wiley Periodicals, Inc.

An abnormally slow proton transfer reaction in a simple HBO derivative due to ultrafast intramolecular-charge transfer events.

PubMed

Alarcos, Noemí; Gutierrez, Mario; Liras, Marta; Sánchez, Félix; Douhal, Abderrazzak

2015-07-07

We report on the steady-state, picosecond and femtosecond time-resolved studies of a charge and proton transfer dye 6-amino-2-(2'-hydroxyphenyl)benzoxazole (6A-HBO) and its methylated derivative 6-amino-2-(2'-methoxyphenyl)benzoxazole (6A-MBO), in different solvents. With femtosecond resolution and comparison with the photobehaviour of 6A-MBO, we demonstrate for 6A-HBO in solution, the photoproduction of an intramolecular charge-transfer (ICT) process at S1 taking place in ∼140 fs or shorter, followed by solvent relaxation in the charge transferred species. The generated structure (syn-enol charge transfer conformer) experiences an excited-state intramolecular proton-transfer (ESIPT) reaction to produce a keto-type tautomer. This subsequent proton motion occurs in 1.2 ps (n-heptane), 14 ps (DCM) and 35 ps (MeOH). In MeOH, it is assisted by the solvent molecules and occurs through tunneling for which we got a large kinetic isotope effect (KIE) of about 13. For the 6A-DBO (deuterated sample in CD3OD) the global proton-transfer reaction takes place in 200 ps, showing a remarkable slow KIE regime. The slow ESIPT reaction in DCM (14 ps), not through tunnelling as it is not sensitive to OH/OD exchange, has however to overcome an energy barrier using intramolecular as well as solvent coordinates. The rich ESIPT dynamics of 6A-HBO in the used solutions is governed by an ICT reaction, triggered by the amino group, and it is solvent dependent. Thus, the charge injection to a 6A-HBO molecular frame makes the ICT species more stable, and the phenol group less acidic, slowing down the subsequent ESIPT reaction. Our findings bring new insights into the coupling between ICT and ESIPT reactions on the potential-energy surfaces of several barriers.

Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study.

PubMed

Omidyan, Reza; Iravani, Maryam

2016-11-14

The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH 2 ) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S 1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S 1 /S 0 ), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study

NASA Astrophysics Data System (ADS)

Omidyan, Reza; Iravani, Maryam

2016-11-01

The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH2) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S1/S0), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

Spiral diffusion of rotating self-propellers with stochastic perturbation

NASA Astrophysics Data System (ADS)

Nourhani, Amir; Ebbens, Stephen J.; Gibbs, John G.; Lammert, Paul E.

2016-09-01

Translationally diffusive behavior arising from the combination of orientational diffusion and powered motion at microscopic scales is a known phenomenon, but the peculiarities of the evolution of expected position conditioned on initial position and orientation have been neglected. A theory is given of the spiral motion of the mean trajectory depending upon propulsion speed, angular velocity, orientational diffusion, and rate of random chirality reversal. We demonstrate the experimental accessibility of this effect using both tadpole-like and Janus sphere dimer rotating motors. Sensitivity of the mean trajectory to the kinematic parameters suggest that it may be a useful way to determine those parameters.

Fetal lung apparent diffusion coefficient measurement using diffusion-weighted MRI at 3 Tesla: Correlation with gestational age.

PubMed

Afacan, Onur; Gholipour, Ali; Mulkern, Robert V; Barnewolt, Carol E; Estroff, Judy A; Connolly, Susan A; Parad, Richard B; Bairdain, Sigrid; Warfield, Simon K

2016-12-01

To evaluate the feasibility of using diffusion-weighted magnetic resonance imaging (DW-MRI) to assess the fetal lung apparent diffusion coefficient (ADC) at 3 Tesla (T). Seventy-one pregnant women (32 second trimester, 39 third trimester) were scanned with a twice-refocused Echo-planar diffusion-weighted imaging sequence with 6 different b-values in 3 orthogonal diffusion orientations at 3T. After each scan, a region-of-interest (ROI) mask was drawn to select a region in the fetal lung and an automated robust maximum likelihood estimation algorithm was used to compute the ADC parameter. The amount of motion in each scan was visually rated. When scans with unacceptable levels of motion were eliminated, the lung ADC values showed a strong association with gestational age (P < 0.01), increasing dramatically between 16 and 27 weeks and then achieving a plateau around 27 weeks. We show that to get reliable estimates of ADC values of fetal lungs, a multiple b-value acquisition, where motion is either corrected or considered, can be performed. J. Magn. Reson. Imaging 2016;44:1650-1655. © 2016 International Society for Magnetic Resonance in Medicine.

Disentangling Random Motion and Flow in a Complex Medium

PubMed Central

Koslover, Elena F.; Chan, Caleb K.; Theriot, Julie A.

2016-01-01

We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined. PMID:26840734

Microscopic Interpretation and Generalization of the Bloch-Torrey Equation for Diffusion Magnetic Resonance

PubMed Central

Seroussi, Inbar; Grebenkov, Denis S.; Pasternak, Ofer; Sochen, Nir

2017-01-01

In order to bridge microscopic molecular motion with macroscopic diffusion MR signal in complex structures, we propose a general stochastic model for molecular motion in a magnetic field. The Fokker-Planck equation of this model governs the probability density function describing the diffusion-magnetization propagator. From the propagator we derive a generalized version of the Bloch-Torrey equation and the relation to the random phase approach. This derivation does not require assumptions such as a spatially constant diffusion coefficient, or ad-hoc selection of a propagator. In particular, the boundary conditions that implicitly incorporate the microstructure into the diffusion MR signal can now be included explicitly through a spatially varying diffusion coefficient. While our generalization is reduced to the conventional Bloch-Torrey equation for piecewise constant diffusion coefficients, it also predicts scenarios in which an additional term to the equation is required to fully describe the MR signal. PMID:28242566

Nanoscopic dynamics of phospholipid in unilamellar vesicles: Effect of gel to fluid phase transition

DOE PAGES

Sharma, V. K.; Mamontov, E.; Anunciado, D. B.; ...

2015-03-04

Dynamics of phospholipids in unilamellar vesicles (ULV) is of interest in biology, medical, and food sciences since these molecules are widely used as biocompatible agents and a mimic of cell membrane systems. We have investigated the nanoscopic dynamics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) phospholipid in ULV as a function of temperature using elastic and quasielastic neutron scattering (QENS). The dependence of the signal on the scattering momentum transfer, which is a critical advantage of neutron scattering techniques, allows the detailed analysis of the lipid motions that cannot be carried out by other means. In agreement with a differential scanning calorimetry measurement, amore » sharp rise in the elastic scattering intensity below ca. 296 K indicates a phase transition from the high-temperature fluid phase to the low-temperature solid gel phase. The microscopic lipid dynamics exhibits qualitative differences between the solid gel phase (in a measurement at 280 K) and the fluid phase (in a measurement at a physiological temperature of 310 K). The data analysis invariably shows the presence of two distinct motions: the whole lipid molecule motion within a monolayer, or lateral diffusion, and the relatively faster internal motion of the DMPC molecule. The lateral diffusion of the whole lipid molecule is found to be Fickian in character, whereas the internal lipid motions are of localized character, consistent with the structure of the vesicles. The lateral motion slows down by an order of magnitude in the solid gel phase, whereas for the internal motion not only the time scale, but also the character of the motion changes upon the phase transition. In the solid gel phase, the lipids are more ordered and undergo uniaxial rotational motion. However, in the fluid phase, the hydrogen atoms of the lipid tails undergo confined translation diffusion rather than uniaxial rotational diffusion. The localized translational diffusion of the hydrogen atoms of the lipid tails is a manifestation of the flexibility of the chains acquired in the fluid phase. Because of this flexibility, both the local diffusivity and the confinement volume for the hydrogen atoms increase linearly from near the lipid s polar head group to the end of its hydrophobic tail. Our results present a quantitative and detailed picture of the effect of the gel-fluid phase transition on the nanoscopic lipid dynamics in ULV. Lastly, the data analysis approach developed here has a potential for probing the dynamic response of lipids to the presence of additional cell membrane components.« less

Femtosecond studies of protein-ligand hydrophobic binding and dynamics: human serum albumin.

PubMed

Zhong, D; Douhal, A; Zewail, A H

2000-12-19

In this contribution, we report studies of the nature of the dynamics and hydrophobic binding in protein-ligand complexes of human serum albumin with 2-(2'-hydroxyphenyl)-4-methyloxazole. With femtosecond time resolution, we examined the orientational motion of the ligand, its intrinsic nuclear motions, and the lifetime changes in the hydrophobic phase. For comparisons, with similar but chemical nanocavities, we also studied the same ligand in micelles and cyclodextrins. The hydrophobic interactions in the binding crevice are much stronger than those observed in cyclodextrins and micelles. The confined geometry restrains the nonradiative decay and significantly lengthens the excited-state lifetime. The observed dynamics over the femtosecond-to-nanosecond time scale indicate that the binding structure is rigid and the local motions of the ligand are nearly "frozen" in the protein. Another major finding is the elucidation of the directed dynamics by the protein. Proton transfer and intramolecular twisting of 2-(2'-hydroxyphenyl)-4-methyloxazole were observed to evolve along two routes: one involves the direct stretching motion in the molecular plane (approximately 200 fs) and is not sensitive to the environment; the second, less dominant, is related to the twisting motion (approximately 3 ps) of the two heterocyclic rings and drastically slows down in the protein hydrophobic pocket.

Anisotropic Brownian motion in ordered phases of DNA fragments.

PubMed

Dobrindt, J; Rodrigo Teixeira da Silva, E; Alves, C; Oliveira, C L P; Nallet, F; Andreoli de Oliveira, E; Navailles, L

2012-01-01

Using Fluorescence Recovery After Photobleaching, we investigate the Brownian motion of DNA rod-like fragments in two distinct anisotropic phases with a local nematic symmetry. The height of the measurement volume ensures the averaging of the anisotropy of the in-plane diffusive motion parallel or perpendicular to the local nematic director in aligned domains. Still, as shown in using a model specifically designed to handle such a situation and predicting a non-Gaussian shape for the bleached spot as fluorescence recovery proceeds, the two distinct diffusion coefficients of the DNA particles can be retrieved from data analysis. In the first system investigated (a ternary DNA-lipid lamellar complex), the magnitude and anisotropy of the diffusion coefficient of the DNA fragments confined by the lipid bilayers are obtained for the first time. In the second, binary DNA-solvent system, the magnitude of the diffusion coefficient is found to decrease markedly as DNA concentration is increased from isotropic to cholesteric phase. In addition, the diffusion coefficient anisotropy measured within cholesteric domains in the phase coexistence region increases with concentration, and eventually reaches a high value in the cholesteric phase.

Influence of image registration on ADC images computed from free-breathing diffusion MRIs of the abdomen

NASA Astrophysics Data System (ADS)

Guyader, Jean-Marie; Bernardin, Livia; Douglas, Naomi H. M.; Poot, Dirk H. J.; Niessen, Wiro J.; Klein, Stefan

2014-03-01

The apparent diffusion coefficient (ADC) is an imaging biomarker providing quantitative information on the diffusion of water in biological tissues. This measurement could be of relevance in oncology drug development, but it suffers from a lack of reliability. ADC images are computed by applying a voxelwise exponential fitting to multiple diffusion-weighted MR images (DW-MRIs) acquired with different diffusion gradients. In the abdomen, respiratory motion induces misalignments in the datasets, creating visible artefacts and inducing errors in the ADC maps. We propose a multistep post-acquisition motion compensation pipeline based on 3D non-rigid registrations. It corrects for motion within each image and brings all DW-MRIs to a common image space. The method is evaluated on 10 datasets of free-breathing abdominal DW-MRIs acquired from healthy volunteers. Regions of interest (ROIs) are segmented in the right part of the abdomen and measurements are compared in the three following cases: no image processing, Gaussian blurring of the raw DW-MRIs and registration. Results show that both blurring and registration improve the visual quality of ADC images, but compared to blurring, registration yields visually sharper images. Measurement uncertainty is reduced both by registration and blurring. For homogeneous ROIs, blurring and registration result in similar median ADCs, which are lower than without processing. In a ROI at the interface between liver and kidney, registration and blurring yield different median ADCs, suggesting that uncorrected motion introduces a bias. Our work indicates that averaging procedures on the scanner should be avoided, as they remove the opportunity to perform motion correction.

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

Imamura, Kayo; Matsuura, Takanori; Ye, Zhengmao

Disproportionating enzyme from potato was crystallized and preliminarily analyzed using X-ray diffraction. Disproportionating enzyme (D-enzyme; EC 2.4.1.25) is a 59 kDa protein that belongs to the α-amylase family. D-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of α-1,4 glucan. A crystal of the D-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. Preliminary X-ray data showed that the crystal diffracts to 2.0 Å resolution and belongs to space group C222{sub 1}, with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 Å.

Mechanism of vibrational energy dissipation of free OH groups at the air-water interface.

PubMed

Hsieh, Cho-Shuen; Campen, R Kramer; Okuno, Masanari; Backus, Ellen H G; Nagata, Yuki; Bonn, Mischa

2013-11-19

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air-water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air-H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces.

Mechanism of vibrational energy dissipation of free OH groups at the air–water interface

PubMed Central

Hsieh, Cho-Shuen; Campen, R. Kramer; Okuno, Masanari; Backus, Ellen H. G.; Nagata, Yuki; Bonn, Mischa

2013-01-01

Interfaces of liquid water play a critical role in a wide variety of processes that occur in biology, a variety of technologies, and the environment. Many macroscopic observations clarify that the properties of liquid water interfaces significantly differ from those of the bulk liquid. In addition to interfacial molecular structure, knowledge of the rates and mechanisms of the relaxation of excess vibrational energy is indispensable to fully understand physical and chemical processes of water and aqueous solutions, such as chemical reaction rates and pathways, proton transfer, and hydrogen bond dynamics. Here we elucidate the rate and mechanism of vibrational energy dissipation of water molecules at the air–water interface using femtosecond two-color IR-pump/vibrational sum-frequency probe spectroscopy. Vibrational relaxation of nonhydrogen-bonded OH groups occurs at a subpicosecond timescale in a manner fundamentally different from hydrogen-bonded OH groups in bulk, through two competing mechanisms: intramolecular energy transfer and ultrafast reorientational motion that leads to free OH groups becoming hydrogen bonded. Both pathways effectively lead to the transfer of the excited vibrational modes from free to hydrogen-bonded OH groups, from which relaxation readily occurs. Of the overall relaxation rate of interfacial free OH groups at the air–H2O interface, two-thirds are accounted for by intramolecular energy transfer, whereas the remaining one-third is dominated by the reorientational motion. These findings not only shed light on vibrational energy dynamics of interfacial water, but also contribute to our understanding of the impact of structural and vibrational dynamics on the vibrational sum-frequency line shapes of aqueous interfaces. PMID:24191016

Uncovering Implicit Assumptions: A Large-Scale Study on Students' Mental Models of Diffusion

ERIC Educational Resources Information Center

Stains, Marilyne; Sevian, Hannah

2015-01-01

Students' mental models of diffusion in a gas phase solution were studied through the use of the Structure and Motion of Matter (SAMM) survey. This survey permits identification of categories of ways students think about the structure of the gaseous solute and solvent, the origin of motion of gas particles, and trajectories of solute particles in…

Orthogonally combined motion- and diffusion-sensitized driven equilibrium (OC-MDSDE) preparation for vessel signal suppression in 3D turbo spin echo imaging of peripheral nerves in the extremities.

PubMed

Cervantes, Barbara; Kirschke, Jan S; Klupp, Elizabeth; Kooijman, Hendrik; Börnert, Peter; Haase, Axel; Rummeny, Ernst J; Karampinos, Dimitrios C

2018-01-01

To design a preparation module for vessel signal suppression in MR neurography of the extremities, which causes minimal attenuation of nerve signal and is highly insensitive to eddy currents and motion. The orthogonally combined motion- and diffusion-sensitized driven equilibrium (OC-MDSDE) preparation was proposed, based on the improved motion- and diffusion-sensitized driven equilibrium methods (iMSDE and FC-DSDE, respectively), with specific gradient design and orientation. OC-MDSDE was desensitized against eddy currents using appropriately designed gradient prepulses. The motion sensitivity and vessel signal suppression capability of OC-MDSDE and its components were assessed in vivo in the knee using 3D turbo spin echo (TSE). Nerve-to-vessel signal ratios were measured for iMSDE and OC-MDSDE in 7 subjects. iMSDE was shown to be highly sensitive to motion with increasing flow sensitization. FC-DSDE showed robustness against motion, but resulted in strong nerve signal loss with diffusion gradients oriented parallel to the nerve. OC-MDSDE showed superior vessel suppression compared to iMSDE and FC-DSDE and maintained high nerve signal. Mean nerve-to-vessel signal ratios in 7 subjects were 0.40 ± 0.17 for iMSDE and 0.63 ± 0.37 for OC-MDSDE. OC-MDSDE combined with 3D TSE in the extremities allows high-near-isotropic-resolution imaging of peripheral nerves with reduced vessel contamination and high nerve signal. Magn Reson Med 79:407-415, 2018. © 2017 Wiley Periodicals, Inc. © 2017 International Society for Magnetic Resonance in Medicine.

Diffusive mixing and Tsallis entropy

DOE PAGES

O'Malley, Daniel; Vesselinov, Velimir V.; Cushman, John H.

2015-04-29

Brownian motion, the classical diffusive process, maximizes the Boltzmann-Gibbs entropy. The Tsallis q-entropy, which is non-additive, was developed as an alternative to the classical entropy for systems which are non-ergodic. A generalization of Brownian motion is provided that maximizes the Tsallis entropy rather than the Boltzmann-Gibbs entropy. This process is driven by a Brownian measure with a random diffusion coefficient. In addition, the distribution of this coefficient is derived as a function of q for 1 < q < 3. Applications to transport in porous media are considered.

Low b-value diffusion-weighted cardiac magnetic resonance imaging: initial results in humans using an optimal time-window imaging approach.

PubMed

Rapacchi, Stanislas; Wen, Han; Viallon, Magalie; Grenier, Denis; Kellman, Peter; Croisille, Pierre; Pai, Vinay M

2011-12-01

Diffusion-weighted imaging (DWI) using low b-values permits imaging of intravoxel incoherent motion in tissues. However, low b-value DWI of the human heart has been considered too challenging because of additional signal loss due to physiological motion, which reduces both signal intensity and the signal-to-noise ratio (SNR). We address these signal loss concerns by analyzing cardiac motion during a heartbeat to determine the time-window during which cardiac bulk motion is minimal. Using this information to optimize the acquisition of DWI data and combining it with a dedicated image processing approach has enabled us to develop a novel low b-value diffusion-weighted cardiac magnetic resonance imaging approach, which significantly reduces intravoxel incoherent motion measurement bias introduced by motion. Simulations from displacement encoded motion data sets permitted the delineation of an optimal time-window with minimal cardiac motion. A number of single-shot repetitions of low b-value DWI cardiac magnetic resonance imaging data were acquired during this time-window under free-breathing conditions with bulk physiological motion corrected for by using nonrigid registration. Principal component analysis (PCA) was performed on the registered images to improve the SNR, and temporal maximum intensity projection (TMIP) was applied to recover signal intensity from time-fluctuant motion-induced signal loss. This PCATMIP method was validated with experimental data, and its benefits were evaluated in volunteers before being applied to patients. Optimal time-window cardiac DWI in combination with PCATMIP postprocessing yielded significant benefits for signal recovery, contrast-to-noise ratio, and SNR in the presence of bulk motion for both numerical simulations and human volunteer studies. Analysis of mean apparent diffusion coefficient (ADC) maps showed homogeneous values among volunteers and good reproducibility between free-breathing and breath-hold acquisitions. The PCATMIP DWI approach also indicated its potential utility by detecting ADC variations in acute myocardial infarction patients. Studying cardiac motion may provide an appropriate strategy for minimizing the impact of bulk motion on cardiac DWI. Applying PCATMIP image processing improves low b-value DWI and enables reliable analysis of ADC in the myocardium. The use of a limited number of repetitions in a free-breathing mode also enables easier application in clinical conditions.

Measuring and modeling diffuse scattering in protein X-ray crystallography

PubMed Central

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Wall, Michael E.

2016-01-01

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering. PMID:27035972

Measuring and modeling diffuse scattering in protein X-ray crystallography

DOE PAGES

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; ...

2016-03-28

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

NASA Astrophysics Data System (ADS)

Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

2002-03-01

Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

Measuring molecular motions inside single cells with improved analysis of single-particle trajectories

NASA Astrophysics Data System (ADS)

Rowland, David J.; Biteen, Julie S.

2017-04-01

Single-molecule super-resolution imaging and tracking can measure molecular motions inside living cells on the scale of the molecules themselves. Diffusion in biological systems commonly exhibits multiple modes of motion, which can be effectively quantified by fitting the cumulative probability distribution of the squared step sizes in a two-step fitting process. Here we combine this two-step fit into a single least-squares minimization; this new method vastly reduces the total number of fitting parameters and increases the precision with which diffusion may be measured. We demonstrate this Global Fit approach on a simulated two-component system as well as on a mixture of diffusing 80 nm and 200 nm gold spheres to show improvements in fitting robustness and localization precision compared to the traditional Local Fit algorithm.

Self-diffusion studies by intra- and inter-molecular spin-lattice relaxometry using field-cycling: Liquids, plastic crystals, porous media, and polymer segments.

PubMed

Kimmich, Rainer; Fatkullin, Nail

2017-08-01

Field-cycling NMR relaxometry is a well-established technique for probing molecular dynamics in a frequency range from typically a few kHz up to several tens of MHz. For the interpretation of relaxometry data, it is quite often assumed that the spin-lattice relaxation process is of an intra-molecular nature so that rotational fluctuations dominate. However, dipolar interactions as the main type of couplings between protons and other dipolar species without quadrupole moments can imply appreciable inter-molecular contributions. These fluctuate due to translational displacements and to a lesser degree also by rotational reorientations in the short-range limit. The analysis of the inter-molecular proton spin-lattice relaxation rate thus permits one to evaluate self-diffusion variables such as the diffusion coefficient or the mean square displacement on a time scale from nanoseconds to several hundreds of microseconds. Numerous applications to solvents, plastic crystals and polymers will be reviewed. The technique is of particular interest for polymer dynamics since inter-molecular spin-lattice relaxation diffusometry bridges the time scales of quasi-elastic neutron scattering and field-gradient NMR diffusometry. This is just the range where model-specific intra-coil mechanisms are assumed to occur. They are expected to reveal themselves by characteristic power laws for the time-dependence of the mean-square segment displacement. These can be favorably tested on this basis. Results reported in the literature will be compared with theoretical predictions. On the other hand, there is a second way for translational diffusion phenomena to affect the spin-lattice relaxation dispersion. If rotational diffusion of molecules is restricted, translational diffusion properties can be deduced even from molecular reorientation dynamics detected by intra-molecular spin-lattice relaxation. This sort of scenario will be relevant for adsorbates on surfaces or polymer segments under entanglement and chain connectivity constraints. Under such conditions, reorientations will be correlated with translational displacements leading to the so-called RMTD relaxation process (reorientation mediated by translational displacements). Applications to porous glasses, protein solutions, lipid bilayers, and clays will be discussed. Finally, we will address the intriguing fact that the various time limits of the segment mean-square displacement of polymers in some cases perfectly reproduce predictions of the tube/reptation model whereas the reorientation dynamics suggests strongly deviating power laws. Copyright © 2017 Elsevier B.V. All rights reserved.

Brownian motion of a self-propelled particle.

PubMed

ten Hagen, B; van Teeffelen, S; Löwen, H

2011-05-18

Overdamped Brownian motion of a self-propelled particle is studied by solving the Langevin equation analytically. On top of translational and rotational diffusion, in the context of the presented model, the 'active' particle is driven along its internal orientation axis. We calculate the first four moments of the probability distribution function for displacements as a function of time for a spherical particle with isotropic translational diffusion, as well as for an anisotropic ellipsoidal particle. In both cases the translational and rotational motion is either unconfined or confined to one or two dimensions. A significant non-Gaussian behaviour at finite times t is signalled by a non-vanishing kurtosis γ(t). To delimit the super-diffusive regime, which occurs at intermediate times, two timescales are identified. For certain model situations a characteristic t(3) behaviour of the mean-square displacement is observed. Comparing the dynamics of real and artificial microswimmers, like bacteria or catalytically driven Janus particles, to our analytical expressions reveals whether their motion is Brownian or not.

Electric-field noise from carbon-adatom diffusion on a Au(110) surface: First-principles calculations and experiments

NASA Astrophysics Data System (ADS)

Kim, E.; Safavi-Naini, A.; Hite, D. A.; McKay, K. S.; Pappas, D. P.; Weck, P. F.; Sadeghpour, H. R.

2017-03-01

The decoherence of trapped-ion quantum gates due to heating of their motional modes is a fundamental science and engineering problem. This heating is attributed to electric-field noise arising from the trap-electrode surfaces. In this work, we investigate the source of this noise by focusing on the diffusion of carbon-containing adsorbates on the surface of Au(110). We show by density functional theory, based on detailed scanning probe microscopy, how the carbon adatom diffusion on the gold surface changes the energy landscape and how the adatom dipole moment varies with the diffusive motion. A simple model for the diffusion noise, which varies quadratically with the variation of the dipole moment, predicts a noise spectrum, in accordance with the measured values.

Nuclear magnetic resonance investigation of dynamics in poly(ethylene oxide) based polyether-ester-sulfonate ionomers

NASA Astrophysics Data System (ADS)

Roach, David J.

Nuclear magnetic resonance (NMR) spectroscopy has been utilized to investigate the dynamics of poly(ethylene oxide)-based lithium sulfonate ionomer samples that have low glass transition temperatures. 1H and 7Li spin-lattice relaxation times (T1) of the bulk polymer and lithium ions, respectively, were measured and analyzed in samples with a range of ion contents. The temperature dependence of T1 values along with the presence of minima in T1 as a function of temperature enabled correlation times and activation energies to be obtained for both the segmental motion of the polymer backbone and the hopping motion of lithium cations. Similar activation energies for motion of both the polymer and lithium ions in the samples with lower ion content indicate that the polymer segmental motion and lithium ion hopping motion are correlated in these samples, even though lithium hopping is about ten times slower than the segmental motion. A divergent trend is observed for correlation times and activation energies of the highest ion content sample with 100% lithium sulfonation due to the presence of ionic aggregation. Details of the polymer and cation dynamics on the nanosecond timescale are discussed and complement the findings of X-ray scattering and Quasi Elastic Neutron Scattering experiments. Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T g) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components and relative mobilities of the polymer backbone of a suite of. lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content. Each of the main backbone components (PEO spacer and isophthalate groups) exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content on PEO mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, determined from the rate of magnetization transfer from 1H to 13C nuclei, in all ionic samples becomes similar for T [special characters omitted] 1.1 Tg, indicating that the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results compliment previous findings and present an improved picture of the dependence of backbone dynamics on cation type and density in these amorphous PEO-based ionomer systems. 7Li PFG NMR experiments provided measurements of the self-diffusion coefficients for Li+ cations in the PEO600-y Li ionomer series over a range of temperatures. When the Tg values are taken into account, the self-diffusion coefficients of Li+ in each sample follow a similar trendline, indicating that lithium diffusion is independent of ion concentration at any given reduced inverse temperature, Tg/T. Ion aggregation increases Tg and slows both lithium cation diffusion and displacement, but there is no further slowing beyond the Tg effect in the PEO600-y Li ionomers samples. The differences in activation energies obtained from diffusion measurements and relaxation times suggest that at least one additional barrier must be overcome for cations emerge from local hopping motion to macroscopic cation transpfort. Using the Nernst- Einstein equation lithium diffusion coefficients were also calculated from conductivity measurements. The differences between the diffusion measured by the two separate techniques indicate the presence of ion pairs. The activation energy of lithium diffusion was found to be nearly identical between the PFG NMR and conductivity, suggesting that the conductivity and ionic diffusion are related to the same ionic dynamics. As the ion content within the PEO600-y Li samples increases the relative concentration of nonconducting ion pairs decrease. Also an increase in temperature causes a fraction of ion pairs to thermally dissociate into positive triple ions.

Diffusive motion with nonlinear friction: apparently Brownian.

PubMed

Goohpattader, Partho S; Chaudhury, Manoj K

2010-07-14

We study the diffusive motion of a small object placed on a solid support using an inertial tribometer. With an external bias and a Gaussian noise, the object slides accompanied with a fluctuation of displacement that exhibits unique characteristics at different powers of the noise. While it exhibits a fluidlike motion at high powers, a stick-slip motion occurs at a low power. Below a critical power, no motion is observed. The signature of a nonlinear friction is evident in this type of stochastic motion both in the reduced mobility in comparison to that governed by a linear kinematic (Stokes-Einstein-like) friction and in the non-Gaussian probability distribution of the displacement fluctuation. As the power of the noise increases, the effect of the nonlinearity appears to play a lesser role, so that the displacement fluctuation becomes more Gaussian. When the distribution is exponential, it also exhibits an asymmetry with its skewness increasing with the applied bias. A new finding of this study is that the stochastic velocities of the object are so poorly correlated that its diffusivity is much lower than either the linear or the nonlinear friction cases studied by de Gennes [J. Stat. Phys. 119, 953 (2005)]. The mobilities at different powers of the noise together with the estimated variances of velocity fluctuations follow an Einstein-like relation.

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

PubMed Central

Papaleo, Elena; Renzetti, Giulia; Tiberti, Matteo

2012-01-01

Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface. PMID:22558199

Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

NASA Astrophysics Data System (ADS)

Chen, Yao; Wang, Xudong; Deng, Weihua

2017-10-01

This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

The Steady-State Transport of Oxygen through Hemoglobin Solutions

PubMed Central

Keller, K. H.; Friedlander, S. K.

1966-01-01

The steady-state transport of oxygen through hemoglobin solutions was studied to identify the mechanism of the diffusion augmentation observed at low oxygen tensions. A novel technique employing a platinum-silver oxygen electrode was developed to measure the effective diffusion coefficient of oxygen in steady-state transport. The measurements were made over a wider range of hemoglobin and oxygen concentrations than previously reported. Values of the Brownian motion diffusion coefficient of oxygen in hemoglobin solution were obtained as well as measurements of facilitated transport at low oxygen tensions. Transport rates up to ten times greater than ordinary diffusion rates were found. Predictions of oxygen flux were made assuming that the oxyhemoglobin transport coefficient was equal to the Brownian motion diffusivity which was measured in a separate set of experiments. The close correlation between prediction and experiment indicates that the diffusion of oxyhemoglobin is the mechanism by which steady-state oxygen transport is facilitated. PMID:5943608

Mechanisms underlying anomalous diffusion in the plasma membrane.

PubMed

Krapf, Diego

2015-01-01

The plasma membrane is a complex fluid where lipids and proteins undergo diffusive motion critical to biochemical reactions. Through quantitative imaging analyses such as single-particle tracking, it is observed that diffusion in the cell membrane is usually anomalous in the sense that the mean squared displacement is not linear with time. This chapter describes the different models that are employed to describe anomalous diffusion, paying special attention to the experimental evidence that supports these models in the plasma membrane. We review models based on anticorrelated displacements, such as fractional Brownian motion and obstructed diffusion, and nonstationary models such as continuous time random walks. We also emphasize evidence for the formation of distinct compartments that transiently form on the cell surface. Finally, we overview heterogeneous diffusion processes in the plasma membrane, which have recently attracted considerable interest. Copyright © 2015. Published by Elsevier Inc.

Analyzing signal attenuation in PFG anomalous diffusion via a non-Gaussian phase distribution approximation approach by fractional derivatives.

PubMed

Lin, Guoxing

2016-11-21

Anomalous diffusion exists widely in polymer and biological systems. Pulsed-field gradient (PFG) techniques have been increasingly used to study anomalous diffusion in nuclear magnetic resonance and magnetic resonance imaging. However, the interpretation of PFG anomalous diffusion is complicated. Moreover, the exact signal attenuation expression including the finite gradient pulse width effect has not been obtained based on fractional derivatives for PFG anomalous diffusion. In this paper, a new method, a Mainardi-Luchko-Pagnini (MLP) phase distribution approximation, is proposed to describe PFG fractional diffusion. MLP phase distribution is a non-Gaussian phase distribution. From the fractional derivative model, both the probability density function (PDF) of a spin in real space and the PDF of the spin's accumulating phase shift in virtual phase space are MLP distributions. The MLP phase distribution leads to a Mittag-Leffler function based PFG signal attenuation, which differs significantly from the exponential attenuation for normal diffusion and from the stretched exponential attenuation for fractional diffusion based on the fractal derivative model. A complete signal attenuation expression E α (-D f b α,β * ) including the finite gradient pulse width effect was obtained and it can handle all three types of PFG fractional diffusions. The result was also extended in a straightforward way to give a signal attenuation expression of fractional diffusion in PFG intramolecular multiple quantum coherence experiments, which has an n β dependence upon the order of coherence which is different from the familiar n 2 dependence in normal diffusion. The results obtained in this study are in agreement with the results from the literature. The results in this paper provide a set of new, convenient approximation formalisms to interpret complex PFG fractional diffusion experiments.

High-density amorphous ice: A path-integral simulation

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2012-09-01

Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

Effects of phonon broadening on x-ray near-edge spectra in molecular crystals

NASA Astrophysics Data System (ADS)

Vinson, John; Jach, Terrence; Elam, Tim; Denlinger, Jonathon

2014-03-01

Calculations of near-edge x-ray spectra are often carried out using the average atomic coordinates from x-ray or neutron scattering experiments or from density functional theory (DFT) energy minimization. This neglects disorder from thermal and zero-point vibrations. Here we look at the nitrogen K-edge of ammonium chloride and ammonium nitrate, comparing Bethe-Salpeter calculations of absorption and fluorescence to experiment. We find that intra-molecular vibrational effects lead to significant, non-uniform broadening of the spectra, and that for some features zero-point motion is the primary source of the observed shape.

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Kalli, Antreas C.; Yasuoka, Kenji; Sansom, Mark S. P.

2017-01-01

Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:28116358

Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model

NASA Astrophysics Data System (ADS)

Yuste, S. B.; Abad, E.; Baumgaertner, A.

2016-07-01

We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ ,P (ℓ ) ˜ℓ-(1 +α ) (α >0 ). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems.

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.

Intermediate scattering function of an anisotropic active Brownian particle

PubMed Central

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-01-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations. PMID:27830719

Intermediate scattering function of an anisotropic active Brownian particle.

PubMed

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-10

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

Intermediate scattering function of an anisotropic active Brownian particle

NASA Astrophysics Data System (ADS)

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

Quantum State Diffusion

NASA Astrophysics Data System (ADS)

Percival, Ian

2005-10-01

1. Introduction; 2. Brownian motion and Itô calculus; 3. Open quantum systems; 4. Quantum state diffusion; 5. Localisation; 6. Numerical methods and examples; 7. Quantum foundations; 8. Primary state diffusion; 9. Classical dynamics of quantum localisation; 10. Semiclassical theory and linear dynamics.

Differential Microscopic Mobility of Components within a Deep Eutectic Solvent

DOE PAGES

Wagle, Durgesh V.; Baker, Gary A.; Mamontov, Eugene

2015-07-13

From macroscopic measurements of deep eutectic solvents such as glyceline (1:2 molar ratio of choline chloride to glycerol), the long-range translational diffusion of the larger cation (choline) is known to be slower compared to that of the smaller hydrogen bond donor (glycerol). However, when the diffusion dynamics are analyzed on the subnanometer length scale, we discover that the displacements associated with the localized diffusive motions are actually larger for choline. This counterintuitive diffusive behavior can be understood as follows. The localized diffusive motions confined in the transient cage of neighbor particles, which precede the cage-breaking long-range diffusion jumps, are moremore » spatially constrained for glycerol than for choline because of the stronger hydrogen bonds the former makes with chloride anions. The implications of differential localized mobility of the constituents should be especially important for applications where deep eutectic solvents are confined on the nanometer length scale and their long-range translational diffusion is strongly inhibited (e.g., within microporous media).« less

Four-dimensional diffusion-weighted MR imaging (4D-DWI): a feasibility study.

PubMed

Liu, Yilin; Zhong, Xiaodong; Czito, Brian G; Palta, Manisha; Bashir, Mustafa R; Dale, Brian M; Yin, Fang-Fang; Cai, Jing

2017-02-01

Diffusion-weighted Magnetic Resonance Imaging (DWI) has been shown to be a powerful tool for cancer detection with high tumor-to-tissue contrast. This study aims to investigate the feasibility of developing a four-dimensional DWI technique (4D-DWI) for imaging respiratory motion for radiation therapy applications. Image acquisition was performed by repeatedly imaging a volume of interest (VOI) using an interleaved multislice single-shot echo-planar imaging (EPI) 2D-DWI sequence in the axial plane. Each 2D-DWI image was acquired with an intermediately low b-value (b = 500 s/mm 2 ) and with diffusion-encoding gradients in x, y, and z diffusion directions. Respiratory motion was simultaneously recorded using a respiratory bellow, and the synchronized respiratory signal was used to retrospectively sort the 2D images to generate 4D-DWI. Cine MRI using steady-state free precession was also acquired as a motion reference. As a preliminary feasibility study, this technique was implemented on a 4D digital human phantom (XCAT) with a simulated pancreas tumor. The respiratory motion of the phantom was controlled by regular sinusoidal motion profile. 4D-DWI tumor motion trajectories were extracted and compared with the input breathing curve. The mean absolute amplitude differences (D) were calculated in superior-inferior (SI) direction and anterior-posterior (AP) direction. The technique was then evaluated on two healthy volunteers. Finally, the effects of 4D-DWI on apparent diffusion coefficient (ADC) measurements were investigated for hypothetical heterogeneous tumors via simulations. Tumor trajectories extracted from XCAT 4D-DWI were consistent with the input signal: the average D value was 1.9 mm (SI) and 0.4 mm (AP). The average D value was 2.6 mm (SI) and 1.7 mm (AP) for the two healthy volunteers. A 4D-DWI technique has been developed and evaluated on digital phantom and human subjects. 4D-DWI can lead to more accurate respiratory motion measurement. This has a great potential to improve the visualization and delineation of cancer tumors for radiotherapy. © 2016 American Association of Physicists in Medicine.

Single-particle tracking: applications to membrane dynamics.

PubMed

Saxton, M J; Jacobson, K

1997-01-01

Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

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.

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.

Active colloidal propulsion over a crystalline surface

NASA Astrophysics Data System (ADS)

Choudhury, Udit; Straube, Arthur V.; Fischer, Peer; Gibbs, John G.; Höfling, Felix

2017-12-01

We study both experimentally and theoretically the dynamics of chemically self-propelled Janus colloids moving atop a two-dimensional crystalline surface. The surface is a hexagonally close-packed monolayer of colloidal particles of the same size as the mobile one. The dynamics of the self-propelled colloid reflects the competition between hindered diffusion due to the periodic surface and enhanced diffusion due to active motion. Which contribution dominates depends on the propulsion strength, which can be systematically tuned by changing the concentration of a chemical fuel. The mean-square displacements (MSDs) obtained from the experiment exhibit enhanced diffusion at long lag times. Our experimental data are consistent with a Langevin model for the effectively two-dimensional translational motion of an active Brownian particle in a periodic potential, combining the confining effects of gravity and the crystalline surface with the free rotational diffusion of the colloid. Approximate analytical predictions are made for the MSD describing the crossover from free Brownian motion at short times to active diffusion at long times. The results are in semi-quantitative agreement with numerical results of a refined Langevin model that treats translational and rotational degrees of freedom on the same footing.

Fractional motion model for characterization of anomalous diffusion from NMR signals.

PubMed

Fan, Yang; Gao, Jia-Hong

2015-07-01

Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

Fractional motion model for characterization of anomalous diffusion from NMR signals

NASA Astrophysics Data System (ADS)

Fan, Yang; Gao, Jia-Hong

2015-07-01

Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes

NASA Astrophysics Data System (ADS)

Nilsen, Ian A.; Osborne, Derek G.; White, Aaron M.; Anna, Jessica M.; Kubarych, Kevin J.

2014-10-01

Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ˜3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.

Contributions of different degrees of freedom to thermal transport in the C60 molecular crystal

NASA Astrophysics Data System (ADS)

Kumar, Sushant; Shao, Cheng; Lu, Simon; McGaughey, Alan J. H.

2018-03-01

Three models of the C60 molecular crystal are studied using molecular dynamics simulations to resolve the roles played by intermolecular and intramolecular degrees of freedom (DOF) in its structural, mechanical, and thermal properties at temperatures between 35 and 400 K. In the full DOF model, all DOF are active. In the rigid body model, the intramolecular DOF are frozen, such that only center of mass (COM) translations and molecular rotations/librations are active. In the point mass model, the molecule is replaced by a point mass, such that only COM translations are active. The zero-pressure lattice constants and bulk moduli predicted from the three models fall within ranges of 0.15 and 20%. The thermal conductivity of the point mass model is the largest across the temperature range, showing a crystal-like temperature dependence (i.e., it decreases with increasing temperature) due to the presence of phonon modes associated with the COM translations. The rigid body model thermal conductivity is the smallest and follows two distinct regimes. It is crystal-like at low temperatures and becomes temperature invariant at high temperatures. The latter is typical of the behavior of an amorphous material. By calculating the rotational diffusion coefficient, the transition between the two regimes is found to occur at the temperature where the molecules begin to rotate freely. Above this temperature, phonons related to COM translations are scattered by the rotational DOF. The full DOF model thermal conductivity is larger than that of the rigid body model, indicating that intramolecular DOF contribute to thermal transport.

High-Resolution Multi-Shot Spiral Diffusion Tensor Imaging with Inherent Correction of Motion-Induced Phase Errors

PubMed Central

Truong, Trong-Kha; Guidon, Arnaud

2014-01-01

Purpose To develop and compare three novel reconstruction methods designed to inherently correct for motion-induced phase errors in multi-shot spiral diffusion tensor imaging (DTI) without requiring a variable-density spiral trajectory or a navigator echo. Theory and Methods The first method simply averages magnitude images reconstructed with sensitivity encoding (SENSE) from each shot, whereas the second and third methods rely on SENSE to estimate the motion-induced phase error for each shot, and subsequently use either a direct phase subtraction or an iterative conjugate gradient (CG) algorithm, respectively, to correct for the resulting artifacts. Numerical simulations and in vivo experiments on healthy volunteers were performed to assess the performance of these methods. Results The first two methods suffer from a low signal-to-noise ratio (SNR) or from residual artifacts in the reconstructed diffusion-weighted images and fractional anisotropy maps. In contrast, the third method provides high-quality, high-resolution DTI results, revealing fine anatomical details such as a radial diffusion anisotropy in cortical gray matter. Conclusion The proposed SENSE+CG method can inherently and effectively correct for phase errors, signal loss, and aliasing artifacts caused by both rigid and nonrigid motion in multi-shot spiral DTI, without increasing the scan time or reducing the SNR. PMID:23450457

Open quantum random walks: Bistability on pure states and ballistically induced diffusion

NASA Astrophysics Data System (ADS)

Bauer, Michel; Bernard, Denis; Tilloy, Antoine

2013-12-01

Open quantum random walks (OQRWs) deal with quantum random motions on a line for systems with internal and orbital degrees of freedom. The internal system behaves as a quantum random gyroscope coding for the direction of the orbital moves. We reveal the existence of a transition, depending on OQRW moduli, in the internal system behaviors from simple oscillations to random flips between two unstable pure states. This induces a transition in the orbital motions from the usual diffusion to ballistically induced diffusion with a large mean free path and large effective diffusion constant at large times. We also show that mixed states of the internal system are converted into random pure states during the process. We touch upon possible experimental realizations.

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

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

Yang, J.; Martí, J., E-mail: jordi.marti@upc.edu; Calero, C.

2014-03-14

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in themore » membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10{sup −5} cm{sup 2}/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10{sup −8} cm{sup 2}/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm{sup −1}, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.« less

A new fundamental model of moving particle for reinterpreting Schroedinger equation

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

Umar, Muhamad Darwis

2012-06-20

The study of Schroedinger equation based on a hypothesis that every particle must move randomly in a quantum-sized volume has been done. In addition to random motion, every particle can do relative motion through the movement of its quantum-sized volume. On the other way these motions can coincide. In this proposed model, the random motion is one kind of intrinsic properties of the particle. The every change of both speed of randomly intrinsic motion and or the velocity of translational motion of a quantum-sized volume will represent a transition between two states, and the change of speed of randomly intrinsicmore » motion will generate diffusion process or Brownian motion perspectives. Diffusion process can take place in backward and forward processes and will represent a dissipative system. To derive Schroedinger equation from our hypothesis we use time operator introduced by Nelson. From a fundamental analysis, we find out that, naturally, we should view the means of Newton's Law F(vector sign) = ma(vector sign) as no an external force, but it is just to describe both the presence of intrinsic random motion and the change of the particle energy.« less

Diffusion Weighted Magnetic Resonance Imaging Assessment of Blood Flow in the Microvasculature of Abdominal Organs

NASA Astrophysics Data System (ADS)

Truica, Loredana Sorina

In this thesis, water diffusion in human liver and placenta is studied using diffusion weighted magnetic resonance imaging. For short, randomly oriented vascular segments, intravascular water motion is diffusion-like. For tissues with large vascular compartments the diffusion decay is bi-exponential with one component corresponding to diffusing water and the other to water in the microvasculature. This model, known as the intravoxel incoherent motion (IVIM) model, is seldom used with abdominal organs because of motion artifacts. This limitation was overcome for the experiments reported here by introducing: 1) parallel imaging, 2) navigator echo respiratory triggering (NRT), 3) a double echo diffusion sequence that inherently compensates for eddy current effects, 4) SPAIR fat suppression and 5) a superior approach to image analysis. In particular, the use of NRT allowed us to use a free breathing protocol instead of the previously required breath hold protocol. The resulting DWI images were of high quality and motion artifact free. Diffusion decays were measured over a larger portion of the decay than had previously been reported and the results are considerably better than those previously reported. For both studies, reliable measurements of the diffusion coefficient (D), pseudo-diffusion coefficient (D) and perfusion fraction (f), were obtained using a region of interest analysis as well as a pixel-by-pixel approach. To within experimental error, all patients had the same values of D (1.10 mum 2/ms +/- 0.16 mum2/ms), D* (46 mum2/ms +/- 17 mum2/ms) and f (44.0% +/- 6.9%) in liver and D (1.8 mum 2/ms +/- 0.2 mum2/ms), D* (30 mum 2/ms +/- 12 mmu2/ms), and f (40% +/- 6%) in the placenta. No dependence on gestational age was found for the placental study. Parametric maps of f and D* were consistent with blood flow patterns in both systems. The model worked well for both investigated organs even though their anatomical structures are quite different. A method for removing rectified noise bias from low intensity magnitude MR images measured with phased array coils is also presented. This algorithm has significance for diffusion decay measurements since it permits the use of low intensity data points which could, for example, allow the acquisition of high resolution parametric maps.

Dielectric studies on mobility of the glycosidic linkage in seven disaccharides.

PubMed

Kaminski, K; Kaminska, E; Wlodarczyk, P; Pawlus, S; Kimla, D; Kasprzycka, A; Paluch, M; Ziolo, J; Szeja, W; Ngai, K L

2008-10-09

Isobaric dielectric relaxation measurements were performed on seven chosen disaccharides. For five of them, i.e., sucrose, maltose, trehalose, lactulose, and leucrose, we were able to observe the temperature evolution of the structural relaxation process. In the case of the other disaccharides studied (lactose and cellobiose), it was impossible to obtain such information because of the large contribution of the dc conductivity and polarization of the capacitor plates to the imaginary and real part of the complex permittivity, respectively. On the other hand, in the glassy state, two secondary relaxations have been identified in the dielectric spectra of all investigated carbohydrates. The faster one (gamma) is a common characteristic feature of the entire sugar family (mono-, di-, oligo-, and polysaccharide). The molecular origin of this process is still not unambiguously identified but is expected to involve intramolecular degrees of freedom as inferred from insensitivity of its relaxation time to pressure found in some monosaccharides (fructose and ribose). The slower one (labeled beta) was recently identified to be intermolecular in origin (i.e., a Johari-Goldstein (JG) beta-relaxation), involving twisting motion of the monosugar rings around the glycosidic bond. The activation energies and dielectric strengths for the beta-relaxation determined herein provide us valuable information about the flexibility of the glycosidic bond and the mobility of this particular linkage in the disaccharides studied. In turn, this information is essential for the control of the diffusivity of drugs or water entrapped in the sugar matrix.

Probing short-range protein Brownian motion in the cytoplasm of living cells.

PubMed

Di Rienzo, Carmine; Piazza, Vincenzo; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

2014-12-23

The translational motion of molecules in cells deviates from what is observed in dilute solutions. Theoretical models provide explanations for this effect but with predictions that drastically depend on the nanoscale organization assumed for macromolecular crowding agents. A conclusive test of the nature of the translational motion in cells is missing owing to the lack of techniques capable of probing crowding with the required temporal and spatial resolution. Here we show that fluorescence-fluctuation analysis of raster scans at variable timescales can provide this information. By using green fluorescent proteins in cells, we measure protein motion at the unprecedented timescale of 1 μs, unveiling unobstructed Brownian motion from 25 to 100 nm, and partially suppressed diffusion above 100 nm. Furthermore, experiments on model systems attribute this effect to the presence of relatively immobile structures rather than to diffusing crowding agents. We discuss the implications of these results for intracellular processes.

Divergent series and memory of the initial condition in the long-time solution of some anomalous diffusion problems.

PubMed

Yuste, S Bravo; Borrego, R; Abad, E

2010-02-01

We consider various anomalous d -dimensional diffusion problems in the presence of an absorbing boundary with radial symmetry. The motion of particles is described by a fractional diffusion equation. Their mean-square displacement is given by r(2) proportional, variant t(gamma)(00 , the emergence of such series in the long-time domain is a specific feature of subdiffusion problems. We present a method to regularize such series, and, in some cases, validate the procedure by using alternative techniques (Laplace transform method and numerical simulations). In the normal diffusion case, we find that the signature of the initial condition on the approach to the steady state rapidly fades away and the solution approaches a single (the main) decay mode in the long-time regime. In remarkable contrast, long-time memory of the initial condition is present in the subdiffusive case as the spatial part Psi1(r) describing the long-time decay of the solution to the steady state is determined by a weighted superposition of all spatial modes characteristic of the normal diffusion problem, the weight being dependent on the initial condition. Interestingly, Psi1(r) turns out to be independent of the anomalous diffusion exponent gamma .

Non-opioid analgesic drug flupirtine: Spectral analysis, DFT computations, in vitro bioactivity and molecular docking study

NASA Astrophysics Data System (ADS)

Leenaraj, D. R.; Hubert Joe, I.

2017-06-01

Spectral features of non-opioid analgesic drug flupirtine have been explored by the Fourier transform infrared, Raman and Nuclear magnetic resonance spectroscopic techniques combined with density functional theory computations. The bioactive conformer of flupirtine is stabilized by an intramolecular Csbnd H⋯N hydrogen bonding resulting by the steric strain of hydrogen atoms. Natural bond orbital and natural population analysis support this result. The charge redistribution also has been analyzed. Antimicrobial activities of flupirtine have been screened by agar well disc diffusion and molecular docking methods, which exposes the importance of triaminopyridine in flupirtine.

Parsing anomalous versus normal diffusive behavior of bedload sediment particles

USGS Publications Warehouse

Fathel, Siobhan; Furbish, David; Schmeeckle, Mark

2016-01-01

Bedload sediment transport is the basic physical ingredient of river evolution. Formulae exist for estimating transport rates, but the diffusive contribution to the sediment flux, and the associated spreading rate of tracer particles, are not clearly understood. The start-and-stop motions of sediment particles transported as bedload on a streambed mimic aspects of the Einstein–Smoluchowski description of the random-walk motions of Brownian particles. Using this touchstone description, recent work suggests the presence of anomalous diffusion, where the particle spreading rate differs from the linear dependence with time of Brownian behavior. We demonstrate that conventional measures of particle spreading reveal different attributes of bedload particle behavior depending on details of the calculation. When we view particle motions over start-and-stop timescales obtained from high-speed (250 Hz) imaging of coarse-sand particles, high-resolution measurements reveal ballistic-like behavior at the shortest (10−2 s) timescale, followed by apparent anomalous behavior due to correlated random walks in transition to normal diffusion (>10−1 s) – similar to Brownian particle behavior but involving distinctly different physics. However, when treated as a ‘virtual plume’ over this timescale range, particles exhibit inhomogeneous diffusive behavior because both the mean and the variance of particle travel distances increase nonlinearly with increasing travel times, a behavior that is unrelated to anomalous diffusion or to Brownian-like behavior. Our results indicate that care is needed in suggesting anomalous behavior when appealing to conventional measures of diffusion formulated for ideal particle systems.

Real-time observation of intramolecular proton transfer in the electronic ground state of chloromalonaldehyde: an ab initio study of time-resolved photoelectron spectra.

PubMed

do N Varella, Márcio T; Arasaki, Yasuki; Ushiyama, Hiroshi; Takatsuka, Kazuo; Wang, Kwanghsi; McKoy, Vincent

2007-02-07

The authors report on studies of time-resolved photoelectron spectra of intramolecular proton transfer in the ground state of chloromalonaldehyde, employing ab initio photoionization matrix elements and effective potential surfaces of reduced dimensionality, wherein the couplings of proton motion to the other molecular vibrational modes are embedded by averaging over classical trajectories. In the simulations, population is transferred from the vibrational ground state to vibrationally hot wave packets by pumping to an excited electronic state and dumping with a time-delayed pulse. These pump-dump-probe simulations demonstrate that the time-resolved photoelectron spectra track proton transfer in the electronic ground state well and, furthermore, that the geometry dependence of the matrix elements enhances the tracking compared with signals obtained with the Condon approximation. Photoelectron kinetic energy distributions arising from wave packets localized in different basins are also distinguishable and could be understood, as expected, on the basis of the strength of the optical couplings in different regions of the ground state potential surface and the Franck-Condon overlaps of the ground state wave packets with the vibrational eigenstates of the ion potential surface.

Time series analysis of particle tracking data for molecular motion on the cell membrane.

PubMed

Ying, Wenxia; Huerta, Gabriel; Steinberg, Stanly; Zúñiga, Martha

2009-11-01

Biophysicists use single particle tracking (SPT) methods to probe the dynamic behavior of individual proteins and lipids in cell membranes. The mean squared displacement (MSD) has proven to be a powerful tool for analyzing the data and drawing conclusions about membrane organization, including features like lipid rafts, protein islands, and confinement zones defined by cytoskeletal barriers. Here, we implement time series analysis as a new analytic tool to analyze further the motion of membrane proteins. The experimental data track the motion of 40 nm gold particles bound to Class I major histocompatibility complex (MHCI) molecules on the membranes of mouse hepatoma cells. Our first novel result is that the tracks are significantly autocorrelated. Because of this, we developed linear autoregressive models to elucidate the autocorrelations. Estimates of the signal to noise ratio for the models show that the autocorrelated part of the motion is significant. Next, we fit the probability distributions of jump sizes with four different models. The first model is a general Weibull distribution that shows that the motion is characterized by an excess of short jumps as compared to a normal random walk. We also fit the data with a chi distribution which provides a natural estimate of the dimension d of the space in which a random walk is occurring. For the biological data, the estimates satisfy 1 < d < 2, implying that particle motion is not confined to a line, but also does not occur freely in the plane. The dimension gives a quantitative estimate of the amount of nanometer scale obstruction met by a diffusing molecule. We introduce a new distribution and use the generalized extreme value distribution to show that the biological data also have an excess of long jumps as compared to normal diffusion. These fits provide novel estimates of the microscopic diffusion constant. Previous MSD analyses of SPT data have provided evidence for nanometer-scale confinement zones that restrict lateral diffusion, supporting the notion that plasma membrane organization is highly structured. Our demonstration that membrane protein motion is autocorrelated and is characterized by an excess of both short and long jumps reinforces the concept that the membrane environment is heterogeneous and dynamic. Autocorrelation analysis and modeling of the jump distributions are powerful new techniques for the analysis of SPT data and the development of more refined models of membrane organization. The time series analysis also provides several methods of estimating the diffusion constant in addition to the constant provided by the mean squared displacement. The mean squared displacement for most of the biological data shows a power law behavior rather the linear behavior of Brownian motion. In this case, we introduce the notion of an instantaneous diffusion constant. All of the diffusion constants show a strong consistency for most of the biological data.

Diffusion and self-assembly of C60 molecules on monolayer graphyne sheets

PubMed Central

Ozmaian, Masoumeh; Fathizadeh, Arman; Jalalvand, Morteza; Ejtehadi, Mohammad Reza; Allaei, S. Mehdi Vaez

2016-01-01

The motion of a fullerene (C60) on 5 different types of graphyne is studied by all-atom molecular dynamics simulations and compared with former studies on the motion of C60 on graphene. The motion shows a diffusive behavior which consists of either a continuous motion or discrete movements between trapping sites depending on the type of the graphyne sheet. For graphyne-4 and graphyne-5, fullerenes could detach from the surface of the graphyne sheet at room temperature which was not reported for similar cases on graphene sheets. Collective motion of a group of fullerenes interacting with a graphyne studied and it is shown that fullerenes exhibit stable assemblies. Depending on the type of graphyne, these assemblies can have either single or double layers. The mobility of the assembled structures is also dependent on the type of the graphyne sheet. The observed properties of the motion suggests novel applications for the complexes of fullerene and monolayer graphynes. PMID:26912386

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

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

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Generalized run-and-turn motions: From bacteria to Lévy walks

NASA Astrophysics Data System (ADS)

Detcheverry, François

2017-07-01

Swimming bacteria exhibit a repertoire of motility patterns, in which persistent motion is interrupted by turning events. What are the statistical properties of such random walks? If some particular instances have long been studied, the general case where turning times do not follow a Poisson process has remained unsolved. We present a generic extension of the continuous time random walks formalism relying on operators and noncommutative calculus. The approach is first applied to a unimodal model of bacterial motion. We examine the existence of a minimum in velocity correlation function and discuss the maximum of diffusivity at an optimal value of rotational diffusion. The model is then extended to bimodal patterns and includes as particular cases all swimming strategies: run-and-tumble, run-stop, run-reverse and run-reverse-flick. We characterize their velocity correlation functions and investigate how bimodality affects diffusivity. Finally, the wider applicability of the method is illustrated by considering curved trajectories and Lévy walks. Our results are relevant for intermittent motion of living beings, be they swimming micro-organisms or crawling cells.

Brownian Motion in a Speckle Light Field: Tunable Anomalous Diffusion and Selective Optical Manipulation

PubMed Central

Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain

2014-01-01

The motion of particles in random potentials occurs in several natural phenomena ranging from the mobility of organelles within a biological cell to the diffusion of stars within a galaxy. A Brownian particle moving in the random optical potential associated to a speckle pattern, i.e., a complex interference pattern generated by the scattering of coherent light by a random medium, provides an ideal model system to study such phenomena. Here, we derive a theory for the motion of a Brownian particle in a speckle field and, in particular, we identify its universal characteristic timescale. Based on this theoretical insight, we show how speckle light fields can be used to control the anomalous diffusion of a Brownian particle and to perform some basic optical manipulation tasks such as guiding and sorting. Our results might broaden the perspectives of optical manipulation for real-life applications. PMID:24496461

Arnold Diffusion of Charged Particles in ABC Magnetic Fields

NASA Astrophysics Data System (ADS)

Luque, Alejandro; Peralta-Salas, Daniel

2017-06-01

We prove the existence of diffusing solutions in the motion of a charged particle in the presence of ABC magnetic fields. The equations of motion are modeled by a 3DOF Hamiltonian system depending on two parameters. For small values of these parameters, we obtain a normally hyperbolic invariant manifold and we apply the so-called geometric methods for a priori unstable systems developed by A. Delshams, R. de la Llave and T.M. Seara. We characterize explicitly sufficient conditions for the existence of a transition chain of invariant tori having heteroclinic connections, thus obtaining global instability (Arnold diffusion). We also check the obtained conditions in a computer-assisted proof. ABC magnetic fields are the simplest force-free-type solutions of the magnetohydrodynamics equations with periodic boundary conditions, and can be considered as an elementary model for the motion of plasma-charged particles in a tokamak.

The rate of collisions due to Brownian or gravitational motion of small drops

NASA Technical Reports Server (NTRS)

Zhang, Xiaoguang; Davis, Robert H.

1991-01-01

Quantitative predictions of the collision rate of two spherical drops undergoing Brownian diffusion or gravitational sedimentation are presented. The diffusion equation for relative Brownian motion of two drops is derived, and the relative motion of pairs of drops in gravitational sedimentation is traced via a trajectory analysis in order to develop theoretical models to determine the collision efficiencies, both with and without interparticle forces applied between the drops. It is concluded that finite collision rates between nondeforming fluid drops are possible for Brownian diffusion or gravitational sedimentation in the absence of attractive forces, in stark contrast to the prediction that lubrication forces prevent rigid spheres from contacting each other unless an attractive force that becomes infinite as the separation approaches zero is applied. Collision rates are shown to increase as the viscosity of the drop-phase decreases. In general, hydrodynamic interactions reduce the collision rates more for gravitational collisions than for Brownian collisions.

Needlelike motion of prolate ellipsoids in the sea of spheres

NASA Astrophysics Data System (ADS)

Vasanthi, R.; Ravichandran, S.; Bagchi, Biman

2001-05-01

Molecular dynamics simulations of translational motion of isolated prolate ellipsoids in the sea of spheres have been carried out for several different values of the aspect ratio (κ), obtained by changing either the length or the diameter of the ellipsoids, at several different solvent densities. The interaction among the spheres is given by the Lennard-Jones pair potential while that between spheres and ellipsoids is given by a modified Gay-Berne potential. Both the mean-square displacements of the center of mass of the ellipsoids and their orientational time correlation function have been calculated. It is found that at short to intermediate times, the motion of ellipsoids is anisotropic and primarily needlelike—the molecules prefer to move parallel to their long axis. The ratio of these two diffusion constants (D∥ and D⊥) approaches κ, suggesting a decoupling of D∥ from the length of the ellipsoid. The diffusion becomes isotropic in the long time with the total diffusion coefficient given by D∥+2D⊥. The crossover from the anisotropic to the isotropic diffusion is surprisingly sharp and clear in most cases.

SU-F-303-13: Initial Evaluation of Four Dimensional Diffusion- Weighted MRI (4D-DWI) and Its Effect On Apparent Diffusion Coefficient (ADC) Measurement

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

Liu, Y; Yin, F; Czito, B

2015-06-15

Purpose: Diffusion-weighted imaging(DWI) has been shown to have superior tumor-to-tissue contrast for cancer detection.This study aims at developing and evaluating a four dimensional DWI(4D-DWI) technique using retrospective sorting method for imaging respiratory motion for radiotherapy planning,and evaluate its effect on Apparent Diffusion Coefficient(ADC) measurement. Materials/Methods: Image acquisition was performed by repeatedly imaging a volume of interest using a multi-slice single-shot 2D-DWI sequence in the axial planes and cine MRI(served as reference) using FIESTA sequence.Each 2D-DWI image were acquired in xyz-diffusion-directions with a high b-value(b=500s/mm2).The respiratory motion was simultaneously recorded using bellows.Retrospective sorting was applied in each direction to reconstruct 4D-DWI.Themore » technique was evaluated using a computer simulated 4D-digital human phantom(XCAT),a motion phantom and a healthy volunteer under an IRB-approved study.Motion trajectories of regions-of-interests(ROI) were extracted from 4D-DWI and compared with reference.The mean motion trajectory amplitude differences(D) between the two was calculated.To quantitatively analyze the motion artifacts,XCAT were controlled to simulate regular motion and the motions of 10 liver cancer patients.4D-DWI,free-breathing DWI(FB- DWI) were reconstructed.Tumor volume difference(VD) of each phase of 4D-DWI and FB-DWI from the input static tumor were calculated.Furthermore, ADC was measured for each phase of 4D-DWI and FB-DWI data,and mean tumor ADC values(M-ADC) were calculated.Mean M-ADC over all 4D-DWI phases was compared with M-ADC calculated from FB-DWI. Results: 4D-DWI of XCAT,the motion phantom and the healthy volunteer demonstrated the respiratory motion clearly.ROI D values were 1.9mm,1.7mm and 2.0mm,respectively.For motion artifacts analysis,XCAT 4D-DWI images show much less motion artifacts compare to FB-DWI.Mean VD for 4D-WDI and FB-DWI were 8.5±1.4% and 108±15%,respectively.Mean M-ADC for ADC measured from 4D-DWI and M-ADC measured from FB-DWI were (2.29±0.04)*0.001*mm2/s and (3.80±0.01)*0.001*mm2/s,respectively.ADC value ground-truth is 2.24*0.001*mm2/s from the input of the simulation. Conclusion: A respiratory correlated 4D-DWI technique has been initially evaluated in phantoms and a human subject.Comparing to free breathing DWI,4D-DWI can lead to more accurate measurement of ADC.« less

Brownian motion of solitons in a Bose-Einstein condensate.

PubMed

Aycock, Lauren M; Hurst, Hilary M; Efimkin, Dmitry K; Genkina, Dina; Lu, Hsin-I; Galitski, Victor M; Spielman, I B

2017-03-07

We observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated [Formula: see text] Bose-Einstein condensates (BECs) and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one dimension (1D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton's diffusive behavior using a quasi-1D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment.

Brownian motion of solitons in a Bose–Einstein condensate

PubMed Central

Aycock, Lauren M.; Hurst, Hilary M.; Efimkin, Dmitry K.; Genkina, Dina; Lu, Hsin-I; Galitski, Victor M.; Spielman, I. B.

2017-01-01

We observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated Rb87 Bose–Einstein condensates (BECs) and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one dimension (1D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton’s diffusive behavior using a quasi-1D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment. PMID:28196896

Motion of charged particles normal to an irregular magnetic field. [astrophysical plasmas

NASA Technical Reports Server (NTRS)

Jokipii, J. R.

1975-01-01

The motion is analyzed of charged particles in a fluctuating magnetic field which varies only in directions normal to its mean direction, such as that which would be generated by an ensemble of magnetosonic waves propagating normal to an ambient magnetic field. The appropriate generalization of gradient-drift motion is derived in terms of the power spectrum of the magnetic fluctuations, and an effective spatial diffusion coefficient is obtained. Several special cases are considered, including a Gaussian power spectrum, a power-law spectrum with a cutoff, and a general power-law spectrum. A possible magnitude is calculated for the spatial diffusion coefficient of the solar wind.

Random diffusivity from stochastic equations: comparison of two models for Brownian yet non-Gaussian diffusion

NASA Astrophysics Data System (ADS)

Sposini, Vittoria; Chechkin, Aleksei V.; Seno, Flavio; Pagnini, Gianni; Metzler, Ralf

2018-04-01

A considerable number of systems have recently been reported in which Brownian yet non-Gaussian dynamics was observed. These are processes characterised by a linear growth in time of the mean squared displacement, yet the probability density function of the particle displacement is distinctly non-Gaussian, and often of exponential (Laplace) shape. This apparently ubiquitous behaviour observed in very different physical systems has been interpreted as resulting from diffusion in inhomogeneous environments and mathematically represented through a variable, stochastic diffusion coefficient. Indeed different models describing a fluctuating diffusivity have been studied. Here we present a new view of the stochastic basis describing time-dependent random diffusivities within a broad spectrum of distributions. Concretely, our study is based on the very generic class of the generalised Gamma distribution. Two models for the particle spreading in such random diffusivity settings are studied. The first belongs to the class of generalised grey Brownian motion while the second follows from the idea of diffusing diffusivities. The two processes exhibit significant characteristics which reproduce experimental results from different biological and physical systems. We promote these two physical models for the description of stochastic particle motion in complex environments.

Electric-field noise from carbon-adatom diffusion on a Au(110) surface: First-principles calculations and experiments

DOE PAGES

Kim, E.; Safavi-Naini, A.; Hite, D. A.; ...

2017-03-01

The decoherence of trapped-ion quantum bits due to heating of their motional modes is a fundamental science and engineering problem. This heating is attributed to electric-field noise arising from processes on the trap-electrode surfaces. In this work, we address the source of this noise by focusing on the diffusion of carbon-containing adsorbates on the surface of Au(110). We show by detailed scanned probe microscopy and density functional theory how the carbon adatom diffusion on the gold surface changes the energy landscape, and how the adatom dipole moment varies with the diffusive motion. Lastly, a simple model for the diffusion noise,more » which varies quadratically with the variation of the dipole moment, qualitatively reproduces the measured noise spectrum, and the estimate of the noise spectral density is in accord with measured values.« less

Relative distance between tracers as a measure of diffusivity within moving aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Zaburdaev, Vasily

2018-02-01

Tracking of particles, be it a passive tracer or an actively moving bacterium in the growing bacterial colony, is a powerful technique to probe the physical properties of the environment of the particles. One of the most common measures of particle motion driven by fluctuations and random forces is its diffusivity, which is routinely obtained by measuring the mean squared displacement of the particles. However, often the tracer particles may be moving in a domain or an aggregate which itself experiences some regular or random motion and thus masks the diffusivity of tracers. Here we provide a method for assessing the diffusivity of tracer particles within mobile aggregates by measuring the so-called mean squared relative distance (MSRD) between two tracers. We provide analytical expressions for both the ensemble and time averaged MSRD allowing for direct identification of diffusivities from experimental data.

Electric-field noise from carbon-adatom diffusion on a Au(110) surface: First-principles calculations and experiments

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

Kim, E.; Safavi-Naini, A.; Hite, D. A.

The decoherence of trapped-ion quantum bits due to heating of their motional modes is a fundamental science and engineering problem. This heating is attributed to electric-field noise arising from processes on the trap-electrode surfaces. In this work, we address the source of this noise by focusing on the diffusion of carbon-containing adsorbates on the surface of Au(110). We show by detailed scanned probe microscopy and density functional theory how the carbon adatom diffusion on the gold surface changes the energy landscape, and how the adatom dipole moment varies with the diffusive motion. Lastly, a simple model for the diffusion noise,more » which varies quadratically with the variation of the dipole moment, qualitatively reproduces the measured noise spectrum, and the estimate of the noise spectral density is in accord with measured values.« less

[Joint correction for motion artifacts and off-resonance artifacts in multi-shot diffusion magnetic resonance imaging].

PubMed

Wu, Wenchuan; Fang, Sheng; Guo, Hua

2014-06-01

Aiming at motion artifacts and off-resonance artifacts in multi-shot diffusion magnetic resonance imaging (MRI), we proposed a joint correction method in this paper to correct the two kinds of artifacts simultaneously without additional acquisition of navigation data and field map. We utilized the proposed method using multi-shot variable density spiral sequence to acquire MRI data and used auto-focusing technique for image deblurring. We also used direct method or iterative method to correct motion induced phase errors in the process of deblurring. In vivo MRI experiments demonstrated that the proposed method could effectively suppress motion artifacts and off-resonance artifacts and achieve images with fine structures. In addition, the scan time was not increased in applying the proposed method.

Surface diffusion of cyclic hydrocarbons on nickel

NASA Astrophysics Data System (ADS)

Silverwood, I. P.; Armstrong, J.

2018-08-01

Surface diffusion of adsorbates is difficult to measure on realistic systems, yet it is of fundamental interest in catalysis and coating reactions. quasielastic neutron scattering (QENS) was used to investigate the diffusion of cyclohexane and benzene adsorbed on a nickel metal sponge catalyst. Molecular dynamics simulations of benzene on a model (111) nickel surface showed localised motion with diffusion by intermittent jumps. The experimental data was therefore fitted to the Singwi-Sjölander model and activation energies for diffusion of 4.0 kJ mol-1 for benzene and 4.3 kJ mol-1 for cyclohexane were calculated for the two dimensional model. Limited motion out-of plane was seen in the dynamics simulations and is discussed, although the resolution of the scattering experiment is insufficient to quantify this. Good agreement is seen between the use of a perfect crystal as a model for a disordered system over short time scales, suggesting that simple models are adequate to describe diffusion over polycrystalline metal surfaces on the timescale of QENS measurement.

Diffusion limit of Lévy-Lorentz gas is Brownian motion

NASA Astrophysics Data System (ADS)

Magdziarz, Marcin; Szczotka, Wladyslaw

2018-07-01

In this paper we analyze asymptotic behaviour of a stochastic process called Lévy-Lorentz gas. This process is aspecial kind of continuous-time random walk in which walker moves in the fixed environment composed of scattering points. Upon each collision the walker performs a flight to the nearest scattering point. This type of dynamics is observed in Lévy glasses or long quenched polymers. We show that the diffusion limit of Lévy-Lorentz gas with finite mean distance between scattering centers is the standard Brownian motion. Thus, for long times the behaviour of the Lévy-Lorentz gas is close to the diffusive regime.

Optimal estimation of diffusion coefficients from single-particle trajectories

NASA Astrophysics Data System (ADS)

Vestergaard, Christian L.; Blainey, Paul C.; Flyvbjerg, Henrik

2014-02-01

How does one optimally determine the diffusion coefficient of a diffusing particle from a single-time-lapse recorded trajectory of the particle? We answer this question with an explicit, unbiased, and practically optimal covariance-based estimator (CVE). This estimator is regression-free and is far superior to commonly used methods based on measured mean squared displacements. In experimentally relevant parameter ranges, it also outperforms the analytically intractable and computationally more demanding maximum likelihood estimator (MLE). For the case of diffusion on a flexible and fluctuating substrate, the CVE is biased by substrate motion. However, given some long time series and a substrate under some tension, an extended MLE can separate particle diffusion on the substrate from substrate motion in the laboratory frame. This provides benchmarks that allow removal of bias caused by substrate fluctuations in CVE. The resulting unbiased CVE is optimal also for short time series on a fluctuating substrate. We have applied our estimators to human 8-oxoguanine DNA glycolase proteins diffusing on flow-stretched DNA, a fluctuating substrate, and found that diffusion coefficients are severely overestimated if substrate fluctuations are not accounted for.

Diffusion of multiple species with excluded-volume effects.

PubMed

Bruna, Maria; Chapman, S Jonathan

2012-11-28

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results.

Ionomers for Ion-Conducting Energy Materials

NASA Astrophysics Data System (ADS)

Colby, Ralph

For ionic actuators and battery separators, it is vital to utilize single-ion conducting ionomers that avoid the detrimental polarization of other ions. Single-ion conducting ionomers are synthesized based on DFT calculations, with low glass transition temperatures (facile dynamics) to prepare ion-conducting membranes for battery separators that conduct Li+ or Na+. Characterization by X-ray scattering, dielectric spectroscopy, FTIR, NMR and linear viscoelasticity collectively develop a coherent picture of ionic aggregation and both counterion and polymer dynamics. 7Li NMR diffusion measurements find that diffusion is faster than expected by conductivity using the Nernst-Einstein equation, which means that the majority of Li diffusion occurs by ion pairs moving with the polymer segmental motion. Segmental motion only contributes to ionic conduction in the rare event that one of these ion pairs has an extra Li (a positive triple ion). This leads us to a new metric for ion-conducting soft materials, the product of the cation number density p0 and their diffusion coefficient D; p0D is the diffusive flux of lithium ions. This new metric has a maximum at intermediate ion content that corresponds to the overlap of ion pair polarizability volumes. At higher ion contents, the ion pairs interact strongly and form larger aggregation states that retard segmental motion of both mobile ion pairs and triple ions.

Resolving High Amplitude Surface Motion with Diffusing Light

NASA Technical Reports Server (NTRS)

Wright, W.; Budakian, R.; Putterman, Seth J.

1996-01-01

A new technique has been developed for the purpose of imaging high amplitude surface motion. With this method one can quantitatively measure the transition to ripple wave turbulence. In addition, one can measure the phase of the turbulent state. These experiments reveal strong coherent structures in turbulent range of motion.

Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications

NASA Astrophysics Data System (ADS)

Torabifard, Hedieh; Reed, Luke; Berry, Matthew T.; Hein, Jason E.; Menke, Erik; Cisneros, G. Andrés

2017-10-01

The development of Li-ion batteries for energy storage has received significant attention. The synthesis and characterization of electrolytes in these batteries are an important component of this development. Ionic liquids (ILs) have been proposed as possible electrolytes in these devices. Thus, the accurate determination of thermophysical properties for these solvents becomes important for determining their applicability as electrolytes. In this contribution, we present the synthesis and experimental/computational characterization of thermodynamic and transport properties of a pyrrolidinium based ionic liquid as a first step to investigate the possible applicability of this class of ILs for Li-ion batteries. A quantum mechanical-based force field with many-body polarizable interactions has been developed for the simulation of spirocyclic pyrrolidinium, [sPyr+], with BF4- and Li+. Molecular dynamics calculations employing intra-molecular polarization predicted larger heat of vaporization and self-diffusion coefficients and smaller densities in comparison with the model without intra-molecular polarization, indicating that the inclusion of this term can significantly effect the inter-ionic interactions. The calculated properties are in good agreement with available experimental data for similar IL pairs and isothermal titration calorimetry data for [sPyr+][BF4-].

Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes.

PubMed

Berry, Hugues; Chaté, Hugues

2014-02-01

In vivo measurements of the passive movements of biomolecules or vesicles in cells consistently report "anomalous diffusion," where mean-squared displacements scale as a power law of time with exponent α<1 (subdiffusion). While the detailed mechanisms causing such behaviors are not always elucidated, movement hindrance by obstacles is often invoked. However, our understanding of how hindered diffusion leads to subdiffusion is based on diffusion amidst randomly located immobile obstacles. Here, we have used Monte Carlo simulations to investigate transient subdiffusion due to mobile obstacles with various modes of mobility. Our simulations confirm that the anomalous regimes rapidly disappear when the obstacles move by Brownian motion. By contrast, mobile obstacles with more confined displacements, e.g., Orstein-Ulhenbeck motion, are shown to preserve subdiffusive regimes. The mean-squared displacement of tracked protein displays convincing power laws with anomalous exponent α that varies with the density of Orstein-Ulhenbeck (OU) obstacles or the relaxation time scale of the OU process. In particular, some of the values we observed are significantly below the universal value predicted for immobile obstacles in two dimensions. Therefore, our results show that subdiffusion due to mobile obstacles with OU type of motion may account for the large variation range exhibited by experimental measurements in living cells and may explain that some experimental estimates are below the universal value predicted for immobile obstacles.

The molecular basis of the solution properties of hyaluronan investigated by confocal fluorescence recovery after photobleaching.

PubMed Central

Gribbon, P; Heng, B C; Hardingham, T E

1999-01-01

Hyaluronan (HA) is a highly hydrated polyanion, which is a network-forming and space-filling component in the extracellular matrix of animal tissues. Confocal fluorescence recovery after photobleaching (confocal-FRAP) was used to investigate intramolecular hydrogen bonding and electrostatic interactions in hyaluronan solutions. Self and tracer lateral diffusion coefficients within hyaluronan solutions were measured over a wide range of concentrations (c), with varying electrolyte and at neutral and alkaline pH. The free diffusion coefficient of fluoresceinamine-labeled HA of 500 kDa in PBS was 7.9 x 10(-8) cm(2) s(-1) and of 830 kDa HA was 5.6 x 10(-8) cm(2) s(-1). Reductions in self- and tracer-diffusion with c followed a stretched exponential model. Electrolyte-induced polyanion coil contraction and destiffening resulted in a 2.8-fold increase in self-diffusion between 0 and 100 mM NaCl. Disruption of hydrogen bonds by strong alkali (0.5 M NaOH) resulted in further larger increases in self- and tracer-diffusion coefficients, consistent with a more dynamic and permeable network. Concentrated hyaluronan solution properties were attributed to hydrodynamic and entanglement interactions between domains. There was no evidence of chain-chain associations. At physiological electrolyte concentration and pH, the greatest contribution to the intrinsic stiffness of hyaluronan appeared to be due to hydrogen bonds between adjacent saccharides. PMID:10512840

Anatomy of Particle Diffusion

ERIC Educational Resources Information Center

Bringuier, E.

2009-01-01

The paper analyses particle diffusion from a thermodynamic standpoint. The main goal of the paper is to highlight the conceptual connection between particle diffusion, which belongs to non-equilibrium statistical physics, and mechanics, which deals with particle motion, at the level of third-year university courses. We start out from the fact…

Variability of non-Gaussian diffusion MRI and intravoxel incoherent motion (IVIM) measurements in the breast.

PubMed

Iima, Mami; Kataoka, Masako; Kanao, Shotaro; Kawai, Makiko; Onishi, Natsuko; Koyasu, Sho; Murata, Katsutoshi; Ohashi, Akane; Sakaguchi, Rena; Togashi, Kaori

2018-01-01

We prospectively examined the variability of non-Gaussian diffusion magnetic resonance imaging (MRI) and intravoxel incoherent motion (IVIM) measurements with different numbers of b-values and excitations in normal breast tissue and breast lesions. Thirteen volunteers and fourteen patients with breast lesions (seven malignant, eight benign; one patient had bilateral lesions) were recruited in this prospective study (approved by the Internal Review Board). Diffusion-weighted MRI was performed with 16 b-values (0-2500 s/mm2 with one number of excitations [NEX]) and five b-values (0-2500 s/mm2, 3 NEX), using a 3T breast MRI. Intravoxel incoherent motion (flowing blood volume fraction [fIVIM] and pseudodiffusion coefficient [D*]) and non-Gaussian diffusion (theoretical apparent diffusion coefficient [ADC] at b value of 0 sec/mm2 [ADC0] and kurtosis [K]) parameters were estimated from IVIM and Kurtosis models using 16 b-values, and synthetic apparent diffusion coefficient (sADC) values were obtained from two key b-values. The variabilities between and within subjects and between different diffusion acquisition methods were estimated. There were no statistical differences in ADC0, K, or sADC values between the different b-values or NEX. A good agreement of diffusion parameters was observed between 16 b-values (one NEX), five b-values (one NEX), and five b-values (three NEX) in normal breast tissue or breast lesions. Insufficient agreement was observed for IVIM parameters. There were no statistical differences in the non-Gaussian diffusion MRI estimated values obtained from a different number of b-values or excitations in normal breast tissue or breast lesions. These data suggest that a limited MRI protocol using a few b-values might be relevant in a clinical setting for the estimation of non-Gaussian diffusion MRI parameters in normal breast tissue and breast lesions.

Variability of non-Gaussian diffusion MRI and intravoxel incoherent motion (IVIM) measurements in the breast

PubMed Central

Kataoka, Masako; Kanao, Shotaro; Kawai, Makiko; Onishi, Natsuko; Koyasu, Sho; Murata, Katsutoshi; Ohashi, Akane; Sakaguchi, Rena; Togashi, Kaori

2018-01-01

We prospectively examined the variability of non-Gaussian diffusion magnetic resonance imaging (MRI) and intravoxel incoherent motion (IVIM) measurements with different numbers of b-values and excitations in normal breast tissue and breast lesions. Thirteen volunteers and fourteen patients with breast lesions (seven malignant, eight benign; one patient had bilateral lesions) were recruited in this prospective study (approved by the Internal Review Board). Diffusion-weighted MRI was performed with 16 b-values (0–2500 s/mm2 with one number of excitations [NEX]) and five b-values (0–2500 s/mm2, 3 NEX), using a 3T breast MRI. Intravoxel incoherent motion (flowing blood volume fraction [fIVIM] and pseudodiffusion coefficient [D*]) and non-Gaussian diffusion (theoretical apparent diffusion coefficient [ADC] at b value of 0 sec/mm2 [ADC0] and kurtosis [K]) parameters were estimated from IVIM and Kurtosis models using 16 b-values, and synthetic apparent diffusion coefficient (sADC) values were obtained from two key b-values. The variabilities between and within subjects and between different diffusion acquisition methods were estimated. There were no statistical differences in ADC0, K, or sADC values between the different b-values or NEX. A good agreement of diffusion parameters was observed between 16 b-values (one NEX), five b-values (one NEX), and five b-values (three NEX) in normal breast tissue or breast lesions. Insufficient agreement was observed for IVIM parameters. There were no statistical differences in the non-Gaussian diffusion MRI estimated values obtained from a different number of b-values or excitations in normal breast tissue or breast lesions. These data suggest that a limited MRI protocol using a few b-values might be relevant in a clinical setting for the estimation of non-Gaussian diffusion MRI parameters in normal breast tissue and breast lesions. PMID:29494639

In Vivo Anomalous Diffusion and Weak Ergodicity Breaking of Lipid Granules

NASA Astrophysics Data System (ADS)

Jeon, Jae-Hyung; Tejedor, Vincent; Burov, Stas; Barkai, Eli; Selhuber-Unkel, Christine; Berg-Sørensen, Kirstine; Oddershede, Lene; Metzler, Ralf

2011-01-01

Combining extensive single particle tracking microscopy data of endogenous lipid granules in living fission yeast cells with analytical results we show evidence for anomalous diffusion and weak ergodicity breaking. Namely we demonstrate that at short times the granules perform subdiffusion according to the laws of continuous time random walk theory. The associated violation of ergodicity leads to a characteristic turnover between two scaling regimes of the time averaged mean squared displacement. At longer times the granule motion is consistent with fractional Brownian motion.

Compressed exponential relaxation in liquid silicon: Universal feature of the crossover from ballistic to diffusive behavior in single-particle dynamics

NASA Astrophysics Data System (ADS)

Morishita, Tetsuya

2012-07-01

We report a first-principles molecular-dynamics study of the relaxation dynamics in liquid silicon (l-Si) over a wide temperature range (1000-2200 K). We find that the intermediate scattering function for l-Si exhibits a compressed exponential decay above 1200 K including the supercooled regime, which is in stark contrast to that for normal "dense" liquids which typically show stretched exponential decay in the supercooled regime. The coexistence of particles having ballistic-like motion and those having diffusive-like motion is demonstrated, which accounts for the compressed exponential decay in l-Si. An attempt to elucidate the crossover from the ballistic to the diffusive regime in the "time-dependent" diffusion coefficient is made and the temperature-independent universal feature of the crossover is disclosed.

Analysis of phase error effects in multishot diffusion-prepared turbo spin echo imaging

PubMed Central

Cervantes, Barbara; Kooijman, Hendrik; Karampinos, Dimitrios C.

2017-01-01

Background To characterize the effect of phase errors on the magnitude and the phase of the diffusion-weighted (DW) signal acquired with diffusion-prepared turbo spin echo (dprep-TSE) sequences. Methods Motion and eddy currents were identified as the main sources of phase errors. An analytical expression for the effect of phase errors on the acquired signal was derived and verified using Bloch simulations, phantom, and in vivo experiments. Results Simulations and experiments showed that phase errors during the diffusion preparation cause both magnitude and phase modulation on the acquired data. When motion-induced phase error (MiPe) is accounted for (e.g., with motion-compensated diffusion encoding), the signal magnitude modulation due to the leftover eddy-current-induced phase error cannot be eliminated by the conventional phase cycling and sum-of-squares (SOS) method. By employing magnitude stabilizers, the phase-error-induced magnitude modulation, regardless of its cause, was removed but the phase modulation remained. The in vivo comparison between pulsed gradient and flow-compensated diffusion preparations showed that MiPe needed to be addressed in multi-shot dprep-TSE acquisitions employing magnitude stabilizers. Conclusions A comprehensive analysis of phase errors in dprep-TSE sequences showed that magnitude stabilizers are mandatory in removing the phase error induced magnitude modulation. Additionally, when multi-shot dprep-TSE is employed the inconsistent signal phase modulation across shots has to be resolved before shot-combination is performed. PMID:28516049

Relativistic diffusive motion in random electromagnetic fields

NASA Astrophysics Data System (ADS)

Haba, Z.

2011-08-01

We show that the relativistic dynamics in a Gaussian random electromagnetic field can be approximated by the relativistic diffusion of Schay and Dudley. Lorentz invariant dynamics in the proper time leads to the diffusion in the proper time. The dynamics in the laboratory time gives the diffusive transport equation corresponding to the Jüttner equilibrium at the inverse temperature β-1 = mc2. The diffusion constant is expressed by the field strength correlation function (Kubo's formula).

On time-dependent diffusion coefficients arising from stochastic processes with memory

NASA Astrophysics Data System (ADS)

Carpio-Bernido, M. Victoria; Barredo, Wilson I.; Bernido, Christopher C.

2017-08-01

Time-dependent diffusion coefficients arise from anomalous diffusion encountered in many physical systems such as protein transport in cells. We compare these coefficients with those arising from analysis of stochastic processes with memory that go beyond fractional Brownian motion. Facilitated by the Hida white noise functional integral approach, diffusion propagators or probability density functions (pdf) are obtained and shown to be solutions of modified diffusion equations with time-dependent diffusion coefficients. This should be useful in the study of complex transport processes.

Estimation of slipping organ motion by registration with direction-dependent regularization.

PubMed

Schmidt-Richberg, Alexander; Werner, René; Handels, Heinz; Ehrhardt, Jan

2012-01-01

Accurate estimation of respiratory motion is essential for many applications in medical 4D imaging, for example for radiotherapy of thoracic and abdominal tumors. It is usually done by non-linear registration of image scans at different states of the breathing cycle but without further modeling of specific physiological motion properties. In this context, the accurate computation of respiration-driven lung motion is especially challenging because this organ is sliding along the surrounding tissue during the breathing cycle, leading to discontinuities in the motion field. Without considering this property in the registration model, common intensity-based algorithms cause incorrect estimation along the object boundaries. In this paper, we present a model for incorporating slipping motion in image registration. Extending the common diffusion registration by distinguishing between normal- and tangential-directed motion, we are able to estimate slipping motion at the organ boundaries while preventing gaps and ensuring smooth motion fields inside and outside. We further present an algorithm for a fully automatic detection of discontinuities in the motion field, which does not rely on a prior segmentation of the organ. We evaluate the approach for the estimation of lung motion based on 23 inspiration/expiration pairs of thoracic CT images. The results show a visually more plausible motion estimation. Moreover, the target registration error is quantified using manually defined landmarks and a significant improvement over the standard diffusion regularization is shown. Copyright © 2011 Elsevier B.V. All rights reserved.

Understanding THz spectra of aqueous solutions: glycine in light and heavy water.

PubMed

Sun, Jian; Niehues, Gudrun; Forbert, Harald; Decka, Dominique; Schwaab, Gerhard; Marx, Dominik; Havenith, Martina

2014-04-02

THz spectroscopy of aqueous solutions has been established as of recently to be a valuable and complementary experimental tool to provide direct insights into the solute-solvent coupling due to hydrogen-bond dynamics involving interfacial water. Despite much experimental progress, understanding THz spectra in terms of molecular motions, akin to mid-infrared spectra, still remains elusive. Here, using the osmoprotectant glycine as a showcase, we demonstrate how this can be achieved by combining THz absorption spectroscopy and ab initio molecular dynamics. The experimental THz spectrum is characterized by broad yet clearly discernible peaks. Based on substantial extensions of available mode-specific decomposition schemes, the experimental spectrum can be reproduced by theory and assigned on an essentially quantitative level. This joint effort reveals an unexpectedly clear picture of the individual contributions of molecular motion to the THz absorption spectrum in terms of distinct modes stemming from intramolecular vibrations, rigid-body-like hindered rotational and translational motion, and specific couplings to interfacial water molecules. The assignment is confirmed by the peak shifts observed in the THz spectrum of deuterated glycine in heavy water, which allow us to separate the distinct modes experimentally.

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

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.

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.

Dynamics of colloidal particles in electrohydrodynamic convection of nematic liquid crystal.

PubMed

Takahashi, Kentaro; Kimura, Yasuyuki

2014-07-01

We have studied the dynamics of micrometer-sized colloidal particles in electrohydrodynamic convection of nematic liquid crystal. Above the onset voltage of electroconvection, the parallel array of convection rolls appears to be perpendicular to the nematic field at first. The particles are forced to rotate by convection flow and are trapped within a single roll in this voltage regime. A slow glide motion along the roll axis is also observed. The frequency of rotational motion and the glide velocity increase with the applied voltage. Under a much larger voltage where the roll axis temporally fluctuates, the particles occasionally hop to the neighbor rolls. In this voltage regime, the motion of the particles becomes two-dimensional. The motion perpendicular to the roll axis exhibits diffusion behavior at a long time period. The effective diffusion constant is 10(3)-10(4) times larger than the molecular one. The observed behavior is compared with the result obtained by a simple stochastic model for the transport of the particles in convection. The enhancement of diffusion can be quantitatively described well by the rotation frequency in a roll, the width of the roll, and the hopping probability to the neighbor rolls.

Diffuse correlation tomography in the transport regime: A theoretical study of the sensitivity to Brownian motion.

PubMed

Tricoli, Ugo; Macdonald, Callum M; Durduran, Turgut; Da Silva, Anabela; Markel, Vadim A

2018-02-01

Diffuse correlation tomography (DCT) uses the electric-field temporal autocorrelation function to measure the mean-square displacement of light-scattering particles in a turbid medium over a given exposure time. The movement of blood particles is here estimated through a Brownian-motion-like model in contrast to ordered motion as in blood flow. The sensitivity kernel relating the measurable field correlation function to the mean-square displacement of the particles can be derived by applying a perturbative analysis to the correlation transport equation (CTE). We derive an analytical expression for the CTE sensitivity kernel in terms of the Green's function of the radiative transport equation, which describes the propagation of the intensity. We then evaluate the kernel numerically. The simulations demonstrate that, in the transport regime, the sensitivity kernel provides sharper spatial information about the medium as compared with the correlation diffusion approximation. Also, the use of the CTE allows one to explore some additional degrees of freedom in the data such as the collimation direction of sources and detectors. Our results can be used to improve the spatial resolution of DCT, in particular, with applications to blood flow imaging in regions where the Brownian motion is dominant.

Diffuse correlation tomography in the transport regime: A theoretical study of the sensitivity to Brownian motion

NASA Astrophysics Data System (ADS)

Tricoli, Ugo; Macdonald, Callum M.; Durduran, Turgut; Da Silva, Anabela; Markel, Vadim A.

2018-02-01

Diffuse correlation tomography (DCT) uses the electric-field temporal autocorrelation function to measure the mean-square displacement of light-scattering particles in a turbid medium over a given exposure time. The movement of blood particles is here estimated through a Brownian-motion-like model in contrast to ordered motion as in blood flow. The sensitivity kernel relating the measurable field correlation function to the mean-square displacement of the particles can be derived by applying a perturbative analysis to the correlation transport equation (CTE). We derive an analytical expression for the CTE sensitivity kernel in terms of the Green's function of the radiative transport equation, which describes the propagation of the intensity. We then evaluate the kernel numerically. The simulations demonstrate that, in the transport regime, the sensitivity kernel provides sharper spatial information about the medium as compared with the correlation diffusion approximation. Also, the use of the CTE allows one to explore some additional degrees of freedom in the data such as the collimation direction of sources and detectors. Our results can be used to improve the spatial resolution of DCT, in particular, with applications to blood flow imaging in regions where the Brownian motion is dominant.

Probing short-range protein Brownian motion in the cytoplasm of living cells

PubMed Central

Di Rienzo, Carmine; Piazza, Vincenzo; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

2014-01-01

The translational motion of molecules in cells deviates from what is observed in dilute solutions. Theoretical models provide explanations for this effect but with predictions that drastically depend on the nanoscale organization assumed for macromolecular crowding agents. A conclusive test of the nature of the translational motion in cells is missing owing to the lack of techniques capable of probing crowding with the required temporal and spatial resolution. Here we show that fluorescence-fluctuation analysis of raster scans at variable timescales can provide this information. By using green fluorescent proteins in cells, we measure protein motion at the unprecedented timescale of 1 μs, unveiling unobstructed Brownian motion from 25 to 100 nm, and partially suppressed diffusion above 100 nm. Furthermore, experiments on model systems attribute this effect to the presence of relatively immobile structures rather than to diffusing crowding agents. We discuss the implications of these results for intracellular processes. PMID:25532887

Self-averaging and weak ergodicity breaking of diffusion in heterogeneous media

NASA Astrophysics Data System (ADS)

Russian, Anna; Dentz, Marco; Gouze, Philippe

2017-08-01

Diffusion in natural and engineered media is quantified in terms of stochastic models for the heterogeneity-induced fluctuations of particle motion. However, fundamental properties such as ergodicity and self-averaging and their dependence on the disorder distribution are often not known. Here, we investigate these questions for diffusion in quenched disordered media characterized by spatially varying retardation properties, which account for particle retention due to physical or chemical interactions with the medium. We link self-averaging and ergodicity to the disorder sampling efficiency Rn, which quantifies the number of disorder realizations a noise ensemble may sample in a single disorder realization. Diffusion for disorder scenarios characterized by a finite mean transition time is ergodic and self-averaging for any dimension. The strength of the sample to sample fluctuations decreases with increasing spatial dimension. For an infinite mean transition time, particle motion is weakly ergodicity breaking in any dimension because single particles cannot sample the heterogeneity spectrum in finite time. However, even though the noise ensemble is not representative of the single-particle time statistics, subdiffusive motion in q ≥2 dimensions is self-averaging, which means that the noise ensemble in a single realization samples a representative part of the heterogeneity spectrum.

IUTAM symposium on hydrodynamic diffusion of suspended particles

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

Davis, R.H.

Hydrodynamic diffusion refers to the fluctuating motion of nonBrownian particles (or droplets or bubbles) which occurs in a dispersion due to multiparticle interactions. For example, in a concentrated sheared suspension, particles do not move along streamlines but instead exhibit fluctuating motions as they tumble around each other. This leads to a net migration of particles down gradients in particle concentration and in shear rate, due to the higher frequency of encounters of a test particle with other particles on the side of the test particle which has higher concentration or shear rate. As another example, suspended particles subject to sedimentation,more » centrifugation, or fluidization, do not generally move relative to the fluid with a constant velocity, but instead experience diffusion-like fluctuations in velocity due to interactions with neighboring particles and the resulting variation in the microstructure or configuration of the suspended particles. In flowing granular materials, the particles interact through direct collisions or contacts (rather than through the surrounding fluid); these collisions also cause the particles to undergo fluctuating motions characteristic of diffusion processes. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.« less

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.

Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains

NASA Astrophysics Data System (ADS)

Nahali, Negar; Rosa, Angelo

2018-05-01

We employ large-scale molecular dynamics computer simulations to study the problem of nanoprobe diffusion in entangled solutions of linear polymers and unknotted and unconcatenated circular (ring) polymers. By tuning both the diameter of the nanoprobe and the density of the solution, we show that nanoprobes of diameter smaller than the entanglement distance (tube diameter) of the solution display the same (Rouse-like) behavior in solutions of both polymer architectures. Instead, nanoprobes with larger diameters appear to diffuse markedly faster in solutions of rings than in solutions of linear chains. Finally, by analysing the distribution functions of spatial displacements, we find that nanoprobe motion in rings' solutions shows both Gaussian and ergodic behaviors, in all regimes considered, while, in solutions of linear chains, nanoprobes exceeding the size of the tube diameter show a transition to non-Gaussian and non-ergodic motion. Our results emphasize the role of chain architecture in the motion of nanoprobes dispersed in polymer solutions.

Active diffusion and microtubule-based transport oppose myosin forces to position organelles in cells

PubMed Central

Lin, Congping; Schuster, Martin; Guimaraes, Sofia Cunha; Ashwin, Peter; Schrader, Michael; Metz, Jeremy; Hacker, Christian; Gurr, Sarah Jane; Steinberg, Gero

2016-01-01

Even distribution of peroxisomes (POs) and lipid droplets (LDs) is critical to their role in lipid and reactive oxygen species homeostasis. How even distribution is achieved remains elusive, but diffusive motion and directed motility may play a role. Here we show that in the fungus Ustilago maydis ∼95% of POs and LDs undergo diffusive motions. These movements require ATP and involve bidirectional early endosome motility, indicating that microtubule-associated membrane trafficking enhances diffusion of organelles. When early endosome transport is abolished, POs and LDs drift slowly towards the growing cell end. This pole-ward drift is facilitated by anterograde delivery of secretory cargo to the cell tip by myosin-5. Modelling reveals that microtubule-based directed transport and active diffusion support distribution, mobility and mixing of POs. In mammalian COS-7 cells, microtubules and F-actin also counteract each other to distribute POs. This highlights the importance of opposing cytoskeletal forces in organelle positioning in eukaryotes. PMID:27251117

Surface diffusion of a carbon-adatom on Au(110) surfaces

NASA Astrophysics Data System (ADS)

Kim, E.; Safavi-Naini, A.; Hite, D. A.; McKay, K. S.; Pappas, D. P.; Weck, P. F.; Sadeghpour, H. R.

We have investigated the surface diffusion of carbon-adatom on gold surfaces using density functional theory and detailed scanning probe microscopy. The decoherence of trapped-ion quantum gates due to heating of their motional modes is a fundamental science and engineering problem. In an effort to understand heating at the trap-electrode surfaces, we investigate the possible source of noise by focusing on the diffusion of carbon-containing adsorbates onto the Au(110) surface. In this study, we show how the diffusive motion of carbon adatom on gold surface significantly affects the energy landscape and adatom dipole moment variation. A simple model for the diffusion noise, which varies quadratically with the variation of the dipole moment, qualitatively reproduces the measured noise spectrum, and the estimate of the noise spectral density is in accord with measured values. Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the United States Department of Energy's NNSA under Contract DE-AC04-94AL85000.

Thermodynamics of the general diffusion process: Equilibrium supercurrent and nonequilibrium driven circulation with dissipation

NASA Astrophysics Data System (ADS)

Qian, H.

2015-07-01

Unbalanced probability circulation, which yields cyclic motions in phase space, is the defining characteristics of a stationary diffusion process without detailed balance. In over-damped soft matter systems, such behavior is a hallmark of the presence of a sustained external driving force accompanied with dissipations. In an under-damped and strongly correlated system, however, cyclic motions are often the consequences of a conservative dynamics. In the present paper, we give a novel interpretation of a class of diffusion processes with stationary circulation in terms of a Maxwell-Boltzmann equilibrium in which cyclic motions are on the level set of stationary probability density function thus non-dissipative, e.g., a supercurrent. This implies an orthogonality between stationary circulation J ss ( x) and the gradient of stationary probability density f ss ( x) > 0. A sufficient and necessary condition for the orthogonality is a decomposition of the drift b( x) = j( x) + D( x)∇φ( x) where ∇ṡ j( x) = 0 and j( x) ṡ∇φ( x) = 0. Stationary processes with such Maxwell-Boltzmann equilibrium has an underlying conservative dynamics , and a first integral ϕ( x) ≡ -ln f ss (x) = const, akin to a Hamiltonian system. At all time, an instantaneous free energy balance equation exists for a given diffusion system; and an extended energy conservation law among an entire family of diffusion processes with different parameter α can be established via a Helmholtz theorem. For the general diffusion process without the orthogonality, a nonequilibrium cycle emerges, which consists of external driven φ-ascending steps and spontaneous φ-descending movements, alternated with iso-φ motions. The theory presented here provides a rich mathematical narrative for complex mesoscopic dynamics, with contradistinction to an earlier one [H. Qian et al., J. Stat. Phys. 107, 1129 (2002)]. This article is supplemented with comments by H. Ouerdane and a final reply by the author.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

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

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Chemistry in motion: tiny synthetic motors.

PubMed

Colberg, Peter H; Reigh, Shang Yik; Robertson, Bryan; Kapral, Raymond

2014-12-16

CONSPECTUS: Diffusion is the principal transport mechanism that controls the motion of solute molecules and other species in solution; however, the random walk process that underlies diffusion is slow and often nonspecific. Although diffusion is an essential mechanism for transport in the biological realm, biological systems have devised more efficient transport mechanisms using molecular motors. Most biological motors utilize some form of chemical energy derived from their surroundings to induce conformational changes in order to carry out specific functions. These small molecular motors operate in the presence of strong thermal fluctuations and in the regime of low Reynolds numbers, where viscous forces dominate inertial forces. Thus, their dynamical behavior is fundamentally different from that of macroscopic motors, and different mechanisms are responsible for the production of useful mechanical motion. There is no reason why our interest should be confined to the small motors that occur naturally in biological systems. Recently, micron and nanoscale motors that use chemical energy to produce directed motion by a number of different mechanisms have been made in the laboratory. These small synthetic motors also experience strong thermal fluctuations and operate in regimes where viscous forces dominate. Potentially, these motors could be directed to perform different transport tasks, analogous to those of biological motors, for both in vivo and in vitro applications. Although some synthetic motors execute conformational changes to effect motion, the majority do not, and, instead, they use other mechanisms to convert chemical energy into directed motion. In this Account, we describe how synthetic motors that operate by self-diffusiophoresis make use of a self-generated concentration gradient to drive motor motion. A description of propulsion by self-diffusiophoresis is presented for Janus particle motors comprising catalytic and noncatalytic faces. The properties of the dynamics of chemically powered motors are illustrated by presenting the results of particle-based simulations of sphere-dimer motors constructed from linked catalytic and noncatalytic spheres. The geometries of both Janus and sphere-dimer motors with asymmetric catalytic activity support the formation of concentration gradients around the motors. Because directed motion can occur only when the system is not in equilibrium, the nature of the environment and the role it plays in motor dynamics are described. Rotational Brownian motion also acts to limit directed motion, and it has especially strong effects for very small motors. We address the following question: how small can motors be and still exhibit effects due to propulsion, even if only to enhance diffusion? Synthetic motors have the potential to transform the manner in which chemical dynamical processes are carried out for a wide range of applications.

Tracer diffusion in active suspensions

NASA Astrophysics Data System (ADS)

Burkholder, Eric W.; Brady, John F.

2017-05-01

We study the diffusion of a Brownian probe particle of size R in a dilute dispersion of active Brownian particles of size a , characteristic swim speed U0, reorientation time τR, and mechanical energy ksTs=ζaU02τR/6 , where ζa is the Stokes drag coefficient of a swimmer. The probe has a thermal diffusivity DP=kBT /ζP , where kBT is the thermal energy of the solvent and ζP is the Stokes drag coefficient for the probe. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. In competition with this steric hindrance is an enhancement driven by the activity of the swimmers. The strength of swimming relative to thermal diffusion is set by Pes=U0a /DP . The active contribution to the diffusivity scales as Pes2 for weak swimming and Pes for strong swimming, but the transition between these two regimes is nonmonotonic. When fluctuations in the probe motion decay on the time scale τR, the active diffusivity scales as ksTs/ζP : the probe moves as if it were immersed in a solvent with energy ksTs rather than kBT .

Salt-Finger Convection in a Stratified Fluid Layer Induced by Thermal and Solutal Capillary Motion

NASA Technical Reports Server (NTRS)

Chen, Chuan F.; Chan, Cho Lik

1996-01-01

Salt-finger convection in a double-diffusive system is a motion driven by the release of gravitational potential due to different diffusion rates. Normally, when the gravitational field is reduced, salt-finger convection together with other convective motions driven by buoyancy forces will be rapidly suppressed. However, because the destabilizing effect of the concentration gradient is amplified by the Lewis number, with values varying from 10(exp 2) for aqueous salt solutions to 10 (exp 4) for liquid metals, salt-finger convection may be generated at much reduced gravity levels. In the microgravity environment, the surface tension gradient assumes a dominant role in causing fluid motion. In this paper, we report on some experimental results showing the generation of salt-finger convection due to capillary motio on the surface of a stratified fluid layer. A numerical simulation is presented to show the cause of salt-finger convection.

Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein

DOE PAGES

Sharma, V. K.; Hayes, Douglas G.; Urban, Volker S.; ...

2017-06-12

Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. In this paper, we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates thatmore » surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants’ hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. Finally, this study demonstrates the utility of QENS for evaluating dynamics of BμEs in nanoscopic region, and that proteins directly affect the microscopic dynamics, which is of relevance for evaluating release kinetics of encapsulated drugs from BμE delivery systems and the use of BμEs as biomembrane mimetic systems for investigating membrane protein–biomembrane interactions.« less

Dynamics of a magnetic active Brownian particle under a uniform magnetic field.

PubMed

Vidal-Urquiza, Glenn C; Córdova-Figueroa, Ubaldo M

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α. In this work, the time-dependent active diffusivity and the crossover time (τ^{cross})-from ballistic to diffusive regimes-are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α, the particle undergoes a directional (or ballistic) propulsive motion at very short times (t≪τ^{cross}). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t≫τ^{cross}), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α=0), the crossover time is equal to the characteristic time scale for rotational diffusion, τ_{rot}. In the presence of a magnetic field (α>0), the correlation function, the active diffusivity, and the crossover time decrease with increasing α. The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τ^{cross}≪τ_{rot}. In the limit of weak fields (α≪1), the crossover time decreases quadratically with α, while in the limit of strong fields (α≫1) it decays asymptotically as α^{-1}. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

Dynamics of a magnetic active Brownian particle under a uniform magnetic field

NASA Astrophysics Data System (ADS)

Vidal-Urquiza, Glenn C.; Córdova-Figueroa, Ubaldo M.

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α . In this work, the time-dependent active diffusivity and the crossover time (τcross)—from ballistic to diffusive regimes—are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α , the particle undergoes a directional (or ballistic) propulsive motion at very short times (t ≪τcross ). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t ≫τcross ), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α =0 ), the crossover time is equal to the characteristic time scale for rotational diffusion, τrot. In the presence of a magnetic field (α >0 ), the correlation function, the active diffusivity, and the crossover time decrease with increasing α . The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τcross≪τrot . In the limit of weak fields (α ≪1 ), the crossover time decreases quadratically with α , while in the limit of strong fields (α ≫1 ) it decays asymptotically as α-1. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

Glycosylases utilize ``stop and go'' motion to locate DNA damage

NASA Astrophysics Data System (ADS)

Nelson, Shane

2015-03-01

Oxidative damage to DNA results in alterations that are mutagenic or even cytotoxic. Base excision repair is a mechanism that functions to identify and correct these lesions, and is present in organisms ranging from bacteria to humans. DNA glycosylases are the first enzymes in this pathway and function to locate and remove oxidatively damaged bases, and do so utilizing only thermal energy. However, the question remains of how these enzymes locate and recognize a damaged base among millions of undamaged bases. Utilizing fluorescence video microscopy with high spatial and temporal resolution, we have observed a number of different fluorescently labeled glycosylases (including bacterial FPG, NEI, and NTH as well as mammalian MutyH and OGG). These enzymes diffuse along DNA tightropes at approximately 0.01 +/- 0.005 μm2/s with binding lifetimes ranging from one second to several minutes. Chemically induced damage to the DNA substrate causes a ~ 50% reduction in diffusion coefficients and a ~ 400% increase in binding lifetimes, while mutation of the key ``wedge residue'' - which has been shown to be responsible for damage detection - results in a 200% increase in the diffusion coefficient. Utilizing a sliding window approach to measure diffusion coefficients within individual trajectories, we observe that distributions of diffusion coefficients are bimodal, consistent with periods of diffusive motion interspersed with immobile periods. Utilizing a unique chemo-mechanical simulation approach, we demonstrate that the motion of these glycosylases can be explained as free diffusion along the helical pitch of the DNA, punctuated with two different types of pauses: 1) rapid, short-lived pauses as the enzyme rapidly probes DNA bases to interrogate for damage and, 2) less frequent, longer lived pauses that reflect the enzyme bound to and catalytically removing a damaged base. These simulations also indicate that the wedge residue is critical for interrogation and recognition of damage, and thus enzymes missing this residue diffuse faster. Similarly, chemically induced damage increases the frequency with which the enzymes encounter damaged bases, resulting in slower diffusion.

Brownian motion and its descendants according to Schrödinger

NASA Astrophysics Data System (ADS)

Garbaczewski, Piotr; Vigier, Jean-Pierre

1992-08-01

We revisit Schrödinger's original suggestion of the existence of a special class of random processes, which have their origin in the Einstein-Smoluchowski theory of Brownian motion. Our principal goal is to clarify the physical nature of links connecting the realistic Brownian motion with the abstract mathematical formalism of Nelson and Bernstein diffusions.

Intravoxel Incoherent Motion MR Imaging in the Head and Neck: Correlation with Dynamic Contrast-Enhanced MR Imaging and Diffusion-Weighted Imaging.

PubMed

Xu, Xiao Quan; Choi, Young Jun; Sung, Yu Sub; Yoon, Ra Gyoung; Jang, Seung Won; Park, Ji Eun; Heo, Young Jin; Baek, Jung Hwan; Lee, Jeong Hyun

2016-01-01

To investigate the correlation between perfusion- and diffusion-related parameters from intravoxel incoherent motion (IVIM) and those from dynamic contrast-enhanced MR imaging (DCE-MRI) and diffusion-weighted imaging in tumors and normal muscles of the head and neck. We retrospectively enrolled 20 consecutive patients with head and neck tumors with MR imaging performed using a 3T MR scanner. Tissue diffusivity (D), pseudo-diffusion coefficient (D(*)), and perfusion fraction (f) were derived from bi-exponential fitting of IVIM data obtained with 14 different b-values in three orthogonal directions. We investigated the correlation between D, f, and D(*) and model-free parameters from the DCE-MRI (wash-in, Tmax, Emax, initial AUC60, whole AUC) and the apparent diffusion coefficient (ADC) value in the tumor and normal masseter muscle using a whole volume-of-interest approach. Pearson's correlation test was used for statistical analysis. No correlation was found between f or D(*) and any of the parameters from the DCE-MRI in all patients or in patients with squamous cell carcinoma (p > 0.05). The ADC was significantly correlated with D values in the tumors (p < 0.001, r = 0.980) and muscles (p = 0.013, r = 0.542), despite its significantly higher value than D. The difference between ADC and D showed significant correlation with f values in the tumors (p = 0.017, r = 0.528) and muscles (p = 0.003, r = 0.630), but no correlation with D(*) (p > 0.05, respectively). Intravoxel incoherent motion shows no significant correlation with model-free perfusion parameters derived from the DCE-MRI but is feasible for the analysis of diffusivity in both tumors and normal muscles of the head and neck.

Molecular dynamics simulations of propane in slit shaped silica nano-pores: direct comparison with quasielastic neutron scattering experiments.

PubMed

Gautam, Siddharth; Le, Thu; Striolo, Alberto; Cole, David

2017-12-13

Molecular motion under confinement has important implications for a variety of applications including gas recovery and catalysis. Propane confined in mesoporous silica aerogel as studied using quasielastic neutron scattering (QENS) showed anomalous pressure dependence in its diffusion coefficient (J. Phys. Chem. C, 2015, 119, 18188). Molecular dynamics (MD) simulations are often employed to complement the information obtained from QENS experiments. Here, we report an MD simulation study to probe the anomalous pressure dependence of propane diffusion in silica aerogel. Comparison is attempted based on the self-diffusion coefficients and on the time scales of the decay of the simulated intermediate scattering functions. While the self-diffusion coefficients obtained from the simulated mean squared displacement profiles do not exhibit the anomalous pressure dependence observed in the experiments, the time scales of the decay of the intermediate scattering functions calculated from the simulation data match the corresponding quantities obtained in the QENS experiment and thus confirm the anomalous pressure dependence of the diffusion coefficient. The origin of the anomaly in pressure dependence lies in the presence of an adsorbed layer of propane molecules that seems to dominate the confined propane dynamics at low pressure, thereby lowering the diffusion coefficient. Further, time scales for rotational motion obtained from the simulations explain the absence of rotational contribution to the QENS spectra in the experiments. In particular, the rotational motion of the simulated propane molecules is found to exhibit large angular jumps at lower pressure. The present MD simulation work thus reveals important new insights into the origin of anomalous pressure dependence of propane diffusivity in silica mesopores and supplements the information obtained experimentally by QENS data.

Anisotropic rotational diffusion studied by passage saturation transfer electron paramagnetic resonance

NASA Astrophysics Data System (ADS)

Robinson, Bruce H.; Dalton, Larry R.

1980-01-01

The stochastic Liouville equation for the spin density matrix is modified to consider the effects of Brownian anisotropic rotational diffusion upon electron paramagnetic resonance (EPR) and saturation transfer electron paramagnetic resonance (ST-EPR) spectra. Spectral shapes and the ST-EPR parameters L″/L, C'/C, and H″/H defined by Thomas, Dalton, and Hyde at X-band microwave frequencies [J. Chem. Phys. 65, 3006 (1976)] are examined and discussed in terms of the rotational times τ∥ and τ⊥ and in terms of other defined correlation times for systems characterized by magnetic tensors of axial symmetry and for systems characterized by nonaxially symmetric magnetic tensors. For nearly axially symmetric magnetic tensors, such as nitroxide spin labels studied employing 1-3 GHz microwaves, ST-EPR spectra for systems undergoing anisotropic rotational diffusion are virtually indistinguishable from spectra for systems characterized by isotropic diffusion. For nonaxially symmetric magnetic tensors, such as nitroxide spin labels studied employing 8-35 GHz microwaves, the high field region of the ST-EPR spectra, and hence the H″/H parameter, will be virtually indistinguishable from spectra, and parameter values, obtained for isotropic diffusion. On the other hand, the central spectral region at x-band microwave frequencies, and hence the C'/C parameter, is sensitive to the anisotropic diffusion model provided that a unique and static relationship exists between the magnetic and diffusion tensors. Random labeling or motion of the spin label relative to the biomolecule whose hydrodynamic properties are to be investigated will destroy spectral sensitivity to anisotropic motion. The sensitivity to anisotropic motion is enhanced in proceeding to 35 GHz with the increased sensitivity evident in the low field half of the EPR and ST-EPR spectra. The L″/L parameter is thus a meaningful indicator of anisotropic motion when compared with H″/H parameter analysis. However, consideration of spectral shapes suggests that the C'/C parameter definition is not meaningfully extended from 9.5 to 35 GHz. Alternative definitions of the L″/L and C'/C parameters are proposed for those microwave frequencies for which the electron Zeeman anisotropy is comparable to or greater than the electron-nitrogen nuclear hyperfine anisotropy.

Dynamics in the Plastic Crystalline Phases of Cyclohexanol and Cyclooctanol Studied by Quasielastic Neutron Scattering.

PubMed

Novak, E; Jalarvo, N; Gupta, S; Hong, K; Förster, S; Egami, T; Ohl, M

2018-06-01

Plastic crystals are a promising candidate for solid state ionic conductors. In this work, quasielastic neutron scattering is employed to investigate the center of mass diffusive motions in two types of plastic crystalline cyclic alcohols: cyclohexanol and cyclooctanol. Two separate motions are observed which are attributed to long-range translational diffusion (α-process) and cage rattling (fast β-process). Residence times and diffusion coefficients are calculated for both processes, along with the confinement distances for the cage rattling. In addition, a binary mixture of these two materials is measured to understand how the dynamics change when a second type of molecule is added to the matrix. It is observed that, upon the addition of the larger cyclooctanol molecules into the cyclohexanol solution, the cage size decreases, which causes a decrease in the observed diffusion rates for both the α- and fast β-processes.

Radial diffusion in magnetodiscs. [charged particle motion in planetary or stellar magnetosphere

NASA Technical Reports Server (NTRS)

Birmingham, T. J.

1985-01-01

The orbits of charged particles in magnetodiscs are considered. The bounce motion is assumed adiabatic except for transits of a small equatorial region of weak magnetic field strength and high field curvature. Previous theory and modeling have shown that particles scatter randomly in pitch angle with each passage through the equator. A peaked distribution thus diffuses in pitch angle on the time scale of many bounces. It is argued in this paper that spatial diffusion is a further consequence when the magnetodisc has a longitudinal asymmetry. A general expression for DLL, the diffusion of equatorial crossing radii, is derived. DLL is evaluated explicitly for ions in Jupiter's 20-35 radii magnetodisc, assumed to be represented by Connerney et al.'s (1982) Voyager model plus a small image dipole asymmetry. Rates are energy, species, and space dependent but can average as much as a few tenths of a planetary radius per bounce period.

Hydrogen species motion in piezoelectrics: A quasi-elastic neutron scattering study

NASA Astrophysics Data System (ADS)

Alvine, K. J.; Tyagi, M.; Brown, C. M.; Udovic, T. J.; Jenkins, T.; Pitman, S. G.

2012-03-01

Hydrogen is known to damage or degrade piezoelectric materials, at low pressure for ferroelectric random access memory applications, and at high pressure for hydrogen-powered vehicle applications. The piezoelectric degradation is in part governed by the motion of hydrogen species within the piezoelectric materials. We present here quasi-elastic neutron scattering (QENS) measurements of the local hydrogen species motion within lead zirconate titanate (PZT) and barium titanate (BTO) on samples charged by exposure to high-pressure gaseous hydrogen (≈17 MPa). Neutron vibrational spectroscopy (NVS) studies of the hydrogen-enhanced vibrational modes are presented as well. Results are discussed in the context of theoretically predicted interstitial hydrogen lattice sites and compared to comparable bulk diffusion studies of hydrogen diffusion in lead zirconate titanate.

Unveiling the mechanism of the promising two-dimensional photoswitch - Hemithioindigo

NASA Astrophysics Data System (ADS)

Li, Donglin; Yang, Yonggang; Li, Chaozheng; Liu, Yufang

2018-07-01

The control of internal molecular motions by outside stimuli is a decisive task in the construction of functional molecules and molecular machines. Light-induced intramolecular rotations of photoswitches have attracted increasing research interests because of the high stability and high reversibility of photoswitches. Recently, Henry et al. reported an unprecedented two-dimensional controlled photoswitch, the hemithioindigo (HTI) derivative Z1, whose single bond rotation in dimethyl sulphoxide (DMSO) solvent and double bond rotation in cyclohexane solvent can be induced by visible light (J. Am. Chem. Soc. 2016, 138, 12,219). Here we investigate the intramolecular rotations of the HTI and Z1 in different polar solvents by time-dependent density functional theory (TDDFT) and Nonadiabatic dynamic simulations. Due to the steric hindrance between methyl and thioindigo fragment, the rotations of Z1 in the excited state are obstructed. Interestingly, the HTI exhibits two distinct rotation paths in DMSO and cyclohexane solvents at about 50 fs. The intermolecular hydrogen bonds between HTI and DMSO play an important role in the rotation of HTI in DMSO solvent. Therefore, the HTI is a more promising two-dimensional photoswitch compared with the Z1. Our finding is thus of fundamental importance to understand the mechanisms of this class of photoswitches and design complex molecular behavior.

Tree-ring cellulose exhibits several distinct intramolecular 13C signals

NASA Astrophysics Data System (ADS)

Wieloch, Thomas; Ehlers, Ina; Frank, David; Gessler, Arthur; Grabner, Michael; Yu, Jun; Schleucher, Jürgen

2017-04-01

Stable carbon isotopes are a key tool in biogeosciences. Present applications including compound-specific isotope analysis measure 13C/12C ratios (δ13C) of bulk material or of whole molecules. However, it is well known that primary metabolites also show large intramolecular 13C variation - also called isotopomer variation. This variation reflects 13C fractionation by enzyme reactions and therefore encodes metabolic information. Furthermore, δ13C must be considered an average of the intramolecular 13C distribution. Here we will present (1) methodology to analyse intramolecular 13C distributions of tree-ring cellulose by quantitative 13C NMR (Chaintreau et al., 2013, Anal Chim Acta, 788, 108-113); (2) intramolecular 13C distributions of an annually-resolved tree ring chronology (Pinus nigra, 1961-1995); (3) isotope parameters and terminology for analysis of intramolecular isotope time series; (4) a method for correcting for heterotrophic C redistribution. We will show that the intramolecular 13C distribution of tree-ring cellulose shows large variation, with differences between isotopomers exceeding 10‰Ṫhus, individual 13C isotopomers of cellulose constitute distinct 13C inputs into major global C pools such as wood and soil organic matter. When glucose units with the observed intramolecular 13C pattern are broken down along alternative catabolic pathways, it must be expected that respired CO2 with strongly differing δ13C will be released; indicating that intramolecular 13C variation affects isotope signals of atmosphere-biosphere C exchange fluxes. taking this variation into account will improve modelling of the global C cycle. Furthermore, cluster analysis shows that tree-ring glucose exhibits several independent intramolecular 13C signals, which constitute distinct ecophysiological information channels. Thus, whole-molecule 13C analysis likely misses a large part of the isotope information stored in tree rings. As we have shown for deuterium (Ehlers et al., 2015, PNAS, 112, 15585), intramolecular isotope signals allow tracing plant acclimation over centuries, and intramolecular 13C distributions will also improve our understanding of 13C signatures of global C fluxes.

Brownian Motion of Asymmetric Boomerang Colloidal Particles

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan; Sun, Kai; Wei, Qi-Huo

2014-03-01

We used video microscopy and single particle tracking to study the diffusion and local behaviors of asymmetric boomerang particles in a quasi-two dimensional geometry. The motion is biased towards the center of hydrodynamic stress (CoH) and the mean square displacements of the particles are linear at short and long times with different diffusion coefficients and in the crossover regime it is sub-diffusive. Our model based on Langevin theory shows that these behaviors arise from the non-coincidence of the CoH with the center of the body. Since asymmetric boomerangs represent a class of rigid bodies of more generals shape, therefore our findings are generic and true for any non-skewed particle in two dimensions. Both experimental and theoretical results will be discussed.

Simulation of moving flat plate with unsteady translational motion using vortex method

NASA Astrophysics Data System (ADS)

Widodo, A. F.; Zuhal, L. R.

2013-10-01

This paper presents simulation of moving flate plate with unsteady translational motion using Lagrangianmeshless numerical simulation named vortex method. The method solves Navier-Stokes equations in term of vorticity. The solving strategy is splitting the equation into diffusion and convection term to be solved separately. The diffusion term is modeled by particles strength exchange(PSE) which is the most accurate of diffusion modeling in vortex method. The convection term that represents transport of particles is calculated by time step integration of velocity. Velocity of particles is natively calculated using Biot-Savart relation but for acceleration, fastmultiple method(FMM) is employed. The simulation is validated experimentally using digital particle image velocimetry(DPIV) and the results give good agreement.

An Alternative Estimate of the Motion of the Capricorn Plate

NASA Astrophysics Data System (ADS)

Burris, S. G.; Gordon, R. G.

2013-12-01

Diffuse plate boundaries cover ~15% of Earth's surface and can exceed 1000 km in across-strike width. Deforming oceanic lithosphere in the equatorial Indian Ocean accommodates the motion between the India and Capricorn plates and serves as their mutual diffuse plate boundary. This deforming lithosphere lies between the Central Indian Ridge to the west and the Sumatra trench to the east; the plates diverge to the west of ≈74°E and converge to the east of it. Many data have shown that the pole of rotation between the India and Capricorn plates lies within this diffuse plate boundary [1,2]. Surprisingly, however, the recently estimated angular velocity in the MORVEL global set of angular velocities [3] places this pole of rotation north of prior poles by several degrees, and north of the diffuse plate boundary. The motion between the India and Capricorn plates can only be estimated indirectly by differencing the motion of the India plate relative to the Somalia plate, on the one hand, and the motion of the Capricorn plate relative to Somalia plate, on the other. While the MORVEL India-Somalia angular velocity is similar to prior estimates, the MORVEL Capricorn-Somalia pole of rotation lies northwest of its predecessors. The difference is not caused by new transform azimuth data incorporated into MORVEL or by the new application of a correction to spreading rates for outward displacement. Instead the difference appears to be caused by a few anomalous spreading rates near the northern end of the Capricorn-Somalia plate boundary along the Central Indian Ridge. Rejecting these data leads to consistency with prior results. Implications for the motion of the Capricorn plate relative to Australia will be discussed. [1] DeMets, C., R. G. Gordon, and J.-Y. Royer, 2005. Motion between the Indian, Capricorn, and Somalian plates since 20 Ma: implications for the timing and magnitude of distributed deformation in the equatorial Indian ocean, Geophys. J. Int., 161, 445-468. [2] Gordon, R. G., Royer, J.-Y., and D. F. Argus, 2008. Space geodetic test of kinematic models for the Indo-Australian composite plate, Geology, 36, 827-830, doi: 10.1130/G25089A.1. [3] DeMets, C., Gordon, R. G., & Argus, D. F., 2010. Geologically current plate motions, Geophys. J. Int., 181, 1-80, doi: 10.1111/j.1365-246X.2009.04491.x.

Non-universal tracer diffusion in crowded media of non-inert obstacles.

PubMed

Ghosh, Surya K; Cherstvy, Andrey G; Metzler, Ralf

2015-01-21

We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.

Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations.

PubMed

Wu, Hao; Noé, Frank

2011-03-01

Diffusion processes are relevant for a variety of phenomena in the natural sciences, including diffusion of cells or biomolecules within cells, diffusion of molecules on a membrane or surface, and diffusion of a molecular conformation within a complex energy landscape. Many experimental tools exist now to track such diffusive motions in single cells or molecules, including high-resolution light microscopy, optical tweezers, fluorescence quenching, and Förster resonance energy transfer (FRET). Experimental observations are most often indirect and incomplete: (1) They do not directly reveal the potential or diffusion constants that govern the diffusion process, (2) they have limited time and space resolution, and (3) the highest-resolution experiments do not track the motion directly but rather probe it stochastically by recording single events, such as photons, whose properties depend on the state of the system under investigation. Here, we propose a general Bayesian framework to model diffusion processes with nonlinear drift based on incomplete observations as generated by various types of experiments. A maximum penalized likelihood estimator is given as well as a Gibbs sampling method that allows to estimate the trajectories that have caused the measurement, the nonlinear drift or potential function and the noise or diffusion matrices, as well as uncertainty estimates of these properties. The approach is illustrated on numerical simulations of FRET experiments where it is shown that trajectories, potentials, and diffusion constants can be efficiently and reliably estimated even in cases with little statistics or nonequilibrium measurement conditions.

Bringing diffuse X-ray scattering into focus

DOE PAGES

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

2018-02-16

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Bringing diffuse X-ray scattering into focus

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

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Spatially constrained incoherent motion method improves diffusion-weighted MRI signal decay analysis in the liver and spleen

PubMed Central

Taimouri, Vahid; Afacan, Onur; Perez-Rossello, Jeannette M.; Callahan, Michael J.; Mulkern, Robert V.; Warfield, Simon K.; Freiman, Moti

2015-01-01

Purpose: To evaluate the effect of the spatially constrained incoherent motion (SCIM) method on improving the precision and robustness of fast and slow diffusion parameter estimates from diffusion-weighted MRI in liver and spleen in comparison to the independent voxel-wise intravoxel incoherent motion (IVIM) model. Methods: We collected diffusion-weighted MRI (DW-MRI) data of 29 subjects (5 healthy subjects and 24 patients with Crohn’s disease in the ileum). We evaluated parameters estimates’ robustness against different combinations of b-values (i.e., 4 b-values and 7 b-values) by comparing the variance of the estimates obtained with the SCIM and the independent voxel-wise IVIM model. We also evaluated the improvement in the precision of parameter estimates by comparing the coefficient of variation (CV) of the SCIM parameter estimates to that of the IVIM. Results: The SCIM method was more robust compared to IVIM (up to 70% in liver and spleen) for different combinations of b-values. Also, the CV values of the parameter estimations using the SCIM method were significantly lower compared to repeated acquisition and signal averaging estimated using IVIM, especially for the fast diffusion parameter in liver (CVIV IM = 46.61 ± 11.22, CVSCIM = 16.85 ± 2.160, p < 0.001) and spleen (CVIV IM = 95.15 ± 19.82, CVSCIM = 52.55 ± 1.91, p < 0.001). Conclusions: The SCIM method characterizes fast and slow diffusion more precisely compared to the independent voxel-wise IVIM model fitting in the liver and spleen. PMID:25832079

Similarities between principal components of protein dynamics and random diffusion

NASA Astrophysics Data System (ADS)

Hess, Berk

2000-12-01

Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.

Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations.

PubMed

Lin, Shiang-Tai; Maiti, Prabal K; Goddard, William A

2010-06-24

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Chelators Exhibiting Triple Fluorescence.

DTIC Science & Technology

1998-08-31

l-NN-dimethylamino-propane, forms an intramolecular 9 exciplex between the phenyl and amino end groups. The formation of an intramolecular exciplex 10...alkyl amino chains. e.g. 3-(4-cyanophenyl)-l-N.N- 21 dimethylaminopropane (CNP3NM, Fig. I b), can form intramolecular exciplexes which arise due to 2...for intramolecular exciplex formation in CNP3NM is indicated by 4 the strong. red-shifted fluorescence observed, and the complete absence of LE

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

Tuning Solvatochromism of Azo Dyes with Intramolecular Hydrogen Bonding in Solution and on Titanium Dioxide Nanoparticles

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

Zhang, Lei; Cole, Jacqueline M.; Liu, Xiaogang

2013-11-25

“Smart tuning” of optical properties in three azo dyes containing intramolecular hydrogen bonding is realized by the judicious control of solvents, when the dyes are in solution or adsorbed onto titanium dioxide nanoparticles. In solution, certain solvents destabilizing intramolecular hydrogen bonding induce a distinctive ≈70 nm “blue-shifted” absorption peak, compared with other solvents. In parallel, the optical properties of azo dye/TiO2 nanocomposites can be tuned using solvents with different hydrogen-bond accepting/donating abilities, giving insights into smart materials and dye-sensitized solar cell device design. It is proposed that intramolecular hydrogen bonding alone plays the leading role in such phenomena, which ismore » fundamentally different to other mechanisms, such as tautomerism and cis–trans isomerization, that explain the optical control of azo dyes. Hybrid density functional theory (DFT) is employed in order to trace the origin of this optical control, and these calculations support the mechanism involving intramolecular hydrogen bonding. Two complementary studies are also reported: 1H NMR spectroscopy is conducted in order to further understand the solvent effects on intramolecular hydrogen bonding; crystal structure analysis from associated research indicates the importance of intramolecular hydrogen bonding on intramolecular charge transfer.« less

Microscopic theory for dynamics in entangled polymer nanocomposites

NASA Astrophysics Data System (ADS)

Yamamoto, Umi

New microscopic theories for describing dynamics in polymer nanocomposites are developed and applied. The problem is addressed from two distinct perspectives and using two different theoretical approaches. The first half of this dissertation studies the long-time and intermediate-time dynamics of nanoparticles in entangled and unentangled polymer melts for dilute particle concentrations. Using a combination of mode-coupling, Brownian motion, and polymer physics ideas, the nanoparticle long-time diffusion coefficients is formulated in terms of multiple length-scales, packing microstructures, and spatially-resolved polymer density fluctuation dynamics. The key motional mechanism is described via the parallel relaxation of the force exerted on the particle controlled by collective polymer constraint-release and the particle self-motion. A sharp but smooth crossover from the hydrodynamic to the non-hydrodynamic regime is predicted based on the Stokes-Einstein violation ratio as a function of all the system variables. Quantitative predictions are made for the recovery of the Stokes-Einstein law, and the diffusivity in the crossover regime agrees surprisingly well with large-scale molecular dynamics simulations for all particle sizes and chain lengths studied. The approach is also extended to address intermediate-time anomalous transport of a single nanoparticle and two-particle relative diffusion. The second half of this dissertation focuses on developing a novel dynamical theory for a liquid of infinitely-thin rods in the presence of hard spherical obstacles, aiming at a technical and conceptual extension of the existing paradigm for entangled polymer dynamics. As a fundamental theoretical development, the two-component generalization of a first-principles dynamic meanfield approach is presented. The theory enforces inter-needle topological uncrossability and needlesphere impenetrability in a unified manner, leading to a generalized theory of entanglements that includes the sphere excluded volume effect. Coupled self-consistent equations for the generalized diffusion tensors are constructed, and the expressions for the transverse localization lengths and the long-time diffusion coefficients are derived. In the static sphere limit, we find the effective tube diameter is generally reduced as a function of a single confinement parameter that quantifies the number of particles penetrating into the pure-polymer tube. A preliminary extension to treat flexible chain melts has also been achieved, and shown to agree reasonably well with simulations. The anisotropic needle diffusion constants are rich functions of the length-scale ratios, needle concentration and particle volume fraction. We show that the steric blocking of the longitudinal motion causes a literal and simultaneous localization of the two diffusion channels, and entangled needles can diffuse via a modified reptation dynamics over a window of polymer concentration but the compression of the tube and the blocking of the reptation motion must be accounted for. Generalization to treat mobile spheres is also possible and fully formulated.

Emergence of complex behavior in pili-based motility in early stages of P. aeruginosa surface adaptation

NASA Astrophysics Data System (ADS)

Brill-Karniely, Yifat; Jin, Fan; Wong, Gerard C. L.; Frenkel, Daan; Dobnikar, Jure

2017-04-01

Pseudomonas aeruginosa move across surfaces by using multiple Type IV Pili (TFP), motorized appendages capable of force generation via linear extension/retraction cycles, to generate surface motions collectively known as twitching motility. Pseudomonas cells arrive at a surface with low levels of piliation and TFP activity, which both progressively increase as the cells sense the presence of a surface. At present, it is not clear how twitching motility emerges from these initial minimal conditions. Here, we build a simple model for TFP-driven surface motility without complications from viscous and solid friction on surfaces. We discover the unanticipated structural requirement that TFP motors need to have a minimal amount of effective angular rigidity in order for cells to perform the various classes of experimentally-observed motions. Moreover, a surprisingly small number of TFP are needed to recapitulate movement signatures associated with twitching: Two TFP can already produce movements reminiscent of recently observed slingshot type motion. Interestingly, jerky slingshot motions characteristic of twitching motility comprise the transition region between different types of observed crawling behavior in the dynamical phase diagram, such as self-trapped localized motion, 2-D diffusive exploration, and super-diffusive persistent motion.

Physicochemical code for quinary protein interactions in Escherichia coli

PubMed Central

Mu, Xin; Choi, Seongil; Lang, Lisa; Mowray, David; Danielsson, Jens; Oliveberg, Mikael

2017-01-01

How proteins sense and navigate the cellular interior to find their functional partners remains poorly understood. An intriguing aspect of this search is that it relies on diffusive encounters with the crowded cellular background, made up of protein surfaces that are largely nonconserved. The question is then if/how this protein search is amenable to selection and biological control. To shed light on this issue, we examined the motions of three evolutionary divergent proteins in the Escherichia coli cytoplasm by in-cell NMR. The results show that the diffusive in-cell motions, after all, follow simplistic physical−chemical rules: The proteins reveal a common dependence on (i) net charge density, (ii) surface hydrophobicity, and (iii) the electric dipole moment. The bacterial protein is here biased to move relatively freely in the bacterial interior, whereas the human counterparts more easily stick. Even so, the in-cell motions respond predictably to surface mutation, allowing us to tune and intermix the protein’s behavior at will. The findings show how evolution can swiftly optimize the diffuse background of protein encounter complexes by just single-point mutations, and provide a rational framework for adjusting the cytoplasmic motions of individual proteins, e.g., for rescuing poor in-cell NMR signals and for optimizing protein therapeutics. PMID:28536196

Investigating the effect of poly-l-lactic acid nanoparticles carrying hypericin on the flow-biased diffusive motion of HeLa cell organelles.

PubMed

Penjweini, Rozhin; Deville, Sarah; Haji Maghsoudi, Omid; Notelaers, Kristof; Ethirajan, Anitha; Ameloot, Marcel

2017-07-19

In this study, we investigate in human cervical epithelial HeLa cells the intracellular dynamics and the mutual interaction with the organelles of the poly-l-lactic acid nanoparticles (PLLA NPs) carrying the naturally occurring hydrophobic photosensitizer hypericin. Temporal and spatiotemporal image correlation spectroscopy was used for the assessment of the intracellular diffusion and directed motion of the nanocarriers by tracking the hypericin fluorescence. Using image cross-correlation spectroscopy and specific fluorescent labelling of endosomes, lysosomes and mitochondria, the NPs dynamics in association with the cell organelles was studied. Static colocalization experiments were interpreted according to the Manders' overlap coefficient. Nanoparticles associate with a small fraction of the whole-organelle population. The organelles moving with NPs exhibit higher directed motion compared to those moving without them. The rate of the directed motion drops substantially after the application of nocodazole. The random component of the organelle motions is not influenced by the NPs. Image correlation and cross-correlation spectroscopy are most appropriate to unravel the motion of the PLLA nanocarrier and to demonstrate that the rate of the directed motion of organelles is influenced by their interaction with the nanocarriers. Not all PLLA-hypericin NPs are associated with organelles. © 2017 Royal Pharmaceutical Society.

Influence of image registration on apparent diffusion coefficient images computed from free-breathing diffusion MR images of the abdomen.

PubMed

Guyader, Jean-Marie; Bernardin, Livia; Douglas, Naomi H M; Poot, Dirk H J; Niessen, Wiro J; Klein, Stefan

2015-08-01

To evaluate the influence of image registration on apparent diffusion coefficient (ADC) images obtained from abdominal free-breathing diffusion-weighted MR images (DW-MRIs). A comprehensive pipeline based on automatic three-dimensional nonrigid image registrations is developed to compensate for misalignments in DW-MRI datasets obtained from five healthy subjects scanned twice. Motion is corrected both within each image and between images in a time series. ADC distributions are compared with and without registration in two abdominal volumes of interest (VOIs). The effects of interpolations and Gaussian blurring as alternative strategies to reduce motion artifacts are also investigated. Among the four considered scenarios (no processing, interpolation, blurring and registration), registration yields the best alignment scores. Median ADCs vary according to the chosen scenario: for the considered datasets, ADCs obtained without processing are 30% higher than with registration. Registration improves voxelwise reproducibility at least by a factor of 2 and decreases uncertainty (Fréchet-Cramér-Rao lower bound). Registration provides similar improvements in reproducibility and uncertainty as acquiring four times more data. Patient motion during image acquisition leads to misaligned DW-MRIs and inaccurate ADCs, which can be addressed using automatic registration. © 2014 Wiley Periodicals, Inc.

Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking

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

Dettmer, Simon L.; Keyser, Ulrich F.; Pagliara, Stefano

In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of thesemore » methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces.« less

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%.

Effect of Varying the 1-4 Intramolecular Scaling Factor in Atomistic Simulations of Long-Chain N-alkanes with the OPLS-AA Model

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

de Almeida, Valmor F; Ye, Xianggui; Cui, Shengting

2013-01-01

A comprehensive molecular dynamics simulation study of n-alkanes using the Optimized Potential for Liquid Simulation-All Atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained bymore » successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better un-derstand the effects of reducing the scaling factor, we analyzed the variation of the torsion potential pro-file with the scaling factor, and the corresponding impact on the gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane. This relatively simple procedure thus allows for more accurate predictions of the thermo-physical properties of longer n-alkanes.« less

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

PubMed Central

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-01-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

Weak Ergodicity Breaking of Receptor Motion in Living Cells Stemming from Random Diffusivity

NASA Astrophysics Data System (ADS)

Manzo, Carlo; Torreno-Pina, Juan A.; Massignan, Pietro; Lapeyre, Gerald J.; Lewenstein, Maciej; Garcia Parajo, Maria F.

2015-01-01

Molecular transport in living systems regulates numerous processes underlying biological function. Although many cellular components exhibit anomalous diffusion, only recently has the subdiffusive motion been associated with nonergodic behavior. These findings have stimulated new questions for their implications in statistical mechanics and cell biology. Is nonergodicity a common strategy shared by living systems? Which physical mechanisms generate it? What are its implications for biological function? Here, we use single-particle tracking to demonstrate that the motion of dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN), a receptor with unique pathogen-recognition capabilities, reveals nonergodic subdiffusion on living-cell membranes In contrast to previous studies, this behavior is incompatible with transient immobilization, and, therefore, it cannot be interpreted according to continuous-time random-walk theory. We show that the receptor undergoes changes of diffusivity, consistent with the current view of the cell membrane as a highly dynamic and diverse environment. Simulations based on a model of an ordinary random walk in complex media quantitatively reproduce all our observations, pointing toward diffusion heterogeneity as the cause of DC-SIGN behavior. By studying different receptor mutants, we further correlate receptor motion to its molecular structure, thus establishing a strong link between nonergodicity and biological function. These results underscore the role of disorder in cell membranes and its connection with function regulation. Because of its generality, our approach offers a framework to interpret anomalous transport in other complex media where dynamic heterogeneity might play a major role, such as those found, e.g., in soft condensed matter, geology, and ecology.

Brownian motion under dynamic disorder: effects of memory on the decay of the non-Gaussianity parameter

NASA Astrophysics Data System (ADS)

Tyagi, Neha; Cherayil, Binny J.

2018-03-01

The increasingly widespread occurrence in complex fluids of particle motion that is both Brownian and non-Gaussian has recently been found to be successfully modeled by a process (frequently referred to as ‘diffusing diffusivity’) in which the white noise that governs Brownian diffusion is itself stochastically modulated by either Ornstein–Uhlenbeck dynamics or by two-state noise. But the model has so far not been able to account for an aspect of non-Gaussian Brownian motion that is also commonly observed: a non-monotonic decay of the parameter that quantifies the extent of deviation from Gaussian behavior. In this paper, we show that the inclusion of memory effects in the model—via a generalized Langevin equation—can rationalise this phenomenon.

Fractional Brownian motion with a reflecting wall

NASA Astrophysics Data System (ADS)

Wada, Alexander H. O.; Vojta, Thomas

2018-02-01

Fractional Brownian motion, a stochastic process with long-time correlations between its increments, is a prototypical model for anomalous diffusion. We analyze fractional Brownian motion in the presence of a reflecting wall by means of Monte Carlo simulations. Whereas the mean-square displacement of the particle shows the expected anomalous diffusion behavior ˜tα , the interplay between the geometric confinement and the long-time memory leads to a highly non-Gaussian probability density function with a power-law singularity at the barrier. In the superdiffusive case α >1 , the particles accumulate at the barrier leading to a divergence of the probability density. For subdiffusion α <1 , in contrast, the probability density is depleted close to the barrier. We discuss implications of these findings, in particular, for applications that are dominated by rare events.

A finite volume method for trace element diffusion and partitioning during crystal growth

NASA Astrophysics Data System (ADS)

Hesse, Marc A.

2012-09-01

A finite volume method on a uniform grid is presented to compute the polythermal diffusion and partitioning of a trace element during the growth of a porphyroblast crystal in a uniform matrix and in linear, cylindrical and spherical geometry. The motion of the crystal-matrix interface and the thermal evolution are prescribed functions of time. The motion of the interface is discretized and it advances from one cell boundary to next as the prescribed interface position passes the cell center. The appropriate conditions for the flux across the crystal-matrix interface are derived from discrete mass conservation. Numerical results are benchmarked against steady and transient analytic solutions for isothermal diffusion with partitioning and growth. Two applications illustrate the ability of the model to reproduce observed rare-earth element patterns in garnets (Skora et al., 2006) and water concentration profiles around spherulites in obsidian (Watkins et al., 2009). Simulations with diffusion inside the growing crystal show complex concentration evolutions for trace elements with high diffusion coefficients, such as argon or hydrogen, but demonstrate that rare-earth element concentrations in typical metamorphic garnets are not affected by intracrystalline diffusion.

Tracer diffusion in active suspensions.

PubMed

Burkholder, Eric W; Brady, John F

2017-05-01

We study the diffusion of a Brownian probe particle of size R in a dilute dispersion of active Brownian particles of size a, characteristic swim speed U_{0}, reorientation time τ_{R}, and mechanical energy k_{s}T_{s}=ζ_{a}U_{0}^{2}τ_{R}/6, where ζ_{a} is the Stokes drag coefficient of a swimmer. The probe has a thermal diffusivity D_{P}=k_{B}T/ζ_{P}, where k_{B}T is the thermal energy of the solvent and ζ_{P} is the Stokes drag coefficient for the probe. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. In competition with this steric hindrance is an enhancement driven by the activity of the swimmers. The strength of swimming relative to thermal diffusion is set by Pe_{s}=U_{0}a/D_{P}. The active contribution to the diffusivity scales as Pe_{s}^{2} for weak swimming and Pe_{s} for strong swimming, but the transition between these two regimes is nonmonotonic. When fluctuations in the probe motion decay on the time scale τ_{R}, the active diffusivity scales as k_{s}T_{s}/ζ_{P}: the probe moves as if it were immersed in a solvent with energy k_{s}T_{s} rather than k_{B}T.

Coupling of active motion and advection shapes intracellular cargo transport.

PubMed

Khuc Trong, Philipp; Guck, Jochen; Goldstein, Raymond E

2012-07-13

Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such cargo-motor motion. Active and advective transport are thus intrinsically coupled as related, yet different representations of the same underlying network structure. A reaction-advection-diffusion system is used here to show that this coupling affects the transport and localization of a passive tracer in a confined geometry. For sufficiently low diffusion, cargo localization to a target zone is optimized either by low reaction kinetics and decoupling of bound and unbound states, or by a mostly disordered cytoskeletal network with only weak directional bias. These generic results may help to rationalize subtle features of cytoskeletal networks, for example as observed for microtubules in fly oocytes.

The rate constant of a quantum-diffusion-controlled bimolecular reaction

NASA Astrophysics Data System (ADS)

Bondarev, B. V.

1986-04-01

A quantum-mechanical equation is derived in the tight-bond approximation which describes the motion and chemical interaction of a pair of species A and B when their displacement in the matrix is caused by tunnelling. Within the framework of the discrete model of random walks, definitions are given of the probability and rate constant of a reaction A + B → P (products) proceeding in a condensed medium. A method is suggested for calculating the rate constant of a quantum-diffusion-controlled bimolecular reaction. By this method, an expression is obtained for the rate constant in the stationary spherically symmetrical case. An equation for the density matrix is also proposed which describes the motion and chemical interaction of a pair of species when the quantum and classical diffusion are competitive.

Chaotic dynamics of large-scale double-diffusive convection in a porous medium

NASA Astrophysics Data System (ADS)

Kondo, Shutaro; Gotoda, Hiroshi; Miyano, Takaya; Tokuda, Isao T.

2018-02-01

We have studied chaotic dynamics of large-scale double-diffusive convection of a viscoelastic fluid in a porous medium from the viewpoint of dynamical systems theory. A fifth-order nonlinear dynamical system modeling the double-diffusive convection is theoretically obtained by incorporating the Darcy-Brinkman equation into transport equations through a physical dimensionless parameter representing porosity. We clearly show that the chaotic convective motion becomes much more complicated with increasing porosity. The degree of dynamic instability during chaotic convective motion is quantified by two important measures: the network entropy of the degree distribution in the horizontal visibility graph and the Kaplan-Yorke dimension in terms of Lyapunov exponents. We also present an interesting on-off intermittent phenomenon in the probability distribution of time intervals exhibiting nearly complete synchronization.

Detecting chaos, determining the dimensions of tori and predicting slow diffusion in Fermi-Pasta-Ulam lattices by the Generalized Alignment Index method

NASA Astrophysics Data System (ADS)

Skokos, C.; Bountis, T.; Antonopoulos, C.

2008-12-01

The recently introduced GALI method is used for rapidly detecting chaos, determining the dimensionality of regular motion and predicting slow diffusion in multi-dimensional Hamiltonian systems. We propose an efficient computation of the GALIk indices, which represent volume elements of k randomly chosen deviation vectors from a given orbit, based on the Singular Value Decomposition (SVD) algorithm. We obtain theoretically and verify numerically asymptotic estimates of GALIs long-time behavior in the case of regular orbits lying on low-dimensional tori. The GALIk indices are applied to rapidly detect chaotic oscillations, identify low-dimensional tori of Fermi-Pasta-Ulam (FPU) lattices at low energies and predict weak diffusion away from quasiperiodic motion, long before it is actually observed in the oscillations.

A Locally Adaptive Regularization Based on Anisotropic Diffusion for Deformable Image Registration of Sliding Organs

PubMed Central

Pace, Danielle F.; Aylward, Stephen R.; Niethammer, Marc

2014-01-01

We propose a deformable image registration algorithm that uses anisotropic smoothing for regularization to find correspondences between images of sliding organs. In particular, we apply the method for respiratory motion estimation in longitudinal thoracic and abdominal computed tomography scans. The algorithm uses locally adaptive diffusion tensors to determine the direction and magnitude with which to smooth the components of the displacement field that are normal and tangential to an expected sliding boundary. Validation was performed using synthetic, phantom, and 14 clinical datasets, including the publicly available DIR-Lab dataset. We show that motion discontinuities caused by sliding can be effectively recovered, unlike conventional regularizations that enforce globally smooth motion. In the clinical datasets, target registration error showed improved accuracy for lung landmarks compared to the diffusive regularization. We also present a generalization of our algorithm to other sliding geometries, including sliding tubes (e.g., needles sliding through tissue, or contrast agent flowing through a vessel). Potential clinical applications of this method include longitudinal change detection and radiotherapy for lung or abdominal tumours, especially those near the chest or abdominal wall. PMID:23899632

A locally adaptive regularization based on anisotropic diffusion for deformable image registration of sliding organs.

PubMed

Pace, Danielle F; Aylward, Stephen R; Niethammer, Marc

2013-11-01

We propose a deformable image registration algorithm that uses anisotropic smoothing for regularization to find correspondences between images of sliding organs. In particular, we apply the method for respiratory motion estimation in longitudinal thoracic and abdominal computed tomography scans. The algorithm uses locally adaptive diffusion tensors to determine the direction and magnitude with which to smooth the components of the displacement field that are normal and tangential to an expected sliding boundary. Validation was performed using synthetic, phantom, and 14 clinical datasets, including the publicly available DIR-Lab dataset. We show that motion discontinuities caused by sliding can be effectively recovered, unlike conventional regularizations that enforce globally smooth motion. In the clinical datasets, target registration error showed improved accuracy for lung landmarks compared to the diffusive regularization. We also present a generalization of our algorithm to other sliding geometries, including sliding tubes (e.g., needles sliding through tissue, or contrast agent flowing through a vessel). Potential clinical applications of this method include longitudinal change detection and radiotherapy for lung or abdominal tumours, especially those near the chest or abdominal wall.

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

NASA Astrophysics Data System (ADS)

Casuso, Ignacio; Khao, Jonathan; Chami, Mohamed; Paul-Gilloteaux, Perrine; Husain, Mohamed; Duneau, Jean-Pierre; Stahlberg, Henning; Sturgis, James N.; Scheuring, Simon

2012-08-01

For cells to function properly, membrane proteins must be able to diffuse within biological membranes. The functions of these membrane proteins depend on their position and also on protein-protein and protein-lipid interactions. However, so far, it has not been possible to study simultaneously the structure and dynamics of biological membranes. Here, we show that the motion of unlabelled membrane proteins can be characterized using high-speed atomic force microscopy. We find that the molecules of outer membrane protein F (OmpF) are widely distributed in the membrane as a result of diffusion-limited aggregation, and while the overall protein motion scales roughly with the local density of proteins in the membrane, individual protein molecules can also diffuse freely or become trapped by protein-protein interactions. Using these measurements, and the results of molecular dynamics simulations, we determine an interaction potential map and an interaction pathway for a membrane protein, which should provide new insights into the connection between the structures of individual proteins and the structures and dynamics of supramolecular membranes.

Subdiffractional tracking of internalized molecules reveals heterogeneous motion states of synaptic vesicles

PubMed Central

Morrow, Isabel C.; Harper, Callista B.

2016-01-01

Our understanding of endocytic pathway dynamics is severely restricted by the diffraction limit of light microscopy. To address this, we implemented a novel technique based on the subdiffractional tracking of internalized molecules (sdTIM). This allowed us to image anti–green fluorescent protein Atto647N-tagged nanobodies trapped in synaptic vesicles (SVs) from live hippocampal nerve terminals expressing vesicle-associated membrane protein 2 (VAMP2)–pHluorin with 36-nm localization precision. Our results showed that, once internalized, VAMP2–pHluorin/Atto647N–tagged nanobodies exhibited a markedly lower mobility than on the plasma membrane, an effect that was reversed upon restimulation in presynapses but not in neighboring axons. Using Bayesian model selection applied to hidden Markov modeling, we found that SVs oscillated between diffusive states or a combination of diffusive and transport states with opposite directionality. Importantly, SVs exhibiting diffusive motion were relatively less likely to switch to the transport motion. These results highlight the potential of the sdTIM technique to provide new insights into the dynamics of endocytic pathways in a wide variety of cellular settings. PMID:27810917

Diffusiophoresis in one-dimensional solute gradients

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

Ault, Jesse T.; Warren, Patrick B.; Shin, Sangwoo

Here, the diffusiophoretic motion of suspended colloidal particles under one-dimensional solute gradients is solved using numerical and analytical techniques. Similarity solutions are developed for the injection and withdrawal dynamics of particles into semi-infinite pores. Furthermore, a method of characteristics formulation of the diffusion-free particle transport model is presented and integrated to realize particle trajectories. Analytical solutions are presented for the limit of small particle diffusiophoretic mobility Γ p relative to the solute diffusivity D s for particle motions in both semi-infinite and finite domains. Results confirm the build up of local maxima and minima in the propagating particle front dynamics.more » The method of characteristics is shown to successfully predict particle motions and the position of the particle front, although it fails to accurately predict suspended particle concentrations in the vicinity of sharp gradients, such as at the particle front peak seen in some injection cases, where particle diffusion inevitably plays an important role. Results inform the design of applications in which the use of applied solute gradients can greatly enhance particle injection into and withdrawal from pores.« less

From quantum stochastic differential equations to Gisin-Percival state diffusion

NASA Astrophysics Data System (ADS)

Parthasarathy, K. R.; Usha Devi, A. R.

2017-08-01

Starting from the quantum stochastic differential equations of Hudson and Parthasarathy [Commun. Math. Phys. 93, 301 (1984)] and exploiting the Wiener-Itô-Segal isomorphism between the boson Fock reservoir space Γ (L2(R+ ) ⊗(Cn⊕Cn ) ) and the Hilbert space L2(μ ) , where μ is the Wiener probability measure of a complex n-dimensional vector-valued standard Brownian motion {B (t ) ,t ≥0 } , we derive a non-linear stochastic Schrödinger equation describing a classical diffusion of states of a quantum system, driven by the Brownian motion B. Changing this Brownian motion by an appropriate Girsanov transformation, we arrive at the Gisin-Percival state diffusion equation [N. Gisin and J. Percival, J. Phys. A 167, 315 (1992)]. This approach also yields an explicit solution of the Gisin-Percival equation, in terms of the Hudson-Parthasarathy unitary process and a randomized Weyl displacement process. Irreversible dynamics of system density operators described by the well-known Gorini-Kossakowski-Sudarshan-Lindblad master equation is unraveled by coarse-graining over the Gisin-Percival quantum state trajectories.

Dynamic Theory of Relativistic Electrons Stochastic Heating by Whistler Mode Waves with Application to the Earth Magnetosphere

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Tel'nikhin, A. A.; Kronberg, T. K.

2007-01-01

In the Hamiltonian approach an electron motion in a coherent packet of the whistler mode waves propagating along the direction of an ambient magnetic field is studied. The physical processes by which these particles are accelerated to high energy are established. Equations governing a particle motion were transformed in to a closed pair of nonlinear difference equations. The solutions of these equations have shown there exists the energetic threshold below that the electron motion is regular, and when the initial energy is above the threshold an electron moves stochastically. Particle energy spectra and pitch angle electron scattering are described by the Fokker-Planck-Kolmogorov equations. Calculating the stochastic diffusion of electrons due to a spectrum of whistler modes is presented. The parametric dependence of the diffusion coefficients on the plasma particle density, magnitude of wave field, and the strength of magnetic field is studies. It is shown that significant pitch angle diffusion occurs for the Earth radiation belt electrons with energies from a few keV up to a few MeV.

Pattern formation, social forces, and diffusion instability in games with success-driven motion

NASA Astrophysics Data System (ADS)

Helbing, Dirk

2009-02-01

A local agglomeration of cooperators can support the survival or spreading of cooperation, even when cooperation is predicted to die out according to the replicator equation, which is often used in evolutionary game theory to study the spreading and disappearance of strategies. In this paper, it is shown that success-driven motion can trigger such local agglomeration and may, therefore, be used to supplement other mechanisms supporting cooperation, like reputation or punishment. Success-driven motion is formulated here as a function of the game-theoretical payoffs. It can change the outcome and dynamics of spatial games dramatically, in particular as it causes attractive or repulsive interaction forces. These forces act when the spatial distributions of strategies are inhomogeneous. However, even when starting with homogeneous initial conditions, small perturbations can trigger large inhomogeneities by a pattern-formation instability, when certain conditions are fulfilled. Here, these instability conditions are studied for the prisoner’s dilemma and the snowdrift game. Furthermore, it is demonstrated that asymmetrical diffusion can drive social, economic, and biological systems into the unstable regime, if these would be stable without diffusion.

Elucidating fluctuating diffusivity in center-of-mass motion of polymer models with time-averaged mean-square-displacement tensor

NASA Astrophysics Data System (ADS)

Miyaguchi, Tomoshige

2017-10-01

There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here a method is developed to elucidate this fluctuating diffusivity from trajectory data. Time-averaged mean-square displacement (MSD), a common tool in single-particle-tracking (SPT) experiments, is generalized to a second-order tensor with which both magnitude and orientation fluctuations of the diffusivity can be clearly detected. This method is used to analyze the center-of-mass motion of four fundamental polymer models: the Rouse model, the Zimm model, a reptation model, and a rigid rodlike polymer. It is found that these models exhibit distinctly different types of magnitude and orientation fluctuations of diffusivity. This is an advantage of the present method over previous ones, such as the ergodicity-breaking parameter and a non-Gaussian parameter, because with either of these parameters it is difficult to distinguish the dynamics of the four polymer models. Also, the present method of a time-averaged MSD tensor could be used to analyze trajectory data obtained in SPT experiments.

Microstructural changes in a cementitious membrane due to the application of a DC electric field.

PubMed

Covelo, Alba; Diaz, Belen; Freire, Lorena; Novoa, X Ramon; Perez, M Consuelo

2008-07-01

The use of electromigration techniques to accelerate chloride ions motion is commonly employed to characterise the permeability of cementitious samples to chlorides, a relevant parameter in reinforced concrete corrosion. This paper is devoted to the study of microstructure's changes occurring in mortar samples when submitted to natural diffusion and migration experiments. The application of an electric field reduces testing time in about one order of magnitude with respect to natural diffusion experiments. Nevertheless, the final sample's microstructure differs in both tests. Impedance Spectroscopy is employed for real time monitoring of microstructural changes. During migration experiments the global impedance undergoes important increase in shorter period of time compared to natural diffusion tests. So, the forced motion of ions through the concrete membrane induces significant variations in the porous structure, as confirmed by Mercury Intrusion Porosimetry. After migration experiments, an important increase in the capillary pore size (10-100 nm) was detected. Conversely, no relevant variations are found after natural diffusion tests. Results presented in this work cast doubt on the significance of diffusion coefficient values obtained under accelerated conditions.

Adsorption, vibration and diffusion of oxygen on Ag(110)

NASA Astrophysics Data System (ADS)

Rawal, Takat; Hong, Sampyo; Pulkkinen, Aki; Alatalo, Matti; Rahman, Talat

2015-03-01

We have performed density functional theory calculations for the adsorption, vibration and diffusion of oxygen on Ag(110). At low coverage, O2 adsorbs at the four-fold hollow (FFH) with the molecular axis aligned along the [ 1 1 0 ] direction. The dissociation of O2 is easier along the [001] direction than along the [ 1 1 0 ] direction. For O2 species in FFH aligned along the [001] the O-O intra-molecular stretching mode is coupled with the substrate vibration and thus its dissociation can be induced by surface phonon. In addition, O diffusion barrier from FFH to next FFH along the [ 1 1 0 ] is small (0.07 eV only) but is by far larger (0.4 eV) along [001]. On the other hand, O species in the short-bride (SB) site prefers to diffuse along the [001] (to FFH) rather than along the [ 1 1 0 ] direction (to next SB). Finally, the preference of atomic oxygen to form O-Ag-O complex on Ag(110) is responsible for disordering of the surface by means of substantial lateral and vertical displacements of Ag atoms in the topmost layer. In fact, such disordering phase of Ag(110) may act as a precursor of the reconstructed phase of Ag(110). Work supported in part by NSF under Grant CHE-1310327.

Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.

Isotopic substitution of a hydrogen bond: A near infrared study of the intramolecular states in (DF)2

NASA Astrophysics Data System (ADS)

Davis, Scott; Anderson, David T.; Farrell, John T., Jr.; Nesbitt, David J.

1996-06-01

High resolution near infrared spectra of the two high frequency intramolecular modes in (DF)2 have been characterized using a slit-jet infrared spectrometer. In total, four pairs of vibration-rotation-tunneling (VRT) bands are observed, corresponding to K=0 and K=1 excitation of both the ν2 (``bound'') and ν1 (``free'') intramolecular DF stretching modes. Analysis of the rotationally resolved spectra provides vibrational origins, rotational constants, tunneling splittings and upper state predissociation lifetimes for all four states. The rotational constants indicate that the deuterated hydrogen bond contracts and bends upon intramolecular excitation, analogous to what has been observed for (HF)2. The isotope and K dependence of tunneling splittings for (HF)2 and (DF)2 in both intramolecular modes is interpreted in terms of a semiclassical 1-D tunneling model. High resolution line shape measurements reveal vibrational predissociation broadening in (DF)2: 56(2) and 3(2) MHz for the ν2 (bound) and ν1 (free) intramolecular stretching modes, respectively. This 20-fold mode specific enhancement parallels the ≥30-fold enhancement observed between analogous intramolecular modes of (HF)2, further elucidating the role of nonstatistical predissociation dynamics in such hydrogen bonded clusters.

Binary Mixtures of Particles with Different Diffusivities Demix.

PubMed

Weber, Simon N; Weber, Christoph A; Frey, Erwin

2016-02-05

The influence of size differences, shape, mass, and persistent motion on phase separation in binary mixtures has been intensively studied. Here we focus on the exclusive role of diffusivity differences in binary mixtures of equal-sized particles. We find an effective attraction between the less diffusive particles, which are essentially caged in the surrounding species with the higher diffusion constant. This effect leads to phase separation for systems above a critical size: A single close-packed cluster made up of the less diffusive species emerges. Experiments for testing our predictions are outlined.

Rotational Dynamics of Solutes with Multiple Single Bond Axes Studied by Infrared Pump-Probe Spectroscopy.

PubMed

Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

2018-02-01

To investigate the relationship between the structural degrees of freedom around a vibrational probe and the rotational relaxation process of a solute in solution, we studied the anisotropy decays of three different N 3 -derivatized amino acids in primary alcohol solutions. By performing polarization-controlled IR pump-probe measurements, we reveal that the anisotropy decays of the vibrational probe molecules in 1-alcohol solutions possess two decay components, at subpicosecond and picosecond time scales. On the basis of results showing that the fast relaxation component is insensitive to the vibrational probe molecule, we suggest that the anisotropy decay of the N 3 group on a subpicosecond time scale results from a local, small-amplitude fluctuation of the flexible vibrational probe, which does not depend on the details of its molecular structure. However, the slow relaxation component depends on the solute: with longer alkyl chains attached to the N 3 group, the anisotropy decay of the slow component is faster. Consequently, we conclude that the slow relaxation component corresponds to the reorientational motion of the N 3 group correlated with other intramolecular rotational motions (e.g., rotational motions of the neighboring alkyl chain). Our experimental results provide important insight into understanding the rotational dynamics of solutes with multiple single bond axes in solution.

Accelerated and Airy-Bloch oscillations

NASA Astrophysics Data System (ADS)

Longhi, Stefano

2016-09-01

A quantum particle subjected to a constant force undergoes an accelerated motion following a parabolic path, which differs from the classical motion just because of wave packet spreading (quantum diffusion). However, when a periodic potential is added (such as in a crystal) the particle undergoes Bragg scattering and an oscillatory (rather than accelerated) motion is found, corresponding to the famous Bloch oscillations (BOs). Here, we introduce an exactly-solvable quantum Hamiltonian model, corresponding to a generalized Wannier-Stark Hamiltonian Ĥ, in which a quantum particle shows an intermediate dynamical behavior, namely an oscillatory motion superimposed to an accelerated one. Such a novel dynamical behavior is referred to as accelerated BOs. Analytical expressions of the spectrum, improper eigenfunctions and propagator of the generalized Wannier-Stark Hamiltonian Ĥ are derived. Finally, it is shown that acceleration and quantum diffusion in the generalized Wannier-Stark Hamiltonian are prevented for Airy wave packets, which undergo a periodic breathing dynamics that can be referred to as Airy-Bloch oscillations.

The Locomotion of Mouse Fibroblasts in Tissue Culture

PubMed Central

Gail, Mitchell H.; Boone, Charles W.

1970-01-01

Time-lapse cinematography was used to investigate the motion of mouse fibroblasts in tissue culture. Observations over successive short time intervals revealed a tendency for the cells to persist in their direction of motion from one 2.5 hr time interval to the next. Over 5.0-hr time intervals, however, the direction of motion appeared random. This fact suggested that D, the diffusion constant of a random walk model, might serve to characterize cellular motility if suitably long observation times were used. We therefore investigated the effect of “persistence” on the pure random walk model, and we found theoretically and confirmed experimentally that the motility of a persisting cell could indeed be characterized by an augmented diffusion constant, D*. A method for determining confidence limits on D* was also developed. Thus a random walk model, modified to comprehend the persistence effect, was found to describe the motion of fibroblasts in tissue culture and to provide a numerical measure of cellular motility. PMID:5531614

Non-equilibrium forces drive the anomalous diffusion of telomeres in the nucleus of mammalian cells

NASA Astrophysics Data System (ADS)

Stadler, Lorenz; Weiss, Matthias

2017-11-01

Telomeres are vital nucleotide sequences at both ends of each chromosome, and their motion reports on the local dynamics of decondensed chromatin in the nucleus of interphase cells. Here, we show that the previously reported subdiffusive motion of telomeres is driven by non-equilibrium cytoskeletal forces. In particular, breaking down microtubules leads to a significantly reduced generalized diffusion coefficient of telomeres. This translates into a markedly reduced effective temperature in the stochastic forces that govern the telomeres’ random walk. Moreover, telomere motion in cells that lack microtubules is well described by the monomer dynamics of a Rouse polymer that is embeddded in a viscoelastic medium. In contrast, active cytoskeletal forces in untreated cells override the environment’s elastic contributions, resulting in the well-known scaling for conventional Rouse dynamics in viscous media. Our data highlight that even subdiffusive motion in cells in most cases may not be a simple thermal transport process but rather is driven by non-equilibrium events.

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

NASA Astrophysics Data System (ADS)

Powers, Thomas R.; Wolgemuth, Charles W.; Goldstein, Raymond E.

1999-11-01

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. The competition between twist diffusion and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist-bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.

Exponential stability of impulsive stochastic genetic regulatory networks with time-varying delays and reaction-diffusion

DOE PAGES

Cao, Boqiang; Zhang, Qimin; Ye, Ming

2016-11-29

We present a mean-square exponential stability analysis for impulsive stochastic genetic regulatory networks (GRNs) with time-varying delays and reaction-diffusion driven by fractional Brownian motion (fBm). By constructing a Lyapunov functional and using linear matrix inequality for stochastic analysis we derive sufficient conditions to guarantee the exponential stability of the stochastic model of impulsive GRNs in the mean-square sense. Meanwhile, the corresponding results are obtained for the GRNs with constant time delays and standard Brownian motion. Finally, an example is presented to illustrate our results of the mean-square exponential stability analysis.

Surge dynamics coupled to pore-pressure evolution in debris flows

USGS Publications Warehouse

Savage, S.B.; Iverson, R.M.; ,

2003-01-01

Temporally and spatially varying pore-fluid pressures exert strong controls on debris-flow motion by mediating internal and basal friction at grain contacts. We analyze these effects by deriving a one-dimensional model of pore-pressure diffusion explicitly coupled to changes in debris-flow thickness. The new pore-pressure equation is combined with Iverson's (1997) extension of the depth-averaged Savage-Hutter (1989, 1991) granular avalanche equations to predict motion of unsteady debris-flow surges with evolving pore-pressure distributions. Computational results illustrate the profound effects of pore-pressure diffusivities on debris-flow surge depths and velocities. ?? 2003 Millpress,.

Physics of ultra-high bioproductivity in algal photobioreactors

NASA Astrophysics Data System (ADS)

Greenwald, Efrat; Gordon, Jeffrey M.; Zarmi, Yair

2012-04-01

Cultivating algae at high densities in thin photobioreactors engenders time scales for random cell motion that approach photosynthetic rate-limiting time scales. This synchronization allows bioproductivity above that achieved with conventional strategies. We show that a diffusion model for cell motion (1) accounts for high bioproductivity at irradiance values previously deemed restricted by photoinhibition, (2) predicts the existence of optimal culture densities and their dependence on irradiance, consistent with available data, (3) accounts for the observed degree to which mixing improves bioproductivity, and (4) provides an estimate of effective cell diffusion coefficients, in accord with independent hydrodynamic estimates.

On the motion of viscous fluids in the presence of diffusion

NASA Astrophysics Data System (ADS)

Secchi, Paolo

1988-01-01

The flow of a viscous incompressible two-component fluid with Fick's-law diffusion is investigated analytically. The existence of a unique global solution for small values of the diffusion coefficient (lambda) is proved for two-dimensional flow. The two- and three-dimensional solutions are also shown to converge toward the solutions of the Navier-Stokes equations for inhomogeneous fluids as lambda approaches zero.

Analysis of Bacteriophage Motion Through a Non-Static Medium

NASA Astrophysics Data System (ADS)

Dickey, Samuel A.

In this work, I investigated the motion of bacteriophages (phages) through their mucosal environment. Recently, biologists here at San Diego State University have proposed a model in which phages move sub-diffusively through mucosal fibers in their hunt for bacteria to prey upon. Through a Hoc protein located upon the capsid of the wild type phages, these phages are allowed to bind to mucosal fibers, and extend the amount of time spent in a single location hunting for bacteria. Contrarily, the delta hoc phages are unable to. The ability of the wild type phages to attach itself to mucosal fibers is what enables its subdiffusive behavior. This study investigates the diffusive behavior of these phages in different mucus concentrations. It expands on previous studies in which only short tracks could be observed. In the study at hand, phages are imaged in a highly doped optical fiber with varying concentrations of mucus present in solution. Through rigorous image processing techniques, trajectories of these phages are created with a minimized noise level. We developed code that created position-versus-time files for each phage present in the experimental data. These files were then further analyzed. The sub-diffusive behavior is investigated via mean squared displacement versus time. The diffusive exponent can be obtained from fits to these data. For large enough time intervals, I always obtained an exponent of one for space and time averaged data. This indicates that the diffusion is normal, or sub-diffusive of the CTRW type. CTRW sub-diffusive motion is characterized by waiting times that resemble a power law distribution and have long tails. I investigate these stuck time distributions, however am unable to determine if a power law or exponential fits the data best. Moreover, the distribution gives the same power law exponent for phages moving through water, or mucus, for wild type and delta hoc phages. These exponents would predict super-diffusive instead of sub-diffusive behavior. We conclude that many of these problems result from the small amount of data available to us and the still primitive conditions of the setup at the time the data were collected.

Steady motion of skyrmions and domains walls under diffusive spin torques

NASA Astrophysics Data System (ADS)

Elías, Ricardo Gabriel; Vidal-Silva, Nicolas; Manchon, Aurélien

2017-03-01

We explore the role of the spin diffusion of conducting electrons in two-dimensional magnetic textures (domain walls and skyrmions) with spatial variation of the order of the spin precession length λex. The effect of diffusion reflects in four additional torques that are third order in spatial derivatives of magnetization and bilinear in λex and in the nonadiabatic parameter β'. In order to study the dynamics of the solitons when these diffusive torques are present, we derive the Thiele equation in the limit of steady motion and we compare the results with the nondiffusive limit. When considering a homogenous current these torques increase the longitudinal velocity of transverse domain walls of width Δ by a factor (λex/Δ)2(α/3), α being the magnetic damping constant. In the case of single skyrmions with core radius r0these new contributions tend to increase the Magnus effect in an amount proportional to (λex/r0) 2(1 +2 α β') .

Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

NASA Astrophysics Data System (ADS)

Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

2017-04-01

DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

REPRESENTATION OF ATMOSPHERIC MOTION IN MODELS OF REGIONAL-SCALE AIR POLLUTION

EPA Science Inventory

A method is developed for generating ensembles of wind fields for use in regional scale (1000 km) models of transport and diffusion. The underlying objective is a methodology for representing atmospheric motion in applied air pollution models that permits explicit treatment of th...

Analytical treatment of particle motion in circularly polarized slab-mode wave fields

NASA Astrophysics Data System (ADS)

Schreiner, Cedric; Vainio, Rami; Spanier, Felix

2018-02-01

Wave-particle interaction is a key process in particle diffusion in collisionless plasmas. We look into the interaction of single plasma waves with individual particles and discuss under which circumstances this is a chaotic process, leading to diffusion. We derive the equations of motion for a particle in the fields of a magnetostatic, circularly polarized, monochromatic wave and show that no chaotic particle motion can arise under such circumstances. A novel and exact analytic solution for the equations is presented. Additional plasma waves lead to a breakdown of the analytic solution and chaotic particle trajectories become possible. We demonstrate this effect by considering a linearly polarized, monochromatic wave, which can be seen as the superposition of two circularly polarized waves. Test particle simulations are provided to illustrate and expand our analytical considerations.

Fractional Brownian motion with a reflecting wall.

PubMed

Wada, Alexander H O; Vojta, Thomas

2018-02-01

Fractional Brownian motion, a stochastic process with long-time correlations between its increments, is a prototypical model for anomalous diffusion. We analyze fractional Brownian motion in the presence of a reflecting wall by means of Monte Carlo simulations. Whereas the mean-square displacement of the particle shows the expected anomalous diffusion behavior 〈x^{2}〉∼t^{α}, the interplay between the geometric confinement and the long-time memory leads to a highly non-Gaussian probability density function with a power-law singularity at the barrier. In the superdiffusive case α>1, the particles accumulate at the barrier leading to a divergence of the probability density. For subdiffusion α<1, in contrast, the probability density is depleted close to the barrier. We discuss implications of these findings, in particular, for applications that are dominated by rare events.

Imaging of optically diffusive media by use of opto-elastography

NASA Astrophysics Data System (ADS)

Bossy, Emmanuel; Funke, Arik R.; Daoudi, Khalid; Tanter, Mickael; Fink, Mathias; Boccara, Claude

2007-02-01

We present a camera-based optical detection scheme designed to detect the transient motion created by the acoustic radiation force in elastic media. An optically diffusive tissue mimicking phantom was illuminated with coherent laser light, and a high speed camera (2 kHz frame rate) was used to acquire and cross-correlate consecutive speckle patterns. Time-resolved transient decorrelations of the optical speckle were measured as the results of localised motion induced in the medium by the radiation force and subsequent propagating shear waves. As opposed to classical acousto-optic techniques which are sensitive to vibrations induced by compressional waves at ultrasonic frequencies, the proposed technique is sensitive only to the low frequency transient motion induced in the medium by the radiation force. It therefore provides a way to assess both optical and shear mechanical properties.

Intravoxel Incoherent Motion in Normal Pituitary Gland: Initial Study with Turbo Spin-Echo Diffusion-Weighted Imaging.

PubMed

Kamimura, K; Nakajo, M; Fukukura, Y; Iwanaga, T; Saito, T; Sasaki, M; Fujisaki, T; Takemura, A; Okuaki, T; Yoshiura, T

2016-12-01

DWI with conventional single-shot EPI of the pituitary gland is hampered by strong susceptibility artifacts. Our purpose was to evaluate the feasibility of intravoxel incoherent motion assessment by using DWI based on TSE of the normal anterior pituitary lobe. The intravoxel incoherent motion parameters, including the true diffusion coefficient (D), the perfusion fraction (f), and the pseudo-diffusion coefficient (D*), were obtained with TSE-DWI in 5 brain regions (the pons, the WM and GM of the vermis, and the genu and splenium of the corpus callosum) in 8 healthy volunteers, and their agreement with those obtained with EPI-DWI was evaluated by using the intraclass correlation coefficient. The 3 intravoxel incoherent motion parameters in the anterior pituitary lobe were compared with those in the brain regions by using the Dunnett test. The agreement between TSE-DWI and EPI-DWI was moderate (intraclass correlation coefficient = 0.571) for D, substantial (0.699) for f', but fair (0.405) for D*. D in the anterior pituitary lobe was significantly higher than in the 5 brain regions (P < .001). The f in the anterior pituitary lobe was significantly higher than in the 5 brain regions (P < .001), except for the vermian GM. The pituitary D* was not significantly different from that in the 5 brain regions. Our results demonstrated the feasibility of intravoxel incoherent motion assessment of the normal anterior pituitary lobe by using TSE-DWI. High D and f values in the anterior pituitary lobe were thought to reflect its microstructural and perfusion characteristics. © 2016 by American Journal of Neuroradiology.

Zooplankton can actively adjust their motility to turbulent flow

PubMed Central

Michalec, François-Gaël; Fouxon, Itzhak

2017-01-01

Calanoid copepods are among the most abundant metazoans in the ocean and constitute a vital trophic link within marine food webs. They possess relatively narrow swimming capabilities, yet are capable of significant self-locomotion under strong hydrodynamic conditions. Here we provide evidence for an active adaptation that allows these small organisms to adjust their motility in response to background flow. We track simultaneously and in three dimensions the motion of flow tracers and planktonic copepods swimming freely at several intensities of quasi-homogeneous, isotropic turbulence. We show that copepods synchronize the frequency of their relocation jumps with the frequency of small-scale turbulence by performing frequent relocation jumps of low amplitude that seem unrelated to localized hydrodynamic signals. We develop a model of plankton motion in turbulence that shows excellent quantitative agreement with our measurements when turbulence is significant. We find that, compared with passive tracers, active motion enhances the diffusion of organisms at low turbulence intensity whereas it dampens diffusion at higher turbulence levels. The existence of frequent jumps in a motion that is otherwise dominated by turbulent transport allows for the possibility of active locomotion and hence to transition from being passively advected to being capable of controlling diffusion. This behavioral response provides zooplankton with the capability to retain the benefits of self-locomotion despite turbulence advection and may help these organisms to actively control their distribution in dynamic environments. Our study reveals an active adaptation that carries strong fitness advantages and provides a realistic model of plankton motion in turbulence. PMID:29229858

Effects of configurational changes on molecular dynamics in polyvinylidene fluoride and poly(vinylidene fluoride-trifluoroethylene) ferroelectric polymers

DOE PAGES

Jalarvo, N.; Pramanick, A.; Do, C.; ...

2015-08-28

Here, we present a comparative study of proton dynamics in unpoled non-ferroelectric polymer polyvinylidene fluoride (PVDF) and in its trifluoroethylene containing ferroelectric copolymer (with 70/30 molar proportion), using quasi-elastic neutron scattering. The neutron data reveal the existence of two distinct types of molecular motions in the temperature range investigated. Moreover, the slower motion, which is characterized in details here, is ascribed to protons jump diffusion along the polymeric carbon chains, while the faster motion could be attributed to localized rotational motion of methylene groups. At temperatures below the Curie point (T-c similar to 385 K) of the composite polymer, themore » slower diffusive mode experiences longer relaxation times in the ferroelectric blend than in the bare PVDF, although the net corresponding diffusion coefficient remains comparatively the same in both polymers with characteristic activation energy of E-A approximate to 27-33 kJ/mol. This arises because of a temperature dependent jump length r(0), which we observe to be effectively longer in the copolymer, possibly due to the formation of ordered ferroelectric domains below Tc. Above Tc, there is no appreciable difference in r(0) between the two systems. Our observation directly relates the known dependence of Tc on molar ratio to changes in r(0), providing fundamental insight into the ferroelectric properties of PVDF-based copolymers.« less

E. coli chemotaxis and super-diffusion

NASA Astrophysics Data System (ADS)

Dobnikar, Jure; Matthäus, Franziska; Jagodic, Marko

2010-03-01

The bacteria E. coli actively propel by switching between clockwise and anti-clockwise rotation of the flagella attached to their cell membranes. This results in two modes of motion: tumbling and swimming. The switching between the two modes is coupled to the ligand sensing through the chemotactic signalling pathway inside the cell. We modelled the signalling pathway and performed numerical simulations of the chemotactic motion of a large number of E. coli bacteria under various external conditions. We have shown that under certain conditions the thermal noise in the level of receptor-bound CheR (an enzyme responsible for methylation of the receptor sites) leads to super-diffusive behaviour (L'evy walk) which is advantageous for the bacterial populations in environments with scarce food. Exerting external pressure we might observe evolution of the wild-type to the super-diffusive populations.

Electric-field noise from carbon-adatom diusion on a Au(110) surface: first-principles calculations and experiments

NASA Astrophysics Data System (ADS)

Sadeghpour, Hossein; Kim, Eunja; Safavi-Naini, Arghavan; Weck, Philippe; Hite, Dustin; McKay, Kyle; Pappas, David

2017-04-01

The decoherence of trapped-ion quantum gates due to heating of their motional modes is a fundamental science and engineering challenge. Mitigating this noise, is fundamental to efficient and scalable operations in ion microtraps. To understand heating at the trap-electrode surfaces, we investigate the possible source of noise by focusing on the diffusion of carbon-containing adsorbates onto the Au(110) surface. Using density functional theory and detailed scanning probe microscopy, we show that the diffusive motion of carbon adatom on gold surface significantly affect the energy landscape and adatom dipole moment variation. A model for the diffusion noise, which varies quadratically with the variation of the dipole moment, qualitatively reproduces the measured noise spectrum, and the estimate of the noise spectral density is in accord with measured values.

Diffusion-weighted imaging in pediatric body MR imaging: principles, technique, and emerging applications.

PubMed

Chavhan, Govind B; Alsabban, Zehour; Babyn, Paul S

2014-01-01

Diffusion-weighted (DW) imaging is an emerging technique in body imaging that provides indirect information about the microenvironment of tissues and lesions and helps detect, characterize, and follow up abnormalities. Two main challenges in the application of DW imaging to body imaging are the decreased signal-to-noise ratio of body tissues compared with neuronal tissues due to their shorter T2 relaxation time, and image degradation related to physiologic motion (eg, respiratory motion). Use of smaller b values and newer motion compensation techniques allow the evaluation of anatomic structures with DW imaging. DW imaging can be performed as a breath-hold sequence or a free-breathing sequence with or without respiratory triggering. Depending on the mobility of water molecules in their microenvironment, different normal tissues have different signals at DW imaging. Some normal tissues (eg, lymph nodes, spleen, ovarian and testicular parenchyma) are diffusion restricted, whereas others (eg, gallbladder, corpora cavernosa, endometrium, cartilage) show T2 shine-through. Epiphyses that contain fatty marrow and bone cortex appear dark on both DW images and apparent diffusion coefficient maps. Current and emerging applications of DW imaging in pediatric body imaging include tumor detection and characterization, assessment of therapy response and monitoring of tumors, noninvasive detection and grading of liver fibrosis and cirrhosis, detection of abscesses, and evaluation of inflammatory bowel disease. RSNA, 2014

Nanoscopic dynamics in hybrid hydroxyapatite-CTAB composite

NASA Astrophysics Data System (ADS)

Dubey, P. S.; Sharma, V. K.; Mitra, S.; Verma, G.; Hassan, P. A.; Dutta, B.; Johnson, M.; Mukhopadhyay, R.

2017-06-01

Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. HAp nanoparticles were synthesized by the co-precipitation method using cetyltrimethylammonium bromide (CTAB) micelles as a template and are characterized using x-ray diffraction, electron microscopy, and thermal gravimetric measurements. Transmission electron microscope (TEM) demonstrates the formation of rod-shaped HAp. Dynamics of CTAB in HAp-CTAB composite as studied by using quasielastic neutron scattering (QENS) technique is reported here. HAp-CTAB composite provides an ideal system for studying the dynamics of CTAB micelles without any aqueous media. QENS data indicate that the observed dynamics are reminiscent of localized motions in ionic micellar systems, consisting of segmental and fast torsional motions. Segmental dynamics has been described with a model, in which hydrogen atoms in the alkyl chain undergoes localized translation diffusion and the CH3 unit associated with the head group undergo 3-fold jump rotation. Within this model, the hydrogen atoms in the alkyl chain undergo diffusion within spherical domains having different radii and diffusivities. A simple linear distribution of the radius and diffusivity has been assumed, in which the CH2 unit nearest to the head group has the least value and the ones furthest from the head group, that is, at the end of the alkyl chain has the largest value. The fast torsional motion is described by a 2-fold jump rotation model. Quantitative estimate of the different parameters characterizing various dynamical motions active within the time scale of the instrument is also presented. We have provided a detailed description of the observed dynamical features in hybrid HAp-CTAB composite, a potential candidate for biomedical applications.

Modeling persistence of motion in a crowded environment: The diffusive limit of excluding velocity-jump processes

NASA Astrophysics Data System (ADS)

Gavagnin, Enrico; Yates, Christian A.

2018-03-01

Persistence of motion is the tendency of an object to maintain motion in a direction for short time scales without necessarily being biased in any direction in the long term. One of the most appropriate mathematical tools to study this behavior is an agent-based velocity-jump process. In the absence of agent-agent interaction, the mean-field continuum limit of the agent-based model (ABM) gives rise to the well known hyperbolic telegraph equation. When agent-agent interaction is included in the ABM, a strictly advective system of partial differential equations (PDEs) can be derived at the population level. However, no diffusive limit of the ABM has been obtained from such a model. Connecting the microscopic behavior of the ABM to a diffusive macroscopic description is desirable, since it allows the exploration of a wider range of scenarios and establishes a direct connection with commonly used statistical tools of movement analysis. In order to connect the ABM at the population level to a diffusive PDE at the population level, we consider a generalization of the agent-based velocity-jump process on a two-dimensional lattice with three forms of agent interaction. This generalization allows us to take a diffusive limit and obtain a faithful population-level description. We investigate the properties of the model at both the individual and population levels and we elucidate some of the models' key characteristic features. In particular, we show an intrinsic anisotropy inherent to the models and we find evidence of a spontaneous form of aggregation at both the micro- and macroscales.

Intramolecular addition of benzylic radicals onto ketenimines. Synthesis of 2-alkylindoles.

PubMed

Alajarín, Mateo; Vidal, Angel; Ortín, María-Mar

2003-12-07

The inter- and intramolecular addition of free radicals onto ketenimines is studied. All the attempts to add intermolecularly several silicon, oxygen or carbon centered radicals to N-(4-methylphenyl)-C,C-diphenyl ketenimine were unsuccessful. In contrast, the intramolecular addition of benzylic radicals, generated from xanthates, onto the central carbon of a ketenimine function with its N atom linked to the ortho position of the aromatic ring occurred under a variety of reaction conditions. These intramolecular cyclizations provide a novel radical-mediated synthesis of 2-alkylindoles.

Local structure in anisotropic systems determined by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Komolkin, Andrei V.; Maliniak, Arnold

In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4'-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, gm2(z1 2, d1 2) and g12(Z1 2, D1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the motional amplitude in the chain. Absence of long range order was confirmed, a feature typical for a nematic liquid crystal.

Intramolecular electrocatalysis of 8-oxo-guanine oxidation: secondary structure control of electron transfer in osmium-labeled oligonucleotides.

PubMed

Holmberg, Rebecca C; Tierney, Mark T; Ropp, Patricia A; Berg, Eric E; Grinstaff, Mark W; Thorp, H Holden

2003-10-06

A phosphoramidite containing Os(bpy)(3)(2+) (Os; bpy, 2,2'-bipyridine) with a three-carbon linker was synthesized and used to prepare oligonucleotides with the Os redox catalyst appended to the 5'-end. The electrogenerated Os(III) is capable of oxidizing 7,8-dihydro-8-oxo-guanine (8G), but 8G is not electrochemically reactive at indium tin oxide electrodes because of poor electrode kinetics for the direct reaction. The hairpin-forming oligonucleotide Os-5'-ATG TCA GAT TAG CAG GCC TGA CAT 8G was synthesized and characterized by thermal denaturation and native gel electrophoresis both in the hairpin form and when hybridized to its Watson-Crick complement. The redox potential in both forms of the appended Os(III/II) couple was 0.63 V (all potentials vs Ag/AgCl), which is identical to that for the free complex. The diffusion coefficients of the hairpin form (10.2 x 10(-)(7) cm(2)/s) and the duplex form (8.7 x 10(-)(7) cm(2)/s) were consistent with values expected from studies of noncovalently bound redox labels, which suggest that the measured diffusion coefficient should be that of the appended DNA molecule. The oligonucleotide was designed such that in the duplex form, the 8G is far from the Os(III/II) couple, but in the hairpin form, the 8G is situated close to the redox center. For the duplex form, cyclic voltammetry studies showed that mediated oxidation of the 8G nucleobase occurred only through bimolecular reaction of the electrogenerated Os(III) of one duplex with the 8G of another duplex. However, in the hairpin form, intramolecular electron transfer from 8G to Os(III) in the same molecule was apparent in both chronoamperometry and cyclic voltammetry.

Detection of Liposome Membrane Viscosity Perturbations with Ratiometric Molecular Rotors

PubMed Central

Nipper, Matthew E.; Dakanali, Marianna; Theodorakis, Emmanuel

2011-01-01

Molecular rotors are a form of fluorescent intramolecular charge-transfer complexes that can undergo intramolecular twisting motion upon photoexcitation. Twisted-state formation leads to non-radiative relaxation that competes with fluorescence emission. In bulk solutions, these molecules exhibit a viscosity-dependent quantum yield. On the molecular scale, the fluorescence emission is a function of the local free volume, which in turn is related to the local microviscosity. Membrane viscosity, and the inverse; fluidity, are characteristic terms used to describe the ease of movement withing the membrane. Often, changes in membrane viscosity govern intracellular processes and are indicative of a disease state. Molecular rotors have been used to investigate viscosity changes in liposomes and cells, but accuracy is affected by local concentration gradients and sample optical properties. We have developed self-calibrating ratiometric molecular rotors to overcome this challenge and integrated the new molecules into a DLPC liposome model exposed to the membrane-fluidizing agent propanol. We show that the ratiometric emission intensity linearly decreases with the pentanol exposure and that the ratiometric intensity is widely independent of the total liposome concentration. Conversely, dye concentration inside liposomes influences the sensitivity of the system. We suggest that the new self-calibrating dyes can be used for real-time viscosity sensing in liposome systems with the advantages of lifetime measurements, but with low-cost steady-state instrumentation. PMID:21354253

Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode.

PubMed

Bastida, Adolfo; Zúñiga, José; Requena, Alberto; Miguel, Beatriz; Candela, María Emilia; Soler, Miguel Angel

2016-01-21

Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.

Critical forces for actin filament buckling and force transmission influence transport in actomyosin networks

NASA Astrophysics Data System (ADS)

Stam, Samantha; Gardel, Margaret

Viscoelastic networks of biopolymers coordinate the motion of intracellular objects during transport. These networks have nonlinear mechanical properties due to events such as filament buckling or breaking of cross-links. The influence of such nonlinear properties on the time and length scales of transport is not understood. Here, we use in vitro networks of actin and the motor protein myosin II to clarify how intracellular forces regulate active diffusion. We observe two transitions in the mean-squared displacement of cross-linked actin with increasing motor concentration. The first is a sharp transition from initially subdiffusive to diffusive-like motion that requires filament buckling but does not cause net contraction of the network. Further increase of the motor density produces a second transition to network rupture and ballistic actin transport. This corresponds with an increase in the correlation of motion and thus may be caused when forces propagate far enough for global motion. We conclude that filament buckling and overall network contraction require different amounts of force and produce distinct transport properties. These nonlinear transitions may act as mechanical switches that can be turned on to produce observed motion within cells.

Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles

NASA Astrophysics Data System (ADS)

Stefferson, Michael W.; Norris, Samantha L.; Vernerey, Franck J.; Betterton, Meredith D.; E Hough, Loren

2017-08-01

Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Examples include membrane proteins or lipids with some entry and diffusion within lipid domains and proteins that can enter into membraneless organelles or compartments such as the nucleolus. Using a lattice model, we studied the diffusive movement of tracer particles which bind to soft obstacles, allowing tracers and obstacles to occupy the same lattice site. For sticky obstacles, bound tracer particles are immobile, while for slippery obstacles, bound tracers can hop without penalty to adjacent obstacles. In both models, binding significantly alters tracer motion. The type and degree of motion while bound is a key determinant of the tracer mobility: slippery obstacles can allow nearly unhindered diffusion, even at high obstacle filling fraction. To mimic compartmentalization in a cell, we examined how obstacle size and a range of bound diffusion coefficients affect tracer dynamics. The behavior of the model is similar in two and three spatial dimensions. Our work has implications for protein movement and interactions within cells.

MRI-based staging of hepatic fibrosis: Comparison of intravoxel incoherent motion diffusion-weighted imaging with magnetic resonance elastography.

PubMed

Ichikawa, Shintaro; Motosugi, Utaroh; Morisaka, Hiroyuki; Sano, Katsuhiro; Ichikawa, Tomoaki; Enomoto, Nobuyuki; Matsuda, Masanori; Fujii, Hideki; Onishi, Hiroshi

2015-07-01

To evaluate the use of intravoxel incoherent motion (IVIM) imaging for staging hepatic fibrosis, and compare its staging ability with that of magnetic resonance elastography (MRE). This study included 129 patients with pathologically staged liver fibrosis, and 53 patients with healthy livers. All patients underwent both MRE and IVIM imaging. Four diffusivity indices were calculated with 11 b-values; slow diffusion coefficient related to molecular diffusion (D), fast diffusion coefficient related to perfusion in micro-vessels (D*), perfusion-related diffusion fraction (f), and apparent diffusion coefficient (ADC). Receiver operating characteristic curve analysis was performed to determine the accuracy of IVIM imaging and MRE for staging hepatic fibrosis. D*, f, and ADC values decreased significantly with fibrosis stage (P < 0.0124), and liver stiffness increased (P < 0.0001). The Az value of MRE was significantly higher than that of D* for all fibrosis stages (D* vs. MRE for ≥ F1, 0.851 vs. 0.992 [P < 0.0001]; ≥ F2, 0.898 vs. 0.998 [P = 0.0003]; ≥ F3, 0.904 vs. 0.995 [P = 0.0004]; F4, 0.885 vs. 0.996 [P < 0.0001]). IVIM imaging is a useful technique for evaluating hepatic fibrosis, but MRE is better able to discriminate fibrosis stages than IVIM imaging. © 2014 Wiley Periodicals, Inc.

Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

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

Wall, Michael E.

X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

MRI assessment of the thigh musculature in dermatomyositis and healthy subjects using diffusion tensor imaging, intravoxel incoherent motion and dynamic DTI.

PubMed

Sigmund, E E; Baete, S H; Luo, T; Patel, K; Wang, D; Rossi, I; Duarte, A; Bruno, M; Mossa, D; Femia, A; Ramachandran, S; Stoffel, D; Babb, J S; Franks, A; Bencardino, J

2018-06-04

Dermatomyositis (DM) is an idiopathic inflammatory myopathy involving severe debilitation in need of diagnostics. We evaluated the proximal lower extremity musculature with diffusion tensor imaging (DTI), intravoxel incoherent motion (IVIM) and dynamic DTI in DM patients and controls and compared with standard clinical workup.  METHODS: In this IRB-approved, HIPAA-compliant study with written informed consent, anatomical, Dixon fat/water and diffusion imaging were collected in bilateral thigh MRI of 22 controls and 27 DM patients in a 3T scanner. Compartments were scored on T1/T2 scales. Single voxel dynamic DTI metrics in quadriceps before and after 3-min leg exercise were measured. Spearman rank correlation and mixed model analysis of variance/covariance (ANOVA/ANCOVA) were used to correlate with T1 and T2 scores and to compare patients with controls. DM patients showed significantly lower pseudo-diffusion and volume in quadriceps than controls. All subjects showed significant correlation between T1 score and signal-weighted fat fraction; tissue diffusion and pseudo-diffusion varied significantly with T1 and T2 score in patients. Radial and mean diffusion exercise response in patients was significantly higher than controls. Static and dynamic diffusion imaging metrics show correlation with conventional imaging scores, reveal spatial heterogeneity, and provide means to differentiate dermatomyositis patients from controls. • Diffusion imaging shows regional differences between thigh muscles of dermatomyositis patients and controls. • Signal-weighted fat fraction and diffusion metrics correlate with T1/T2 scores of disease severity. • Dermatomyositis patients show significantly higher radial diffusion exercise response than controls.

Fractional phenomenology of cosmic ray anomalous diffusion

NASA Astrophysics Data System (ADS)

Uchaikin, V. V.

2013-11-01

We review the evolution of the cosmic ray diffusion concept from the ordinary (Einstein) model of Brownian motion to the fractional models that appeared in the last decade. The mathematical and physical foundations of these models are discussed, as are their consequences, related problems, and prospects for further development.

Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water

NASA Astrophysics Data System (ADS)

Habershon, Scott; Manolopoulos, David E.

2009-12-01

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Zero point energy leakage in condensed phase dynamics: an assessment of quantum simulation methods for liquid water.

PubMed

Habershon, Scott; Manolopoulos, David E

2009-12-28

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Holographic grating relaxation technique for soft matter science

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

Lesnichii, Vasilii, E-mail: vasilii.lesnichii@physchem.uni-freiburg.de; ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101; Kiessling, Andy

2016-06-17

The holographic grating relaxation technique also known as forced Rayleigh scattering consists basically in writing a holographic grating in the specimen of interest and monitoring its diffraction efficiency as a function of time, from which valuable information on mass or heat transfer and photoinduced transformations can be extracted. In a more detailed view, the shape of the relaxation curve and the relaxation rate as a function of the grating period were found to be affected by the architecture of diffusing species (molecular probes) that constitute the grating, as well as that of the environment they diffuse in, thus making itmore » possible to access and study spatial heterogeneity of materials and different modes of e.g., polymer motion. Minimum displacements and spatial domains approachable by the technique are in nanometer range, well below spatial periods of holographic gratings. In the present paper, several cases of holographic relaxation in heterogeneous media and complex motions are exemplified. Nano- to micro-structures or inhomogeneities comparable in spatial scale with holographic gratings manifest themselves in relaxation experiments via non-exponential decay (stepwise or stretched), spatial-period-dependent apparent diffusion coefficient, or unusual dependence of diffusion coefficient on molecular volume of diffusing probes.« less

Subdiffusion in Membrane Permeation of Small Molecules.

PubMed

Chipot, Christophe; Comer, Jeffrey

2016-11-02

Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t 0.7 , in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.

Diffusion with Varying Drag; the Runaway Problem.

NASA Astrophysics Data System (ADS)

Rollins, David Kenneth

We study the motion of electrons in an ionized plasma of electrons and ions in an external electric field. A probability distribution function describes the electron motion and is a solution of a Fokker-Planck equation. In zero field, the solution approaches an equilibrium Maxwellian. For arbitrarily small field, electrons overcome the diffusive effects and are freely accelerated by the field. This is the electron runaway phenomenon. We treat the electric field as a small perturbation. We consider various diffusion coefficients for the one dimensional problem and determine the runaway current as a function of the field strength. Diffusion coefficients, non-zero on a finite interval are examined. Some non-trivial cases of these can be solved exactly in terms of known special functions. The more realistic case where the diffusion coefficient decays with velocity are then considered. To determine the runaway current, the equivalent Schrodinger eigenvalue problem is analysed. The smallest eigenvalue is shown to be equal to the runaway current. Using asymptotic matching a solution can be constructed which is then used to evaluate the runaway current. The runaway current is exponentially small as a function of field strength. This method is used to extract results from the three dimensional problem.

Dependence of Ion Dynamics on the Polymer Chain Length in Poly(ethylene oxide)-Based Polymer Electrolytes.

PubMed

Chattoraj, Joyjit; Knappe, Marisa; Heuer, Andreas

2015-06-04

It is known from experiments that in the polymer electrolyte system, which contains poly(ethylene oxide) chains (PEO), lithium-cations (Li(+)), and bis(trifluoromethanesulfonyl)imide-anions (TFSI(-)), the cation and the anion diffusion and the ionic conductivity exhibit a similar chain-length dependence: with increasing chain length, they start dropping steadily, and later, they saturate to constant values. These results are surprising because Li-cations are strongly correlated with the polymer chains, whereas TFSI-anions do not have such bonding. To understand this phenomenon, we perform molecular dynamics simulations of this system for four different polymer chain lengths. The diffusion results obtained from our simulations display excellent agreement with the experimental data. The cation transport model based on the Rouse dynamics can successfully quantify the Li-diffusion results, which correlates Li diffusion with the polymer center-of-mass motion and the polymer segmental motion. The ionic conductivity as a function of the chain length is then estimated based on the chain-length-dependent ion diffusion, which shows a temperature-dependent deviation for short chain lengths. We argue that in the first regime, counterion correlations modify the conductivity, whereas for the long chains, the system behaves as a strong electrolyte.

Intramolecular interactions in the polar headgroup of sphingosine: serinol.

PubMed

Loru, Donatella; Peña, Isabel; Alonso, José L; Sanz, M Eugenia

2016-03-04

The intramolecular interactions in the lipid sphingosine have been elucidated through the investigation of the amino alcohol serinol which mimics its polar headgroup. Intricate networks of intramolecular hydrogen bonds involving the hydroxyl groups and the amino group contribute to the stabilisation of five different conformations observed in the broadband rotational spectrum.

TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4‧-dimethylaminoflavonol in ethanol solvent

NASA Astrophysics Data System (ADS)

Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

2015-02-01

Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4‧-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule.

Two Decades of Advances in High-Resolution Spectroscopy of Large-Amplitude Motions in N-Fold Potential Wells, as Illustrated by Methanol

NASA Astrophysics Data System (ADS)

Xu, Li-Hong

2016-06-01

Methanol is a simple and intensively studied organic molecule possessing one large-amplitude torsional motion. It has, for nearly a century, been a favorite of researchers in many fields, e.g., instrument builders, for whom methanol is often the first molecule chosen for testing an improved or a newly built instrument (including HIFI, the Heterodyne Instrument for the Far Infrared on board the Herschel space mission); theorists and/or dynamicists studying the challenging effects of a large-amplitude motion coupling with small-amplitude motions to enhance intramolecular vibrational energy redistribution; astronomers who have elevated methanol to their #1 interstellar weed because of its rich and omnipresent spectrum in the interstellar garden, where it serves as a unique probe for diagnosing conditions in star-forming regions; astrochemists studying isotopic ratios as clues to the chemical evolution of the universe; and fundamentalists seeking possible time variation of the proton/electron mass ratio in the standard model; just to name a few. From high-resolution to high-precision spectroscopy, the large-amplitude internal rotation of the methyl top against its OH framework in methanol has never failed to produce new surprises in spectral regions from the microwave all the way to the near IR. The very recent observation of completely unexpected large methanol hyperfine splittings is a vivid testimonial that the large-amplitude torsional motion can still lead us to unexplored landscapes. This talk will focus on the complicated vibration-torsion-rotation energy networks and interactions deduced from high resolution spectra; our efforts to understand some of them using ab-initio-assisted approaches and the modeling of torsion-rotation and torsionally mediated spin-rotation hyperfine splittings in methanol. These topics represent one part of the much larger fascinating world inhabited by methanolics.

Evaluation of bacterial motility from non-Gaussianity of finite-sample trajectories using the large deviation principle

NASA Astrophysics Data System (ADS)

Hanasaki, Itsuo; Kawano, Satoyuki

2013-11-01

Motility of bacteria is usually recognized in the trajectory data and compared with Brownian motion, but the diffusion coefficient is insufficient to evaluate it. In this paper, we propose a method based on the large deviation principle. We show that it can be used to evaluate the non-Gaussian characteristics of model Escherichia coli motions and to distinguish combinations of the mean running duration and running speed that lead to the same diffusion coefficient. Our proposed method does not require chemical stimuli to induce the chemotaxis in a specific direction, and it is applicable to various types of self-propelling motions for which no a priori information of, for example, threshold parameters for run and tumble or head/tail direction is available. We also address the issue of the finite-sample effect on the large deviation quantities, but we propose to make use of it to characterize the nature of motility.

Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra.

PubMed

Ryabov, Yaroslav

2015-09-01

In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Intramolecular hydrogen bonding in malonaldehyde and its radical analogues.

PubMed

Lin, Chen; Kumar, Manoj; Finney, Brian A; Francisco, Joseph S

2017-09-28

High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA RS , and cis-MA RA , both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA RA , in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA RS , in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ * orbital of acceptor O-H bond (n → σ * OH ). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA RS .

Molecular motion in cell membranes: Analytic study of fence-hindered random walks

NASA Astrophysics Data System (ADS)

Kenkre, V. M.; Giuggioli, L.; Kalay, Z.

2008-05-01

A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads to explicit usable solutions including expressions for the molecular mean square displacement and effective diffusion constants. One outcome is a detailed understanding of the dependence of the time variation of the mean square displacement on the initial placement of the molecule within the confined region. How to use the calculations is illustrated by extracting (confinement) compartment sizes from experimentally reported published observations from single particle tracking experiments on the diffusion of gold-tagged G -protein coupled μ -opioid receptors in the normal rat kidney cell membrane, and by further comparing the analytical results to observations on the diffusion of phospholipids, also in normal rat kidney cells.

Magnetic diffusion and flare energy buildup

NASA Technical Reports Server (NTRS)

Wu, S. T.; Yin, C. L.; Yang, W.-H.

1992-01-01

Photospheric motion shears or twists solar magnetic fields to increase magnetic energy in the corona, because this process may change a current-free state of a coronal field to force-free states which carry electric current. This paper analyzes both linear and nonlinear 2D force-free magnetic field models and derives relations of magnetic energy buildup with photospheric velocity field. When realistic data of solar magnetic field and photospheric velocity field are used, it is found that 3-4 hours are needed to create an amount of free magnetic energy which is of the order of the current-free field energy. Furthermore, the paper studies situations in which finite magnetic diffusivities in photospheric plasma are introduced. The shearing motion increases coronal magnetic energy, while the photospheric diffusion reduces the energy. The variation of magnetic energy in the coronal region, then, depends on which process dominates.

Size-dependent quantum diffusion of Gd atoms within Fe nano-corrals

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

Hu, J.; Cao, R. X.; Miao, B. F.

2013-12-01

We systematically studied the size-dependent quantum diffusion of Gd atoms within Fe circular quantum corrals on Ag(111). By varying the size of the quantum corrals, different types of patterns are observed inside the corrals, including a single dot and circular orbits for the diffusion of Gd adatoms. In addition, the motion of the adatoms also forms circular-like orbits outside the corral. Via quantitative analysis, we confirm that the regions with adatoms' high visiting probability are consistent with the positions of the local electronic density-of-states maxima, both inside and outside the corrals within a < 0.2 nm offset. The results agreemore » well with kinetic Monte Carlo simulations that utilize the experimentally determined interaction between Gd and Fe circular corrals. These findings demonstrate that one can engineer adatom motion by controlling the size of the quantum corrals.« less

Following fluctuating signs: Anomalous active superdiffusion of swimmers in anisotropic media

NASA Astrophysics Data System (ADS)

Toner, John; Löwen, Hartmut; Wensink, Henricus H.

2016-06-01

Active (i.e., self-propelled or swimming) particles moving through an isotropic fluid exhibit conventional diffusive behavior. We report anomalous diffusion of an active particle moving in an anisotropic nematic background. While the translational motion parallel to the nematic director shows ballistic behavior, the long-time transverse motion is superdiffusive, with an anomalous scaling proportional to t lnt of the mean-square displacement with time t . This behavior is predicted by an analytical theory that we present here and is corroborated by numerical simulation of active particle diffusion in a simple lattice model for a nematic liquid crystal. It is universal for any collection of self-propelled elements (e.g., bacteria or active rods) moving in a nematic background, provided only that the swimmers are sufficiently dilute that their interactions with each other can be neglected and that they do not perform hairpin turns.

In Silico Neuro-Oncology: Brownian Motion-Based Mathematical Treatment as a Potential Platform for Modeling the Infiltration of Glioma Cells into Normal Brain Tissue.

PubMed

Antonopoulos, Markos; Stamatakos, Georgios

2015-01-01

Intensive glioma tumor infiltration into the surrounding normal brain tissues is one of the most critical causes of glioma treatment failure. To quantitatively understand and mathematically simulate this phenomenon, several diffusion-based mathematical models have appeared in the literature. The majority of them ignore the anisotropic character of diffusion of glioma cells since availability of pertinent truly exploitable tomographic imaging data is limited. Aiming at enriching the anisotropy-enhanced glioma model weaponry so as to increase the potential of exploiting available tomographic imaging data, we propose a Brownian motion-based mathematical analysis that could serve as the basis for a simulation model estimating the infiltration of glioblastoma cells into the surrounding brain tissue. The analysis is based on clinical observations and exploits diffusion tensor imaging (DTI) data. Numerical simulations and suggestions for further elaboration are provided.

Path-length-resolved dynamic light scattering in highly scattering random media: The transition to diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Bizheva, Kostadinka K.; Siegel, Andy M.; Boas, David A.

1998-12-01

We used low coherence interferometry to measure Brownian motion within highly scattering random media. A coherence gate was applied to resolve the optical path-length distribution and to separate ballistic from diffusive light. Our experimental analysis provides details on the transition from single scattering to light diffusion and its dependence on the system parameters. We found that the transition to the light diffusion regime occurs at shorter path lengths for media with higher scattering anisotropy or for larger numerical aperture of the focusing optics.

Time-delayed feedback control of diffusion in random walkers.

PubMed

Ando, Hiroyasu; Takehara, Kohta; Kobayashi, Miki U

2017-07-01

Time delay in general leads to instability in some systems, while specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a stochastic process, i.e., a random walk, and observe its diffusion phenomenon with time-delayed feedback. As a result, the diffusion coefficient decreases with increasing delay time. We analytically illustrate this suppression of diffusion by using stochastic delay differential equations and justify the feasibility of this suppression by applying time-delayed feedback to a molecular dynamics model.

Fractional Dynamics of Single File Diffusion in Dusty Plasma Ring

NASA Astrophysics Data System (ADS)

Muniandy, S. V.; Chew, W. X.; Asgari, H.; Wong, C. S.; Lim, S. C.

2011-11-01

Single file diffusion (SFD) refers to the constrained motion of particles in quasi-one-dimensional channel such that the particles are unable to pass each other. Possible SFD of charged dust confined in biharmonic annular potential well with screened Coulomb interaction is investigated. Transition from normal diffusion to anomalous sub-diffusion behaviors is observed. Deviation from SFD's mean square displacement scaling behavior of 1/2-exponent may occur in strongly interacting systems. A phenomenological model based on fractional Langevin equation is proposed to account for the anomalous SFD behavior in dusty plasma ring.

A Study of Brownian Motion Using Light Scattering

ERIC Educational Resources Information Center

Clark, Noel A.; And Others

1970-01-01

Presents an advanced laboratory experiment and lecture demonstration by which the intensity spectrum of light scattered by a suspension of particles in a fluid can be studied. From this spectrum, it is possible to obtain quantitative information about the motion of the particles, including an accurate determination of their diffusion constant.…

Disparity, motion, and color information improve gloss constancy performance.

PubMed

Wendt, Gunnar; Faul, Franz; Ekroll, Vebjørn; Mausfeld, Rainer

2010-09-01

S. Nishida and M. Shinya (1998) found that observers have only a limited ability to recover surface-reflectance properties under changes in surface shape. Our aim in the present study was to investigate how the degree of surface-reflectance constancy depends on the availability of information that may help to infer the reflectance and shape properties of surfaces. To this end, we manipulated the availability of (i) motion-induced information (static vs. dynamic presentation), (ii) disparity information (with the levels "monocular," "surface disparity," and "surface + highlight disparity"), and (iii) color information (grayscale stimuli vs. hue differences between diffuse and specular reflections). The task of the subjects was to match the perceived lightness and glossiness between two surfaces with different spatial frequency and amplitude by manipulating the diffuse component and the exponent of the Phong lighting model in one of the surfaces. Our results indicate that all three types of information improve the constancy of glossiness matches--both in isolation and in combination. The lightness matching data only revealed an influence of motion and color information. Our results indicate, somewhat counterintuitively, that motion information has a detrimental effect on lightness constancy.

Multimodal transport and dispersion of organelles in narrow tubular cells

NASA Astrophysics Data System (ADS)

Mogre, Saurabh S.; Koslover, Elena F.

2018-04-01

Intracellular components explore the cytoplasm via active motor-driven transport in conjunction with passive diffusion. We model the motion of organelles in narrow tubular cells using analytical techniques and numerical simulations to study the efficiency of different transport modes in achieving various cellular objectives. Our model describes length and time scales over which each transport mode dominates organelle motion, along with various metrics to quantify exploration of intracellular space. For organelles that search for a specific target, we obtain the average capture time for given transport parameters and show that diffusion and active motion contribute to target capture in the biologically relevant regime. Because many organelles have been found to tether to microtubules when not engaged in active motion, we study the interplay between immobilization due to tethering and increased probability of active transport. We derive parameter-dependent conditions under which tethering enhances long-range transport and improves the target capture time. These results shed light on the optimization of intracellular transport machinery and provide experimentally testable predictions for the effects of transport regulation mechanisms such as tethering.

Seismic Velocity Measurements at Expanded Seismic Network Sites

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

Woolery, Edward W; Wang, Zhenming

2005-01-01

Structures at the Paducah Gaseous Diffusion Plant (PGDP), as well as at other locations in the northern Jackson Purchase of western Kentucky may be subjected to large far-field earthquake ground motions from the New Madrid seismic zone, as well as those from small and moderate-sized local events. The resultant ground motion a particular structure is exposed from such event will be a consequence of the earthquake magnitude, the structures' proximity to the event, and the dynamic and geometrical characteristics of the thick soils upon which they are, of necessity, constructed. This investigation evaluated the latter. Downhole and surface (i.e., refractionmore » and reflection) seismic velocity data were collected at the Kentucky Seismic and Strong-Motion Network expansion sites in the vicinity of the Paducah Gaseous Diffusion Plant (PGDP) to define the dynamic properties of the deep sediment overburden that can produce modifying effects on earthquake waves. These effects are manifested as modifications of the earthquake waves' amplitude, frequency, and duration. Each of these three ground motion manifestations is also fundamental to the assessment of secondary earthquake engineering hazards such as liquefaction.« less

Chromosomal locus tracking with proper accounting of static and dynamic errors

PubMed Central

Backlund, Mikael P.; Joyner, Ryan; Moerner, W. E.

2015-01-01

The mean-squared displacement (MSD) and velocity autocorrelation (VAC) of tracked single particles or molecules are ubiquitous metrics for extracting parameters that describe the object’s motion, but they are both corrupted by experimental errors that hinder the quantitative extraction of underlying parameters. For the simple case of pure Brownian motion, the effects of localization error due to photon statistics (“static error”) and motion blur due to finite exposure time (“dynamic error”) on the MSD and VAC are already routinely treated. However, particles moving through complex environments such as cells, nuclei, or polymers often exhibit anomalous diffusion, for which the effects of these errors are less often sufficiently treated. We present data from tracked chromosomal loci in yeast that demonstrate the necessity of properly accounting for both static and dynamic error in the context of an anomalous diffusion that is consistent with a fractional Brownian motion (FBM). We compare these data to analytical forms of the expected values of the MSD and VAC for a general FBM in the presence of these errors. PMID:26172745

Spontaneous Mechanical Buckling in Two-Dimensional Materials: A Power Source for Ambient Vibration Energy Harvesters

NASA Astrophysics Data System (ADS)

Thibado, Paul; Kumar, Pradeep; Singh, Surendra

Internet-of-Things (IoT) is projected to become a multi-trillion-dollar market, but most applications cannot afford replacing batteries on such a large scale, driving the need for battery alternatives. We recently discovered that freestanding graphene membranes are in perpetual motion when held at room temperature. Surprisingly, the random up-down motion of the membrane does not follow classical Brownian motion, but instead is super-diffusive at short times and sub-diffusive at long times. Furthermore, the velocity probability distribution function is non-Gaussian and follows the heavy-tailed Cauchy-Lorentz distribution, consistent with Lévy flights. Molecular dynamics simulations reveal that mechanical buckling is spontaneously occurring, and that this is the mechanism responsible for the anomalous movement. Bucking in this system occurs when the local material suddenly flips from concave to convex. The higher kinetic energy associated with this motion is derived from the surrounding thermal waste heat, and it may be converted into an electrical current and used as the active component of small power generators known as ambient vibration energy harvesters. thibado@uark.edu.

Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface.

PubMed

Nordstierna, Lars; Yushmanov, Pavel V; Furó, István

2006-08-21

Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.

Triggered intravoxel incoherent motion MRI for the assessment of calf muscle perfusion during isometric intermittent exercise.

PubMed

Mastropietro, Alfonso; Porcelli, Simone; Cadioli, Marcello; Rasica, Letizia; Scalco, Elisa; Gerevini, Simonetta; Marzorati, Mauro; Rizzo, Giovanna

2018-06-01

The main aim of this paper was to propose triggered intravoxel incoherent motion (IVIM) imaging sequences for the evaluation of perfusion changes in calf muscles before, during and after isometric intermittent exercise. Twelve healthy volunteers were involved in the study. The subjects were asked to perform intermittent isometric plantar flexions inside the MRI bore. MRI of the calf muscles was performed on a 3.0 T scanner and diffusion-weighted (DW) images were obtained using eight different b values (0 to 500 s/mm 2 ). Acquisitions were performed at rest, during exercise and in the subsequent recovery phase. A motion-triggered echo-planar imaging DW sequence was implemented to avoid movement artifacts. Image quality was evaluated using the average edge strength (AES) as a quantitative metric to assess the motion artifact effect. IVIM parameters (diffusion D, perfusion fraction f and pseudo-diffusion D*) were estimated using a segmented fitting approach and evaluated in gastrocnemius and soleus muscles. No differences were observed in quality of IVIM images between resting state and triggered exercise, whereas the non-triggered images acquired during exercise had a significantly lower value of AES (reduction of more than 20%). The isometric intermittent plantar-flexion exercise induced an increase of all IVIM parameters (D by 10%; f by 90%; D* by 124%; fD* by 260%), in agreement with the increased muscle perfusion occurring during exercise. Finally, IVIM parameters reverted to the resting values within 3 min during the recovery phase. In conclusion, the IVIM approach, if properly adapted using motion-triggered sequences, seems to be a promising method to investigate muscle perfusion during isometric exercise. Copyright © 2018 John Wiley & Sons, Ltd.

Motion-based prediction is sufficient to solve the aperture problem

PubMed Central

Perrinet, Laurent U; Masson, Guillaume S

2012-01-01

In low-level sensory systems, it is still unclear how the noisy information collected locally by neurons may give rise to a coherent global percept. This is well demonstrated for the detection of motion in the aperture problem: as luminance of an elongated line is symmetrical along its axis, tangential velocity is ambiguous when measured locally. Here, we develop the hypothesis that motion-based predictive coding is sufficient to infer global motion. Our implementation is based on a context-dependent diffusion of a probabilistic representation of motion. We observe in simulations a progressive solution to the aperture problem similar to physiology and behavior. We demonstrate that this solution is the result of two underlying mechanisms. First, we demonstrate the formation of a tracking behavior favoring temporally coherent features independently of their texture. Second, we observe that incoherent features are explained away while coherent information diffuses progressively to the global scale. Most previous models included ad-hoc mechanisms such as end-stopped cells or a selection layer to track specific luminance-based features as necessary conditions to solve the aperture problem. Here, we have proved that motion-based predictive coding, as it is implemented in this functional model, is sufficient to solve the aperture problem. This solution may give insights in the role of prediction underlying a large class of sensory computations. PMID:22734489

Mathematical Development and Computational Analysis of Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) Based on Bloch Nuclear Magnetic Resonance (NMR) Diffusion Model for Myocardial Motion.

PubMed

Dada, Michael O; Jayeoba, Babatunde; Awojoyogbe, Bamidele O; Uno, Uno E; Awe, Oluseyi E

2017-09-13

Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) is a tagged image analysis method that can measure myocardial motion and strain in near real-time and is considered a potential candidate to make magnetic resonance tagging clinically viable. However, analytical expressions of radially tagged transverse magnetization in polar coordinates (which is required to appropriately describe the shape of the heart) have not been explored because the physics required to directly connect myocardial deformation of tagged Nuclear Magnetic Resonance (NMR) transverse magnetization in polar geometry and the appropriate harmonic phase parameters are not yet available. The analytical solution of Bloch NMR diffusion equation in spherical geometry with appropriate spherical wave tagging function is important for proper analysis and monitoring of heart systolic and diastolic deformation with relevant boundary conditions. In this study, we applied Harmonic Phase MRI method to compute the difference between tagged and untagged NMR transverse magnetization based on the Bloch NMR diffusion equation and obtained radial wave tagging function for analysis of myocardial motion. The analytical solution of the Bloch NMR equations and the computational simulation of myocardial motion as developed in this study are intended to significantly improve healthcare for accurate diagnosis, prognosis and treatment of cardiovascular related deceases at the lowest cost because MRI scan is still one of the most expensive anywhere. The analysis is fundamental and significant because all Magnetic Resonance Imaging techniques are based on the Bloch NMR flow equations.

Effects of configurational changes on molecular dynamics in polyvinylidene fluoride and poly(vinylidene fluoride-trifluoroethylene) ferroelectric polymers

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

Jalarvo, N., E-mail: jalarvonh@ornl.gov, E-mail: abhijit.pramanick@gmail.com, E-mail: omardiallos@ornl.gov; Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831; Pramanick, A., E-mail: jalarvonh@ornl.gov, E-mail: abhijit.pramanick@gmail.com, E-mail: omardiallos@ornl.gov

2015-08-24

We present a comparative study of proton dynamics in unpoled non-ferroelectric polymer polyvinylidene fluoride (PVDF) and in its trifluoroethylene containing ferroelectric copolymer (with 70/30 molar proportion), using quasi-elastic neutron scattering. The neutron data reveal the existence of two distinct types of molecular motions in the temperature range investigated. The slower motion, which is characterized in details here, is ascribed to protons jump diffusion along the polymeric carbon chains, while the faster motion could be attributed to localized rotational motion of methylene groups. At temperatures below the Curie point (T{sub c} ∼ 385 K) of the composite polymer, the slower diffusive mode experiences longermore » relaxation times in the ferroelectric blend than in the bare PVDF, although the net corresponding diffusion coefficient remains comparatively the same in both polymers with characteristic activation energy of E{sub A} ≈ 27–33 kJ/mol. This arises because of a temperature dependent jump length r{sub 0}, which we observe to be effectively longer in the copolymer, possibly due to the formation of ordered ferroelectric domains below T{sub c}. Above T{sub c}, there is no appreciable difference in r{sub 0} between the two systems. This observation directly relates the known dependence of T{sub c} on molar ratio to changes in r{sub 0}, providing fundamental insight into the ferroelectric properties of PVDF-based copolymers.« less

Multi-Objective Memetic Search for Robust Motion and Distortion Correction in Diffusion MRI.

PubMed

Hering, Jan; Wolf, Ivo; Maier-Hein, Klaus H

2016-10-01

Effective image-based artifact correction is an essential step in the analysis of diffusion MR images. Many current approaches are based on retrospective registration, which becomes challenging in the realm of high b -values and low signal-to-noise ratio, rendering the corresponding correction schemes more and more ineffective. We propose a novel registration scheme based on memetic search optimization that allows for simultaneous exploitation of different signal intensity relationships between the images, leading to more robust registration results. We demonstrate the increased robustness and efficacy of our method on simulated as well as in vivo datasets. In contrast to the state-of-art methods, the median target registration error (TRE) stayed below the voxel size even for high b -values (3000 s ·mm -2 and higher) and low SNR conditions. We also demonstrate the increased precision in diffusion-derived quantities by evaluating Neurite Orientation Dispersion and Density Imaging (NODDI) derived measures on a in vivo dataset with severe motion artifacts. These promising results will potentially inspire further studies on metaheuristic optimization in diffusion MRI artifact correction and image registration in general.

Nanoscopic compartmentalization of membrane protein motion at the axon initial segment.

PubMed

Albrecht, David; Winterflood, Christian M; Sadeghi, Mohsen; Tschager, Thomas; Noé, Frank; Ewers, Helge

2016-10-10

The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single-particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton. We observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of ∼190-nm-spaced segments along the AIS axis as early as day in vitro 4, and this pattern alternates with actin rings. Mathematical modeling shows that diffusion barriers between the segments significantly reduce lateral diffusion along the axon. © 2016 Albrecht et al.

Diffusion in Single Supported Lipid Bilayers

NASA Astrophysics Data System (ADS)

Armstrong, C. L.; Trapp, M.; Rheinstädter, M. C.

2011-03-01

Despite their potential relevance for the development of functionalized surfaces and biosensors, the study of single supported membranes using neutron scattering has been limited by the challenge of obtaining relevant dynamic information from a sample with minimal material. Using state of the art neutron instrumentation we have, for the first time, modeled lipid diffusion in single supported lipid bilayers. While we find that the diffusion coefficient for the single bilayer system is comparable to a multi-lamellar lipid system, the molecular mechanism for lipid motion in the single bilayer is a continuous diffusion process with no sign of the flow-like ballistic motion reported in the stacked membrane system. In the future, these membranes will be used to hold and align proteins, mimicking physiological conditions enabling the study of protein structure, function and interactions in relevant and highly topical membrane/protein systems with minimal sample material. C.L. Armstrong, M.D. Kaye, M. Zamponi, E. Mamontov, M. Tyagi, T. Jenkins and M.C. Rheinstädter, Soft Matter Communication, 2010, Advance Article, DOI: 10.1039/C0SM00637H

Role of spin diffusion in current-induced domain wall motion for disordered ferromagnets

NASA Astrophysics Data System (ADS)

Akosa, Collins Ashu; Kim, Won-Seok; Bisig, André; Kläui, Mathias; Lee, Kyung-Jin; Manchon, Aurélien

2015-03-01

Current-induced spin transfer torque and magnetization dynamics in the presence of spin diffusion in disordered magnetic textures is studied theoretically. We demonstrate using tight-binding calculations that weak, spin-conserving impurity scattering dramatically enhances the nonadiabaticity. To further explore this mechanism, a phenomenological drift-diffusion model for incoherent spin transport is investigated. We show that incoherent spin diffusion indeed produces an additional spatially dependent torque of the form ˜∇2[m ×(u .∇ ) m ] +ξ ∇2[(u .∇ ) m ] , where m is the local magnetization direction, u is the direction of injected current, and ξ is a parameter characterizing the spin dynamics (precession, dephasing, and spin-flip). This torque, which scales as the inverse square of the domain wall width, only weakly enhances the longitudinal velocity of a transverse domain wall but significantly enhances the transverse velocity of vortex walls. The spatial-dependent spin transfer torque uncovered in this study is expected to have significant impact on the current-driven motion of abrupt two-dimensional textures such as vortices, skyrmions, and merons.

Molecular model for the diffusion of associating telechelic polymer networks

NASA Astrophysics Data System (ADS)

Ramirez, Jorge; Dursch, Thomas; Olsen, Bradley

Understanding the mechanisms of motion and stress relaxation of associating polymers at the molecular level is critical for advanced technological applications such as enhanced oil-recovery, self-healing materials or drug delivery. In associating polymers, the strength and rates of association/dissociation of the reversible physical crosslinks govern the dynamics of the network and therefore all the macroscopic properties, like self-diffusion and rheology. Recently, by means of forced Rayleigh scattering experiments, we have proved that associating polymers of different architectures show super-diffusive behavior when the free motion of single molecular species is slowed down by association/dissociation kinetics. Here we discuss a new molecular picture for unentangled associating telechelic polymers that considers concentration, molecular weight, number of arms of the molecules and equilibrium and rate constants of association/dissociation. The model predicts super-diffusive behavior under the right combination of values of the parameters. We discuss some of the predictions of the model using scaling arguments, show detailed results from Brownian dynamics simulations of the FRS experiments, and attempt to compare the predictions of the model to experimental data.

Improved atomistic simulation of diffusion and sorption in metal oxides

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

2001-01-01

Gas diffusion and sorption on the surface of metal oxides are investigated using atomistic simulations, that make use of two different force fields for the description of the intramolecular and intermolecular interactions. MD and MC computations are presented and estimates of the mean residence time, Henry's constant, and the heat of adsorption are provided for various common gases (CO, CO2, O2, CH4, Xe), and semiconducting substrates that hold promise for gas sensor applications (SnO2, BaTiO3). Comparison is made between the performance of a simple, first generation force field (Universal) and a more detailed, second generation field (COMPASS) under the same conditions and the same assumptions regarding the generation of the working configurations. It is found that the two force fields yield qualitatively similar results in all cases examined here. However, direct comparison with experimental data reveals that the accuracy of the COMPASS-based computations is not only higher than that of the first generation force field but exceeds even that of published specialized methods, based on ab initio computations.

Composite and Component Plates, Plate Non-rigidity, and the Steadiness of Plate Motion From Marine Geophysical and Space Geodetic Data

NASA Astrophysics Data System (ADS)

Gordon, R. G.; Argus, D. F.; DeMets, C.

2017-12-01

Plate tectonic theory has evolved since its birth 50 years ago. In particular, we now recognize that some of the originally proposed plates such as the Indo-Australia plate, the Africa plate, and the America plate are what we term "composite" plates—entities that contain no traditionally defined narrow plate boundaries, but are composed of multiple approximately rigid regions, which we term "component" plates, separated by diffuse plate boundaries. The best example of a composite plate is the Indo-Australia composite plate, which consists of the India, Capricorn, Australia, and Macquarie component plates and multiple intervening diffuse oceanic plate boundaries. The poles of relative rotation between component plates tend to lie in their mutual diffuse plate boundary. Outside of diffuse boundaries, plate rigidity has proven to be an excellent approximation, but the non-closure of some plate circuits indicates that stable plate interiors have a small but significant non-rigidity that may add up to 1 to 2 mm/a across any individual plate and may be partly due to horizontal thermal contraction of oceanic lithosphere. The greatest observational challenge to plate rigidity is posed by the Pacific-Cocos-Nazca plate circuit, which fails closure by 15 ±4 mm/a. The most rapid deformation of the plates observed with space geodesy is generated by solid Earth's viscous response to unloading of the late Pleistocene ice sheets. Differences between different realizations of global plate velocities from space geodesy appear in some cases to be due to differing assumptions about the motion of the geocenter, which affects estimated plate relative angular velocities and estimated vertical motion at geodetic sites. Comparison of space geodetic and marine geophysical plate motion rates and directions has demonstrated that plate motion is nearly steady, which allows plate boundary conditions to be applied to inter-seismic strain accumulation due to locking of specific faults. In detail it appears, however, that plate velocities over the past few decades have in several cases been significantly different from plate motions averaged over geologic time. Some of the largest changes have been decreases in rates across convergent plate boundaries: Nazca-South America and the velocities of Nubia, Arabia, and India relative to Eurasia.

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation.

PubMed

Safdari, Hadiseh; Cherstvy, Andrey G; Chechkin, Aleksei V; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation

NASA Astrophysics Data System (ADS)

Safdari, Hadiseh; Cherstvy, Andrey G.; Chechkin, Aleksei V.; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

In vivo free-breathing DTI and IVIM of the whole human heart using a real-time slice-followed SE-EPI navigator-based sequence: A reproducibility study in healthy volunteers.

PubMed

Moulin, Kevin; Croisille, Pierre; Feiweier, Thorsten; Delattre, Benedicte M A; Wei, Hongjiang; Robert, Benjamin; Beuf, Olivier; Viallon, Magalie

2016-07-01

In this study, we proposed an efficient free-breathing strategy for rapid and improved cardiac diffusion-weighted imaging (DWI) acquisition using a single-shot spin-echo echo planar imaging (SE-EPI) sequence. A real-time slice-following technique during free-breathing was combined with a sliding acquisition-window strategy prior Principal Component Analysis temporal Maximum Intensity Projection (PCAtMIP) postprocessing of in-plane co-registered diffusion-weighted images. This methodology was applied to 10 volunteers to quantify the performance of the motion correction technique and the reproducibility of diffusion parameters. The slice-following technique offers a powerful head-foot respiratory motion management solution for SE-EPI cDWI with the advantage of a 100% duty cycle scanning efficiency. The level of co-registration was further improved using nonrigid motion corrections and was evaluated with a co-registration index. Vascular fraction f and the diffusion coefficients D and D* were determined to be 0.122 ± 0.013, 1.41 ± 0.09 × 10(-3) mm(2) /s and 43.6 ± 9.2 × 10(-3) mm(2) /s, respectively. From the multidirectional dataset, the measured mean diffusivity was 1.72 ± 0.09 × 10(-3) mm(2) /s and the fractional anisotropy was 0.36 ± 0.02. The slice-following DWI SE-EPI sequence is a promising solution for clinical implementation, offering a robust improved workflow for further evaluation of DWI in cardiology. Magn Reson Med 76:70-82, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Diffusion Tensor Imaging and Resting-State Functional MRI-Scanning in 5- and 6-Year-Old Children: Training Protocol and Motion Assessment

PubMed Central

Theys, Catherine; Wouters, Jan; Ghesquière, Pol

2014-01-01

Advanced Magnetic Resonance Imaging (MRI) techniques such as Diffusion Tensor Imaging (DTI) and resting-state functional MRI (rfMRI) are widely used to study structural and functional neural connectivity. However, as these techniques are highly sensitive to motion artifacts and require a considerable amount of time for image acquisition, successful acquisition of these images can be challenging to complete with certain populations. This is especially true for young children. This paper describes a new approach termed the ‘submarine protocol’, designed to prepare 5- and 6-year-old children for advanced MRI scanning. The submarine protocol aims to ensure that successful scans can be acquired in a time- and resource-efficient manner, without the need for sedation. This manuscript outlines the protocol and details its outcomes, as measured through the number of children who completed the scanning procedure and analysis of the degree of motion present in the acquired images. Seventy-six children aged between 5.8 and 6.9 years were trained using the submarine protocol and subsequently underwent DTI and rfMRI scanning. After completing the submarine protocol, 75 of the 76 children (99%) completed their DTI-scan and 72 children (95%) completed the full 35-minute scan session. Results of diffusion data, acquired in 75 children, showed that the motion in 60 of the scans (80%) did not exceed the threshold for excessive motion. In the rfMRI scans, this was the case for 62 of the 71 scans (87%). When placed in the context of previous studies, the motion data of the 5- and 6-year-old children reported here were as good as, or better than those previously reported for groups of older children (i.e., 8-year-olds). Overall, this study shows that the submarine protocol can be used successfully to acquire DTI and rfMRI scans in 5 and 6-year-old children, without the need for sedation or lengthy training procedures. PMID:24718364

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.

Molecular dynamics study of nanodroplet diffusion on smooth solid surfaces

NASA Astrophysics Data System (ADS)

Niu, Zhao-Xia; Huang, Tao; Chen, Yong

2018-10-01

We perform molecular dynamics simulations of Lennard-Jones particles in a canonical ensemble to study the diffusion of nanodroplets on smooth solid surfaces. Using the droplet-surface interaction to realize a hydrophilic or hydrophobic surface and calculating the mean square displacement of the center-of-mass of the nanodroplets, the random motion of nanodroplets could be characterized by shorttime subdiffusion, intermediate-time superdiffusion, and long-time normal diffusion. The short-time subdiffusive exponent increases and almost reaches unity (normal diffusion) with decreasing droplet size or enhancing hydrophobicity. The diffusion coefficient of the droplet on hydrophobic surfaces is larger than that on hydrophilic surfaces.

Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

PubMed

Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

2012-11-28

Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

A Numerical Method for the Simulation of Skew Brownian Motion and its Application to Diffusive Shock Acceleration of Charged Particles

NASA Astrophysics Data System (ADS)

McEvoy, Erica L.

Stochastic differential equations are becoming a popular tool for modeling the transport and acceleration of cosmic rays in the heliosphere. In diffusive shock acceleration, cosmic rays diffuse across a region of discontinuity where the up- stream diffusion coefficient abruptly changes to the downstream value. Because the method of stochastic integration has not yet been developed to handle these types of discontinuities, I utilize methods and ideas from probability theory to develop a conceptual framework for the treatment of such discontinuities. Using this framework, I then produce some simple numerical algorithms that allow one to incorporate and simulate a variety of discontinuities (or boundary conditions) using stochastic integration. These algorithms were then modified to create a new algorithm which incorporates the discontinuous change in diffusion coefficient found in shock acceleration (known as Skew Brownian Motion). The originality of this algorithm lies in the fact that it is the first of its kind to be statistically exact, so that one obtains accuracy without the use of approximations (other than the machine precision error). I then apply this algorithm to model the problem of diffusive shock acceleration, modifying it to incorporate the additional effect of the discontinuous flow speed profile found at the shock. A steady-state solution is obtained that accurately simulates this phenomenon. This result represents a significant improvement over previous approximation algorithms, and will be useful for the simulation of discontinuous diffusion processes in other fields, such as biology and finance.

Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry

PubMed Central

Engen, John R.; Wales, Thomas E.; Chen, Shugui; Marzluff, Elaine M.; Hassell, Kerry M.; Weis, David D.; Smithgall, Thomas E.

2013-01-01

Many proteins do not exist in a single rigid conformation. Protein motions, or dynamics, exist and in many cases are important for protein function. The analysis of protein dynamics relies on biophysical techniques that can distinguish simultaneously existing populations of molecules and their rates of interconversion. Hydrogen exchange (HX) detected by mass spectrometry (MS) is contributing to our understanding of protein motions by revealing unfolding and dynamics on a wide timescale, ranging from seconds to hours to days. In this review we discuss HX MS-based analyses of protein dynamics, using our studies of multi-domain kinases as examples. Using HX MS, we have successfully probed protein dynamics and unfolding in the isolated SH3, SH2 and kinase domains of the c-Src and Abl kinase families, as well as the role of inter- and intra-molecular interactions in the global control of kinase function. Coupled with high-resolution structural information, HX MS has proved to be a powerful and versatile tool for the analysis of the conformational dynamics in these kinase systems, and has provided fresh insight regarding the regulatory control of these important signaling proteins. HX MS studies of dynamics are applicable not only to the proteins we illustrate here, but to a very wide range of proteins and protein systems, and should play a role in both classification of and greater understanding of the prevalence of protein motion. PMID:23682200

The Hills are Alive: Dynamic Ridges and Valleys in a Strike-Slip Environment

NASA Astrophysics Data System (ADS)

Duvall, A. R.; Tucker, G. E.

2014-12-01

Strike-slip fault zones have long been known for characteristic landforms such as offset and deflected rivers, linear strike-parallel valleys, and shutter ridges. Despite their common presence, questions remain about the mechanics of how these landforms arise or how their form varies as a function of slip rate, geomorphic process, or material properties. We know even less about what happens far from the fault, in drainage basin headwaters, as a result of strike-slip motion. Here we explore the effects of horizontal fault slip rate, bedrock erodibility, and hillslope diffusivity on river catchments that drain across an active strike-slip fault using the CHILD landscape evolution model. Model calculations demonstrate that lateral fault motion induces a permanent state of landscape disequilibrium brought about by fault offset-generated river lengthening alternating with abrupt shortening due to stream capture. This cycle of shifting drainage patterns and base level change continues until fault motion ceases thus creating a perpetual state of transience unique to strike-slip systems. Our models also make the surprising prediction that, in some cases, hillslope ridges oriented perpendicular to the fault migrate laterally in conjunction with fault motion. Ridge migration happens when slip rate is slow enough and/or diffusion and river incision are fast enough that the hillslopes can respond to the disequilibrium brought about by strike-slip motion. In models with faster slip rates, stronger rocks or less-diffusive hillslopes, ridge mobility is limited or arrested despite the fact that the process of river lengthening and capture continues. Fast-slip cases also develop prominent steep fault-facing hillslope facets proximal to the fault valley and along-strike topographic profiles with reduced local relief between ridges and valleys. Our results demonstrate the dynamic nature of strike-slip landscapes that vary systematically with a ratio of bedrock erodibility (K) and hillslope diffusivity (D) to the rate of horizontal advection of topography (v). These results also reveal a potential set of recognizable geomorphic signatures within strike-slip systems that should be looked to as indicators of fault activity and/or material properties.

Spectral Analysis and Computation of Effective Diffusivities for Steady Random Flows

DTIC Science & Technology

2016-04-28

even in the motion of sea ice floes influenced by winds and ocean currents. The long time, large scale behavior of such systems is equivalent to an...flow plays a key role in many important processes in the global climate system [55] and Earth’s ecosys- tems [14]. Advection of geophysical fluids...HOMOGENIZATION OF THE ADVECTION-DIFFUSION EQUATION The dispersion of a cloud of passive scalars with density φ diffusing with molecular dif- fusivity ε and

Survival probability for a diffusive process on a growing domain

NASA Astrophysics Data System (ADS)

Simpson, Matthew J.; Sharp, Jesse A.; Baker, Ruth E.

2015-04-01

We consider the motion of a diffusive population on a growing domain, 0

FCS diffusion laws in two-phase lipid membranes: determination of domain mean size by experiments and Monte Carlo simulations.

PubMed

Favard, Cyril; Wenger, Jérôme; Lenne, Pierre-François; Rigneault, Hervé

2011-03-02

Many efforts have been undertaken over the last few decades to characterize the diffusion process in model and cellular lipid membranes. One of the techniques developed for this purpose, fluorescence correlation spectroscopy (FCS), has proved to be a very efficient approach, especially if the analysis is extended to measurements on different spatial scales (referred to as FCS diffusion laws). In this work, we examine the relevance of FCS diffusion laws for probing the behavior of a pure lipid and a lipid mixture at temperatures below, within and above the phase transitions, both experimentally and numerically. The accuracy of the microscopic description of the lipid mixtures found here extends previous work to a more complex model in which the geometry is unknown and the molecular motion is driven only by the thermodynamic parameters of the system itself. For multilamellar vesicles of both pure lipid and lipid mixtures, the FCS diffusion laws recorded at different temperatures exhibit large deviations from pure Brownian motion and reveal the existence of nanodomains. The variation of the mean size of these domains with temperature is in perfect correlation with the enthalpy fluctuation. This study highlights the advantages of using FCS diffusion laws in complex lipid systems to describe their temporal and spatial structure. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Nonmonotonic diffusion in crowded environments

PubMed Central

Putzel, Gregory Garbès; Tagliazucchi, Mario; Szleifer, Igal

2015-01-01

We study the diffusive motion of particles among fixed spherical crowders. The diffusers interact with the crowders through a combination of a hard-core repulsion and a short-range attraction. The long-time effective diffusion coefficient of the diffusers is found to depend non-monotonically on the strength of their attraction to the crowders. That is, for a given concentration of crowders, a weak attraction to the crowders enhances diffusion. We show that this counterintuitive fact can be understood in terms of the mesoscopic excess chemical potential landscape experienced by the diffuser. The roughness of this excess chemical potential landscape quantitatively captures the nonmonotonic dependence of the diffusion rate on the strength of crowder-diffuser attraction; thus it is a purely static predictor of dynamic behavior. The mesoscopic view given here provides a unified explanation for enhanced diffusion effects that have been found in various systems of technological and biological interest. PMID:25302920

Determination of malignancy and characterization of hepatic tumor type with diffusion-weighted magnetic resonance imaging: comparison of apparent diffusion coefficient and intravoxel incoherent motion-derived measurements.

PubMed

Doblas, Sabrina; Wagner, Mathilde; Leitao, Helena S; Daire, Jean-Luc; Sinkus, Ralph; Vilgrain, Valérie; Van Beers, Bernard E

2013-10-01

The objective of this study was to compare the value of the apparent diffusion coefficient (ADC) determined with 3 b values and the intravoxel incoherent motion (IVIM)-derived parameters in the determination of malignancy and characterization of hepatic tumor type. Seventy-six patients with 86 solid hepatic lesions, including 8 hemangiomas, 20 lesions of focal nodular hyperplasia, 9 adenomas, 30 hepatocellular carcinomas, 13 metastases, and 6 cholangiocarcinomas, were assessed in this prospective study. Diffusion-weighted images were acquired with 11 b values to measure the ADCs (with b = 0, 150, and 500 s/mm) and the IVIM-derived parameters, namely, the pure diffusion coefficient and the perfusion-related diffusion fraction and coefficient. The diffusion parameters were compared between benign and malignant tumors and between tumor types, and their diagnostic value in identifying tumor malignancy was assessed. The apparent and pure diffusion coefficients were significantly higher in benign than in malignant tumors (benign: 2.32 [0.87] × 10 mm/s and 1.42 [0.37] × 10 mm/s vs malignant: 1.64 [0.51] × 10 mm/s and 1.14 [0.28] × 10 mm/s, respectively; P < 0.0001 and P = 0.0005), whereas the perfusion-related diffusion parameters did not differ significantly between the 2 groups. The apparent and pure diffusion coefficients provided similar accuracy in assessing tumor malignancy (areas under the receiver operating characteristic curve of 0.770 and 0.723, respectively). In the multigroup analysis, the ADC was found to be significantly higher in hemangiomas than in hepatocellular carcinomas, metastases, and cholangiocarcinomas. In the same manner, it was higher in lesions of focal nodular hyperplasia than in metastases and cholangiocarcinomas. However, the pure diffusion coefficient was significantly higher only in hemangiomas versus hepatocellular and cholangiocellular carcinomas. Compared with the ADC, the diffusion parameters derived from the IVIM model did not improve the determination of malignancy and characterization of hepatic tumor type.

Analysis and Comparison with DNS of a Stochastic Model for the Relative Motion of High-Stokes-Number Particles in Isotropic Turbulence

NASA Astrophysics Data System (ADS)

Dhariwal, Rohit; Rani, Sarma; Koch, Donald

2015-11-01

In an earlier work, Rani, Dhariwal, and Koch (JFM, Vol. 756, 2014) developed an analytical closure for the diffusion current in the PDF transport equation describing the relative motion of high-Stokes-number particle pairs in isotropic turbulence. In this study, an improved closure was developed for the diffusion coefficient, such that the motion of the particle-pair center of mass is taken into account. Using the earlier and the new analytical closures, Langevin simulations of pair relative motion were performed for four particle Stokes numbers, Stη = 10 , 20 , 40 , 80 and at two Taylor micro-scale Reynolds numbers Reλ = 76 , 131 . Detailed comparisons of the analytical model predictions with those of DNS were undertaken. It is seen that the pair relative motion statistics obtained from the improved theory show excellent agreement with the DNS statistics. The radial distribution functions (RDFs), and relative velocity PDFs obtained from the improved-closure-based Langevin simulations are found to be in very good agreement with those from DNS. It was found that the RDFs and relative velocity RMS increased with Reλ for all Stη . The collision kernel also increased strongly with Reλ , since it depended on the RDF and the radial relative velocities.

Two-dimensional nature of the active Brownian motion of catalytic microswimmers at solid and liquid interfaces

NASA Astrophysics Data System (ADS)

Dietrich, Kilian; Renggli, Damian; Zanini, Michele; Volpe, Giovanni; Buttinoni, Ivo; Isa, Lucio

2017-06-01

Colloidal particles equipped with platinum patches can establish chemical gradients in H2O2-enriched solutions and undergo self-propulsion due to local diffusiophoretic migration. In bulk (3D), this class of active particles swim in the direction of the surface heterogeneities introduced by the patches and consequently reorient with the characteristic rotational diffusion time of the colloids. In this article, we present experimental and numerical evidence that planar 2D confinements defy this simple picture. Instead, the motion of active particles both on solid substrates and at flat liquid-liquid interfaces is captured by a 2D active Brownian motion model, in which rotational and translational motion are constrained in the xy-plane. This leads to an active motion that does not follow the direction of the surface heterogeneities and to timescales of reorientation that do not match the free rotational diffusion times. Furthermore, 2D-confinement at fluid-fluid interfaces gives rise to a unique distribution of swimming velocities: the patchy colloids uptake two main orientations leading to two particle populations with velocities that differ up to one order of magnitude. Our results shed new light on the behavior of active colloids in 2D, which is of interest for modeling and applications where confinements are present.

MRI quantification of diffusion and perfusion in bone marrow by intravoxel incoherent motion (IVIM) and non-negative least square (NNLS) analysis.

PubMed

Marchand, A J; Hitti, E; Monge, F; Saint-Jalmes, H; Guillin, R; Duvauferrier, R; Gambarota, G

2014-11-01

To assess the feasibility of measuring diffusion and perfusion fraction in vertebral bone marrow using the intravoxel incoherent motion (IVIM) approach and to compare two fitting methods, i.e., the non-negative least squares (NNLS) algorithm and the more commonly used Levenberg-Marquardt (LM) non-linear least squares algorithm, for the analysis of IVIM data. MRI experiments were performed on fifteen healthy volunteers, with a diffusion-weighted echo-planar imaging (EPI) sequence at five different b-values (0, 50, 100, 200, 600 s/mm2), in combination with an STIR module to suppress the lipid signal. Diffusion signal decays in the first lumbar vertebra (L1) were fitted to a bi-exponential function using the LM algorithm and further analyzed with the NNLS algorithm to calculate the values of the apparent diffusion coefficient (ADC), pseudo-diffusion coefficient (D*) and perfusion fraction. The NNLS analysis revealed two diffusion components only in seven out of fifteen volunteers, with ADC=0.60±0.09 (10(-3) mm(2)/s), D*=28±9 (10(-3) mm2/s) and perfusion fraction=14%±6%. The values obtained by the LM bi-exponential fit were: ADC=0.45±0.27 (10(-3) mm2/s), D*=63±145 (10(-3) mm2/s) and perfusion fraction=27%±17%. Furthermore, the LM algorithm yielded values of perfusion fraction in cases where the decay was not bi-exponential, as assessed by NNLS analysis. The IVIM approach allows for measuring diffusion and perfusion fraction in vertebral bone marrow; its reliability can be improved by using the NNLS, which identifies the diffusion decays that display a bi-exponential behavior. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Unusual Circularly Polarized and Aggregation-Induced Near-Infrared Phosphorescence of Helical Platinum(II) Complexes with Tetradentate Salen Ligands.

PubMed

Song, Jintong; Wang, Man; Zhou, Xiangge; Xiang, Haifeng

2018-05-17

A series of chiral and helical Pt II -Salen complexes with 1,1'-binaphthyl linkers were synthesized and characterized. Owing to the restriction of intramolecular motions of central 1,1'-binaphthyls, the complexes exhibit unusual near-infrared aggregation-induced phosphorescence (AIP). The (R)/(S) enantiopure complexes were characterized by X-ray diffraction, circular dichroism spectra, time-dependent density functional theory calculations, and circularly polarized luminescence (CPL). The present work explores the use of tetradentate ligands that can be easily prepared from commercially available enantiopure compounds, and the subsequent preparation of stable CPL-active square planar Pt II complexes with AIP effect that may have interest in many applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of polycyclic molecules by double C(sp2)-H/C(sp3)-H arylations with a single palladium catalyst.

PubMed

Pierre, Cathleen; Baudoin, Olivier

2011-04-01

Polycyclic molecules were obtained in good yields by double C(sp(2))-H/C(sp(3))-H arylations mediated by a single palladium/phosphine catalyst. Both double intermolecular/intramolecular and intramolecular/intramolecular C-C couplings were performed successfully, which indicates that this concept has a broad applicability for the rapid construction of molecular complexity.

Dynamic and Inherent B0 Correction for DTI Using Stimulated Echo Spiral Imaging

PubMed Central

Avram, Alexandru V.; Guidon, Arnaud; Truong, Trong-Kha; Liu, Chunlei; Song, Allen W.

2013-01-01

Purpose To present a novel technique for high-resolution stimulated echo (STE) diffusion tensor imaging (DTI) with self-navigated interleaved spirals (SNAILS) readout trajectories that can inherently and dynamically correct for image artifacts due to spatial and temporal variations in the static magnetic field (B0) resulting from eddy currents, tissue susceptibilities, subject/physiological motion, and hardware instabilities. Methods The Hahn spin echo formed by the first two 90° radio-frequency pulses is balanced to consecutively acquire two additional images with different echo times (TE) and generate an inherent field map, while the diffusion-prepared STE signal remains unaffected. For every diffusion-encoding direction, an intrinsically registered field map is estimated dynamically and used to effectively and inherently correct for off-resonance artifacts in the reconstruction of the corresponding diffusion-weighted image (DWI). Results After correction with the dynamically acquired field maps, local blurring artifacts are specifically removed from individual STE DWIs and the estimated diffusion tensors have significantly improved spatial accuracy and larger fractional anisotropy. Conclusion Combined with the SNAILS acquisition scheme, our new method provides an integrated high-resolution short-TE DTI solution with inherent and dynamic correction for both motion-induced phase errors and off-resonance effects. PMID:23630029

Correlation time and diffusion coefficient imaging: application to a granular flow system.

PubMed

Caprihan, A; Seymour, J D

2000-05-01

A parametric method for spatially resolved measurements for velocity autocorrelation functions, R(u)(tau) = , expressed as a sum of exponentials, is presented. The method is applied to a granular flow system of 2-mm oil-filled spheres rotated in a half-filled horizontal cylinder, which is an Ornstein-Uhlenbeck process with velocity autocorrelation function R(u)(tau) = e(- ||tau ||/tau(c)), where tau(c) is the correlation time and D = tau(c) is the diffusion coefficient. The pulsed-field-gradient NMR method consists of applying three different gradient pulse sequences of varying motion sensitivity to distinguish the range of correlation times present for particle motion. Time-dependent apparent diffusion coefficients are measured for these three sequences and tau(c) and D are then calculated from the apparent diffusion coefficient images. For the cylinder rotation rate of 2.3 rad/s, the axial diffusion coefficient at the top center of the free surface was 5.5 x 10(-6) m(2)/s, the correlation time was 3 ms, and the velocity fluctuation or granular temperature was 1.8 x 10(-3) m(2)/s(2). This method is also applicable to study transport in systems involving turbulence and porous media flows. Copyright 2000 Academic Press.

Dynamics in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Clarke, Nigel

2015-03-01

Since nanoparticles are increasingly being added to polymers to impart mechanical and functional properties, we are exploring how nanoparticles impact polymer dynamics with a focus on the diffusion coefficients. In high molecular weight polymer melts, chain diffusion is well described by the reptation model. Motion proceeds as a snake-like diffusion of the chain as a whole, along the contour of a tube that mimics the role of physical entanglements, or topological constraints, with other chains. In polymer nanocomposites there are additional constraints due to the dispersed nanoparticles in the polymer matrix. Chain motion can be altered by nanoparticle size, shape , aspect ratio, surface area, loading and the nature of the interactions between the nanoparticles and the polymer matrix. We have observed a minimum in the diffusion coefficient as a function of nanoparticle concentration when the nanoparticles are rod-like and a collapse of the diffusion coefficient onto a master curve when the nanoparticles are spherical. We are simulating the dynamics using molecular and dissipative particle simulations in order to provide physical insight into the local structure and dynamics, and have also carried out highly coarse grained Monte Carlo simulations of entangled polymers to explore how reptation is affected by the presence of larger scale obstacles. We acknowledge support from the NSF/EPSRC Materials World Network Program.

Connection between encounter volume and diffusivity in geophysical flows

NASA Astrophysics Data System (ADS)

Rypina, Irina I.; Smith, Stefan G. Llewellyn; Pratt, Larry J.

2018-04-01

Trajectory encounter volume - the volume of fluid that passes close to a reference fluid parcel over some time interval - has been recently introduced as a measure of mixing potential of a flow. Diffusivity is the most commonly used characteristic of turbulent diffusion. We derive the analytical relationship between the encounter volume and diffusivity under the assumption of an isotropic random walk, i.e., diffusive motion, in one and two dimensions. We apply the derived formulas to produce maps of encounter volume and the corresponding diffusivity in the Gulf Stream region of the North Atlantic based on satellite altimetry, and discuss the mixing properties of Gulf Stream rings. Advantages offered by the derived formula for estimating diffusivity from oceanographic data are discussed, as well as applications to other disciplines.

Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals

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

Polikanov, Yury S.; Moore, Peter B.

2015-09-26

The diffuse scattering pattern produced by frozen crystals of the 70S ribosome fromThermus thermophilusis as highly structured as it would be if it resulted entirely from domain-scale motions within these particles. However, the qualitative properties of the scattering pattern suggest that acoustic displacements of the crystal lattice make a major contribution to it.

Transition density of one-dimensional diffusion with discontinuous drift

NASA Technical Reports Server (NTRS)

Zhang, Weijian

1990-01-01

The transition density of a one-dimensional diffusion process with a discontinuous drift coefficient is studied. A probabilistic representation of the transition density is given, illustrating the close connections between discontinuities of the drift and Brownian local times. In addition, some explicit results are obtained based on the trivariate density of Brownian motion, its occupation, and local times.

Normal versus anomalous self-diffusion in two-dimensional fluids: memory function approach and generalized asymptotic Einstein relation.

PubMed

Shin, Hyun Kyung; Choi, Bongsik; Talkner, Peter; Lee, Eok Kyun

2014-12-07

Based on the generalized Langevin equation for the momentum of a Brownian particle a generalized asymptotic Einstein relation is derived. It agrees with the well-known Einstein relation in the case of normal diffusion but continues to hold for sub- and super-diffusive spreading of the Brownian particle's mean square displacement. The generalized asymptotic Einstein relation is used to analyze data obtained from molecular dynamics simulations of a two-dimensional soft disk fluid. We mainly concentrated on medium densities for which we found super-diffusive behavior of a tagged fluid particle. At higher densities a range of normal diffusion can be identified. The motion presumably changes to sub-diffusion for even higher densities.

Normal versus anomalous self-diffusion in two-dimensional fluids: Memory function approach and generalized asymptotic Einstein relation

NASA Astrophysics Data System (ADS)

Shin, Hyun Kyung; Choi, Bongsik; Talkner, Peter; Lee, Eok Kyun

2014-12-01

Based on the generalized Langevin equation for the momentum of a Brownian particle a generalized asymptotic Einstein relation is derived. It agrees with the well-known Einstein relation in the case of normal diffusion but continues to hold for sub- and super-diffusive spreading of the Brownian particle's mean square displacement. The generalized asymptotic Einstein relation is used to analyze data obtained from molecular dynamics simulations of a two-dimensional soft disk fluid. We mainly concentrated on medium densities for which we found super-diffusive behavior of a tagged fluid particle. At higher densities a range of normal diffusion can be identified. The motion presumably changes to sub-diffusion for even higher densities.

Anomalous diffusion for bed load transport with a physically-based model

NASA Astrophysics Data System (ADS)

Fan, N.; Singh, A.; Foufoula-Georgiou, E.; Wu, B.

2013-12-01

Diffusion of bed load particles shows both normal and anomalous behavior for different spatial-temporal scales. Understanding and quantifying these different types of diffusion is important not only for the development of theoretical models of particle transport but also for practical purposes, e.g., river management. Here we extend a recently proposed physically-based model of particle transport by Fan et al. [2013] to further develop an Episodic Langevin equation (ELE) for individual particle motion which reproduces the episodic movement (start and stop) of sediment particles. Using the proposed ELE we simulate particle movements for a large number of uniform size particles, incorporating different probability distribution functions (PDFs) of particle waiting time. For exponential PDFs of waiting times, particles reveal ballistic motion in short time scales and turn to normal diffusion at long time scales. The PDF of simulated particle travel distances also shows a change in its shape from exponential to Gamma to Gaussian with a change in timescale implying different diffusion scaling regimes. For power-law PDF (with power - μ) of waiting times, the asymptotic behavior of particles at long time scales reveals both super-diffusion and sub-diffusion, however, only very heavy tailed waiting times (i.e. 1.0 < μ < 1.5) could result in sub-diffusion. We suggest that the contrast between our results and previous studies (for e.g., studies based on fractional advection-diffusion models of thin/heavy tailed particle hops and waiting times) results could be due the assumption in those studies that the hops are achieved instantaneously, but in reality, particles achieve their hops within finite times (as we simulate here) instead of instantaneously, even if the hop times are much shorter than waiting times. In summary, this study stresses on the need to rethink the alternative models to the previous models, such as, fractional advection-diffusion equations, for studying the anomalous diffusion of bed load particles. The implications of these results for modeling sediment transport are discussed.

Intravoxel Incoherent Motion MR Imaging in the Differentiation of Benign and Malignant Sinonasal Lesions: Comparison with Conventional Diffusion-Weighted MR Imaging.

PubMed

Xiao, Z; Tang, Z; Qiang, J; Wang, S; Qian, W; Zhong, Y; Wang, R; Wang, J; Wu, L; Tang, W; Zhang, Z

2018-01-25

Intravoxel incoherent motion is a promising method for the differentiation of sinonasal lesions. This study aimed to evaluate the value of intravoxel incoherent motion in the differentiation of benign and malignant sinonasal lesions and to compare the diagnostic performance of intravoxel incoherent motion with that of conventional DWI. One hundred thirty-one patients with histologically proved solid sinonasal lesions (56 benign and 75 malignant) who underwent conventional DWI and intravoxel incoherent motion were recruited in this study. The diffusion coefficient ( D ), pseudodiffusion coefficient ( D *), and perfusion fraction ( f ) values derived from intravoxel incoherent motion and ADC values derived from conventional DWI were measured and compared between the 2 groups using the Student t test. Receiver operating characteristic curve analysis, logistic regression analysis, and 10-fold cross-validation were performed to evaluate the diagnostic performance of single-parametric and multiparametric models. The mean ADC and D values were significantly lower in malignant sinonasal lesions than in benign sinonasal lesions (both P < .001). The mean f value was higher in malignant lesions than in benign lesions ( P = .003). Multiparametric models can significantly improve the cross-validated areas under the curve for the differentiation of sinonasal lesions compared with single-parametric models (all corrected P < .05 except the D value). The model of D + f provided a better diagnostic performance than the ADC value (corrected P < .001). Intravoxel incoherent motion appears to be a more effective MR imaging technique than conventional DWI in the differentiation of benign and malignant sinonasal lesions. © 2018 by American Journal of Neuroradiology.

Trouble with diffusion: Reassessing hillslope erosion laws with a particle-based model

NASA Astrophysics Data System (ADS)

Tucker, Gregory E.; Bradley, D. Nathan

2010-03-01

Many geomorphic systems involve a broad distribution of grain motion length scales, ranging from a few particle diameters to the length of an entire hillslope or stream. Studies of analogous physical systems have revealed that such broad motion distributions can have a significant impact on macroscale dynamics and can violate the assumptions behind standard, local gradient flux laws. Here, a simple particle-based model of sediment transport on a hillslope is used to study the relationship between grain motion statistics and macroscopic landform evolution. Surface grains are dislodged by random disturbance events with probabilities and distances that depend on local microtopography. Despite its simplicity, the particle model reproduces a surprisingly broad range of slope forms, including asymmetric degrading scarps and cinder cone profiles. At low slope angles the dynamics are diffusion like, with a short-range, thin-tailed hop length distribution, a parabolic, convex upward equilibrium slope form, and a linear relationship between transport rate and gradient. As slope angle steepens, the characteristic grain motion length scale begins to approach the length of the slope, leading to planar equilibrium forms that show a strongly nonlinear correlation between transport rate and gradient. These high-probability, long-distance motions violate the locality assumption embedded in many common gradient-based geomorphic transport laws. The example of a degrading scarp illustrates the potential for grain motion dynamics to vary in space and time as topography evolves. This characteristic renders models based on independent, stationary statistics inapplicable. An accompanying analytical framework based on treating grain motion as a survival process is briefly outlined.

Diffusion tensor imaging (DTI) with retrospective motion correction for large-scale pediatric imaging.

PubMed

Holdsworth, Samantha J; Aksoy, Murat; Newbould, Rexford D; Yeom, Kristen; Van, Anh T; Ooi, Melvyn B; Barnes, Patrick D; Bammer, Roland; Skare, Stefan

2012-10-01

To develop and implement a clinical DTI technique suitable for the pediatric setting that retrospectively corrects for large motion without the need for rescanning and/or reacquisition strategies, and to deliver high-quality DTI images (both in the presence and absence of large motion) using procedures that reduce image noise and artifacts. We implemented an in-house built generalized autocalibrating partially parallel acquisitions (GRAPPA)-accelerated diffusion tensor (DT) echo-planar imaging (EPI) sequence at 1.5T and 3T on 1600 patients between 1 month and 18 years old. To reconstruct the data, we developed a fully automated tailored reconstruction software that selects the best GRAPPA and ghost calibration weights; does 3D rigid-body realignment with importance weighting; and employs phase correction and complex averaging to lower Rician noise and reduce phase artifacts. For select cases we investigated the use of an additional volume rejection criterion and b-matrix correction for large motion. The DTI image reconstruction procedures developed here were extremely robust in correcting for motion, failing on only three subjects, while providing the radiologists high-quality data for routine evaluation. This work suggests that, apart from the rare instance of continuous motion throughout the scan, high-quality DTI brain data can be acquired using our proposed integrated sequence and reconstruction that uses a retrospective approach to motion correction. In addition, we demonstrate a substantial improvement in overall image quality by combining phase correction with complex averaging, which reduces the Rician noise that biases noisy data. Copyright © 2012 Wiley Periodicals, Inc.

Performance of U-net based pyramidal lucas-kanade registration on free-breathing multi-b-value diffusion MRI of the kidney.

PubMed

Lv, Jun; Huang, Wenjian; Zhang, Jue; Wang, Xiaoying

2018-06-01

In free-breathing multi-b-value diffusion-weighted imaging (DWI), a series of images typically requires several minutes to collect. During respiration the kidney is routinely displaced and may also undergo deformation. These respiratory motion effects generate artifacts and these are the main sources of error in the quantification of intravoxel incoherent motion (IVIM) derived parameters. This work proposes a fully automated framework that combines a kidney segmentation to improve the registration accuracy. 10 healthy subjects were recruited to participate in this experiment. For the segmentation, U-net was adopted to acquire the kidney's contour. The segmented kidney then served as a region of interest (ROI) for the registration method, known as pyramidal Lucas-Kanade. Our proposed framework confines the kidney's solution range, thus increasing the pyramidal Lucas-Kanade's accuracy. To demonstrate the feasibility of our presented framework, eight regions of interest were selected in the cortex and medulla, and data stability was estimated by comparing the normalized root-mean-square error (NRMSE) values of the fitted data from the bi-exponential intravoxel incoherent motion model pre- and post- registration. The results show that the NRMSE was significantly lower after registration both in the cortex (p < 0.05) and medulla (p < 0.01) during free-breathing measurements. In addition, expert visual scoring of the derived apparent diffusion coefficient (ADC), f, D and D* maps indicated there were significant improvements in the alignment of the kidney in the post-registered image. The proposed framework can effectively reduce the motion artifacts of misaligned multi-b-value DWIs and the inaccuracies of the ADC, f, D and D* estimations. Advances in knowledge: This study demonstrates the feasibility of our proposed fully automated framework combining U-net based segmentation and pyramidal Lucas-Kanade registration method for improving the alignment of multi-b-value diffusion-weighted MRIs and reducing the inaccuracy of parameter estimation during free-breathing.

Excited stilbene: intramolecular vibrational redistribution and solvation studied by femtosecond stimulated Raman spectroscopy.

PubMed

Weigel, A; Ernsting, N P

2010-06-17

Excited-state relaxation of cis- and trans-stilbene is traced with femtosecond stimulated Raman spectroscopy, exploiting S(n) <-- S(1) resonance conditions. For both isomers, decay in Raman intensity, shift of spectral positions, and broadening of the bands indicate intramolecular vibrational redistribution (IVR). In n-hexane this process effectively takes 0.5-0.7 ps. Analysis of the intensity decay allows us to further distinguish two phases for trans-stilbene: fast IVR within a subset of modes (approximately 0.3 ps) followed by slower equilibration over the full vibrational manifold (approximately 0.9 ps). In acetonitrile IVR completes with 0.15 ps; this acceleration may originate from symmetry breakage induced by the polar solvent. Another process, dynamic solvation by acetonitrile, is seen as spectral narrowing and characteristic band shifts of the C=C stretch and phenyl bending modes with 0.69 ps. Wavepacket motion is observed in both isomers as oscillation of low-frequency bands with their pertinent mode frequency (90 or 195 cm(-1) in trans-stilbene; 250 cm(-1) in cis-stilbene). Anharmonic coupling shows up as a modulation of high-frequency peak positions by phenyl/ethylene torsion modes of 57 and 90 cm(-1). Decay and shift of the 90 cm(-1) inverse Raman band within the first 0.3 ps suggests a gradual involvement of phenyl/ethylene torsion in relaxation. In cis- and trans-stilbene, low-frequency spectral changes are found within 0.15 ps, indicating an additional ultrafast process.

Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains.

PubMed

Zhou, Huan-Xiang

2006-11-01

Flexible linkers are often found to tether binding sequence motifs or connect protein domains. Here we analyze three usages of flexible linkers: 1), intramolecular binding of proline-rich peptides (PRPs) to SH3 domains for kinase regulation; 2), intramolecular binding of PRP for increasing the folding stability of SH3 domains; and 3), covalent linking of PRPs and other ligands for high-affinity bivalent binding. The basis of these analyses is a quantitative relation between intermolecular and intramolecular binding constants. This relation has the form K(i) = K(e0)p for intramolecular binding and K(e) = K(e01)K(e02)p for bivalent binding. The effective concentration p depends on the length of the linker and the distance between the linker attachment points in the bound state. Several applications illustrate the usefulness of the quantitative relation. These include intramolecular binding to the Itk SH3 domain by an internal PRP and to a circular permutant of the alpha-spectrin SH3 domain by a designed PRP, and bivalent binding to the two SH3 domains of Grb2 by two linked PRPs. These and other examples suggest that flexible linkers and sequence motifs tethered to them, like folded protein domains, are also subject to tight control during evolution.

Rotational and translational diffusions of fluorescent probes during gelation process

NASA Astrophysics Data System (ADS)

Hattori, Yusuke; Panizza, Pascal; Letamendia, Louis; Ushiki, Hideharu

2006-04-01

Gelation process has been investigated by using light scattering techniques in recent years. We measured both of rotational and translational motions of fluorescent probes during gelation process. The measurements were performed after the temperature quenched at 30 °C. As the results, rotational diffusion coefficient of fluorescein was decreased after 6.0 × 10 4 s and energy transfer rate was reduced after 2.0 × 10 4 s. We sorted the gelation process into the following three parts, (I) pre-gelation, (II) reduction of translational diffusion (aging), and (III) reduction of rotational diffusion with saturating translational diffusion (post-gelation). The time scale of the process was completely different from the results of other methods.

On the autonomous motion of active drops or bubbles.

PubMed

Ryazantsev, Yuri S; Velarde, Manuel G; Guzman, Eduardo; Rubio, Ramón G; Ortega, Francisco; Montoya, Juan-Jose

2018-05-19

Thermo-capillary stresses on the surface of a drop can be the result of a non-isothermal surface chemical conversion of a reactant dissolved in the host fluid. The strength of heat production (with e.g. absorption) on the surface is ruled by the diffusion of the reactant and depends on the state of motion of the drop. Such thermo-capillary stresses can provoke the motion of the drop or its motionless state in the presence of an external body force. If in the balance of forces, including indeed viscous drag, the net resultant force vanishes there is the possibility of autonomous motion with constant velocity of the drop. Focusing on drops with radii in the millimeter range provided here is a quantitative study of the possibility of such autonomous motion when the drop, considered as active unit, is seat of endo- or exo-thermic reactive processes that dominate its motion. The framework is restricted to Stokes flows in the hydrodynamics, negligible heat Peclet number while the solute Peclet number is considered very high. A boundary layer approximation is used in the description of reactant diffusion. Those processes eventually end up in the action being expressed by surface tension gradients and the Marangoni effect. Explicit expressions of the force acting on the drop and the velocity fields inside and outside the drop are provided. Some significant particular cases are discussed to illustrate the usefulness of the theory. Copyright © 2018. Published by Elsevier Inc.

Subcontinental-scale crustal velocity changes along the Pacific-North America plate boundary.

PubMed

Davis, J L; Wernicke, B P; Bisnath, S; Niemi, N A; Elósegui, P

2006-06-29

Transient tectonic deformation has long been noted within approximately 100 km of plate boundary fault zones and within active volcanic regions, but it is unknown whether transient motions also occur at larger scales within plates. Relatively localized transients are known to occur as both seismic and episodic aseismic events, and are generally ascribed to motions of magma bodies, aseismic creep on faults, or elastic or viscoelastic effects associated with earthquakes. However, triggering phenomena and systematic patterns of seismic strain release at subcontinental (approximately 1,000 km) scale along diffuse plate boundaries have long suggested that energy transfer occurs at larger scale. Such transfer appears to occur by the interaction of stresses induced by surface wave propagation and magma or groundwater in the crust, or from large-scale stress diffusion within the oceanic mantle in the decades following clusters of great earthquakes. Here we report geodetic evidence for a coherent, subcontinental-scale change in tectonic velocity along a diffuse approximately 1,000-km-wide deformation zone. Our observations are derived from continuous GPS (Global Positioning System) data collected over the past decade across the Basin and Range province, which absorbs approximately 25 per cent of Pacific-North America relative plate motion. The observed changes in site velocity define a sharp boundary near the centre of the province oriented roughly parallel to the north-northwest relative plate motion vector. We show that sites to the west of this boundary slowed relative to sites east of it by approximately 1 mm yr(-1) starting in late 1999.

Femtosecond dynamics in hydrogen-bonded solvents

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

Castner, E.W. Jr.; Chang, Y.J.

1993-09-01

We present results on the ultrafast dynamics of pure hydrogen-bonding solvents, obtained using femtosecond Fourier-transform optical-heterodyne-detected, Raman-induced Kerr effect spectroscopy. Solvent systems we have studied include the formamides, water, ethylene glycol, and acetic acid. Inertial and diffusive motions are clearly resolved. We comment on the effect that such ultrafast solvent motions have on chemical reactions in solution.

Microphysics of liquid complex plasmas in equilibrium and non-equilibrium systems

NASA Astrophysics Data System (ADS)

Piel, Alexander; Block, Dietmar; Melzer, André; Mulsow, Matthias; Schablinski, Jan; Schella, André; Wieben, Frank; Wilms, Jochen

2018-05-01

The dynamic evolution of the microscopic structure of solid and liquid phases of complex plasmas is studied experimentally and by means of molecular dynamics (MD) simulations. In small finite systems, the cooperative motion can be described in terms of discrete modes. These modes are studied with different experimental approaches. Using diffuse scattered laser light, applying laser tweezer forces to individual particles, and periodic laser pulses, the excitation of modes is investigated. The instantaneous normal mode analysis of experimental data from two-dimensional liquid clusters gives access to the local dynamics of the liquid phase. Our investigations shed light on the role of compressional and shear modes as well as the determination of diffusion constants and melting temperatures in finite systems. Special attention is paid to hydrodynamic situations with a stationary inhomogeneous dust flow. MD simulations allow to study the collective motion in the shell of nearest neighbors, which can be linked to smooth and sudden changes of the macroscopic flow. Finally, the observed micro-motion in all situations above allows to shed light on the preference of shear-like over compressional motion in terms of a minimized potential energy and a dynamic incompressibility.

Ab initio study of edge effect on relative motion of walls in carbon nanotubes

NASA Astrophysics Data System (ADS)

Popov, Andrey M.; Lebedeva, Irina V.; Knizhnik, Andrey A.; Lozovik, Yurii E.; Potapkin, Boris V.

2013-01-01

Interwall interaction energies of double-walled nanotubes with long inner and short outer walls are calculated as functions of coordinates describing relative rotation and displacement of the walls using van der Waals corrected density functional theory. The magnitude of corrugation and the shape of the potential energy relief are found to be very sensitive to changes of the shorter wall length at subnanometer scale and atomic structure of the edges if at least one of the walls is chiral. Threshold forces required to start relative motion of the short walls and temperatures at which the transition between diffusive and free motion of the short walls takes place are estimated. The edges are also shown to provide a considerable contribution to the barrier to relative rotation of commensurate nonchiral walls. For such walls, temperatures of orientational melting, i.e., the crossover from rotational diffusion to free relative rotation, are estimated. The possibility to produce nanotube-based bolt/nut pairs and nanobearings is discussed.

Brownian motion of tethered nanowires.

PubMed

Ota, Sadao; Li, Tongcang; Li, Yimin; Ye, Ziliang; Labno, Anna; Yin, Xiaobo; Alam, Mohammad-Reza; Zhang, Xiang

2014-05-01

Brownian motion of slender particles near a boundary is ubiquitous in biological systems and in nanomaterial assembly, but the complex hydrodynamic interaction in those systems is still poorly understood. Here, we report experimental and computational studies of the Brownian motion of silicon nanowires tethered on a substrate. An optical interference method enabled direct observation of microscopic rotations of the slender bodies in three dimensions with high angular and temporal resolutions. This quantitative observation revealed anisotropic and angle-dependent hydrodynamic wall effects: rotational diffusivity in inclined and azimuth directions follows different power laws as a function of the length, ∼ L(-2.5) and ∼ L(-3), respectively, and is more hindered for smaller inclined angles. In parallel, we developed an implicit simulation technique that takes the complex wire-wall hydrodynamic interactions into account efficiently, the result of which agreed well with the experimentally observed angle-dependent diffusion. The demonstrated techniques provide a platform for studying the microrheology of soft condensed matters, such as colloidal and biological systems near interfaces, and exploring the optimal self-assembly conditions of nanostructures.

Rotational diffusion of a molecular cat

NASA Astrophysics Data System (ADS)

Katz-Saporta, Ori; Efrati, Efi

We show that a simple isolated system can perform rotational random walk on account of internal excitations alone. We consider the classical dynamics of a ''molecular cat'': a triatomic molecule connected by three harmonic springs with non-zero rest lengths, suspended in free space. In this system, much like for falling cats, the angular momentum constraint is non-holonomic allowing for rotations with zero overall angular momentum. The geometric nonlinearities arising from the non-zero rest lengths of the springs suffice to break integrability and lead to chaotic dynamics. The coupling of the non-integrability of the system and its non-holonomic nature results in an angular random walk of the molecule. We study the properties and dynamics of this angular motion analytically and numerically. For low energy excitations the system displays normal-mode-like motion, while for high enough excitation energy we observe regular random-walk. In between, at intermediate energies we observe an angular Lévy-walk type motion associated with a fractional diffusion coefficient interpolating between the two regimes.

Experimental Studies of the Brownian Diffusion of Boomerang Colloidal Particle in a Confined Geometry

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Wang, Feng; Joshi, Bhuwan; Wei, Qi-Huo

2011-03-01

Recent studies shows that the boomerang shaped molecules can form various kinds of liquid crystalline phases. One debated topic related to boomerang molecules is the existence of biaxial nematic liquid crystalline phase. Developing and optical microscopic studies of colloidal systems of boomerang particles would allow us to gain better understanding of orientation ordering and dynamics at ``single molecule'' level. Here we report the fabrication and experimental studies of the Brownian motion of individual boomerang colloidal particles confined between two glass plates. We used dark-field optical microscopy to directly visualize the Brownian motion of the single colloidal particles in a quasi two dimensional geometry. An EMCCD was used to capture the motion in real time. An indigenously developed imaging processing algorithm based on MatLab program was used to precisely track the position and orientation of the particles with sub-pixel accuracy. The experimental finding of the Brownian diffusion of a single boomerang colloidal particle will be discussed.

Diffusion of myosin light chain kinase on actin: A mechanism to enhance myosin phosphorylation rates in smooth muscle.

PubMed

Hong, Feng; Brizendine, Richard K; Carter, Michael S; Alcala, Diego B; Brown, Avery E; Chattin, Amy M; Haldeman, Brian D; Walsh, Michael P; Facemyer, Kevin C; Baker, Josh E; Cremo, Christine R

2015-10-01

Smooth muscle myosin (SMM) light chain kinase (MLCK) phosphorylates SMM, thereby activating the ATPase activity required for muscle contraction. The abundance of active MLCK, which is tightly associated with the contractile apparatus, is low relative to that of SMM. SMM phosphorylation is rapid despite the low ratio of MLCK to SMM, raising the question of how one MLCK rapidly phosphorylates many SMM molecules. We used total internal reflection fluorescence microscopy to monitor single molecules of streptavidin-coated quantum dot-labeled MLCK interacting with purified actin, actin bundles, and stress fibers of smooth muscle cells. Surprisingly, MLCK and the N-terminal 75 residues of MLCK (N75) moved on actin bundles and stress fibers of smooth muscle cell cytoskeletons by a random one-dimensional (1-D) diffusion mechanism. Although diffusion of proteins along microtubules and oligonucleotides has been observed previously, this is the first characterization to our knowledge of a protein diffusing in a sustained manner along actin. By measuring the frequency of motion, we found that MLCK motion is permitted only if acto-myosin and MLCK-myosin interactions are weak. From these data, diffusion coefficients, and other kinetic and geometric considerations relating to the contractile apparatus, we suggest that 1-D diffusion of MLCK along actin (a) ensures that diffusion is not rate limiting for phosphorylation, (b) allows MLCK to locate to areas in which myosin is not yet phosphorylated, and (c) allows MLCK to avoid getting "stuck" on myosins that have already been phosphorylated. Diffusion of MLCK along actin filaments may be an important mechanism for enhancing the rate of SMM phosphorylation in smooth muscle. © 2015 Hong et al.

Time‐efficient and flexible design of optimized multishell HARDI diffusion

PubMed Central

Tournier, J. Donald; Price, Anthony N.; Cordero‐Grande, Lucilio; Hughes, Emer J.; Malik, Shaihan; Steinweg, Johannes; Bastiani, Matteo; Sotiropoulos, Stamatios N.; Jbabdi, Saad; Andersson, Jesper; Edwards, A. David; Hajnal, Joseph V.

2017-01-01

Purpose Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time‐efficient and flexible diffusion acquisition capability with built‐in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods Complete flexibility in the sampling of diffusion space combined with free choice of phase‐encode‐direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split‐diffusion‐gradient preparation, multiband acceleration, and a restart capacity were added. Results The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high‐angular resolution, maximally time‐efficient (20 min) multishell protocol with 300 diffusion‐weighted volumes was acquired in >400 neonates. An optimal design of a high‐resolution (1.2 × 1.2 mm2) two‐shell acquisition with 54 diffusion weighted volumes was obtained using a split‐gradient design. Conclusion The presented framework provides flexibility to generate time‐efficient and motion‐robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub‐optimal choices. Magn Reson Med 79:1276–1292, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:28557055

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2015-10-01

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratio for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.

Models of collective cell spreading with variable cell aspect ratio: a motivation for degenerate diffusion models.

PubMed

Simpson, Matthew J; Baker, Ruth E; McCue, Scott W

2011-02-01

Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multiscale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (PME). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the PME to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models.

Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions

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

Zhang, Rui; Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu

2015-10-14

We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratiomore » for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.« less

Surface Transient Binding-Based Fluorescence Correlation Spectroscopy (STB-FCS), a Simple and Easy-to-Implement Method to Extend the Upper Limit of the Time Window to Seconds.

PubMed

Peng, Sijia; Wang, Wenjuan; Chen, Chunlai

2018-05-10

Fluorescence correlation spectroscopy is a powerful single-molecule tool that is able to capture kinetic processes occurring at the nanosecond time scale. However, the upper limit of its time window is restricted by the dwell time of the molecule of interest in the confocal detection volume, which is usually around submilliseconds for a freely diffusing biomolecule. Here, we present a simple and easy-to-implement method, named surface transient binding-based fluorescence correlation spectroscopy (STB-FCS), which extends the upper limit of the time window to seconds. We further demonstrated that STB-FCS enables capture of both intramolecular and intermolecular kinetic processes whose time scales cross several orders of magnitude.

Chaotic Motion of Relativistic Electrons Driven by Whistler Waves

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Telnikhin, A. A.; Kronberg, Tatiana K.

2007-01-01

Canonical equations governing an electron motion in electromagnetic field of the whistler mode waves propagating along the direction of an ambient magnetic field are derived. The physical processes on which the equations of motion are based .are identified. It is shown that relativistic electrons interacting with these fields demonstrate chaotic motion, which is accompanied by the particle stochastic heating and significant pitch angle diffusion. Evolution of distribution functions is described by the Fokker-Planck-Kolmogorov equations. It is shown that the whistler mode waves could provide a viable mechanism for stochastic energization of electrons with energies up to 50 MeV in the Jovian magnetosphere.

Effect of micro-stirring on enzymatic reaction kinetics inside a biomimetic container

NASA Astrophysics Data System (ADS)

Gozen, Irep; Horowitz, Viva; Chambers, Zachary; Manoharan, Vinothan

The intracellular environment is dynamic, influenced by the motion of active machinery such as cytoskeleton filaments and molecular motors. To understand whether and how such activity affects the rates of diffusion-limited reactions, we construct a model system consisting of a phospholipid vesicle encapsulating a small number of micro- or nanoparticles, the active motion of which can be induced by chemical or magnetic cues. We aim to determine a relation between active motion of particles and rates of enzymatic reactions in the confined volume. Our findings might illuminate how active motion influences cytoplasmic reaction dynamics, or may have played a role in protocell genetics.

Intramolecular oxidative deselenization of acylselenoureas: a facile synthesis of benzoxazole amides and carbonic anhydrase inhibitors.

PubMed

Angeli, A; Peat, T S; Bartolucci, G; Nocentini, A; Supuran, C T; Carta, F

2016-12-28

A mild, efficient and one pot procedure to access benzoxazoles using easily accessible acylselenoureas as starting materials has been discovered. Mechanistic studies revealed a pH dependent intramolecular oxidative deselenization, with ring closure due to an intramolecular nucleophilic attack of a phenoxide ion. All the benzoxazoles herein reported possessed a primary sulfonamide zinc binding group and showed effective inhibitory action on the enzymes, carbonic anhydrases.

Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene Macromolecules - Synthesis and Characterization

DTIC Science & Technology

2016-04-12

AFRL-AFOSR-CL-TR-2016-0012 Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene Macromolecules Ronald Ziolo CIQA Final Report 07/07...3. DATES COVERED (From - To)  15 Aug 2014 to 14 Jan 2016 4. TITLE AND SUBTITLE Intramolecular Charge Transfer of Conjugated Liquid Crystal Ferrocene...characterization of a new series of conjugated macromolecules bearing ferrocene as a highly efficient electron donor material coupled to 2,5-di(alcoxy) benzene

Formation of benzo[f]-1-indanone frameworks by regulable intramolecular annulations of gem-dialkylthio trienynes.

PubMed

Fang, Zhongxue; Liu, Ying; Barry, Badru-Deen; Liao, Peiqiu; Bi, Xihe

2015-02-20

An atom-economic route to benzo[f]-1-indanone frameworks has been developed starting from the readily available gem-dialkylthio trienynes by intramolecular annulations. The chemoselectivity of the intramolecular cyclizations can be regulated by both the base and the type of gas atmosphere used in the reaction, thus allowing the divergent synthesis of the corresponding functionalized benzo[f]-1-indanones in good to excellent yields.

Active motion assisted by correlated stochastic torques.

PubMed

Weber, Christian; Radtke, Paul K; Schimansky-Geier, Lutz; Hänggi, Peter

2011-07-01

The stochastic dynamics of an active particle undergoing a constant speed and additionally driven by an overall fluctuating torque is investigated. The random torque forces are expressed by a stochastic differential equation for the angular dynamics of the particle determining the orientation of motion. In addition to a constant torque, the particle is supplemented by random torques, which are modeled as an Ornstein-Uhlenbeck process with given correlation time τ(c). These nonvanishing correlations cause a persistence of the particles' trajectories and a change of the effective spatial diffusion coefficient. We discuss the mean square displacement as a function of the correlation time and the noise intensity and detect a nonmonotonic dependence of the effective diffusion coefficient with respect to both correlation time and noise strength. A maximal diffusion behavior is obtained if the correlated angular noise straightens the curved trajectories, interrupted by small pirouettes, whereby the correlated noise amplifies a straightening of the curved trajectories caused by the constant torque.

Generalized quantum Fokker-Planck, diffusion, and Smoluchowski equations with true probability distribution functions.

PubMed

Banik, Suman Kumar; Bag, Bidhan Chandra; Ray, Deb Shankar

2002-05-01

Traditionally, quantum Brownian motion is described by Fokker-Planck or diffusion equations in terms of quasiprobability distribution functions, e.g., Wigner functions. These often become singular or negative in the full quantum regime. In this paper a simple approach to non-Markovian theory of quantum Brownian motion using true probability distribution functions is presented. Based on an initial coherent state representation of the bath oscillators and an equilibrium canonical distribution of the quantum mechanical mean values of their coordinates and momenta, we derive a generalized quantum Langevin equation in c numbers and show that the latter is amenable to a theoretical analysis in terms of the classical theory of non-Markovian dynamics. The corresponding Fokker-Planck, diffusion, and Smoluchowski equations are the exact quantum analogs of their classical counterparts. The present work is independent of path integral techniques. The theory as developed here is a natural extension of its classical version and is valid for arbitrary temperature and friction (the Smoluchowski equation being considered in the overdamped limit).

Velocity relaxation of a particle in a confined compressible fluid

NASA Astrophysics Data System (ADS)

Tatsumi, Rei; Yamamoto, Ryoichi

2013-05-01

The velocity relaxation of an impulsively forced spherical particle in a fluid confined by two parallel plane walls is studied using a direct numerical simulation approach. During the relaxation process, the momentum of the particle is transmitted in the ambient fluid by viscous diffusion and sound wave propagation, and the fluid flow accompanied by each mechanism has a different character and affects the particle motion differently. Because of the bounding walls, viscous diffusion is hampered, and the accompanying shear flow is gradually diminished. However, the sound wave is repeatedly reflected and spreads diffusely. As a result, the particle motion is governed by the sound wave and backtracks differently in a bulk fluid. The time when the backtracking of the particle occurs changes non-monotonically with respect to the compressibility factor ɛ = ν/ac and is minimized at the characteristic compressibility factor. This factor depends on the wall spacing, and the dependence is different at small and large wall spacing regions based on the different mechanisms causing the backtracking.

Directing energy transport in organic photovoltaic cells using interfacial exciton gates.

PubMed

Menke, S Matthew; Mullenbach, Tyler K; Holmes, Russell J

2015-04-28

Exciton transport in organic semiconductors is a critical, mediating process in many optoelectronic devices. Often, the diffusive and subdiffusive nature of excitons in these systems can limit device performance, motivating the development of strategies to direct exciton transport. In this work, directed exciton transport is achieved with the incorporation of exciton permeable interfaces. These interfaces introduce a symmetry-breaking imbalance in exciton energy transfer, leading to directed motion. Despite their obvious utility for enhanced exciton harvesting in organic photovoltaic cells (OPVs), the emergent properties of these interfaces are as yet uncharacterized. Here, directed exciton transport is conclusively demonstrated in both dilute donor and energy-cascade OPVs where judicious optimization of the interface allows exciton transport to the donor-acceptor heterojunction to occur considerably faster than when relying on simple diffusion. Generalized systems incorporating multiple exciton permeable interfaces are also explored, demonstrating the ability to further harness this phenomenon and expeditiously direct exciton motion, overcoming the diffusive limit.

Nanoscale Rheology and Anisotropic Diffusion Using Single Gold Nanorod Probes

NASA Astrophysics Data System (ADS)

Molaei, Mehdi; Atefi, Ehsan; Crocker, John C.

2018-03-01

The complex rotational and translational Brownian motion of anisotropic particles depends on their shape and the viscoelasticity of their surroundings. Because of their strong optical scattering and chemical versatility, gold nanorods would seem to provide the ultimate probes of rheology at the nanoscale, but the suitably accurate orientational tracking required to compute rheology has not been demonstrated. Here we image single gold nanorods with a laser-illuminated dark-field microscope and use optical polarization to determine their three-dimensional orientation to better than one degree. We convert the rotational diffusion of single nanorods in viscoelastic polyethylene glycol solutions to rheology and obtain excellent agreement with bulk measurements. Extensions of earlier models of anisotropic translational diffusion to three dimensions and viscoelastic fluids give excellent agreement with the observed motion of single nanorods. We find that nanorod tracking provides a uniquely capable approach to microrheology and provides a powerful tool for probing nanoscale dynamics and structure in a range of soft materials.

Vibration-Rotation-Tunneling Levels of the Water Dimer from an ab Initio Potential Surface with Flexible Monomers

NASA Astrophysics Data System (ADS)

Leforestier, Claude; van Harrevelt, Rob; van der Avoird, Ad

2009-05-01

The 12-dimensional ab initio potential for the water dimer with flexible monomers from Huang et al. (J. Chem. Phys. 2008, 128, 034312) was used in accurate calculations of the vibration-rotation-tunneling (VRT) levels of (H2O)2 and (D2O)2 involving the intermolecular rovibrational and tunneling states as well as the intramolecular vibrations. For the intermolecular VRT levels we used a 6 + 6d model in which the fast intramolecular vibrations are adiabatically separated from the much slower intermolecular vibrations, tunneling motions, and overall rotations. We also tested two six-dimensional (6d) rigid monomer models in which the monomers were frozen either at their equilibrium geometry or at their ground state vibrationally averaged geometry. All the results from the 6 + 6d model agree well with the large amount of detailed experimental data available from high-resolution spectroscopy. For most of the parameters characterizing the spectra the results of the two 6d rigid monomer models do not significantly differ from the 6 + 6d results. An exception is the relatively large acceptor tunneling splitting, which was the only quantity for which the 6d model with the monomers frozen at their equilibrium geometry was not in good agreement with the experimental data. The 6d model with monomers at their vibrationally averaged geometry performs considerably better, and the full 6 + 6d results agree with the measurements also for this quantity. For the excited intramolecular vibrations we tested two 6 + 6d models. In the first model the excitation was assumed to be either on the donor in the hydrogen bond or on the acceptor, and to hop from one monomer to the other upon donor-acceptor interchange. In the second model the monomer excitation remains localized on a given monomer for all dimer geometries. Almost the same frequencies of the intramolecular vibrations were found for the two models. The calculations show considerable variations in the frequencies of the intramolecular modes for transitions involving different tunneling levels and different values of the rotational quantum number K. For K = 0 → 0 transitions these variations largely cancel, however. A comparison with experimental data is difficult, except for the acceptor asymmetric stretch mode observed in high-resolution spectra, because it is not clear how much the different transitions contribute to the (unresolved) peaks in most of the experimental spectra. The large red shift of the donor bound OH stretch mode is correctly predicted, but the value calculated for this red shift is too small by more than 20%. Also in the smaller shifts of the other modes we find relatively large errors. It is useful, however, that our detailed calculations including all ground and excited state tunneling levels provide an explanation for the splitting of the acceptor asymmetric stretch band observed in He nanodroplet spectra, as well as for the fact that the other bands in these spectra show much smaller or no splittings.

Mapping the exciton diffusion in semiconductor nanocrystal solids.

PubMed

Kholmicheva, Natalia; Moroz, Pavel; Bastola, Ebin; Razgoniaeva, Natalia; Bocanegra, Jesus; Shaughnessy, Martin; Porach, Zack; Khon, Dmitriy; Zamkov, Mikhail

2015-03-24

Colloidal nanocrystal solids represent an emerging class of functional materials that hold strong promise for device applications. The macroscopic properties of these disordered assemblies are determined by complex trajectories of exciton diffusion processes, which are still poorly understood. Owing to the lack of theoretical insight, experimental strategies for probing the exciton dynamics in quantum dot solids are in great demand. Here, we develop an experimental technique for mapping the motion of excitons in semiconductor nanocrystal films with a subdiffraction spatial sensitivity and a picosecond temporal resolution. This was accomplished by doping PbS nanocrystal solids with metal nanoparticles that force the exciton dissociation at known distances from their birth. The optical signature of the exciton motion was then inferred from the changes in the emission lifetime, which was mapped to the location of exciton quenching sites. By correlating the metal-metal interparticle distance in the film with corresponding changes in the emission lifetime, we could obtain important transport characteristics, including the exciton diffusion length, the number of predissociation hops, the rate of interparticle energy transfer, and the exciton diffusivity. The benefits of this approach to device applications were demonstrated through the use of two representative film morphologies featuring weak and strong interparticle coupling.

Thermal motion of a nonlinear localized pattern in a quasi-one-dimensional system.

PubMed

Dessup, Tommy; Coste, Christophe; Saint Jean, Michel

2016-07-01

We study the dynamics of localized nonlinear patterns in a quasi-one-dimensional many-particle system near a subcritical pitchfork bifurcation. The normal form at the bifurcation is given and we show that these patterns can be described as solitary-wave envelopes. They are stable in a large temperature range and can diffuse along the chain of interacting particles. During their displacements the particles are continually redistributed on the envelope. This change of particle location induces a small modulation of the potential energy of the system, with an amplitude that depends on the transverse confinement. At high temperature, this modulation is irrelevant and the thermal motion of the localized patterns displays all the characteristics of a free quasiparticle diffusion with a diffusion coefficient that may be deduced from the normal form. At low temperature, significant physical effects are induced by the modulated potential. In particular, the localized pattern may be trapped at very low temperature. We also exhibit a series of confinement values for which the modulation amplitudes vanishes. For these peculiar confinements, the mean-square displacement of the localized patterns also evidences free-diffusion behavior at low temperature.

Hydrodynamics of soap films probed by two-particle microrheology

NASA Astrophysics Data System (ADS)

Prasad, Vikram; Weeks, Eric R.

2007-11-01

A soap film consists of a thin water layer that is separated from two bulk air phases above and below it by surfactant monolayers. The flow fields in the soap film created in response to a perturbation depend on coupling between these different phases, the exact nature of which is unknown. In order to determine this coupling, we use polystyrene spheres as tracer particles and track their diffusive motions in the soap film. The correlated Brownian motion of pairs of particles (two-particle microrheology) maps out the flow field, and provides a measure of the surface viscosity of the soap film as well. This measured surface viscosity agrees well with the value obtained from self diffusion of single particles (one-particle microrheology) in the film.

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

NASA Astrophysics Data System (ADS)

Wolgemuth, Charles; Powers, Thomas; Goldstein, Raymond

1999-10-01

The stability of forced elastic filaments arise in several important biological settings involving bend and twist elasticity at low Reynolds number. Examples include DNA transcription and replication and bacterial flagellar motion. In order to elucidate fundamental processes common to these systems, we consider the model problem of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes seperated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. Experiments are proposed to examine these phenomena and the consequences for swimming investigated.

Asymmetric skew Bessel processes and their applications to finance

NASA Astrophysics Data System (ADS)

Decamps, Marc; Goovaerts, Marc; Schoutens, Wim

2006-02-01

In this paper, we extend the Harrison and Shepp's construction of the skew Brownian motion (1981) and we obtain a diffusion similar to the two-dimensional Bessel process with speed and scale densities discontinuous at one point. Natural generalizations to multi-dimensional and fractional order Bessel processes are then discussed as well as invariance properties. We call this family of diffusions asymmetric skew Bessel processes in opposition to skew Bessel processes as defined in Barlow et al. [On Walsh's Brownian motions, Seminaire de Probabilities XXIII, Lecture Notes in Mathematics, vol. 1372, Springer, Berlin, New York, 1989, pp. 275-293]. We present factorizations involving (asymmetric skew) Bessel processes with random time. Finally, applications to the valuation of perpetuities and Asian options are proposed.

Swarming bacteria migrate by Lévy Walk

NASA Astrophysics Data System (ADS)

Ariel, Gil; Rabani, Amit; Benisty, Sivan; Partridge, Jonathan D.; Harshey, Rasika M.; Be'Er, Avraham

2015-09-01

Individual swimming bacteria are known to bias their random trajectories in search of food and to optimize survival. The motion of bacteria within a swarm, wherein they migrate as a collective group over a solid surface, is fundamentally different as typical bacterial swarms show large-scale swirling and streaming motions involving millions to billions of cells. Here by tracking trajectories of fluorescently labelled individuals within such dense swarms, we find that the bacteria are performing super-diffusion, consistent with Lévy walks. Lévy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Lévy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought.

Solution of a modified fractional diffusion equation

NASA Astrophysics Data System (ADS)

Langlands, T. A. M.

2006-07-01

Recently, a modified fractional diffusion equation has been proposed [I. Sokolov, J. Klafter, From diffusion to anomalous diffusion: a century after Einstein's brownian motion, Chaos 15 (2005) 026103; A.V. Chechkin, R. Gorenflo, I.M. Sokolov, V.Yu. Gonchar, Distributed order time fractional diffusion equation, Frac. Calc. Appl. Anal. 6 (3) (2003) 259279; I.M. Sokolov, A.V. Checkin, J. Klafter, Distributed-order fractional kinetics, Acta. Phys. Pol. B 35 (2004) 1323.] for describing processes that become less anomalous as time progresses by the inclusion of a second fractional time derivative acting on the diffusion term. In this letter we give the solution of the modified equation on an infinite domain. In contrast to the solution of the traditional fractional diffusion equation, the solution of the modified equation requires an infinite series of Fox functions instead of a single Fox function.

Anomaly diffuse and dielectric relaxation in strontium doped lanthanum molybdate

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

Liu, Xiao; Fan, Huiqing, E-mail: hqfan3@163.com; Shi, Jing

2011-12-15

Highlights: Black-Right-Pointing-Pointer The anomaly diffuse and dielectric relaxation behaviors are fitted by the Cole-Cole approach. Black-Right-Pointing-Pointer The peak in the LSMO is corresponding to different oxygen ion diffusion process. Black-Right-Pointing-Pointer We first give better explanation about the strange conductivity change caused by doping. Black-Right-Pointing-Pointer The oxygen ion diffusion is due to a combination of the dipolar relaxation and the motion of ions. -- Abstract: The dielectric properties of the La{sub 2-x}Sr{sub x}Mo{sub 2}O{sub 9-{delta}} (x = 0-0.2) ceramics were investigated in the temperature range of 300-800 K. Dielectric measurement reveals that two dielectric anomalies, associated with the oxygen ion diffusion,more » exist in frequency spectrum with x = 0.5. The broad dielectric peaks in tan {delta}({omega}) can be well fitted by a modified Cole-Cole approach. When x = 0.1, only one dielectric relaxation peak is observed, corresponding to different oxygen ion diffusion processes, as distinct from the only relaxation peak in the pure La{sub 2}Mo{sub 2}O{sub 9}. The relaxation parameters {tau}{sub 0}, the dielectric relaxation strength {Delta}, and the activation energy E{sub a} were obtained. The result of this work shows that, the conductivity change caused by doping between the two phases is due to the combination of the dipolar effects and motion of ions.« less

The Dynamics of Controlled Flow Separation within a Diverter Duct Diffuser

NASA Astrophysics Data System (ADS)

Peterson, C. J.; Vukasinovic, B.; Glezer, A.

2016-11-01

The evolution and receptivity to fluidic actuation of the flow separation within a rectangular, constant-width, diffuser that is branched off of a primary channel is investigated experimentally at speeds up to M = 0.4. The coupling between the diffuser's adverse pressure gradient and the internal separation that constricts nearly half of the flow passage through the duct is controlled using a spanwise array of fluidic actuators on the surface upstream of the diffuser's inlet plane. The dynamics of the separating surface vorticity layer in the absence and presence of actuation are investigated using high-speed particle image velocimetry combined with surface pressure measurements and total pressure distributions at the primary channel's exit plane. It is shown that the actuation significantly alters the incipient dynamics of the separating vorticity layer as the characteristic cross stream scales of the boundary layer upstream of separation and of the ensuing vorticity concentrations within the separated flow increase progressively with actuation level. It is argued that the dissipative (high frequency) actuation alters the balance between large- and small-scale motions near separation by intensifying the large-scale motions and limiting the small-scale dynamics. Controlling separation within the diffuser duct also has a profound effect on the global flow. In the presence of actuation, the mass flow rate in the primary duct increases 10% while the fraction of the diverted mass flow rate in the diffuser increases by more than 45% at 0.7% actuation mass fraction. Supported by the Boeing Company.

Atomistic Simulation Studies of Cholesteryl Oleates: Model for the Core of Lipoprotein Particles

PubMed Central

Heikelä, Mikko; Vattulainen, Ilpo; Hyvönen, Marja T.

2006-01-01

We have conducted molecular dynamics simulations to gain insight into the atomic-scale properties of an isotropic system of cholesteryl oleate (CO) molecules. Cholesteryl esters are major constituents of low density lipoprotein particles, the key players in the formation of atherosclerosis, as well as the storage form of cholesterol. Here the aim is to clarify structural and dynamical properties of CO molecules under conditions, which are suggestive of those in the core of low density lipoprotein particles. The simulations in the fluid phase indicate that the system of CO molecules is characterized by an absence of translational order, as expected, while the orientational order between distinct CO molecules is significant at short distances, persisting over a molecular size. As for intramolecular properties, the bonds along the oleate chain are observed to be weakly ordered with respect to the sterol structure, unlike the bonds along the short hydrocarbon chain of cholesterol where the ordering is significant. The orientational distribution of the oleate chain as a whole with respect to the sterol moiety is of broad nature, having a major amount of extended and a less considerable proportion of bended structures. Distinct transient peaks at specific angles also appear. The diffusion of CO molecules is found to be a slow process and characterized by a diffusion coefficient of the order of 2 × 10−9 cm2/s. This is considerably slower than diffusion, e.g., in ordered domains of lipid membranes rich in sphingomyelin and cholesterol. Analysis of the rotational diffusion rates and trans-to-gauche transition rates yield results consistent with experiments. PMID:16399839

Brownian Motion and the Temperament of Living Cells

NASA Astrophysics Data System (ADS)

Tsekov, Roumen; Lensen, Marga C.

2013-07-01

The migration of living cells usually obeys the laws of Brownian motion. While the latter is due to the thermal motion of the surrounding matter, the locomotion of cells is generally associated with their vitality. We study what drives cell migration and how to model memory effects in the Brownian motion of cells. The concept of temperament is introduced as an effective biophysical parameter driving the motion of living biological entities in analogy with the physical parameter of temperature, which dictates the movement of lifeless physical objects. The locomemory of cells is also studied via the generalized Langevin equation. We explore the possibility of describing cell locomemory via the Brownian self-similarity concept. An heuristic expression for the diffusion coefficient of cells on structured surfaces is derived.

Preparation of 3D Architecture Graphdiyne Nanosheets for High-Performance Sodium-Ion Batteries and Capacitors.

PubMed

Wang, Kun; Wang, Ning; He, Jianjiang; Yang, Ze; Shen, Xiangyan; Huang, Changshui

2017-11-22

Here, we apply three-dimensional (3D) architecture graphdiyne nanosheet (GDY-NS) as anode materials for sodium-ion storage devices achieving high energy and power performance along with excellent cyclic ability. The contribution of 3D architecture nanostructure and intramolecular pores of the GDY-NS can substantially optimize the sodium storage behavior through the accommodated intramolecular pore, 3D interconnective porous structure, and increased activity sites to facilitate a fast sodium-ion-diffusion channel. The contribution of butadiyne linkages and the formation of a stable solid electrolyte interface layer are directly confirmed through the in situ Raman measurement. The GDY-NS-based sodium-ion batteries exhibit a stable reversible capacity of approximately 812 mAh g -1 at a current density of 0.05 A g -1 ; they maintain more than 405 mAh g -1 over 1000 cycles at a current density of 1 A g -1 . Furthermore, the sodium-ion capacitors could deliver a capacitance more than 200 F g -1 over 3000 cycles at 1 A g -1 and display an initial specific energy as high as 182.3 Wh kg -1 at a power density of 300 W kg -1 and maintain specific energy of 166 Wh kg -1 even at a power density of 15 000 W kg -1 . The high energy and power density along with excellent cyclic performance based on the GDY-NS anode offers a great potential toward application on next-generation energy storage devices.

Triplet-Triplet Annihilation Photon Upconversion in Polymer Thin Film: Sensitizer Design.

PubMed

Jiang, Xinpeng; Guo, Xinyan; Peng, Jiang; Zhao, Dahui; Ma, Yuguo

2016-05-11

Efficient visible-to-UV photon upconversion via triplet-triplet annihilation (TTA) is accomplished in polyurethane (PU) films by developing new, powerful photosensitizers fully functional in the solid-state matrix. These rationally designed triplet sensitizers feature a bichromophoric scaffold comprising a tris-cyclometalated iridium(III) complex covalently tethered to a suitable organic small molecule. The very rapid intramolecular triplet energy transfer from the former to the latter is pivotal for achieving the potent sensitizing ability, because this process out-competes the radiative and nonradiative decays inherent to the metal complex and produces long-lived triplet excitons localized with the acceptor moiety readily available for intermolecular transfer and TTA. Nonetheless, compared to the solution state, the molecular diffusion is greatly limited in solid matrices, which even creates difficulty for the Dexter-type intramolecular energy transfer. This is proven by the experimental results showing that the sensitizing performance of the bichromophoric molecules strongly depends on the spatial distance separating the donor (D) and acceptor (A) units and that incorporating a longer linker between the D and A evidently curbs the TTA upconversion efficiency in PU films. Using a rationally optimized sensitizer structure in combination with 2,7-di-tert-butylpyrene as the annihilator/emitter, the doped polyurethane (PU) films demonstrate effective visible-to-UV upconverted emission signal under noncoherent-light irradiation, attaining an upconversion quantum yield of 2.6%. Such quantum efficiency is the highest value so far reported for the visible-to-UV TTA systems in solid matrices.

Kinetics of end-to-end collision in short single-stranded nucleic acids.

PubMed

Wang, Xiaojuan; Nau, Werner M

2004-01-28

A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescent state of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-end collision in short single-stranded oligodeoxyribonucleotides of the type 5'-DBO-(X)n-dG with X = dA, dC, dT, or dU and n = 2 or 4. The fluorophore was covalently attached to the 5' end and dG was introduced as an efficient intrinsic quencher at the 3' terminus. The end-to-end collision rates, which can be directly related to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 x 10(6) s(-1). They were strongly dependent on the strand length, the base sequence, as well as the temperature. Oligonucleotides containing dA in the backbone displayed much slower collision rates and significantly higher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsic rigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecular collision is significantly faster than the nucleation step of hairpin closing. This is consistent with the configurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc.Natl. Acad. Sci. USA 2001, 98, 7771-7776), in which the formation of misfolded loops is thought to slow hairpin formation.

Decoupling of rotational and translational diffusion in supercooled colloidal fluids

PubMed Central

Edmond, Kazem V.; Elsesser, Mark T.; Hunter, Gary L.; Pine, David J.; Weeks, Eric R.

2012-01-01

We use confocal microscopy to directly observe 3D translational and rotational diffusion of tetrahedral clusters, which serve as tracers in colloidal supercooled fluids. We find that as the colloidal glass transition is approached, translational and rotational diffusion decouple from each other: Rotational diffusion remains inversely proportional to the growing viscosity whereas translational diffusion does not, decreasing by a much lesser extent. We quantify the rotational motion with two distinct methods, finding agreement between these methods, in contrast with recent simulation results. The decoupling coincides with the emergence of non-Gaussian displacement distributions for translation whereas rotational displacement distributions remain Gaussian. Ultimately, our work demonstrates that as the glass transition is approached, the sample can no longer be approximated as a continuum fluid when considering diffusion. PMID:23071311

Crossover of two power laws in the anomalous diffusion of a two lipid membrane

NASA Astrophysics Data System (ADS)

Bakalis, Evangelos; Höfinger, Siegfried; Venturini, Alessandro; Zerbetto, Francesco

2015-06-01

Molecular dynamics simulations of a bi-layer membrane made by the same number of 1-palmitoyl-2-oleoyl-glycero-3-phospho-ethanolamine and palmitoyl-oleoyl phosphatidylserine lipids reveal sub-diffusional motion, which presents a crossover between two different power laws. Fractional Brownian motion is the stochastic mechanism that governs the motion in both regimes. The location of the crossover point is justified with simple geometrical arguments and is due to the activation of the mechanism of circumrotation of lipids about each other.

Crossover of two power laws in the anomalous diffusion of a two lipid membrane

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

Bakalis, Evangelos, E-mail: ebakalis@gmail.com, E-mail: francesco.zerbetto@unibo.it; Höfinger, Siegfried; Zerbetto, Francesco, E-mail: ebakalis@gmail.com, E-mail: francesco.zerbetto@unibo.it

2015-06-07

Molecular dynamics simulations of a bi-layer membrane made by the same number of 1-palmitoyl-2-oleoyl-glycero-3-phospho-ethanolamine and palmitoyl-oleoyl phosphatidylserine lipids reveal sub-diffusional motion, which presents a crossover between two different power laws. Fractional Brownian motion is the stochastic mechanism that governs the motion in both regimes. The location of the crossover point is justified with simple geometrical arguments and is due to the activation of the mechanism of circumrotation of lipids about each other.

Crossover of two power laws in the anomalous diffusion of a two lipid membrane.

PubMed

Bakalis, Evangelos; Höfinger, Siegfried; Venturini, Alessandro; Zerbetto, Francesco

2015-06-07

Molecular dynamics simulations of a bi-layer membrane made by the same number of 1-palmitoyl-2-oleoyl-glycero-3-phospho-ethanolamine and palmitoyl-oleoyl phosphatidylserine lipids reveal sub-diffusional motion, which presents a crossover between two different power laws. Fractional Brownian motion is the stochastic mechanism that governs the motion in both regimes. The location of the crossover point is justified with simple geometrical arguments and is due to the activation of the mechanism of circumrotation of lipids about each other.

Contrasting intermolecular and intramolecular exciplex formation of a 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad.

PubMed

Imoto, Mitsutaka; Ikeda, Hiroshi; Fujii, Takayuki; Taniguchi, Hisaji; Tamaki, Akihiro; Takeda, Motonori; Mizuno, Kazuhiko

2010-05-07

An intramolecular exciplex is formed upon excitation of the cyclohexane solution of the 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad, but little if any intramolecular CT complex exists in the ground state of this substance in solution. In contrast, in the crystalline state, the dyad forms an intermolecular mixed-stack CT complex in the ground state and an intermolecular exciplex when it is photoexcited.

PROPELLER for motion-robust imaging of in vivo mouse abdomen at 9.4 T.

PubMed

Teh, Irvin; Golay, Xavier; Larkman, David J

2010-11-01

In vivo high-field MRI in the abdomen of small animals is technically challenging because of the small voxel sizes, short T(2) and physiological motion. In standard Cartesian sampling, respiratory and gastrointestinal motion can lead to ghosting artefacts. Although respiratory triggering and navigator echoes can either avoid or compensate for motion, they can lead to variable TRs, require invasive intubation and ventilation, or extend TEs. A self-navigated fast spin echo (FSE)-based periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) acquisition was implemented at 9.4 T to enable high-resolution in vivo MRI of mouse abdomen without the use of additional navigators or triggering. T(2)-weighted FSE-PROPELLER data were compared with single-shot FSE and multi-shot FSE data with and without triggering. Single-shot methods, although rapid and robust to motion, demonstrated strong blurring. Multi-shot FSE data showed better resolution, but suffered from marked blurring in the phase-encoding direction and motion in between shots, leading to ghosting artefacts. When respiratory triggering was used, motion artefacts were largely avoided. However, TRs and acquisition times were lengthened by up to approximately 20%. The PROPELLER data showed a 25% and 61% improvement in signal-to-noise ratio and contrast-to-noise ratio, respectively, compared with multi-shot FSE data, together with a 35% reduction in artefact power. A qualitative comparison between acquisition methods using diffusion-weighted imaging was performed. The results were similar, with the exception that respiratory triggering was unable to exclude major motion artefacts as a result of the sensitisation to motion by the diffusion gradients. The PROPELLER data were of consistently higher quality. Considerations specific to the use of PROPELLER at high field are discussed, including the selection of practical blade widths and the effects on contrast, resolution and artefacts.

Diffusion behavior of the fluorescent proteins eGFP and Dreiklang in solvents of different viscosity monitored by fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Junghans, Cornelia; Schmitt, Franz-Josef; Vukojević, Vladana; Friedrich, Thomas

2016-12-01

Fluorescence correlation spectroscopy relies on temporal autocorrelation analysis of fluorescence intensity fluctuations that spontaneously arise in systems at equilibrium due to molecular motion and changes of state that cause changes in fluorescence, such as triplet state transition, photoisomerization and other photophysical transformations, to determine the rates of these processes. The stability of a fluorescent molecule against dark state conversion is of particular concern for chromophores intended to be used as reference tags for comparing diffusion processes on multiple time scales. In this work, we analyzed properties of two fluorescent proteins, the photoswitchable Dreiklang and its parental eGFP, in solvents of different viscosity to vary the diffusion time through the observation volume element by several orders of magnitude. In contrast to eGFP, Dreiklang undergoes a dark-state conversion on the time scale of tens to hundreds of microseconds under conditions of intense fluorescence excitation, which results in artificially shortened diffusion times if the diffusional motion through the observation volume is sufficiently slowed down. Such photophysical quenching processes have also been observed in FCS studies on other photoswitchable fluorescent proteins including Citrine, from which Dreiklang was derived by genetic engineering. This property readily explains the discrepancies observed previously between the diffusion times of eGFP- and Dreiklang-labeled plasma membrane protein complexes.

Differentiation between phyllodes tumours and fibroadenomas using intravoxel incoherent motion magnetic resonance imaging: comparison with conventional diffusion-weighted imaging.

PubMed

Kawashima, Hiroko; Miyati, Tosiaki; Ohno, Naoki; Ohno, Masako; Inokuchi, Masafumi; Ikeda, Hiroko; Gabata, Toshifumi

2018-04-01

To investigate whether the parameters derived from intravoxel incoherent motion (IVIM) MRI could differentiate phyllodes tumours (PTs) from fibroadenomas (FAs) by comparing the apparent diffusion coefficient (ADC) values. This retrospective study included 7 FAs, 10 benign PTs (BPTs), 4 borderline PTs, and one malignant PT. Biexponential analyses of IVIM were performed using a 3 T MRI scanner. Quantitative IVIM parameters [pure diffusion coefficient (D), perfusion-related diffusion coefficient (D*), and fraction (f)] were calculated. The ADC was also calculated using monoexponential fitting. The D and ADC values showed an increasing tendency in the order of FA, BPT, and borderline or malignant PT (BMPT). No significant difference was found in the D value among the three groups. The ADC value of the BMPT group was significantly higher than that of the FA group (p = 0.048). The D* value showed an increasing tendency in the order of BMPT, BPT, and FA, and the D* value of the BMPT group was significantly lower than that of the FA group (p = 0.048). The D* derived from IVIM and the ADC were helpful for differentiating between FA and BMPT. Advances in knowledge: IVIM MRI examination showed that the perfusion-related diffusion coefficient is lower in borderline and malignant PTs than in FAs and the opposite is true for the ADC.

Chemical origin of blue- and redshifted hydrogen bonds: intramolecular hyperconjugation and its coupling with intermolecular hyperconjugation.

PubMed

Li, An Yong

2007-04-21

Upon formation of a H bond Y...H-XZ, intramolecular hyperconjugation n(Z)-->sigma*(X-H) of the proton donor plays a key role in red- and blueshift characters of H bonds and must be introduced in the concepts of hyperconjugation and rehybridization. Intermolecular hyperconjugation transfers electron density from Y to sigma*(X-H) and causes elongation and stretch frequency redshift of the X-H bond; intramolecular hyperconjugation couples with intermolecular hyperconjugation and can adjust electron density in sigma*(X-H); rehybridization causes contraction and stretch frequency blueshift of the X-H bond on complexation. The three factors--intra- and intermolecular hyperconjugations and rehybridization--determine commonly red- or blueshift of the formed H bond. A proton donor that has strong intramolecular hyperconjugation often forms blueshifted H bonds.

Intramolecular aggregation and optical limiting properties of triazine-linked mono-, bis- and tris-phthalocyanines.

PubMed

Chen, Jun; Zhang, Tao; Wang, Shuangqing; Hu, Rui; Li, Shayu; Ma, Jin Shi; Yang, Guoqiang

2015-10-05

A series of triazine-linked mono-, bis- and tris-phthalocyanines are synthesized, intramolecular aggregation is found in bis- and tris-phthalocyanines via π-π stacking interaction. Theoretical and experimental studies reveal the formation of the intramolecular aggregation. The spectrographic, photophysical and nonlinear optical properties of these compounds are adjusted for the formation of the intramolecular aggregation. The bis-phthalocyanine dimer presents smaller fluorescence quantum yield, lower triplet formation yield and the triplet-minus-ground state extinction coefficient, which causes poorer optical limiting performance. It is interesting that the tris-phthalocyanine is composed of a mono-phthalocyanine part and a bis-phthalocyanine part, the optical limiting property of the tris-phthalocyanine is similar to that of mono-phthalocyanine. Copyright © 2015 Elsevier B.V. All rights reserved.

Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser

DOE PAGES

Levantino, Matteo; Schirò, Giorgio; Lemke, Henrik Till; ...

2015-04-02

Light absorption can trigger biologically relevant protein conformational changes. The light induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it undergoes damped oscillations withmore » a ~3.6-picosecond time period. Our results unambiguously show how initially localized chemical changes can propagate at the level of the global protein conformation in the picosecond timescale.« less

Giant transversal particle diffusion in a longitudinal magnetic ratchet.

PubMed

Tierno, Pietro; Reimann, Peter; Johansen, Tom H; Sagués, Francesc

2010-12-03

We study the transversal motion of paramagnetic particles on a uniaxial garnet film, exhibiting a longitudinal ratchet effect in the presence of an oscillating magnetic field. Without the field, the thermal diffusion coefficient obtained by video microscopy is D(0) ≈ 3 × 10(-4)  μm2/s. With the field, the transversal diffusion exhibits a giant enhancement by almost four decades and a pronounced maximum as a function of the driving frequency. We explain the experimental findings with a theoretical interpretation in terms of random disorder effects within the magnetic film.

Explosion investigation of asphalt-salt mixtures in a reprocessing plant.

PubMed

Hasegawa, K; Li, Y

2000-12-15

Cause investigation of a fire and explosion at the nuclear fuel waste reprocessing plant indicated that self-heating ignition of an asphalt-salt-waste, bituminized, mixture (AS) caused the disaster. A 220l drum was filled with the AS at a temperature of about 180 degrees C. About 20h later the drum ignited and burned as it was being cooled. It is estimated that the AS contained approximately 55wt.% blown asphalt, 25wt.% NaNO(3), 5wt.% NaNO(2), 8wt.% Na(2)CO(3), 2wt.% NaH(2)PO(4), 1wt.% Ba (OH)(2), 1wt.% K(4)[Fe(CN)(6)], and possibly 3wt.% of other materials. To determine the reaction promoting factors and pertinent chemical reaction rates, self-reaction of the AS has been investigated by the use of a C80D heat flux reaction calorimeter. The oxidizing reactions with asphalt are ruled by NaNO(2) rather than by NaNO(3), in spite of a lower concentration of NaNO(2). The kinetic rates of the interfacial reaction between salt particles and asphalt for the reaction controlled and diffusion controlled steps have been formulated as a function of salt particle size for both NaNO(2) and NaNO(3). Numerical solution of the heat balance equations formulating the heterogeneous reaction scheme indicates that a runaway reaction occurs when the AS-filling temperature is 208 degrees C for a drum filled with an AS mixture produced under standard operating conditions. Molecules containing intramolecular hydrogen, such as Na(2)HPO(4) and NaHCO(3), do not oxidize asphalt directly, however, their presence chemically promotes the oxidizing reaction of NaNO(2). Moreover, NaHCO(3) decomposition which produces gases creates many micro holes in the interior of the salt particles. This in turn promotes the oxidizing reactions that are diffusion controlled. Finally, the consequence of a runaway reaction at 180 degrees C or lower is qualitatively explained by taking into account the chemical effect of intramolecular hydrogen and the physical effect of the NaHCO(3) decomposition gases.

Effects of alcohols on the stability and low-frequency local motions that control the slow changes in structural dynamics of ferrocytochrome c.

PubMed

Jain, Rishu; Sharma, Deepak; Kumar, Rajesh

2013-10-01

To determine the effects of alcohols on the low-frequency local motions that control slow changes in structural dynamics of native-like compact states of proteins, we have studied the effects of alcohols on structural fluctuation of M80-containing Ω-loop by measuring the rate of thermally driven CO dissociation from a natively folded carbonmonoxycytochrome c under varying concentrations of alcohols (methanol, ethanol, 1-propanol, 2-propanol, 3°-butanol, 2,2,2-trifluoroethanol). As alcohol is increased, the rate coefficient of CO dissociation (k(diss)) first decreases in subdenaturing region and then increases on going from subdenaturing to denaturing milieu. This decrease in k(diss) is more for 2,2,2-trifluroethanol and 1-propanol and least for methanol, indicating that the first phase of motional constraint is due to the hydrophobicity of alcohols and intramolecular protein cross-linking effect of alcohols, which results in conformational entropy loss of protein. The thermal denaturation midpoint for ferrocytochrome c decreases with increase in alcohol, indicating that alcohol decrease the global stability of protein. The stabilization free energy (ΔΔG) in alcohols' solution was calculated from the slope of the Wyman-Tanford plot and water activity. The m-values obtained from the slope of ΔΔG versus alcohols plot were found to be more negative for longer and linear chain alcohols, indicating destabilization of proteins by alcohols through disturbance of hydrophobic interactions and hydrogen bonding.

Bivariate Gaussian bridges: directional factorization of diffusion in Brownian bridge models.

PubMed

Kranstauber, Bart; Safi, Kamran; Bartumeus, Frederic

2014-01-01

In recent years high resolution animal tracking data has become the standard in movement ecology. The Brownian Bridge Movement Model (BBMM) is a widely adopted approach to describe animal space use from such high resolution tracks. One of the underlying assumptions of the BBMM is isotropic diffusive motion between consecutive locations, i.e. invariant with respect to the direction. Here we propose to relax this often unrealistic assumption by separating the Brownian motion variance into two directional components, one parallel and one orthogonal to the direction of the motion. Our new model, the Bivariate Gaussian bridge (BGB), tracks movement heterogeneity across time. Using the BGB and identifying directed and non-directed movement within a trajectory resulted in more accurate utilisation distributions compared to dynamic Brownian bridges, especially for trajectories with a non-isotropic diffusion, such as directed movement or Lévy like movements. We evaluated our model with simulated trajectories and observed tracks, demonstrating that the improvement of our model scales with the directional correlation of a correlated random walk. We find that many of the animal trajectories do not adhere to the assumptions of the BBMM. The proposed model improves accuracy when describing the space use both in simulated correlated random walks as well as observed animal tracks. Our novel approach is implemented and available within the "move" package for R.

Neuroperformance Imaging

DTIC Science & Technology

2012-10-01

EMBC10.1722. 10. Mitra, P.P., Halperin, B.I.: Effects of finite gradient-pulse widths in pulsed- field - gradient diffusion measurements . Journal of Magnetic ...December 2011 ABSTRACT: The addition of a pair of magnetic field gradient pulses had initially enabled the measurement of spin motion to nuclear mag- netic...introduced a pair of (homogenous) magnetic field gradients into the spin echo experi- ment with the purpose of accurately measuring the scalar diffusion

Meaningful interpretation of subdiffusive measurements in living cells (crowded environment) by fluorescence fluctuation microscopy.

PubMed

Baumann, Gerd; Place, Robert F; Földes-Papp, Zeno

2010-08-01

In living cell or its nucleus, the motions of molecules are complicated due to the large crowding and expected heterogeneity of the intracellular environment. Randomness in cellular systems can be either spatial (anomalous) or temporal (heterogeneous). In order to separate both processes, we introduce anomalous random walks on fractals that represented crowded environments. We report the use of numerical simulation and experimental data of single-molecule detection by fluorescence fluctuation microscopy for detecting resolution limits of different mobile fractions in crowded environment of living cells. We simulate the time scale behavior of diffusion times tau(D)(tau) for one component, e.g. the fast mobile fraction, and a second component, e.g. the slow mobile fraction. The less the anomalous exponent alpha the higher the geometric crowding of the underlying structure of motion that is quantified by the ratio of the Hausdorff dimension and the walk exponent d(f)/d(w) and specific for the type of crowding generator used. The simulated diffusion time decreases for smaller values of alpha # 1 but increases for a larger time scale tau at a given value of alpha # 1. The effect of translational anomalous motion is substantially greater if alpha differs much from 1. An alpha value close to 1 contributes little to the time dependence of subdiffusive motions. Thus, quantitative determination of molecular weights from measured diffusion times and apparent diffusion coefficients, respectively, in temporal auto- and crosscorrelation analyses and from time-dependent fluorescence imaging data are difficult to interpret and biased in crowded environments of living cells and their cellular compartments; anomalous dynamics on different time scales tau must be coupled with the quantitative analysis of how experimental parameters change with predictions from simulated subdiffusive dynamics of molecular motions and mechanistic models. We first demonstrate that the crowding exponent alpha also determines the resolution of differences in diffusion times between two components in addition to photophysical parameters well-known for normal motion in dilute solution. The resolution limit between two different kinds of single molecule species is also analyzed under translational anomalous motion with broken ergodicity. We apply our theoretical predictions of diffusion times and lower limits for the time resolution of two components to fluorescence images in human prostate cancer cells transfected with GFP-Ago2 and GFP-Ago1. In order to mimic heterogeneous behavior in crowded environments of living cells, we need to introduce so-called continuous time random walks (CTRW). CTRWs were originally performed on regular lattice. This purely stochastic molecule behavior leads to subdiffusive motion with broken ergodicity in our simulations. For the first time, we are able to quantitatively differentiate between anomalous motion without broken ergodicity and anomalous motion with broken ergodicity in time-dependent fluorescence microscopy data sets of living cells. Since the experimental conditions to measure a selfsame molecule over an extended period of time, at which biology is taken place, in living cells or even in dilute solution are very restrictive, we need to perform the time average over a subpopulation of different single molecules of the same kind. For time averages over subpopulations of single molecules, the temporal auto- and crosscorrelation functions are first found. Knowing the crowding parameter alpha for the cell type and cellular compartment type, respectively, the heterogeneous parameter gamma can be obtained from the measurements in the presence of the interacting reaction partner, e.g. ligand, with the same alpha value. The product alpha x gamma = gamma is not a simple fitting parameter in the temporal auto- and two-color crosscorrelation functions because it is related to the proper physical models of anomalous (spatial) and heterogeneous (temporal) randomness in cellular systems.We have already derived an analytical solution gamma for in the special case of gamma = 3/2. In the case of two-color crosscorrelation or/and two-color fluorescence imaging (co-localization experiments), the second component is also a two-color species gr, for example a different molecular complex with an additional ligand. Here, we first show that plausible biological mechanisms from FCS/ FCCS and fluorescence imaging in living cells are highly questionable without proper quantitative physical models of subdiffusive motion and temporal randomness. At best, such quantitative FCS/ FCCS and fluorescence imaging data are difficult to interpret under crowding and heterogeneous conditions. It is challenging to translate proper physical models of anomalous (spatial) and heterogeneous (temporal) randomness in living cells and their cellular compartments like the nucleus into biological models of the cell biological process under study testable by single-molecule approaches. Otherwise, quantitative FCS/FCCS and fluorescence imaging measurements in living cells are not well described and cannot be interpreted in a meaningful way.

Diffusion control for a tempered anomalous diffusion system using fractional-order PI controllers.

PubMed

Juan Chen; Zhuang, Bo; Chen, YangQuan; Cui, Baotong

2017-05-09

This paper is concerned with diffusion control problem of a tempered anomalous diffusion system based on fractional-order PI controllers. The contribution of this paper is to introduce fractional-order PI controllers into the tempered anomalous diffusion system for mobile actuators motion and spraying control. For the proposed control force, convergence analysis of the system described by mobile actuator dynamical equations is presented based on Lyapunov stability arguments. Moreover, a new Centroidal Voronoi Tessellation (CVT) algorithm based on fractional-order PI controllers, henceforth called FOPI-based CVT algorithm, is provided together with a modified simulation platform called Fractional-Order Diffusion Mobile Actuator-Sensor 2-Dimension Fractional-Order Proportional Integral (FO-Diff-MAS2D-FOPI). Finally, extensive numerical simulations for the tempered anomalous diffusion process are presented to verify the effectiveness of our proposed fractional-order PI controllers. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

TURBULENCE IN THE SOLAR WIND MEASURED WITH COMET TAIL TEST PARTICLES

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

DeForest, C. E.; Howard, T. A.; Matthaeus, W. H.

2015-10-20

By analyzing the motions of test particles observed remotely in the tail of Comet Encke, we demonstrate that the solar wind undergoes turbulent processing enroute from the Sun to the Earth and that the kinetic energy entrained in the large-scale turbulence is sufficient to explain the well-known anomalous heating of the solar wind. Using the heliospheric imaging (HI-1) camera on board NASA's STEREO-A spacecraft, we have observed an ensemble of compact features in the comet tail as they became entrained in the solar wind near 0.4 AU. We find that the features are useful as test particles, via mean-motion analysismore » and a forward model of pickup dynamics. Using population analysis of the ensemble's relative motion, we find a regime of random-walk diffusion in the solar wind, followed, on larger scales, by a surprising regime of semiconfinement that we attribute to turbulent eddies in the solar wind. The entrained kinetic energy of the turbulent motions represents a sufficient energy reservoir to heat the solar wind to observed temperatures at 1 AU. We determine the Lagrangian-frame diffusion coefficient in the diffusive regime, derive upper limits for the small scale coherence length of solar wind turbulence, compare our results to existing Eulerian-frame measurements, and compare the turbulent velocity with the size of the observed eddies extrapolated to 1 AU. We conclude that the slow solar wind is fully mixed by turbulence on scales corresponding to a 1–2 hr crossing time at Earth; and that solar wind variability on timescales shorter than 1–2 hr is therefore dominated by turbulent processing rather than by direct solar effects.« less

Time scale of diffusion in molecular and cellular biology

NASA Astrophysics Data System (ADS)

Holcman, D.; Schuss, Z.

2014-05-01

Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

Single-crystal diffuse scattering studies on polymorphs of molecular crystals. I. The room-temperature polymorphs of the drug benzocaine.

PubMed

Chan, E J; Welberry, T R; Goossens, D J; Heerdegen, A P; Beasley, A G; Chupas, P J

2009-06-01

The drug benzocaine (ethyl 4-aminobenzoate), commonly used as a local anaesthetic, is a bimorphic solid at room temperature. Form (I) is monoclinic P2(1)/c, while the metastable form (II) is orthorhombic P2(1)2(1)2(1). Three-dimensional diffuse X-ray scattering data have been collected for the two forms on the 11-ID-B beamline at the Advanced Photon Source (APS). Both forms show strong and highly structured diffuse scattering. The data have been interpreted and analysed using Monte Carlo (MC) modelling on the basis that the scattering is purely thermal in origin and indicates the presence of highly correlated molecular motions. In both forms (I) and (II) broad diffuse streaks are observed in the 0kl section which indicate strong longitudinal displacement correlations between molecules in the 031 directions, extending over distances of up to 50 A. Streaks extending between Bragg peaks in the hk0 section normal to [100] correspond to correlated motions of chains of molecules extending along a that are linked by N-H...O=C hydrogen bonds and which occur together as coplanar ribbon pairs. The main difference between the two forms is in the dynamical behaviour of the ribbon pairs and in particular how they are able to slide relative to each other. While for form (I) a model involving harmonic springs is able to describe the motion satisfactorily, as simple excursions away from the average structure, there is evidence in form (II) of anharmonic effects that are precursors of a phase transition to a new low-temperature phase, form (III), that was subsequently found.

Lateral diffusion and retrograde movements of individual cell surface components on single motile cells observed with Nanovid microscopy

PubMed Central

1991-01-01

A recently introduced extension of video-enhanced light microscopy, called Nanovid microscopy, documents the dynamic reorganization of individual cell surface components on living cells. 40-microns colloidal gold probes coupled to different types of poly-L-lysine label negative cell surface components of PTK2 cells. Evidence is provided that they bind to negative sialic acid residues of glycoproteins, probably through nonspecific electrostatic interactions. The gold probes, coupled to short poly-L-lysine molecules (4 kD) displayed Brownian motion, with a diffusion coefficient in the range 0.1-0.2 micron2/s. A diffusion coefficient in the 0.1 micron2/s range was also observed with 40-nm gold probes coupled to an antibody against the lipid-linked Thy-1 antigen on 3T3 fibroblasts. Diffusion of these probes is largely confined to apparent microdomains of 1-2 microns in size. On the other hand, the gold probes, coupled to long poly-L-lysine molecules (240 kD) molecules and bound to the leading lamella, were driven rearward, toward the boundary between lamelloplasm and perinuclear cytoplasm at a velocity of 0.5-1 micron/min by a directed ATP-dependent mechanism. This uniform motion was inhibited by cytochalasin, suggesting actin microfilament involvement. A similar behavior on MO cells was observed when the antibody-labeled gold served as a marker for the PGP-1 (GP-80) antigen. These results show that Nanovid microscopy, offering the possibility to observe the motion of individual specific cell surface components, provides a new and powerful tool to study the dynamic reorganization of the cell membrane during locomotion and in other biological contexts as well. PMID:1670778

Nonholonomic diffusion of a stochastic sled

NASA Astrophysics Data System (ADS)

Jung, Peter; Marchegiani, Giampiero; Marchesoni, Fabio

2016-01-01

A sled is a stylized mechanical model of a system which is constrained to move in space in a specific orientation, i.e., in the direction of the runners of the sled or a blade. The negation of motion transverse to the runners renders the sled a nonholonomic mechanical system. In this paper we report on the unexpected and fascinating richness of the dynamics of such a sled if it is subject to random forces. Specifically we show that the ensuing random dynamics is characterized by relatively smooth sections of motion interspersed by episodes of persistent tumbling (change of orientation) and sharp reversals resembling the random walks of bacterial cells. In the presence of self-propulsion, the diffusivity of the sled can be enhanced and suppressed depending on the directionality and strength of the propulsive force.

Approximation of super-ions for single-file diffusion of multiple ions through narrow pores.

PubMed

Kharkyanen, Valery N; Yesylevskyy, Semen O; Berezetskaya, Natalia M

2010-11-01

The general theory of the single-file multiparticle diffusion in the narrow pores could be greatly simplified in the case of inverted bell-like shape of the single-particle energy profile, which is often observed in biological ion channels. There is a narrow and deep groove in the energy landscape of multiple interacting ions in such profiles, which corresponds to the pre-defined optimal conduction pathway in the configurational space. If such groove exists, the motion of multiple ions can be reduced to the motion of single quasiparticle, called the superion, which moves in one-dimensional effective potential. The concept of the superions dramatically reduces the computational complexity of the problem and provides very clear physical interpretation of conduction phenomena in the narrow pores.

Divergent Synthesis of Solanidine and 22-epi-Solanidine.

PubMed

Hou, Ling-Li; Shi, Yong; Zhang, Zhi-Dan; Wu, Jing-Jing; Yang, Qing-Xiong; Tian, Wei-Sheng

2017-07-21

A divergent synthesis of solanidine and 22-epi-solanidine, two 25S natural steroidal alkaloids, from 25R-configured diosgenin acetate, is described. Initially, solanidine was synthesized through a series of transformations including a cascade ring-switching process of furostan-26-acid, an epimerization of C25 controlled by the conformation of six-membered lactone ring, an intramolecular Schmidt reaction, and an imine reduction/intramolecular aminolysis process. To address the epimerization issue during Schmidt reaction, an improved synthesis was developed, which also led to a synthesis of 22-epi-solanidine. In this synthesis, selective transformation of azido lactone to azido diol and amino diol was realized through a reduction relay tactic. The azido diol was transformed to solanidine via an intramolecular Schmidt reaction/N-alkylation/reduction process and to 22-epi-solanidine via an intramolecular double N-alkylation process.

Intramolecular Benzoin Reaction Catalyzed by Benzaldehyde Lyase from Pseudomonas Fluorescens Biovar I.

PubMed

Hernández, Karel; Parella, Teodor; Petrillo, Giovanna; Usón, Isabel; Wandtke, Claudia M; Joglar, Jesús; Bujons, Jordi; Clapés, Pere

2017-05-02

Intramolecular benzoin reactions catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I (BAL) are reported. The structure of the substrates envisaged for this reaction consists of two benzaldehyde derivatives linked by an alkyl chain. The structural requirements needed to achieve the intramolecular carbon-carbon bond reaction catalyzed by BAL were established. Thus, a linker consisting of a linear alkyl chain of three carbon atoms connected through ether-type bonds to the 2 and 2' positions of two benzaldehyde moieties, which could be substituted with either Cl, Br, or OCH 3 at either the 3 and 3' or 5 and 5' positions, were suitable substrates for BAL. Reactions with 61-84 % yields of the intramolecular product and ee values between 64 and 98 %, were achieved. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vinylcyclopropylacyl and polyeneacyl radicals. Intramolecular ketene alkyl radical additions in ring synthesis.

PubMed

De Boeck, Benoit; Herbert, Nicola M A; Harrington-Frost, Nicole M; Pattenden, Gerald

2005-01-21

Treatment of a variety of substituted vinylcyclopropyl selenyl esters, e.g. 11, with Bu(3)SnH-AIBN in refluxing benzene leads to the corresponding acyl radical intermediates, which undergo rearrangement and intramolecular cyclisations via their ketene alkyl radical equivalents producing cyclohexenones in 50-60% yield. By contrast, treatment of conjugated triene selenyl esters, e.g. 32, with Bu(3)SnH-AIBN produces substituted 2-cyclopentenones via intramolecular cyclisations of their ketene alkyl radical intermediates. Under the same radical-initiating conditions the selenyl esters derived from o-vinylbenzoic acid and o-vinylcinnamic acid undergo intramolecular cyclisations producing 1-indanone and 5,6-dihydrobenzocyclohepten-7-one respectively in 60-70% yields. A tandem radical cyclisation from the alpha,beta,gamma,delta-diene selenyl ester 31 provides an expeditious synthesis of the diquinane 35 in 69% yield.

Role of Intramolecular Aromatic π-π Interactions in the Self-Assembly of Di-l-Phenylalanine Dipeptide Driven by Intermolecular Interactions: Effect of Alanine Substitution.

PubMed

Reddy, Samala Murali Mohan; Shanmugam, Ganesh

2016-09-19

Although the role of intermolecular aromatic π-π interactions in the self-assembly of di-l-phenylalanine (l-Phe-l-Phe, FF), a peptide that is known for hierarchical structure, is well established, the influence of intramolecular π-π interactions on the morphology of the self-assembled structure of FF has not been studied. Herein, the role of intramolecular aromatic π-π interactions is investigated for FF and analogous alanine (Ala)-containing dipeptides, namely, l-Phe-l-Ala (FA) and l-Ala-l-Phe (AF). The results reveal that these dipeptides not only form self-assemblies, but also exhibit remarkable differences in structural morphology. The morphological differences between FF and the analogues indicate the importance of intramolecular π-π interactions, and the structural difference between FA and AF demonstrates the crucial role of the nature of intramolecular side-chain interactions (aromatic-aliphatic or aliphatic-aromatic), in addition to intermolecular interactions, in deciding the final morphology of the self-assembled structure. The current results emphasise that intramolecular aromatic π-π interaction may not be essential to induce self-assembly in smaller peptides, and π (aromatic)-alkyl or alkyl-π (aromatic) interactions may be sufficient. This work also illustrates the versatility of aromatic and a combination of aromatic and aliphatic residues in dipeptides in the formation of structurally diverse self-assembled structures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Folding time dependence of the motions of a molecular motor in an amorphous medium

NASA Astrophysics Data System (ADS)

Ciobotarescu, Simona; Bechelli, Solene; Rajonson, Gabriel; Migirditch, Samuel; Hester, Brooke; Hurduc, Nicolae; Teboul, Victor

2017-12-01

We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time τf. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very slowly with τf, while for rapid foldings (regime II) the diffusion increases strongly with τf(D ≈τf-2 ), suggesting two different physical mechanisms. We find that in regime I the motor's displacement during the folding process is counteracted by a reverse displacement during the unfolding, while in regime II this counteraction is much weaker. We notice that regime I behavior is reminiscent of the scallop theorem that holds for larger motors in a continuous medium. We find that the difference in the efficiency of the motor's motion explains most of the observed difference between the two regimes. For fast foldings the motor trajectories differ significantly from the opposite trajectories induced by the following unfolding process, resulting in a more efficient global motion than for slow foldings. This result agrees with the fluctuation theorems expectation for time reversal mechanisms. In agreement with the fluctuation theorems we find that the motors are unexpectedly more efficient when they are generating more entropy, a result that can be used to increase dramatically the motor's motion.

Vibration isolation technology: Sensitivity of selected classes of experiments to residual accelerations

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.

1990-01-01

The solution was sought of a 2-D axisymmetric moving boundary problem for the sensitivity of isothermal and nonisothermal liquid columns and the sensitivity of thermo-capillary flows to buoyancy driven convection caused by residual accelerations. The sensitivity of a variety of space experiments to residual accelerations are examined. In all the cases discussed, the sensitivity is related to the dynamic response of a fluid. In some cases the sensitivity can be defined by the magnitude of the response of the velocity field. This response may involve motion of the fluid associated with internal density gradients, or the motion of a free liquid surface. For fluids with internal density gradients, the type of acceleration to which the experiment is sensitive will depend on whether buoyancy driven convection must be small in comparison to other types of fluid motion (such as thermocapillary flow), or fluid motion must be suppressed or eliminated (such as in diffusion studies, or directional solidification experiments). The effect of the velocity on the composition and temperature field must be considered, particularly in the vicinity of the melt crystal interface. As far as the response to transient disturbances is concerned the sensitivity is determined by both the magnitude and frequency the acceleration and the characteristic momentum and solute diffusion times.

Swim stress, motion, and deformation of active matter: effect of an external field.

PubMed

Takatori, Sho C; Brady, John F

2014-12-21

We analyze the stress, dispersion, and average swimming speed of self-propelled particles subjected to an external field that affects their orientation and speed. The swimming trajectory is governed by a competition between the orienting influence (i.e., taxis) associated with the external (e.g., magnetic, gravitational, thermal, nutrient concentration) field versus the effects that randomize the particle orientations (e.g., rotary Brownian motion and/or an intrinsic tumbling mechanism like the flagella of bacteria). The swimmers' motion is characterized by a mean drift velocity and an effective translational diffusivity that becomes anisotropic in the presence of the orienting field. Since the diffusivity yields information about the micromechanical stress, the anisotropy generated by the external field creates a normal stress difference in the recently developed "swim stress" tensor [Takatori, Yan, and Brady, Phys. Rev. Lett., 2014]. This property can be exploited in the design of soft, compressible materials in which their size, shape, and motion can be manipulated and tuned by loading the material with active swimmers. Since the swimmers exert different normal stresses in different directions, the material can compress/expand, elongate, and translate depending on the external field strength. Such an active system can be used as nano/micromechanical devices and motors. Analytical solutions are corroborated by Brownian dynamics simulations.

Statistical assessment of bi-exponential diffusion weighted imaging signal characteristics induced by intravoxel incoherent motion in malignant breast tumors

PubMed Central

Wong, Oi Lei; Lo, Gladys G.; Chan, Helen H. L.; Wong, Ting Ting; Cheung, Polly S. Y.

2016-01-01

Background The purpose of this study is to statistically assess whether bi-exponential intravoxel incoherent motion (IVIM) model better characterizes diffusion weighted imaging (DWI) signal of malignant breast tumor than mono-exponential Gaussian diffusion model. Methods 3 T DWI data of 29 malignant breast tumors were retrospectively included. Linear least-square mono-exponential fitting and segmented least-square bi-exponential fitting were used for apparent diffusion coefficient (ADC) and IVIM parameter quantification, respectively. F-test and Akaike Information Criterion (AIC) were used to statistically assess the preference of mono-exponential and bi-exponential model using region-of-interests (ROI)-averaged and voxel-wise analysis. Results For ROI-averaged analysis, 15 tumors were significantly better fitted by bi-exponential function and 14 tumors exhibited mono-exponential behavior. The calculated ADC, D (true diffusion coefficient) and f (pseudo-diffusion fraction) showed no significant differences between mono-exponential and bi-exponential preferable tumors. Voxel-wise analysis revealed that 27 tumors contained more voxels exhibiting mono-exponential DWI decay while only 2 tumors presented more bi-exponential decay voxels. ADC was consistently and significantly larger than D for both ROI-averaged and voxel-wise analysis. Conclusions Although the presence of IVIM effect in malignant breast tumors could be suggested, statistical assessment shows that bi-exponential fitting does not necessarily better represent the DWI signal decay in breast cancer under clinically typical acquisition protocol and signal-to-noise ratio (SNR). Our study indicates the importance to statistically examine the breast cancer DWI signal characteristics in practice. PMID:27709078

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

NASA Astrophysics Data System (ADS)

Ghosh, Surya K.; Cherstvy, Andrey G.; Grebenkov, Denis S.; Metzler, Ralf

2016-01-01

A topic of intense current investigation pursues the question of how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of extensive simulations of the motion of a finite sized tracer particle in a heterogeneously crowded environment made up of quenched distributions of monodisperse crowders of varying sizes in finite circular two-dimensional domains. For given spatial distributions of monodisperse crowders we demonstrate how anomalous diffusion with strongly non-Gaussian features arises in this model system. We investigate both biologically relevant situations of particles released either at the surface of an inner domain or at the outer boundary, exhibiting distinctly different features of the observed anomalous diffusion for heterogeneous distributions of crowders. Specifically we reveal an asymmetric spreading of tracers even at moderate crowding. In addition to the mean squared displacement (MSD) and local diffusion exponent we investigate the magnitude and the amplitude scatter of the time averaged MSD of individual tracer trajectories, the non-Gaussianity parameter, and the van Hove correlation function. We also quantify how the average tracer diffusivity varies with the position in the domain with a heterogeneous radial distribution of crowders and examine the behaviour of the survival probability and the dynamics of the tracer survival probability. Inter alia, the systems we investigate are related to the passive transport of lipid molecules and proteins in two-dimensional crowded membranes or the motion in colloidal solutions or emulsions in effectively two-dimensional geometries, as well as inside supercrowded, surface adhered cells.

Rapid-Onset Diffuse Skeletal Fluorosis from Inhalant Abuse: A Case Report.

PubMed

Cohen, Eric; Hsu, Raymond Y; Evangelista, Peter; Aaron, Roy; Rubin, Lee E

A thirty-year-old man presented with severely debilitating left hip pain and stiffness. Radiographs demonstrated diffuse osteosclerosis and heterotopic bone formation with near ankylosis of the left hip. The patient underwent successful joint-preserving surgery to restore hip range of motion. After disclosing a history of inhalant abuse, which was confirmed by elevated serum fluoride levels, he was diagnosed with diffuse skeletal fluorosis. To the best of our knowledge, we present the first reported case of diffuse skeletal fluorosis caused by inhalant abuse of 1,1-difluoroethane. Skeletal fluorosis is uncommon in the United States but is important to consider in the differential diagnosis when a patient presents with otherwise unexplained joint pain and osteosclerosis.

Perpendicular diffusion of a dilute beam of charged dust particles in a strongly coupled dusty plasma

NASA Astrophysics Data System (ADS)

Liu, Bin; Goree, J.

2014-06-01

The diffusion of projectiles drifting through a target of strongly coupled dusty plasma is investigated in a simulation. A projectile's drift is driven by a constant force F. We characterize the random walk of the projectiles in the direction perpendicular to their drift. The perpendicular diffusion coefficient Dp⊥ is obtained from the simulation data. The force dependence of Dp⊥ is found to be a power law in a high force regime, but a constant at low forces. A mean kinetic energy Wp for perpendicular motion is also obtained. The diffusion coefficient is found to increase with Wp with a linear trend at higher energies, but an exponential trend at lower energies.

Mesoscopic description of random walks on combs

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Iomin, Alexander; Campos, Daniel; Horsthemke, Werner

2015-12-01

Combs are a simple caricature of various types of natural branched structures, which belong to the category of loopless graphs and consist of a backbone and branches. We study continuous time random walks on combs and present a generic method to obtain their transport properties. The random walk along the branches may be biased, and we account for the effect of the branches by renormalizing the waiting time probability distribution function for the motion along the backbone. We analyze the overall diffusion properties along the backbone and find normal diffusion, anomalous diffusion, and stochastic localization (diffusion failure), respectively, depending on the characteristics of the continuous time random walk along the branches, and compare our analytical results with stochastic simulations.

Theoretical verification of nonthermal microwave effects on intramolecular reactions.

PubMed

Kanno, Manabu; Nakamura, Kosuke; Kanai, Eri; Hoki, Kunihito; Kono, Hirohiko; Tanaka, Motohiko

2012-03-08

There have been a growing number of articles that report dramatic improvements in the experimental performance of chemical reactions by microwave irradiation compared to that under conventional heating conditions. We theoretically examined whether nonthermal microwave effects on intramolecular reactions exist or not, in particular, on Newman-Kwart rearrangements and intramolecular Diels-Alder reactions. The reaction rates of the former calculated by the transition state theory, which consider only the thermal effects of microwaves, agree quantitatively with experimental data, and thus, the increases in reaction rates can be ascribed to dielectric heating of the solvent by microwaves. In contrast, for the latter, the temperature dependence of reaction rates can be explained qualitatively by thermal effects but the possibility of nonthermal effects still remains regardless of whether competitive processes are present or not. The effective intramolecular potential energy surface in the presence of a microwave field suggests that nonthermal effects arising from potential distortion are vanishingly small in intramolecular reactions. It is useful in the elucidation of the reaction mechanisms of microwave synthesis to apply the present theoretical approach with reference to the experiments where thermal and nonthermal effects are separated by screening microwave fields.

Molecular dynamics simulations of melting and the glass transition of nitromethane.

PubMed

Zheng, Lianqing; Luo, Sheng-Nian; Thompson, Donald L

2006-04-21

Molecular dynamics simulations have been used to investigate the thermodynamic melting point of the crystalline nitromethane, the melting mechanism of superheated crystalline nitromethane, and the physical properties of crystalline and glassy nitromethane. The maximum superheating and glass transition temperatures of nitromethane are calculated to be 316 and 160 K, respectively, for heating and cooling rates of 8.9 x 10(9) Ks. Using the hysteresis method [Luo et al., J. Chem. Phys. 120, 11640 (2004)] and by taking the glass transition temperature as the supercooling temperature, we calculate a value of 251.1 K for the thermodynamic melting point, which is in excellent agreement with the two-phase result [Agrawal et al., J. Chem. Phys. 119, 9617 (2003)] of 255.5 K and measured value of 244.73 K. In the melting process, the nitromethane molecules begin to rotate about their lattice positions in the crystal, followed by translational freedom of the molecules. A nucleation mechanism for the melting is illustrated by the distribution of the local translational order parameter. The critical values of the Lindemann index for the C and N atoms immediately prior to melting (the Lindemann criterion) are found to be around 0.155 at 1 atm. The intramolecular motions and molecular structure of nitromethane undergo no abrupt changes upon melting, indicating that the intramolecular degrees of freedom have little effect on the melting. The thermal expansion coefficient and bulk modulus are predicted to be about two or three times larger in crystalline nitromethane than in glassy nitromethane. The vibrational density of states is almost identical in both phases.

Solvent dynamical control of ultrafast ground state electron transfer: implications for Class II-III mixed valency.

PubMed

Lear, Benjamin J; Glover, Starla D; Salsman, J Catherine; Londergan, Casey H; Kubiak, Clifford P

2007-10-24

We relate the solvent and temperature dependence of the rates of intramolecular electron transfer (ET) of mixed valence complexes of the type {[Ru3O(OAc)6(CO)(L)]2-BL}-1, where L = pyridyl ligand and BL = pyrazine. Complexes were reduced chemically or electrochemically to obtain the mixed valence anions in seven solvents: acetonitrile, methylene chloride, dimethylformamide, tetrahydrofuran, dimethylsulfoxide, chloroform, and hexamethylphosphoramide. Rate constants for intramolecular ET were estimated by simulating the observed degree of nu(CO) IR band shape coalescence in the mixed valence state. Correlations between rate constants for ET and solvent properties including static dielectric constant, optical dielectric constant, the quantity 1/epsilonop - 1/epsilonS, microscopic solvent polarity, viscosity, cardinal rotational moments of inertia, and solvent relaxation times were examined. In the temperature study, the complexes displayed a sharp increase in the ket as the freezing points of the solvents methylene chloride and acetonitrile were approached. The solvent phase transition causes a localized-to-delocalized transition in the mixed valence ions and an acceleration in the rate of ET. This is explained in terms of decoupling the slower solvent motions involved in the frequency factor nuN which increases the value of nuN. The observed solvent and temperature dependence of the ket for these complexes is used in order to formulate a new definition for Robin-Day class II-III mixed valence compounds. Specifically, it is proposed that class II-III compounds are those for which thermodynamic properties of the solvent exert no control over ket, but the dynamic properties of the solvent still influence ket.

Convergence of sampling in protein simulations

NASA Astrophysics Data System (ADS)

Hess, Berk

2002-03-01

With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations, but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling.