Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis.

PubMed

Wijnrocx, K; François, L; Stinckens, A; Janssens, S; Buys, N

2016-10-01

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. © 2016 Blackwell Verlag GmbH.

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

Effect of dynamic high pressure on emulsifying and encapsulant properties of cashew tree gum.

PubMed

Porto, Bruna Castro; Cristianini, Marcelo

2018-04-15

Dynamic high pressure (DHP) has been applied in the physical modification of biopolymers as polysaccharides, proteins and gums. It is known that DHP is able to promote degradation of polysaccharides (e.g. molecular weight reduction). However, few studies have assessed the effect of DHP on the emulsifying and encapsulating properties of polysaccharides. Thus, this study aimed to investigate the effect of DHP on the emulsifying (average droplet size and particle size distribution, optical and confocal scanning laser microscopy, rheology, zeta potential and electric conductivity, creaming index, and turbidity) and encapsulating (scanning electronic microscopy, flavor retention, average droplet size, and particle size distribution) properties of cashew tree gum (CG). The application of DHP process improved the emulsifying capacity of cashew tree gum (CG) by reducing the medium droplet size (D3,2 and D4,3), increasing the turbidity and improving the emulsion stability. However, no effect of DHP was observed on the encapsulating capacity of CG. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modelling heat conduction in polycrystalline hexagonal boron-nitride films

PubMed Central

Mortazavi, Bohayra; Pereira, Luiz Felipe C.; Jiang, Jin-Wu; Rabczuk, Timon

2015-01-01

We conducted extensive molecular dynamics simulations to investigate the thermal conductivity of polycrystalline hexagonal boron-nitride (h-BN) films. To this aim, we constructed large atomistic models of polycrystalline h-BN sheets with random and uniform grain configuration. By performing equilibrium molecular dynamics (EMD) simulations, we investigated the influence of the average grain size on the thermal conductivity of polycrystalline h-BN films at various temperatures. Using the EMD results, we constructed finite element models of polycrystalline h-BN sheets to probe the thermal conductivity of samples with larger grain sizes. Our multiscale investigations not only provide a general viewpoint regarding the heat conduction in h-BN films but also propose that polycrystalline h-BN sheets present high thermal conductivity comparable to monocrystalline sheets. PMID:26286820

Structure and stabilizing interactions of casein micelles probed by high-pressure light scattering and FTIR.

PubMed

Gebhardt, Ronald; Takeda, Naohiro; Kulozik, Ulrich; Doster, Wolfgang

2011-03-17

Caseins form heterogeneous micelles composed of three types of disordered protein chains (α, β, κ), which include protein-bound calcium phosphate particles. We probe the stability limits of the micelle by applying hydrostatic pressure. The resulting changes of the size distribution and the average molecular weight are recorded in situ with static and dynamic light scattering. Pressure induces irreversible dissociation of the micelles into monomers above a critical value depending on their size. The critical pressure increases with temperature, pH, and calcium concentration due to the interplay of hydrophobic and electrostatic interactions. The pressure transition curves are biphasic, reflecting the equilibrium of two micelle states with different stability, average size, entropy, and calcium bound. The fast process of pressure dissociation is used to probe the slow equilibrium of the two micelle states under various conditions. Binding and release of β-casein from the micelle is suggested as the molecular mechanism of stabilization associated with the two states. In situ FTIR spectroscopy covering the P-O stretching region indicates that bound calcium phosphate particles are released from serine phosphate residues at pressures above 100 MPa. The resulting imbalance of charge triggers the complete decomposition of the micelle. © 2011 American Chemical Society

An evaluation of the effects of PEO/PEG molecular weights on extruded alumina rods

NASA Astrophysics Data System (ADS)

Bolger, Nancy Beth

1998-12-01

Alumina rods were piston extruded from bodies containing polyethylene glycols (PEGs) and polyethylene oxides (PEOs) with molecular weights ranging from 1,300 to 3,800,000 g/mol. A blend of aluminas possessing different particle size distributions was evaluated with regard to its extrusion pressure by varying the amount of PEG/PEO addition. Behavior exhibited by the alumina blend was dependent upon the additive that was used. The higher molecular weight binders with average molecular weight of 200,000 g/mol and 3,350,000 g/mol displayed the most severe behaviors of near dilatant and dilatant respectively. Physical properties of the green and fired states, as well as the binder burnout, were investigated with the changing additions. Correlation between the green and fired strengths and the changing molecular weights were examined. The additive present influenced the surface properties of the rods, which affected the green strengths. The highest average molecular weight polyethylene glycols showed higher green strengths, while the lowest green strengths were observed for the high molecular weight polyethylene oxides. Fired strengths generally ranged from approximately 12,000 psi to 16,000 psi for additive batches. Alumina pellets containing twelve separate combinations of polyethylene glycol with polyethylene oxide were dry pressed. Physical properties of the green and fired states were examined. Statistical analysis was performed upon the data and seven combinations of polyethylene glycol with polyethylene oxide were deemed significant. These combinations in conjunction with the same alumina blend were then piston extruded. The addition of polyethylene glycol reduced the near dilatant behavior exhibited by the 200,000 g/mol average molecular weight polyethylene oxide. Dilatant behavior was completely eliminated from the 3,350,000 g/mol average molecular weight polyethylene oxide batches. Physical properties of the green and fired states were again investigated with the changing additions. Polyethylene oxide, in combination with polyethylene glycol, did show an increase in green strength versus the polyethylene oxide alone. Strengths were still lower than those displayed by the polyethylene glycols alone. Reductions or degradations in molecular weight of the polymers due to mixing and extrusion processes may account for lower green strength of bodies, especially those containing polyethylene oxides.

Kinetic energy distribution of multiply charged ions in Coulomb explosion of Xe clusters.

PubMed

Heidenreich, Andreas; Jortner, Joshua

2011-02-21

We report on the calculations of kinetic energy distribution (KED) functions of multiply charged, high-energy ions in Coulomb explosion (CE) of an assembly of elemental Xe(n) clusters (average size (n) = 200-2171) driven by ultra-intense, near-infrared, Gaussian laser fields (peak intensities 10(15) - 4 × 10(16) W cm(-2), pulse lengths 65-230 fs). In this cluster size and pulse parameter domain, outer ionization is incomplete∕vertical, incomplete∕nonvertical, or complete∕nonvertical, with CE occurring in the presence of nanoplasma electrons. The KEDs were obtained from double averaging of single-trajectory molecular dynamics simulation ion kinetic energies. The KEDs were doubly averaged over a log-normal cluster size distribution and over the laser intensity distribution of a spatial Gaussian beam, which constitutes either a two-dimensional (2D) or a three-dimensional (3D) profile, with the 3D profile (when the cluster beam radius is larger than the Rayleigh length) usually being experimentally realized. The general features of the doubly averaged KEDs manifest the smearing out of the structure corresponding to the distribution of ion charges, a marked increase of the KEDs at very low energies due to the contribution from the persistent nanoplasma, a distortion of the KEDs and of the average energies toward lower energy values, and the appearance of long low-intensity high-energy tails caused by the admixture of contributions from large clusters by size averaging. The doubly averaged simulation results account reasonably well (within 30%) for the experimental data for the cluster-size dependence of the CE energetics and for its dependence on the laser pulse parameters, as well as for the anisotropy in the angular distribution of the energies of the Xe(q+) ions. Possible applications of this computational study include a control of the ion kinetic energies by the choice of the laser intensity profile (2D∕3D) in the laser-cluster interaction volume.

Molecular weight distribution characterization of hydrophobe-modified hydroxyethyl cellulose by size-exclusion chromatography.

PubMed

Li, Yongfu; Meunier, David M; Partain, Emmett M

2014-09-12

Size-exclusion chromatography (SEC) of hydrophobe-modified hydroxyethyl cellulose (HmHEC) is challenging because polymer chains are not isolated in solution due to association of hydrophobic groups and hydrophobic interaction with column packing materials. An approach to neutralize these hydrophobic interactions was developed by adding β-cyclodextrin (β-CD) to the aqueous eluent. SEC mass recovery, especially for the higher molecular weight chains, increased with increasing concentration of β-CD in the eluent. A β-CD concentration of 0.75wt% in the eluent was determined to be optimal for the HmHEC polymers studied. These conditions enabled precise determinations of apparent molecular weight distributions exhibiting less than 2% relative standard deviation in the measured weight-average molecular weight (MW) for five injections on three studied samples and showed no significant differences in MW determined on two different days. The developed technology was shown to be very robust for characterizing HmHEC having MW from 500kg/mol to 2000kg/mol, and it can be potentially applied to other hydrophobe-modified polymers. Copyright © 2014 Elsevier B.V. All rights reserved.

A new analytical approach to understanding nanoscale lead-iron interactions in drinking water distribution systems.

PubMed

Trueman, Benjamin F; Gagnon, Graham A

2016-07-05

High levels of iron in distributed drinking water often accompany elevated lead release from lead service lines and other plumbing. Lead-iron interactions in drinking water distribution systems are hypothesized to be the result of adsorption and transport of lead by iron oxide particles. This mechanism was explored using point-of-use drinking water samples characterized by size exclusion chromatography with UV and multi-element (ICP-MS) detection. In separations on two different stationary phases, high apparent molecular weight (>669 kDa) elution profiles for (56)Fe and (208)Pb were strongly correlated (average R(2)=0.96, N=73 samples representing 23 single-unit residences). Moreover, (56)Fe and (208)Pb peak areas exhibited an apparent linear dependence (R(2)=0.82), consistent with mobilization of lead via adsorption to colloidal particles rich in iron. A UV254 absorbance peak, coincident with high molecular weight (56)Fe and (208)Pb, implied that natural organic matter was interacting with the hypothesized colloidal species. High molecular weight UV254 peak areas were correlated with both (56)Fe and (208)Pb peak areas (R(2)=0.87 and 0.58, respectively). On average, 45% (std. dev. 10%) of total lead occurred in the size range 0.05-0.45 μm. Copyright © 2016 Elsevier B.V. All rights reserved.

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

PubMed

Roy, Ambrish; Skolnick, Jeffrey

2015-02-15

Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. Supplementary data are available at Bioinformatics online. skolnick@gatech.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Study of Nanoscale Friction Behaviors of Graphene on Gold Substrates Using Molecular Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Pengzhe; Li, Rui

2018-02-01

In this paper, we investigate the friction behaviors of graphene flakes sliding on a gold substrate using molecular dynamics simulations. The effects of flake size, flake shape, relative rotation angle between flake and substrate, and crystal orientation of substrate on the friction process are thoroughly studied. It is found that under the same load, the average friction forces per atom are smaller for a bigger graphene flake, which exhibits an obvious size effect. It is also shown that flake shape is critical in determining the friction in the sliding process. The average friction forces per atom for the square flake are much bigger than those for the triangular and round flakes. Moreover, the average friction forces per atom for the triangular flake are the smallest. We also find that the orientation of graphene flake relative to gold substrate plays a vital role in the friction process. The friction forces for the graphene flake sliding along the armchair direction are much bigger than those for the flakes with rotation. In addition, it is also found that single crystalline gold substrate exhibits a significant anisotropic effect of friction, which is attributed to the anisotropic effect of potential energy corrugation. These understandings not only shed light on the underlying mechanisms of graphene flake sliding on the gold substrates but also may guide the design and fabrication of nanoscale graphene-based devices.

Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

2009-10-01

Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.

Effect of surface roughness on liquid property measurements using mechanically oscillating sensors

NASA Technical Reports Server (NTRS)

Jain, Mahaveer K.; Grimes, Craig A.

2002-01-01

The resonant frequency and quality factor Q of a liquid immersed magnetoelastic sensor are shown to shift linearly with the liquid viscosity and density product. Measurements using different grade oils, organic chemicals, and glycerol-water mixtures show that the surface roughness of the sensor in combination with the molecular size of the liquid play important roles in determining measurement sensitivity, which can be controlled through adjusting the surface roughness of the sensor surface. A theoretical model describing the sensor resonant frequency and quality factor Q as a function of liquid properties is developed using a novel equivalent circuit approach. Experimental results are in agreement with theory when the liquid molecule size is larger than the average surface roughness. However, when the molecular size of the liquid is small relative to the surface roughness features molecules are trapped, and the trapped molecules act both as a mass load and viscous load; the result is higher viscous damping of the sensor than expected. c2002 Elsevier Science B.V. All rights reserved.

Optimal descriptor as a translator of eclectic information into the prediction of membrane damage: the case of a group of ZnO and TiO2 nanoparticles.

PubMed

Toropova, Alla P; Toropov, Andrey A; Benfenati, Emilio; Puzyn, Tomasz; Leszczynska, Danuta; Leszczynski, Jerzy

2014-10-01

The development of quantitative structure-activity relationships for nanomaterials needs representation of molecular structure of extremely complex molecular systems. Obviously, various characteristics of nanomaterial could impact associated biochemical endpoints. Following features of TiO2 and ZnO nanoparticles (n=42) are considered here: (i) engineered size (nm); (ii) size in water suspension (nm); (iii) size in phosphate buffered saline (PBS, nm); (iv) concentration (mg/L); and (v) zeta potential (mV). The damage to cellular membranes (units/L) is selected as an endpoint. Quantitative features-activity relationships (QFARs) are calculated by the Monte Carlo technique for three distributions of data representing values associated with membrane damage into the training and validation sets. The obtained models are characterized by the following average statistics: 0.78

Size effect on atomic structure in low-dimensional Cu-Zr amorphous systems.

PubMed

Zhang, W B; Liu, J; Lu, S H; Zhang, H; Wang, H; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

2017-08-04

The size effect on atomic structure of a Cu 64 Zr 36 amorphous system, including zero-dimensional small-size amorphous particles (SSAPs) and two-dimensional small-size amorphous films (SSAFs) together with bulk sample was investigated by molecular dynamics simulations. We revealed that sample size strongly affects local atomic structure in both Cu 64 Zr 36 SSAPs and SSAFs, which are composed of core and shell (surface) components. Compared with core component, the shell component of SSAPs has lower average coordination number and average bond length, higher degree of ordering, and lower packing density due to the segregation of Cu atoms on the shell of Cu 64 Zr 36 SSAPs. These atomic structure differences in SSAPs with various sizes result in different glass transition temperatures, in which the glass transition temperature for the shell component is found to be 577 K, which is much lower than 910 K for the core component. We further extended the size effect on the structure and glasses transition temperature to Cu 64 Zr 36 SSAFs, and revealed that the T g decreases when SSAFs becomes thinner due to the following factors: different dynamic motion (mean square displacement), different density of core and surface and Cu segregation on the surface of SSAFs. The obtained results here are different from the results for the size effect on atomic structure of nanometer-sized crystalline metallic alloys.

Atomic density effects on temperature characteristics and thermal transport at grain boundaries through a proper bin size selection

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

Vo, Truong Quoc; Kim, BoHung, E-mail: muratbarisik@iyte.edu.tr, E-mail: bohungk@ulsan.ac.kr; Barisik, Murat, E-mail: muratbarisik@iyte.edu.tr, E-mail: bohungk@ulsan.ac.kr

2016-05-21

This study focuses on the proper characterization of temperature profiles across grain boundaries (GBs) in order to calculate the correct interfacial thermal resistance (ITR) and reveal the influence of GB geometries onto thermal transport. The solid-solid interfaces resulting from the orientation difference between the (001), (011), and (111) copper surfaces were investigated. Temperature discontinuities were observed at the boundary of grains due to the phonon mismatch, phonon backscattering, and atomic forces between dissimilar structures at the GBs. We observed that the temperature decreases gradually in the GB area rather than a sharp drop at the interface. As a result, threemore » distinct temperature gradients developed at the GB which were different than the one observed in the bulk solid. This behavior extends a couple molecular diameters into both sides of the interface where we defined a thickness at GB based on the measured temperature profiles for characterization. Results showed dependence on the selection of the bin size used to average the temperature data from the molecular dynamics system. The bin size on the order of the crystal layer spacing was found to present an accurate temperature profile through the GB. We further calculated the GB thickness of various cases by using potential energy (PE) distributions which showed agreement with direct measurements from the temperature profile and validated the proper binning. The variation of grain crystal orientation developed different molecular densities which were characterized by the average atomic surface density (ASD) definition. Our results revealed that the ASD is the primary factor affecting the structural disorders and heat transfer at the solid-solid interfaces. Using a system in which the planes are highly close-packed can enhance the probability of interactions and the degree of overlap between vibrational density of states (VDOS) of atoms forming at interfaces, leading to a reduced ITR. Thus, an accurate understanding of thermal characteristics at the GB can be formulated by selecting a proper bin size.« less

Molecular size and origin do not influence the harmful side effects of hydroxyethyl starch on human proximal tubule cells (HK-2) in vitro.

PubMed

Bruno, Raphael R; Neuhaus, Winfried; Roewer, Norbert; Wunder, Christian; Schick, Martin A

2014-09-01

Recently, clinical trials revealed renal impairment induced by hydroxyethyl starch (HES) in septic patients. In prior studies, we managed to demonstrate that HES accumulated in renal proximal tubule cells (PTCs). The related pathomechanism has not yet been discovered. To validate our hypothesis that the HES molecule itself is harmful, regardless of its molecule size or origin, we conducted a comprehensive study to elucidate the influences of different HES preparations on PTC viability in vitro. Cell viability of human PTC was measured with a cytotoxicity assay, quantifying the reduction of tetrazolium salt to colored formazan. Experiments were performed by assessing the influence of different carrier solutions of HES (balanced, nonbalanced, culture medium), different average molecular weights (70, 130, 200 kDa), different origins (potato or corn derived), and various durations of incubation (2-21 hours). Furthermore, HES 130/0.4 was fractionated by ultrafiltration, and the impact on cell viability of average single-size fractions with <3, 3 to 10, 10 to 30, 30 to 50, 50 to 100, and >100 kDa was investigated. We also tested the possible synergistic effects of inflammation induced by tumor necrosis factor-α. All tested HES solutions, regardless of origin or carrier matrix, decreased cell viability in an equivalent, dose-dependent manner. Coincubation with tumor necrosis factor-α did not reduce HES-induced reduction of cell viability. Minor differences were detected comparing 70, 130, and 200 kDa preparations. Analysis of fractionated HES revealed that each fraction decreased cell viability. Even small HES molecules (10-30 kDa) were significantly deleterious. For the first time, we were able to show that only the total mass of HES molecules applied is responsible for the harmful impact on renal PTC in vitro. Neither molecular size nor their origin showed any relevance.

Atomic density effects on temperature characteristics and thermal transport at grain boundaries through a proper bin size selection

NASA Astrophysics Data System (ADS)

Vo, Truong Quoc; Barisik, Murat; Kim, BoHung

2016-05-01

This study focuses on the proper characterization of temperature profiles across grain boundaries (GBs) in order to calculate the correct interfacial thermal resistance (ITR) and reveal the influence of GB geometries onto thermal transport. The solid-solid interfaces resulting from the orientation difference between the (001), (011), and (111) copper surfaces were investigated. Temperature discontinuities were observed at the boundary of grains due to the phonon mismatch, phonon backscattering, and atomic forces between dissimilar structures at the GBs. We observed that the temperature decreases gradually in the GB area rather than a sharp drop at the interface. As a result, three distinct temperature gradients developed at the GB which were different than the one observed in the bulk solid. This behavior extends a couple molecular diameters into both sides of the interface where we defined a thickness at GB based on the measured temperature profiles for characterization. Results showed dependence on the selection of the bin size used to average the temperature data from the molecular dynamics system. The bin size on the order of the crystal layer spacing was found to present an accurate temperature profile through the GB. We further calculated the GB thickness of various cases by using potential energy (PE) distributions which showed agreement with direct measurements from the temperature profile and validated the proper binning. The variation of grain crystal orientation developed different molecular densities which were characterized by the average atomic surface density (ASD) definition. Our results revealed that the ASD is the primary factor affecting the structural disorders and heat transfer at the solid-solid interfaces. Using a system in which the planes are highly close-packed can enhance the probability of interactions and the degree of overlap between vibrational density of states (VDOS) of atoms forming at interfaces, leading to a reduced ITR. Thus, an accurate understanding of thermal characteristics at the GB can be formulated by selecting a proper bin size.

Early-stage aggregation in three-dimensional charged granular gas.

PubMed

Singh, Chamkor; Mazza, Marco G

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Early-stage aggregation in three-dimensional charged granular gas

NASA Astrophysics Data System (ADS)

Singh, Chamkor; Mazza, Marco G.

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

PubMed

Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A

2012-06-01

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.

The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity

PubMed Central

Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A.

2012-01-01

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population’s phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models. PMID:22426879

Characterization and migration of oil and solids in oily sludge during centrifugation.

PubMed

Wang, Jun; Han, Xu; Huang, Qunxing; Ma, Zengyi; Chi, Yong; Yan, Jianhua

2018-05-01

The migration behaviors of oil, water and solids in sludge during centrifugation were elaborated. Size distribution, surface topography and lypohydrophilic properties were studied in detail. The average size of solids was 61 μm in original sludge, 31 μm in upper layer and 235 μm in bottom layer. The result shows that solvent is essential to separate oil phase into molecular light and weight fractions during centrifugation. With solvent/oil ratio increases from 1:2, 1:1, 2:1 to 5:1, molecular weight in upper layer decreases from 1044, 1043, 1020 to 846 combined with that in bottom layer increases. A model was proposed to calculate the oil residue content in solid phases after sedimentation. The findings of this paper provide information for optimizing the oil recovery and clean treatment.

High Coverages of Hydrogen on a (10,0) Carbon Nanotube

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

2001-01-01

The binding energy of H to a (10,0) carbon nanotube is calculated at 24, 50, and 100% coverage. Several different bonding configurations are considered for the 50% coverage case. Using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) approach, the average C-H bond energy for the most stable 50% coverage and for the 100% coverage are 57.3 and 38.6 kcal/mol, respectively. Considering the size of the bond energy of H2, these values suggest that it will be difficult to achieve 100% atomic H coverage on a (10,0) nanotube.

Scaling of number, size, and metabolic rate of cells with body size in mammals.

PubMed

Savage, Van M; Allen, Andrew P; Brown, James H; Gillooly, James F; Herman, Alexander B; Woodruff, William H; West, Geoffrey B

2007-03-13

The size and metabolic rate of cells affect processes from the molecular to the organismal level. We present a quantitative, theoretical framework for studying relationships among cell volume, cellular metabolic rate, body size, and whole-organism metabolic rate that helps reveal the feedback between these levels of organization. We use this framework to show that average cell volume and average cellular metabolic rate cannot both remain constant with changes in body size because of the well known body-size dependence of whole-organism metabolic rate. Based on empirical data compiled for 18 cell types in mammals, we find that many cell types, including erythrocytes, hepatocytes, fibroblasts, and epithelial cells, follow a strategy in which cellular metabolic rate is body size dependent and cell volume is body size invariant. We suggest that this scaling holds for all quickly dividing cells, and conversely, that slowly dividing cells are expected to follow a strategy in which cell volume is body size dependent and cellular metabolic rate is roughly invariant with body size. Data for slowly dividing neurons and adipocytes show that cell volume does indeed scale with body size. From these results, we argue that the particular strategy followed depends on the structural and functional properties of the cell type. We also discuss consequences of these two strategies for cell number and capillary densities. Our results and conceptual framework emphasize fundamental constraints that link the structure and function of cells to that of whole organisms.

Multi-scale study of condensation in water jets using ellipsoidal-statistical Bhatnagar-Gross-Krook and molecular dynamics modeling

NASA Astrophysics Data System (ADS)

Li, Zheng; Borner, Arnaud; Levin, Deborah A.

2014-06-01

Homogeneous water condensation and ice formation in supersonic expansions to vacuum for stagnation pressures from 12 to 1000 mbar are studied using the particle-based Ellipsoidal-Statistical Bhatnagar-Gross-Krook (ES-BGK) method. We find that when condensation starts to occur, at a stagnation pressure of 96 mbar, the increase in the degree of condensation causes an increase in the rotational temperature due to the latent heat of vaporization. The simulated rotational temperature profiles along the plume expansion agree well with measurements confirming the kinetic homogeneous condensation models and the method of simulation. Comparisons of the simulated gas and cluster number densities, cluster size for different stagnation pressures along the plume centerline were made and it is found that the cluster size increase linearly with respect to stagnation pressure, consistent with classical nucleation theory. The sensitivity of our results to cluster nucleation model and latent heat values based on bulk water, specific cluster size, or bulk ice are examined. In particular, the ES-BGK simulations are found to be too coarse-grained to provide information on the phase or structure of the clusters formed. For this reason, molecular dynamics simulations of water condensation in a one-dimensional free expansion to simulate the conditions in the core of a plume are performed. We find that the internal structure of the clusters formed depends on the stagnation temperature. A larger cluster of average size 21 was tracked down the expansion, and a calculation of its average internal temperature as well as a comparison of its radial distribution functions (RDFs) with values measured for solid amorphous ice clusters lead us to conclude that this cluster is in a solid-like rather than liquid form. In another molecular-dynamics simulation at a much lower stagnation temperature, a larger cluster of size 324 and internal temperature 200 K was extracted from an expansion plume and equilibrated to determine its RDF and self-diffusion coefficient. The value of the latter shows that this cluster is formed in a supercooled liquid state rather than in an amorphous solid state.

Discreteness-induced concentration inversion in mesoscopic chemical systems.

PubMed

Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F; Grima, Ramon

2012-04-10

Molecular discreteness is apparent in small-volume chemical systems, such as biological cells, leading to stochastic kinetics. Here we present a theoretical framework to understand the effects of discreteness on the steady state of a monostable chemical reaction network. We consider independent realizations of the same chemical system in compartments of different volumes. Rate equations ignore molecular discreteness and predict the same average steady-state concentrations in all compartments. However, our theory predicts that the average steady state of the system varies with volume: if a species is more abundant than another for large volumes, then the reverse occurs for volumes below a critical value, leading to a concentration inversion effect. The addition of extrinsic noise increases the size of the critical volume. We theoretically predict the critical volumes and verify, by exact stochastic simulations, that rate equations are qualitatively incorrect in sub-critical volumes.

Membranes with functionalized carbon nanotube pores for selective transport

DOEpatents

Bakajin, Olgica; Noy, Aleksandr; Fornasiero, Francesco; Park, Hyung Gyu; Holt, Jason K; Kim, Sangil

2015-01-27

Provided herein composition and methods for nanoporous membranes comprising single walled, double walled, or multi-walled carbon nanotubes embedded in a matrix material. Average pore size of the carbon nanotube can be 6 nm or less. These membranes are a robust platform for the study of confined molecular transport, with applications in liquid and gas separations and chemical sensing including desalination, dialysis, and fabric formation.

Resolution of molecular weight distributions in slightly pyrolyzed cellulose using the weibull function

Treesearch

A. Broido; Hsiukang Yow

1977-01-01

Even before weight loss in the low-temperature pyrolysis of cellulose becomes significant, the average degree of polymerization of the partially pyrolyzed samples drops sharply. The gel permeation chromatograms of nitrated derivatives of the samples can be described in terms of a small number of mixed size populations—each component fitted within reasonable limits by a...

Nanostructural control of the release of macromolecules from silica sol–gels

PubMed Central

Radin, Shula; Bhattacharyya, Sanjib; Ducheyne, Paul

2013-01-01

The therapeutic use of biological molecules such as growth factors and monoclonal antibodies is challenging in view of their limited half-life in vivo. This has elicited the interest in delivery materials that can protect these molecules until released over extended periods of time. Although previous studies have shown controlled release of biologically functional BMP-2 and TGF-β from silica sol–gels, more versatile release conditions are desirable. This study focuses on the relationship between room temperature processed silica sol–gel synthesis conditions and the nanopore size and size distribution of the sol–gels. Furthermore, the effect on release of large molecules with a size up to 70 kDa is determined. Dextran, a hydrophilic polysaccharide, was selected as a large model molecule at molecular sizes of 10, 40 and 70 kDa, as it enabled us to determine a size effect uniquely without possible confounding chemical effects arising from the various molecules used. Previously, acid catalysis was performed at a pH value of 1.8 below the isoelectric point of silica. Herein the silica synthesis was pursued using acid catalysis at either pH 1.8 or 3.05 first, followed by catalysis at higher values by adding base. This results in a mesoporous structure with an abundance of pores around 3.5 nm. The data show that all molecular sizes can be released in a controlled manner. The data also reveal a unique in vivo approach to enable release of large biological molecules: the use more labile sol–gel structures by acid catalyzing above the pH value of the isoelectric point of silica; upon immersion in a physiological fluid the pores expand to reach an average size of 3.5 nm, thereby facilitating molecular out-diffusion. PMID:23643607

Near-infrared scattering as a dust diagnostic

NASA Astrophysics Data System (ADS)

Saajasto, Mika; Juvela, Mika; Malinen, Johanna

2018-06-01

Context. Regarding the evolution of dust grains from diffuse regions of space to dense molecular cloud cores, many questions remain open. Scattering at near-infrared wavelengths, or "cloudshine", can provide information on cloud structure, dust properties, and the radiation field that is complementary to mid-infrared "coreshine" and observations of dust emission at longer wavelengths. Aims: We examine the possibility of using near-infrared scattering to constrain the local radiation field and the dust properties, the scattering and absorption efficiency, the size distribution of the grains, and the maximum grain size. Methods: We use radiative transfer modelling to examine the constraints provided by the J, H, and K bands in combination with mid-infrared surface brightness at 3.6 μm. We use spherical one-dimensional and elliptical three-dimensional cloud models to study the observable effects of different grain size distributions with varying absorption and scattering properties. As an example, we analyse observations of a molecular cloud in Taurus, TMC-1N. Results: The observed surface brightness ratios of the bands change when the dust properties are changed. However, even a change of ±10% in the surface brightness of one band changes the estimated power-law exponent of the size distribution γ by up to 30% and the estimated strength of the radiation field KISRF by up to 60%. The maximum grain size Amax and γ are always strongly anti-correlated. For example, overestimating the surface brightness by 10% changes the estimated radiation field strength by 20% and the exponent of the size distribution by 15%. The analysis of our synthetic observations indicates that the relative uncertainty of the parameter distributions are on average Amax, γ 25%, and the deviation between the estimated and correct values ΔQ < 15%. For the TMC-1N observations, a maximum grain size Amax > 1.5μm and a size distribution with γ > 4.0 have high probability. The mass weighted average grain size is ⟨am⟩ = 0.113μm. Conclusions: We show that scattered infrared light can be used to derive meaningful limits for the dust parameters. However, errors in the surface brightness data can result in considerable uncertainties on the derived parameters.

One-Pot Process in Scalable Bath for Water-Dispersed ZnS Nanocrystals with the Tailored Size

DOE PAGES

Jung, Hyunsung; Phelps, Tommy J.; Rondinone, Adam J.; ...

2017-05-01

Well-dispersed ZnS nanocrystals with tailored size in aqueous solutions were synthesized by employing cysteine-sulfur (Cys-S) complexes with low molecular weight in a scalable anoxic vessel. High yield production of water-dispersed ZnS nanocrystals on a 10-L scale was demonstrated in an aqueous solution process. The average crystallite size of ZnS was controlled by changing the ratio of the cysteine to sulfide in the applied Cys-S complexes. A decrease in the crystallite size of ZnS likely resulted in both the blue shift of peak positions and the relative variation of peak intensities in the photoluminescence properties. In addition, the pH-dependent stability againstmore » aggregation of ZnS nanocrystals was investigated to reduce agglomeration.« less

Crossover in growth laws for phase-separating binary fluids: molecular dynamics simulations.

PubMed

Ahmad, Shaista; Das, Subir K; Puri, Sanjay

2012-03-01

Pattern and dynamics during phase separation in a symmetrical binary (A+B) Lennard-Jones fluid are studied via molecular dynamics simulations after quenching homogeneously mixed critical (50:50) systems to temperatures below the critical one. The morphology of the domains, rich in A or B particles, is observed to be bicontinuous. The early-time growth of the average domain size is found to be consistent with the Lifshitz-Slyozov law for diffusive domain coarsening. After a characteristic time, dependent on the temperature, we find a clear crossover to an extended viscous hydrodynamic regime where the domains grow linearly with time. Pattern formation in the present system is compared with that in solid binary mixtures, as a function of temperature. Important results for the finite-size and temperature effects on the small-wave-vector behavior of the scattering function are also presented.

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

PubMed Central

Mortlock, Sally-Anne; Khatkar, Mehar S.; Williamson, Peter

2016-01-01

Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial. PMID:26824579

Is telomere length a molecular marker of past thermal stress in wild fish?

PubMed

Debes, Paul V; Visse, Marko; Panda, Bineet; Ilmonen, Petteri; Vasemägi, Anti

2016-11-01

Telomeres protect eukaryotic chromosomes; variation in telomere length has been linked (primarily in homoeothermic animals) to variation in stress, cellular ageing and disease risk. Moreover, telomeres have been suggested to function as biomarker for quantifying past environmental stress, but studies in wild animals remain rare. Environmental stress, such as extreme environmental temperatures in poikilothermic animals, may result in oxidative stress that accelerates telomere attrition. However, growth, which may depend on temperature, can also contribute to telomere attrition. To test for associations between multitissue telomere length and past water temperature while accounting for the previous individual growth, we used quantitative PCR to analyse samples from 112 young-of-the-year brown trout from 10 natural rivers with average water temperature differences of up to 6°C (and an absolute maximum of 23°C). We found negative associations between relative telomere length (RTL) and both average river temperature and individual body size. We found no indication of RTL-temperature association differences among six tissues, but we did find indications for differences among the tissues for associations between RTL and body size; size trends, albeit nonsignificant in their differences, were strongest in muscle and weakest in fin. Although causal relationships among temperature, growth, oxidative stress, and cross-sectional telomere length remain largely unknown, our results indicate that telomere-length variation in a poikilothermic wild animal is associated with both past temperature and growth. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Geometry of phase-separated domains in phospholipid bilayers by diffraction-contrast electron microscopy.

PubMed Central

Hui, S W

1981-01-01

The sizes and shapes of solidus (gel) phase domains in the hydrated molecular bilayers of dilauroylphosphatidylcholine/dipalmitoylphasphatidylcholine (DLPC/DPPC) (1:1) and phosphatidylserine (PS)/DPPC (1:2) are visualized directly by low dose diffraction-contrast electron microscopy. The temperature and humidity of the bilayers are controlled by an environmental chamber set in an electron microscope. The contrast between crystalline domains is enhanced by electron optical filtering of the diffraction patterns of the bilayers. The domains are seen as a patchwork in the plane of the bilayer, with an average width of 0.2-0.5 micrometer. The percentage of solidus area measured from diffraction-contrast micrographs at various temperatures agrees in general with those depicted by known phase diagrams. The shape and size of the domains resemble those seen by freeze-fracture in multilamellar vesicles. Temperature-related changes in domain size and in phase boundary per unit area are more pronounced in the less miscible DLPC/DPPC mixture. No significant change in these geometric parameters with temperature is found in the PS/DPPC mixture. Mapping domains by their molecular diffraction signals not only verifies the existance of areas of different molecular packing during phase separation but also provides a quantitative measurement of structural boundaries and defects in lipid bilayers. Images FIGURE 1 FIGURE 3 FIGURE 6 PMID:6894707

The effect of baking and enzymatic treatment on the structural properties of wheat starch.

PubMed

Fuentes, Catalina; Zielke, Claudia; Prakash, Manish; Kumar, Puneeth; Peñarrieta, J Mauricio; Eliasson, Ann-Charlotte; Nilsson, Lars

2016-12-15

In this study, bread was baked with and without the addition of α-amylase. Starch was extracted from the baked bread and its molecular properties were characterized using (1)H NMR and asymmetric flow field-flow fractionation (AF4) connected to multi-angle light scattering (MALS) and other detectors. The approach allows determination of molar mass, root- mean-square radius and apparent density as well as the average degree of branching of amylopectin. The results show that starch size and structure is affected as a result of the baking process. The effect is larger when α-amylase is added. The changes include both a decrease molar mass and size as well as an increase in apparent density. Moreover, an increase in average degree of branching and the number of reducing ends H-1(β-r) and H-1(α-r) can be observed. Copyright © 2016. Published by Elsevier Ltd.

Identification of Characteristic Macromolecules of Escherichia coli Genotypes by Atomic Force Microscope Nanoscale Mechanical Mapping

NASA Astrophysics Data System (ADS)

Chang, Alice Chinghsuan; Liu, Bernard Haochih

2018-02-01

The categorization of microbial strains is conventionally based on the molecular method, and seldom are the morphological characteristics in the bacterial strains studied. In this research, we revealed the macromolecular structures of the bacterial surface via AFM mechanical mapping, whose resolution was not only determined by the nanoscale tip size but also the mechanical properties of the specimen. This technique enabled the nanoscale study of membranous structures of microbial strains with simple specimen preparation and flexible working environments, which overcame the multiple restrictions in electron microscopy and label-enable biochemical analytical methods. The characteristic macromolecules located among cellular surface were considered as surface layer proteins and were found to be specific to the Escherichia coli genotypes, from which the averaged molecular sizes were characterized with diameters ranging from 38 to 66 nm, and the molecular shapes were kidney-like or round. In conclusion, the surface macromolecular structures have unique characteristics that link to the E. coli genotype, which suggests that the genomic effects on cellular morphologies can be rapidly identified using AFM mechanical mapping. [Figure not available: see fulltext.

Encapsidation of Linear Polyelectrolyte in a Viral Nanocontainer

NASA Astrophysics Data System (ADS)

Hu, Yufang

2005-03-01

We present the results from a combined experimental and theoretical study on the self-assembly of a model icosahedral virus, Cowpea Chlorotic Mottle Virus (CCMV). The formation of native CCMV capsids is believed to be driven primarily by the electrostatic interactions between the viral RNA and the positively charged capsid interior, as well as by the hydrophobic interactions between capsid protein subunits. To probe these molecular interactions, in vitro self-assembly reactions are carried out using the CCMV capsid protein and a synthetic linear polyelectrolyte, sodium polystyrene sulfonate (NaPSS), which functions as the analog of viral RNA. Under appropriate solutions conditions, NaPSS is encapsidated by the viral capsid. The molecular weight of NaPSS is systematically varied and the resulting average capsid size, size distribution, and particle morphology are measured by transmission electron microscopy. The correlation between capsid size and packaged cargo size, as well as the upper limit of capsid packaging capacity, are characterized. To elucidate the physical role played by the encapsidated polyelectrolyte in determining the preferred size of spherical viruses, we have used a mean-field approach to calculate the free energy of the virus-like particle as a function of chain length (and of the strength of chain/capsid attractive interaction). We find good agreement with our analytical calculations and experimental results.

Bottleneck Effect on Evolutionary Rate in the Nearly Neutral Mutation Model

PubMed Central

Araki, H.; Tachida, H.

1997-01-01

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N(1) and N(2) (N(1) > N(2)), in the simulations. The overdispersion is observed if 2N(2)σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock. PMID:9335622

Liquid Chromatography at Critical Conditions: Balancing size exclusion and adsorption in nanopores

NASA Astrophysics Data System (ADS)

Abdulahad, Asem; Amos, Jeffrey; Ryu, Chang

2009-03-01

Liquid chromatography at critical condition (LCCC) is a measure to identify thermodynamic conditions, in which polymers elute independently of molar mass during high performance liquid chromatography. Under these critical conditions the entropic exclusions that dominate size exclusion chromatography (SEC) and the enthalpic adsorption that governs adsorption-based interaction chromatography (IC) are said to negate one another resulting in simultaneous elution of the polymer of different molecular weights. Using multiple C18-bonded silica columns with different average nanopore sizes (from 5 nm to 30 nm), we will study the LCCC conditions of PS in methylene chloride/acetonitrile solvent mixture at different temperature. In addition, we will show that the separation of polystyrene can be fine tuned using a refined temperature gradient interaction chromatography (TGIC) that employs multiple columns of varying pore size in sequence.

Melting/freezing behavior of a fluid confined in porous glasses and MCM-41: Dielectric spectroscopy and molecular simulation

NASA Astrophysics Data System (ADS)

Sliwinska-Bartkowiak, Malgorzata; Dudziak, Grazyna; Sikorski, Roman; Gras, Roman; Radhakrishnan, Ravi; Gubbins, Keith E.

2001-01-01

We report both experimental measurements and molecular simulations of the melting and freezing behavior of fluids in nanoporous media. The experimental studies are for nitrobenzene in the silica-based pores of controlled pore glass, Vycor, and MCM-41. Dielectric relaxation spectroscopy is used to determine melting points and the orientational relaxation times of the nitrobenzene molecules in the bulk and the confined phase. Monte Carlo simulations, together with a bond orientational order parameter method, are used to determine the melting point and fluid structure inside cylindrical pores modeled on silica. Qualitative comparison between experiment and simulation are made for the shift in the freezing temperatures and the structure of confined phases. From both the experiments and the simulations, it is found that the confined fluid freezes into a single crystalline structure for average pore diameters greater than 20σ, where σ is the diameter of the fluid molecule. For average pore sizes between 20σ and 15σ, part of the confined fluid freezes into a frustrated crystal structure with the rest forming an amorphous region. For pore sizes smaller than 15σ, even the partial crystallization did not occur. Our measurements and calculations show clear evidence of a novel intermediate "contact layer" phase lying between liquid and crystal; the contact layer is the confined molecular layer adjacent to the pore wall and experiences a deeper fluid-wall potential energy compared to the inner layers. We also find evidence of a liquid to "hexatic" transition in the quasi-two-dimensional contact layer at high temperatures.

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

PubMed Central

Bonet, Julio; Girona, Elena Lopez; Sargent, Daniel J; Muñoz-Torres, Monica C; Monfort, Amparo; Abbott, Albert G; Arús, Pere; Simpson, David W; Davik, Jahn

2009-01-01

Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN). Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR. PMID:19772672

Measurement of Size-dependent Dynamic Shape Factors of Quartz Particles in Two Flow Regimes

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

Alexander, Jennifer M.; Bell, David M.; Imre, D.

2016-08-02

Understanding and modeling the behavior of quartz dust particles, commonly found in the atmosphere, requires knowledge of many relevant particles properties, including particle shape. This study uses a single particle mass spectrometer, a differential mobility analyzer, and an aerosol particle mass analyzer to measure quartz aerosol particles mobility, aerodynamic, and volume equivalent diameters, mass, composition, effective density, and dynamic shape factor as a function of particle size, in both the free molecular and transition flow regimes. The results clearly demonstrate that dynamic shape factors can vary significantly as a function of particle size. For the quartz samples studied here, themore » dynamic shape factors increase with size, indicating that larger particles are significantly more aspherical than smaller particles. In addition, dynamic shape factors measured in the free-molecular (χv) and transition (χt) flow regimes can be significantly different, and these differences vary with the size of the quartz particles. For quartz, χv of small (d < 200 nm) particles is 1.25, while χv of larger particles (d ~ 440 nm) is 1.6, with a continuously increasing trend with particle size. In contrast χt, of small particles starts at 1.1 increasing slowly to 1.34 for 550 nm diameter particles. The multidimensional particle characterization approach used here goes beyond determination of average properties for each size, to provide additional information about how the particle dynamic shape factor may vary even for particles with the same mass and volume equivalent diameter.« less

Exploring glycogen biosynthesis through Monte Carlo simulation.

PubMed

Zhang, Peng; Nada, Sharif S; Tan, Xinle; Deng, Bin; Sullivan, Mitchell A; Gilbert, Robert G

2018-05-08

Glycogen, a complex branched polymer of glucose (average chain length ~10 monomer units), is the blood-sugar reservoir in humans and other animals. Certain aspects of its molecular structure relevant to its biological functions are currently unamenable to experimental exploration. Knowledge of these is needed to develop future models for quantitative data-fitting to obtain mechanistic understanding of the biosynthetic processes that give rise to glycogen structure. Monte Carlo simulations of the biosynthesis of this structure with realistic macromolecular parameters reveal how chain growth and stoppage (the latter assumed to be through both the action of glycogen branching enzyme and other degradative enzymes, and by hindrance) control structural features. The simulated chain-length, pair-distance and radial density distributions agree semi-quantitatively with the limited available data. The simulations indicate that a steady state in molecular structure and size is rapidly obtained, that molecular density reaches a maximum near the center of the particle (not at the periphery, as is the case with dendrimers), and that particle size is controlled by both enzyme activity and hindrance. This knowledge will aid in the understanding of diabetes (loss of blood-sugar control), which has been found to involve subtle differences in glycogen molecular structure. Copyright © 2018 Elsevier B.V. All rights reserved.

Swelling Kinetics of Waxy Maize Starch

NASA Astrophysics Data System (ADS)

Desam, Gnana Prasuna Reddy

Starch pasting behavior greatly influences the texture of a variety of food products such as canned soup, sauces, baby foods, batter mixes etc. The annual consumption of starch in the U.S. is 3 million metric tons. It is important to characterize the relationship between the structure, composition and architecture of the starch granules with its pasting behavior in order to arrive at a rational methodology to design modified starch of desirable digestion rate and texture. In this research, polymer solution theory was applied to predict the evolution of average granule size of starch at different heating temperatures in terms of its molecular weight, second virial coefficient and extent of cross-link. Evolution of granule size distribution of waxy native maize starch when subjected to heating at constant temperatures of 65, 70, 75, 80, 85 and 90 C was characterized using static laser light scattering. As expected, granule swelling was more pronounced at higher temperatures and resulted in a shift of granule size distribution to larger sizes with a corresponding increase in the average size by 100 to 120% from 13 mum to 25-28 mum. Most of the swelling occurred within the first 10 min of heating. Pasting behavior of waxy maize at different temperatures was also characterized from the measurements of G' and G" for different heating times. G' was found to increase with temperature at holding time of 2 min followed by its decrease at larger holding times. This behavior is believed to be due to the predominant effect of swelling at small times. However, G" was insensitive to temperature and holding times. The structure of waxy maize starch was characterized by cryoscanning electron microscopy. Experimental data of average granule size vs time at different temperatures were compared with model predictions. Also the Experimental data of particle size distribution vs particle size at different times and temperatures were compared with model predictions.

Determination of molecular mass values of chondroitin sulfates by fluorophore-assisted carbohydrate electrophoresis (FACE).

PubMed

Buzzega, Dania; Maccari, Francesca; Volpi, Nicola

2010-03-11

Fluorophore-assisted carbohydrate electrophoresis (FACE) was applied to determine the molecular mass (M) values of various chondroitin sulfate (CS) samples. After labeling with 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS), FACE was able to resolve each CS sample as a discrete band depending on the M value. After densitometric acquisition, the migration distance of each CS standard was acquired and the third grade polynomial calibration standard curve was determined by plotting the logarithms of the M values as a function of migration ratio. Purified CS samples of different origin and the European Pharmacopeia CS standard were analyzed by both FACE and conventional high-performance size-exclusion liquid chromatography (HPSEC) methods. The molecular weight value on the top of the chromatographic peak (M(p)), the number-average M(n), weight-average M(w), and polydispersity (M(w)/M(n)) were examined by both techniques and found to be quite similar. This study demonstrates that FACE analysis is a suitable, sensitive and simple method for the determination of the M values of CS macromolecules with possible utilization in virtually any kind of research and development such as quality control laboratories. Copyright 2009 Elsevier B.V. All rights reserved.

Cellulosic nanowhiskers. Theory and application of light scattering from polydisperse spheroids in the Rayleigh-Gans-Debye regime.

PubMed

Braun, Birgit; Dorgan, John R; Chandler, John P

2008-04-01

Mathematical treatment of light scattering within the Rayleigh-Gans-Debye limit for spheroids with polydispersity in both length and diameter is developed and experimentally tested using cellulosic nanowhiskers (CNW). Polydispersity indices are obtained by fitting the theoretical formfactor to experimental data. Good agreement is achieved using a polydispersity of 2.3 for the length, independent of the type of acid used. Diameter polydispersities are 2.1 and 3.0 for sulfuric and hydrochloric acids, respectively. These polydispersities allow the determination of average dimensions from the z-average mean-square radius (z) and the weight-average molecular weight (M w) easily obtained from Berry plots. For cotton linter hydrolyzed by hydrochloric acid, the average length and diameter are 244 and 22 nm. This compares to average length and diameter of 272 and 13 nm for sulfuric acid. This study establishes a new light-scattering methodology as a quick and robust tool for size characterization of polydisperse spheroidal nanoparticles.

Production and structural analysis of the polysaccharide secreted by Trametes (Coriolus) versicolor ATCC 200801.

PubMed

Rau, Udo; Kuenz, Anja; Wray, Victor; Nimtz, Manfred; Wrenger, Julika; Cicek, Hasan

2009-01-01

Trametes versicolor ATCC 200801 secretes 4.1 g L(-1) of exopolysaccharide (EPS) when synthetic minimal medium and low-shear bioreactor cultivation technique are used. Structural and compositional analyses by thin layer chromatography, gas chromatography-mass spectrometry, electrospray ionization tandem mass spectrometry, and nuclear magnetic resonance spectroscopy yielded predominantly glucose and small amounts of galactose, mannose, arabinose, and xylose. The main EPS is composed of beta-1,3/beta-1,6-linked D-glucose molecules which is identical with Schizophyllan but does not possess a triple helical arrangement as secondary structure. Two molar mass fractions were detected by size exclusion chromatography yielding weight-average molecular weights of 4,100 and 2.6 kDa. Protein content varies between 2-3.6% (w/w). The exopolysaccharide is different in the nature of the glycosidic linkage, composition of monosaccharides, protein content, and weight-average molecular weight compared to the well-known polysaccharopeptide (PSP) and polysaccharopeptide Krestin (PSK).

Vitreous floaters (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kershaw, K.; Nguyen, Derek; Yee, Kenneth; Nguyen, Justin A.; Harrington, Michael G.; Sebag, Jerry

2017-02-01

BACKGROUND: Vitreous opacities and posterior vitreous detachment (PVD) disturb vision by degrading contrast sensitivity (AJO 172:7-12, 2016). Increased light scattering is the presumed mechanism. To test this hypothesis, dynamic light scattering (DLS) was performed on excised vitreous of patients with clinically significant floaters, and compared to macular pucker controls. METHODS: Undiluted, unfixed vitreous was procured during 25-gauge vitrectomy in 14 subjects (age = 59 +/- 6.6 years) with clinically significant vitreous floaters, and 6 controls (age = 66.5 +/- 8.7 years; P = 0.10) with macular pucker. Total protein concentration was determined by fluorescent Quant-iTTM protein assay kit (Invitrogen/Molecular Probes, Eugene, OR) with bovine serum albumin (0500 ng/ml) as a standard. Fluorescence (excitation at 470 nm and emission at 570 nm) was measured using a Gemini XPS Dual-Scanning Microplate Spectrofluorometer and data analyzed using SoftMax Pro software (Molecular Devices, Sunnyvale, CA). DLS (NS300, Malvern Instruments, Westborough, MA) measurements were performed in each specimen after 10-fold dilution in phosphate buffered saline to optimize concentration in each specimen and determine the mean number of particles, the particle size distributions, and the average particle sizes. RESULTS: Total protein concentration in vitreous specimens trended higher in macular pucker controls (1037 +/- 1038 μg/mL) than eyes with vitreous floaters (353.7 +/- 141.1 μg/mL P = 0.08). When normalized to total protein concentration, the number of particles in vitreous from floater eyes was more than 2-fold greater than controls (P < 0.04). Particle size distributions were similarly two-fold greater in vitreous from floater subjects as compared to controls (P < 0.05). The average particle size in vitreous from floater eyes was 315.8 +/- 194.6 nm, compared to 147.7 +/- 129.3 nm in macular pucker controls (P = 0.039). CONCLUSIONS: Vitreous from eyes with clinically significant floaters contains more particles of larger sizes as compared to controls, likely accounting for the degradation of contrast sensitivity previously found in these patients (Retina 34:1062-8, 2014; IOVS 56:1611-7, 2015; AJO 172:7-12, 2016). DLS could elucidate the underlying molecular abnormalities in patients afflicted with bothersome vitreous floaters and help develop clinical tools to better measure vitreous floaters as well as test the efficacy of various therapies.

Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

1998-01-01

A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

Synthesis and characterization of functional acrylic copolymers via RAFT mini-emulsion polymerization

NASA Astrophysics Data System (ADS)

Yılmaz, Onur; Özkan, ćiǧdem Kılıçarislan; Yılmaz, Catalina N.; Yorgancıoǧlu, Ali; Özgünay, Hasan; Karavana, Hüseyin Ata

2017-12-01

Copolymers bearing reactive functional groups with controlled molecular weights are of importance since they can be used in many fields such as composites, coatings, membranes, catalysis, biology, optoelectronics, pharmaceuticals, etc. In the present study low molecular weight copolymers based on butyl acrylate (BA) and methyl methacrylate (MMA) in combination with reactive functional monomers of vinyl trietoxysilane (VTES), 3-trimetoxysilylpropyl methacrylate (TMSPMA) and glycidyl methacrylate (GMA) were synthesized via RAFT mini-emulsion technique using 2-cyano 2-propyldodecyldithiocarbonate as CTA agent. The results showed that the average molecular weights of copolymers were close to the theoretical values. On the other hand, PDI values were found to be higher than conventional RAFT polymers. The particle sizes of the latexes were small with very homogenous distributions and good stability. FTIR, H-NMR and TGA results verified the success of copolymer syntheses.

Thermodynamic limits on the size and size distribution of nucleic acids synthesized in vitro: the role of pyrophosphate hydrolysis.

PubMed

Peller, L

1977-02-08

The free-energy change of phosphodiester bond formation from nucleoside triphosphates is more favorable than with nucleoside diphosphates as substrates. Base-stacking interactions can make significant contributions to both delta G degrees ' values. Pyrophosphate hydrolysis when it accompanies the former reaction dominates all thermodynamic considerations. Three experimental situations are discussed in which high-molecular-weight polynucleotides are synthesized without a strong driving force for covalent bond formation. For one of these, a kinetic scheme is presented which encompasses an early narrow Poisson distribution of chain lengths with ultimate passage to a disperse equilibrium population of chain sizes. Hydrolytic removal of pyrophosphate expands the time scale for this undesirable process by a factor of 10(9), while it enormously elevates the thermodynamic ceiling for the average degrees of polymerization in the other two examples. The electron micrographically revealed broad size population from an early study of partial replication of a T7 DNA template is found to adhere (fortuitously) to a disperse most probable representation. Some possible origins are examined for the branched structures in this product, as well as in a later investigation of replication of this nucleic acid. The achievement of both very high molecular weights and sharply peaked size distributions in polynucleotides synthesized in vitro will require coupling to inorganic pyrophosphatase action as in vivo.

Reduced Sampling Size with Nanopipette for Tapping-Mode Scanning Probe Electrospray Ionization Mass Spectrometry Imaging

PubMed Central

Kohigashi, Tsuyoshi; Otsuka, Yoichi; Shimazu, Ryo; Matsumoto, Takuya; Iwata, Futoshi; Kawasaki, Hideya; Arakawa, Ryuichi

2016-01-01

Mass spectrometry imaging (MSI) with ambient sampling and ionization can rapidly and easily capture the distribution of chemical components in a solid sample. Because the spatial resolution of MSI is limited by the size of the sampling area, reducing sampling size is an important goal for high resolution MSI. Here, we report the first use of a nanopipette for sampling and ionization by tapping-mode scanning probe electrospray ionization (t-SPESI). The spot size of the sampling area of a dye molecular film on a glass substrate was decreased to 6 μm on average by using a nanopipette. On the other hand, ionization efficiency increased with decreasing solvent flow rate. Our results indicate the compatibility between a reduced sampling area and the ionization efficiency using a nanopipette. MSI of micropatterns of ink on a glass and a polymer substrate were also demonstrated. PMID:28101441

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

The effect of the averaged structural and energetic features on the cohesive energy of nanocrystals

NASA Astrophysics Data System (ADS)

Ali Safaei

2010-03-01

The size dependency of the cohesive energy of nanocrystals is obtained in terms of their averaged structural and energetic properties, which are in direct proportion with their cohesive energies. The significance of the effect of the geometrical shape of nanoparticles on their thermal stability has been discussed. The model has been found to have good prediction for the case of Cu and Al nanoparticles, with sizes in the ranges of 1-22 nm and 2-22 nm, respectively. Defining a new parameter, named as the surface-to-volume energy-contribution ratio, the relative thermal stabilities of different nanoclusters and their different surface-crystalline faces are discussed and compared to the molecular dynamic (MD) simulation results of copper nanoclusters. Finally, based on the size dependency of the cohesive energy, a formula for the size-dependent diffusion coefficient has been presented which includes the structural and energetic effects. Using this formula, the faster-than-expected interdiffusion/alloying of Au(core)-Ag(shell) nanoparticles with the core-shell structure, the Au-core diameter of 20 nm and the Ag-shell thickness of 2.91 nm, has been discussed and the calculated diffusion coefficient has been found to be consistent with its corresponding experimental value.

The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Xu, Jian; Huai, Ping; Deng, Huiqiu; Hu, Wangyu

2016-02-01

Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the HeN and HeNV1SIA1 clusters, the average length of He-He bonds shortens, but it elongates for the HeNV1 clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of HeNVM cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

Protein-protein conjugate nanoparticles for malaria antigen delivery and enhanced immunogenicity

PubMed Central

Scaria, Puthupparampil V.; Jones, David S.; Barnafo, Emma; Fischer, Elizabeth R.; Anderson, Charles; MacDonald, Nicholas J.; Lambert, Lynn; Rausch, Kelly M.; Narum, David L.

2017-01-01

Chemical conjugation of polysaccharide to carrier proteins has been a successful strategy to generate potent vaccines against bacterial pathogens. We developed a similar approach for poorly immunogenic malaria protein antigens. Our lead candidates in clinical trials are the malaria transmission blocking vaccine antigens, Pfs25 and Pfs230D1, individually conjugated to the carrier protein Exoprotein A (EPA) through thioether chemistry. These conjugates form nanoparticles that show enhanced immunogenicity compared to unconjugated antigens. In this study, we examined the broad applicability of this technology as a vaccine development platform, by comparing the immunogenicity of conjugates prepared by four different chemistries using different malaria antigens (PfCSP, Pfs25 and Pfs230D1), and carriers such as EPA, TT and CRM197. Several conjugates were synthesized using thioether, amide, ADH and glutaraldehyde chemistries, characterized for average molecular weight and molecular weight distribution, and evaluated in mice for humoral immunogenicity. Conjugates made with the different chemistries, or with different carriers, showed no significant difference in immunogenicity towards the conjugated antigens. Since particle size can influence immunogenicity, we tested conjugates with different average size in the range of 16–73 nm diameter, and observed greater immunogenicity of smaller particles, with significant differences between 16 and 73 nm particles. These results demonstrate the multiple options with respect to carriers and chemistries that are available for protein-protein conjugate vaccine development. PMID:29281708

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Inorganic dual-layer microporous supported membranes

DOEpatents

Brinker, C. Jeffrey; Tsai, Chung-Yi; Lu, Yungfeng

2003-03-25

The present invention provides for a dual-layer inorganic microporous membrane capable of molecular sieving, and methods for production of the membranes. The inorganic microporous supported membrane includes a porous substrate which supports a first inorganic porous membrane having an average pore size of less than about 25 .ANG. and a second inorganic porous membrane coating the first inorganic membrane having an average pore size of less than about 6 .ANG.. The dual-layered membrane is produced by contacting the porous substrate with a surfactant-template polymeric sol, resulting in a surfactant sol coated membrane support. The surfactant sol coated membrane support is dried, producing a surfactant-templated polymer-coated substrate which is calcined to produce an intermediate layer surfactant-templated membrane. The intermediate layer surfactant-templated membrane is then contacted with a second polymeric sol producing a polymeric sol coated substrate which is dried producing an inorganic polymeric coated substrate. The inorganic polymeric coated substrate is then calcined producing an inorganic dual-layered microporous supported membrane in accordance with the present invention.

Pattern, growth, and aging in aggregation kinetics of a Vicsek-like active matter model

NASA Astrophysics Data System (ADS)

Das, Subir K.

2017-01-01

Via molecular dynamics simulations, we study kinetics in a Vicsek-like phase-separating active matter model. Quantitative results, for isotropic bicontinuous pattern, are presented on the structure, growth, and aging. These are obtained via the two-point equal-time density-density correlation function, the average domain length, and the two-time density autocorrelation function. Both the correlation functions exhibit basic scaling properties, implying self-similarity in the pattern dynamics, for which the average domain size exhibits a power-law growth in time. The equal-time correlation has a short distance behavior that provides reasonable agreement between the corresponding structure factor tail and the Porod law. The autocorrelation decay is a power-law in the average domain size. Apart from these basic similarities, the overall quantitative behavior of the above-mentioned observables is found to be vastly different from those of the corresponding passive limit of the model which also undergoes phase separation. The functional forms of these have been quantified. An exceptionally rapid growth in the active system occurs due to fast coherent motion of the particles, mean-squared-displacements of which exhibit multiple scaling regimes, including a long time ballistic one.

Quantitative LC-MS of polymers: determining accurate molecular weight distributions by combined size exclusion chromatography and electrospray mass spectrometry with maximum entropy data processing.

PubMed

Gruendling, Till; Guilhaus, Michael; Barner-Kowollik, Christopher

2008-09-15

We report on the successful application of size exclusion chromatography (SEC) combined with electrospray ionization mass spectrometry (ESI-MS) and refractive index (RI) detection for the determination of accurate molecular weight distributions of synthetic polymers, corrected for chromatographic band broadening. The presented method makes use of the ability of ESI-MS to accurately depict the peak profiles and retention volumes of individual oligomers eluting from the SEC column, whereas quantitative information on the absolute concentration of oligomers is obtained from the RI-detector only. A sophisticated computational algorithm based on the maximum entropy principle is used to process the data gained by both detectors, yielding an accurate molecular weight distribution, corrected for chromatographic band broadening. Poly(methyl methacrylate) standards with molecular weights up to 10 kDa serve as model compounds. Molecular weight distributions (MWDs) obtained by the maximum entropy procedure are compared to MWDs, which were calculated by a conventional calibration of the SEC-retention time axis with peak retention data obtained from the mass spectrometer. Comparison showed that for the employed chromatographic system, distributions below 7 kDa were only weakly influenced by chromatographic band broadening. However, the maximum entropy algorithm could successfully correct the MWD of a 10 kDa standard for band broadening effects. Molecular weight averages were between 5 and 14% lower than the manufacturer stated data obtained by classical means of calibration. The presented method demonstrates a consistent approach for analyzing data obtained by coupling mass spectrometric detectors and concentration sensitive detectors to polymer liquid chromatography.

Determination of the presence of hyaluronic acid in preparations containing amino acids: the molecular weight characterization.

PubMed

Bellomaria, A; Nepravishta, R; Mazzanti, U; Marchetti, M; Piccioli, P; Paci, M

2014-10-15

Several pharmaceutical preparations contain hyaluronic acid in the presence of a large variety of low molecular weight charged molecules like amino acids. In these mixtures, it is particularly difficult to determine the concentration and the molecular weight of the hyaluronic acid fragments. In fact zwitterionic compounds in high concentration behave by masking the hyaluronic acid due to the electrostatic interactions between amino acids and hyaluronic acid. In such conditions the common colorimetric test of the hyaluronic acid determination appears ineffective and in the (1)H NMR spectra the peaks of the polymer disappear completely. By a simple separation procedure the presence of hyaluronic acid was revealed by the DMAB test and (1)H NMR while its average molecular weight in the final product was determined by DOSY NMR spectroscopy alone. The latter determination is very important due to the healthy effects of some sizes of this polymer's fragments. Copyright © 2014 Elsevier B.V. All rights reserved.

Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

NASA Astrophysics Data System (ADS)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Highly repeatable room temperature negative differential resistance in AlN/GaN resonant tunneling diodes grown by molecular beam epitaxy

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

Growden, Tyler A.; Fakhimi, Parastou; Berger, Paul R., E-mail: pberger@ieee.org

AlN/GaN resonant tunneling diodes grown on low dislocation density semi-insulating bulk GaN substrates via plasma-assisted molecular-beam epitaxy are reported. The devices were fabricated using a six mask level, fully isolated process. Stable room temperature negative differential resistance (NDR) was observed across the entire sample. The NDR exhibited no hysteresis, background light sensitivity, or degradation of any kind after more than 1000 continuous up-and-down voltage sweeps. The sample exhibited a ∼90% yield of operational devices which routinely displayed an average peak current density of 2.7 kA/cm{sup 2} and a peak-to-valley current ratio of ≈1.15 across different sizes.

Effects of temperature and pressure on the nucleation and growth of silver clusters from supersaturated vapor: A molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Wang, Qin; Xie, Hui; Chen, Yongshi; Liu, Chao

2017-04-01

The nucleation and growth of silver nanoparticles in the supersaturated system are investigated by molecular dynamics simulation at different temperatures and pressures. The variety of the atoms in the biggest cluster and the size of average clusters in the system versus the time are estimated to reveal the relationship between the nucleation as well as cluster growth. The nucleation rates in different situations are calculated with the threshold method. The effect of temperature and pressure on the nucleation rate is identified as obeying a linear function. Finally, the development of basal elements, such as monomers, dimers and trimmers, is revealed how the temperature and pressure affect the nucleation and growth of the silver cluster.

Radiologic, pathologic and molecular attributes of two types of papillary renal adenocarcinomas.

PubMed

Mydlo, J H; Weinstein, R; Misseri, R; Axiotis, C; Thelmo, W

2001-09-01

Most papillary renal tumors are not as aggressive as clear cell carcinomas and thus carry a better prognosis. However, several reports in the literature have demonstrated a subset of patients with papillary tumors that have a more aggressive biology and advanced stage at presentation. We compared several parameters of these subsets of renal tumors in an effort to characterize these lesions. We reviewed 391 cases of nephrectomies that were performed for cancer over a 20-year period from four institutions. Of these, 41 were documented as papillary adenocarcinomas. We reviewed these cases with respect to stage at presentation, size, vascularity on (computerized tomography) CT scan, histology, and cytokeratin immunohistology. Thirty-two of the lesions presented in the fifth, sixth, seventh and eighth decades of life (Type I), while most of the remaining 9 tumors (Type II) presented in the fourth decade of life, and in more advanced stages. Tumor volumes ranged from 84 cm3 to 1660 cm3. Type I tumors had an average size of 515 cm3 and an enhancement on CT of 36 +/- 4 Hounsfield units, compared with Type II tumors which had an average size of 164 cm3 and an enhancement on CT of 92 +/- 8 Hounsfield units. Type II tumors also had a higher mean Fuhrman score of nuclear pleomorphism than Type I, and a greater expression of cytokeratin. We found that the more common Type I variant of papillary renal adenocarcinoma was less vascular on CT scan, larger in size, and had a lower amount of nuclear pleomorphism as well as decreased expression of cytokeratin 7. The more aggressive biological variant, Type II, presented in the earlier decades of life, with a smaller, but more vascular, cancer and had a greater nuclear pleomorphism. Nuclear pleomorphism still appears to have the best prognostic assessment. However, other molecular and genetic parameters of these tumors, as well as long-term survival data will be necessary to determine the significance of these findings.

Determination of the molecular weight of low-molecular-weight heparins by using high-pressure size exclusion chromatography on line with a triple detector array and conventional methods.

PubMed

Bisio, Antonella; Mantegazza, Alessandra; Vecchietti, Davide; Bensi, Donata; Coppa, Alessia; Torri, Giangiacomo; Bertini, Sabrina

2015-03-19

The evaluation of weight average molecular weight (Mw) and molecular weight distribution represents one of the most controversial aspects concerning the characterization of low molecular weight heparins (LMWHs). As the most commonly used method for the measurement of such parameters is high performance size exclusion chromatography (HP-SEC), the soundness of results mainly depends on the appropriate calibration of the chromatographic columns used. With the aim of meeting the requirement of proper Mw standards for LMWHs, in the present work the determination of molecular weight parameters (Mw and Mn) by HP-SEC combined with a triple detector array (TDA) was performed. The HP-SEC/TDA technique permits the evaluation of polymeric samples by exploiting the combined and simultaneous action of three on-line detectors: light scattering detectors (LALLS/RALLS); refractometer and viscometer. Three commercial LMWH samples, enoxaparin, tinzaparin and dalteparin, a γ-ray depolymerized heparin (γ-Hep) and its chromatographic fractions, and a synthetic pentasaccharide were analysed by HP-SEC/TDA. The same samples were analysed also with a conventional HP-SEC method employing refractive index (RI) and UV detectors and two different chromatographic column set, silica gel and polymeric gel columns. In both chromatographic systems, two different calibration curves were built up by using (i) γ-Hep chromatographic fractions and the corresponding Mw parameters obtained via HP-SEC/TDA; (ii) the whole γ-Hep preparation with broad Mw dispersion and the corresponding cumulative distribution function calculated via HP-SEC/TDA. In addition, also a chromatographic column calibration according to European Pharmacopoeia indication was built up. By comparing all the obtained results, some important differences among Mw and size distribution values of the three LMWHs were found with the five different calibration methods and with HP-SEC/TDA method. In particular, the detection of the lower molecular weight components turned out to be the most critical aspect. Whereas HP-SEC/TDA may underestimate species under 2 KDa when present in low concentration, other methods appeared to emphasize their content.

Molecular dynamics simulations of void defects in the energetic material HMX.

PubMed

Duan, Xiao Hui; Li, Wen Peng; Pei, Chong Hua; Zhou, Xiao Qing

2013-09-01

A molecular dynamics (MD) simulation was carried out to characterize the dynamic evolution of void defects in crystalline octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX). Different models were constructed with the same concentration of vacancies (10 %) to discuss the size effects of void. Energetic ground state properties were determined by annealing simulations. The void formation energy per molecule removed was found to be 55-63 kcal/mol(-1), and the average binding energy per molecule was between 32 and 34 kcal/mol(-1) according to the change in void size. Voids with larger size had lower formation energy. Local binding energies for molecules directly on the void surface decreased greatly compared to those in defect-free lattice, and then gradually increased until the distance away from the void surface was around 10 Å. Analysis of 1 ns MD simulations revealed that the larger the void size, the easier is void collapse. Mean square displacements (MSDs) showed that HMX molecules that had collapsed into void present liquid structure characteristics. Four unique low-energy conformers were found for HMX molecules in void: two whose conformational geometries corresponded closely to those found in HMX polymorphs and two, additional, lower energy conformers that were not seen in the crystalline phases. The ratio of different conformers changed with the simulated temperature, in that the ratio of α conformer increased with the increase in temperature.

Mass spectrometric identification of water-soluble gold nanocluster fractions from sequential size-selective precipitation.

PubMed

Yang, Xiupei; Su, Yan; Paau, Man Chin; Choi, Martin M F

2012-02-07

This paper presents a simple and convenient methodology to separate and characterize water-soluble gold nanocluster stabilized with penicillamine ligands (AuNC-SR) in aqueous medium by sequential size-selective precipitation (SSSP) and mass spectrometry (MS). The highly polydisperse crude AuNC-SR product with an average core diameter of 2.1 nm was initially synthesized by a one-phase solution method. AuNCs were then precipitated and separated successively from larger to smaller ones by progressively increasing the concentration of acetone in the aqueous AuNCs solution. The SSSP fractions were analyzed by UV-vis spectroscopy, matrix-assisted laser desorption/ionization time-of-flight-MS, and thermogravimetric analysis (TGA). The MS and TGA data confirmed that the fractions precipitated from 36, 54, 72, and 90% v/v acetone (F(36%), F(54%), F(72%), and F(90%)) comprised families of close core size AuNCs with average molecular formulas of Au(38)(SR)(18), Au(28)(SR)(15), Au(18)(SR)(12), and Au(11)(SR)(8), respectively. In addition, F(36%), F(54%), F(72%), and F(90%) contained also the typical magic-sized gold nanoparticles of Au(38), Au(25), Au(18), and Au(11), respectively, together with some other AuNCs. This study shed light on the potential use of SSSP for simple and large-scale preliminary separation of polydisperse water-soluble AuNCs into different fractions with a relatively narrower size distribution. © 2012 American Chemical Society

Fast pyrolysis of palm kernel shells: influence of operation parameters on the bio-oil yield and the yield of phenol and phenolic compounds.

PubMed

Kim, Seon-Jin; Jung, Su-Hwa; Kim, Joo-Sik

2010-12-01

Palm kernel shells were pyrolyzed in a pyrolysis plant equipped with a fluidized-bed reactor and a char-separation system. The influence of reaction temperature, feed size and feed rate on the product spectrum was also investigated. In addition, the effect of reaction temperature on the yields of phenol and phenolic compounds in the bio-oil was examined. The maximum bio-oil yield was 48.7 wt.% of the product at 490 degrees C. The maximum yield of phenol plus phenolic compounds amounted to about 70 area percentage at 475 degrees C. The yield of pyrolytic lignin after its isolation from the bio-oil was approximately 46 wt.% based on the water and ash free oil. The pyrolytic lignin was mainly composed of phenol, phenolic compounds and oligomers of coniferyl, sinapyl and p-coumaryl alcohols. From the result of a GPC analysis, the number average molecular weight and the weight average molecular weight were 325 and 463 g/mol, respectively. 2010 Elsevier Ltd. All rights reserved.

Scanning near-field optical microscopy.

PubMed

Vobornik, Dusan; Vobornik, Slavenka

2008-02-01

An average human eye can see details down to 0,07 mm in size. The ability to see smaller details of the matter is correlated with the development of the science and the comprehension of the nature. Today's science needs eyes for the nano-world. Examples are easily found in biology and medical sciences. There is a great need to determine shape, size, chemical composition, molecular structure and dynamic properties of nano-structures. To do this, microscopes with high spatial, spectral and temporal resolution are required. Scanning Near-field Optical Microscopy (SNOM) is a new step in the evolution of microscopy. The conventional, lens-based microscopes have their resolution limited by diffraction. SNOM is not subject to this limitation and can offer up to 70 times better resolution.

Investigation of Sclerotinia sclerotiorum strains variability in Brazil.

PubMed

Abreu, M J; Souza, E A

2015-06-18

White mold is a common bean disease caused by the fungus Sclerotinia sclerotiorum, resulting in economic losses in Brazil and worldwide. Lack of knowledge about the population structure of the pathogen makes it difficult to control the disease. The aim of this study was to characterize strains of S. sclerotiorum obtained from ex-perimental and commercial common bean fields in Brazil. We analyzed 50 strains of S. sclerotiorum collected at several locations in the state of Minas Gerais. The strains were characterized according to their ability and time for developing apothecia. Morphological and physiological analyses such as the mycelial growth index, colony color, the time re-quired to form the first sclerotia on media, the number of sclerotia per plate, average sclerotium size, and sclerotium shape were performed. We determined the mycelial compatibility, conducted molecular analy-sis of microsatellites, and evaluated the aggressiveness of 28 strains. Most strains had the ability to form apothecia. A small group of strains showed mycelial compatibility, and the strains showed different aggres-siveness levels. Overall, the population studied here demonstrated wide variability based on the morphological, physiological, and molecular traits analyzed. The average size and shape of sclerotia presented a cor-relation of 0.617, whereas the times required to form sclerotia and the number of sclerotia per plate showed a correlation of -0.455. The char-acterization of the pathogen population described herein will provide an important tool for promoting the development of bean cultivars re-sistant to white mold.

Synthesis and Characterization of Graft Copolymers Poly(isoprene-g-styrene) of High Molecular Weight by a Combination of Anionic Polymerization and Emulsion Polymerization

DOE PAGES

Wang, Wenwen; Wang, Weiyu; Li, Hui; ...

2015-01-14

In this study, high molecular weight “comb-shaped” graft copolymers, poly(isoprene-g-styrene), with polyisoprene as the backbone and polystyrene as side chains, were synthesized via free radical emulsion polymerization by copolymerization of isoprene with a polystyrene macromonomer synthesized using anionic polymerization. A small amount of toluene was used in order to successfully disperse the macromonomer. Both a redox and thermal initiation system were used in the emulsion polymerization, and the latex particle size and distribution were investigated by dynamic light scattering. The structural characteristics of the macromonomer and comb graft copolymers were investigated through use of size exclusion chromatography, spectroscopy, microscopy, thermalmore » analysis, and rheology. While the macromonomer was successfully copolymerized to obtain the desired multigraft copolymers, small amounts of unreacted macromonomer remained in the products, reflecting its reduced reactivity due to steric effects. Nevertheless, the multigraft copolymers obtained were very high in molecular weight (5–12 × 10 5 g/mol) and up to 10 branches per chain, on average, could be incorporated. A material incorporating 29 wt% polystyrene exhibits a disordered microphase separated morphology and elastomeric properties. As a result, these materials show promise as new, highly tunable, and potentially low cost thermoplastic elastomers.« less

The ART of mating: alternative reproductive tactics and mating success in a nest-guarding fish.

PubMed

Mascolino, S; Benvenuto, C; Gubili, C; Sacchi, C; Boufana, B; Mariani, S

2016-12-01

Behavioural observations in the field of male Mediterranean damselfish Chromis chromis were combined with molecular analyses, using bi-parentally and maternally inherited markers, to investigate reproductive success patterns of alternative reproductive tactics (ARTs) in terms of number of eggs sired and number of females contributing to each nest. Cuckoldry was observed in every nest sampled, with at least two and up to seven sneaker males per nest. The nesting male, however, always significantly fertilized the greater number of eggs (on average 49%) in each clutch, whereas each sneaker fertilized around 7% of the clutch. The average number of females whose eggs were fertilized by nesting males was 6·76 (range 2-13), while each sneaker on average fertilized the eggs of 1·74 (range 1-8) females. Using this sibship reconstruction, some of the factors involved in the regulation of the dynamic equilibrium of reproductive success were investigated between the two ARTs shown by C. chromis males. Results show that the sneakers' reproductive success was positively linked to egg clutch size; the density of individuals in the nesting area negatively affected the size of egg clutches; the rate of defence behaviours performed by nesting males negatively influenced the number of females contributing to each nest. © 2016 The Fisheries Society of the British Isles.

Validation of a high-performance size-exclusion chromatography method to determine and characterize β-glucans in beer wort using a triple-detector array.

PubMed

Tomasi, Ivan; Marconi, Ombretta; Sileoni, Valeria; Perretti, Giuseppe

2017-01-01

Beer wort β-glucans are high-molecular-weight non-starch polysaccharides of that are great interest to the brewing industries. Because glucans can increase the viscosity of the solutions and form gels, hazes, and precipitates, they are often related to poor lautering performance and beer filtration problems. In this work, a simple and suitable method was developed to determine and characterize β-glucans in beer wort using size exclusion chromatography coupled with a triple-detector array, which is composed of a light scatterer, a viscometer, and a refractive-index detector. The method performances are comparable to the commercial reference method as result from the statistical validation and enable one to obtain interesting parameters of β-glucan in beer wort, such as the molecular weight averages, fraction description, hydrodynamic radius, intrinsic viscosity, polydispersity and Mark-Houwink parameters. This characterization can be useful in brewing science to understand filtration problems, which are not always explained through conventional analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular dynamics simulations of diffusion and clustering along critical isotherms of medium-chain n-alkanes.

PubMed

Mutoru, J W; Smith, W; O'Hern, C S; Firoozabadi, A

2013-01-14

Understanding the transport properties of molecular fluids in the critical region is important for a number of industrial and natural systems. In the literature, there are conflicting reports on the behavior of the self diffusion coefficient D(s) in the critical region of single-component molecular systems. For example, D(s) could decrease to zero, reach a maximum, or remain unchanged and finite at the critical point. Moreover, there is no molecular-scale understanding of the behavior of diffusion coefficients in molecular fluids in the critical regime. We perform extensive molecular dynamics simulations in the critical region of single-component fluids composed of medium-chain n-alkanes-n-pentane, n-decane, and n-dodecane-that interact via anisotropic united-atom potentials. For each system, we calculate D(s), and average molecular cluster sizes κ(cl) and numbers N(cl) at various cluster lifetimes τ, as a function of density ρ in the range 0.2ρ(c) ≤ ρ ≤ 2.0ρ(c) at the critical temperature T(c). We find that D(s) decreases with increasing ρ but remains finite at the critical point. Moreover, for any given τ < 1.2 × 10(-12) s, κ(cl) increases with increasing ρ but is also finite at the critical point.

Equilibrium Limit of Boundary Scattering in Carbon Nanostructures: Molecular Dynamics Calculations of Thermal Transport

NASA Technical Reports Server (NTRS)

Haskins, Justin; Kinaci, Alper; Sevik, Cem; Cagin, Tahir

2012-01-01

It is widely known that graphene and many of its derivative nanostructures have exceedingly high reported thermal conductivities (up to 4000 W/mK at 300 K). Such attractive thermal properties beg the use of these structures in practical devices; however, to implement these materials while preserving transport quality, the influence of structure on thermal conductivity should be thoroughly understood. For graphene nanostructures, having average phonon mean free paths on the order of one micron, a primary concern is how size influences the potential for heat conduction. To investigate this, we employ a novel technique to evaluate the lattice thermal conductivity from the Green-Kubo relations and equilibrium molecular dynamics in systems where phonon-boundary scattering dominates heat flow. Specifically, the thermal conductivities of graphene nanoribbons and carbon nanotubes are calculated in sizes up to 3 microns, and the relative influence of boundary scattering on thermal transport is determined to be dominant at sizes less than 1 micron, after which the thermal transport largely depends on the quality of the nanostructure interface. The method is also extended to carbon nanostructures (fullerenes) where phonon confinement, as opposed to boundary scattering, dominates, and general trends related to the influence of curvature on thermal transport in these materials are discussed.

Identification of Structural Features of Condensed Tannins That Affect Protein Aggregation

PubMed Central

Ropiak, Honorata M.; Lachmann, Peter; Ramsay, Aina; Green, Rebecca J.; Mueller-Harvey, Irene

2017-01-01

A diverse panel of condensed tannins was used to resolve the confounding effects of size and subunit composition seen previously in tannin-protein interactions. Turbidimetry revealed that size in terms of mean degree of polymerisation (mDP) or average molecular weight (amw) was the most important tannin parameter. The smallest tannin with the relatively largest effect on protein aggregation had an mDP of ~7. The average size was significantly correlated with aggregation of bovine serum albumin, BSA (mDP: r = -0.916; amw: r = -0.925; p<0.01; df = 27), and gelatin (mDP: r = -0.961; amw: r = -0.981; p<0.01; df = 12). The procyanidin/prodelphinidin and cis-/trans-flavan-3-ol ratios gave no significant correlations. Tryptophan fluorescence quenching indicated that procyanidins and cis-flavan-3-ol units contributed most to the tannin interactions on the BSA surface and in the hydrophobic binding pocket (r = 0.677; p<0.05; df = 9 and r = 0.887; p<0.01; df = 9, respectively). Circular dichroism revealed that higher proportions of prodelphinidins decreased the apparent α-helix content (r = -0.941; p<0.01; df = 5) and increased the apparent β-sheet content (r = 0.916; p<0.05; df = 5) of BSA. PMID:28125657

Identification of Structural Features of Condensed Tannins That Affect Protein Aggregation.

PubMed

Ropiak, Honorata M; Lachmann, Peter; Ramsay, Aina; Green, Rebecca J; Mueller-Harvey, Irene

2017-01-01

A diverse panel of condensed tannins was used to resolve the confounding effects of size and subunit composition seen previously in tannin-protein interactions. Turbidimetry revealed that size in terms of mean degree of polymerisation (mDP) or average molecular weight (amw) was the most important tannin parameter. The smallest tannin with the relatively largest effect on protein aggregation had an mDP of ~7. The average size was significantly correlated with aggregation of bovine serum albumin, BSA (mDP: r = -0.916; amw: r = -0.925; p<0.01; df = 27), and gelatin (mDP: r = -0.961; amw: r = -0.981; p<0.01; df = 12). The procyanidin/prodelphinidin and cis-/trans-flavan-3-ol ratios gave no significant correlations. Tryptophan fluorescence quenching indicated that procyanidins and cis-flavan-3-ol units contributed most to the tannin interactions on the BSA surface and in the hydrophobic binding pocket (r = 0.677; p<0.05; df = 9 and r = 0.887; p<0.01; df = 9, respectively). Circular dichroism revealed that higher proportions of prodelphinidins decreased the apparent α-helix content (r = -0.941; p<0.01; df = 5) and increased the apparent β-sheet content (r = 0.916; p<0.05; df = 5) of BSA.

The Determination of Molecular Structure from Rotational Spectra

DOE R&D Accomplishments Database

Laurie, V. W.; Herschbach, D. R.

1962-07-01

An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

DNA methylation intratumor heterogeneity in localized lung adenocarcinomas.

PubMed

Quek, Kelly; Li, Jun; Estecio, Marcos; Zhang, Jiexin; Fujimoto, Junya; Roarty, Emily; Little, Latasha; Chow, Chi-Wan; Song, Xingzhi; Behrens, Carmen; Chen, Taiping; William, William N; Swisher, Stephen; Heymach, John; Wistuba, Ignacio; Zhang, Jianhua; Futreal, Andrew; Zhang, Jianjun

2017-03-28

Cancers are composed of cells with distinct molecular and phenotypic features within a given tumor, a phenomenon termed intratumor heterogeneity (ITH). Previously, we have demonstrated genomic ITH in localized lung adenocarcinomas; however, the nature of methylation ITH in lung cancers has not been well investigated. In this study, we generated methylation profiles of 48 spatially separated tumor regions from 11 localized lung adenocarcinomas and their matched normal lung tissues using Illumina Infinium Human Methylation 450K BeadChip array. We observed methylation ITH within the same tumors, but to a much less extent compared to inter-individual heterogeneity. On average, 25% of all differentially methylated probes compared to matched normal lung tissues were shared by all regions from the same tumors. This is in contrast to somatic mutations, of which approximately 77% were shared events amongst all regions of individual tumors, suggesting that while the majority of somatic mutations were early clonal events, the tumor-specific DNA methylation might be associated with later branched evolution of these 11 tumors. Furthermore, our data showed that a higher extent of DNA methylation ITH was associated with larger tumor size (average Euclidean distance of 35.64 (> 3cm, median size) versus 27.24 (<= 3cm), p = 0.014), advanced age (average Euclidean distance of 34.95 (above 65) verse 28.06 (below 65), p = 0.046) and increased risk of postsurgical recurrence (average Euclidean distance of 35.65 (relapsed patients) versus 29.03 (patients without relapsed), p = 0.039).

Oligomeric cationic polymethacrylates: a comparison of methods for determining molecular weight.

PubMed

Locock, Katherine E S; Meagher, Laurence; Haeussler, Matthias

2014-02-18

This study compares three common laboratory methods, size-exclusion chromatography (SEC), (1)H nuclear magnetic resonance (NMR), and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), to determine the molecular weight of oligomeric cationic copolymers. The potential bias for each method was examined across a series of polymers that varied in molecular weight and cationic character (both choice of cation (amine versus guanidine) and relative proportion present). SEC was found to be the least accurate, overestimating Mn by an average of 140%, owing to the lack of appropriate cationic standards available, and the complexity involved in estimating the hydrodynamic volume of copolymers. MALDI-TOF approximated Mn well for the highly monodisperse (Đ < 1.1), low molecular weight (degree of polymerization (DP) <50) species but appeared unsuitable for the largest polymers in the series due to the mass bias associated with the technique. (1)H NMR was found to most accurately estimate Mn in this study, differing to theoretical values by only 5.2%. (1)H NMR end-group analysis is therefore an inexpensive and facile, primary quantitative method to estimate the molecular weight of oliogomeric cationic polymethacrylates if suitably distinct end-groups signals are present in the spectrum.

Simultaneous determination of molecular weights and contents of water-soluble polysaccharides and their fractions from Lycium barbarum collected in China.

PubMed

Wu, Ding-Tao; Lam, Shing-Chung; Cheong, Kit-Leong; Wei, Feng; Lin, Peng-Cheng; Long, Ze-Rong; Lv, Xiao-Jie; Zhao, Jing; Ma, Shuang-Cheng; Li, Shao-Ping

2016-09-10

Molecular weights and contents of water-soluble polysaccharides and their fractions in fifty batches of fruits of Lycium barbarum (wolfberry) collected from different regions of China, including Qinghai, Ningxia, Inner Mongolia, Xinjiang, and Gansu, were simultaneously determined using high performance size exclusion chromatography (HPSEC) coupled with multi angle laser light scattering (MALLS) and refractive index detector (RID) with the refractive index increment (dn/dc). Results showed that HPSEC chromatograms and molecular weight distributions of polysaccharides in L. barbarum collected from different regions of China were similar. Furthermore, the average contents of each polysaccharide fraction (peaks 1, 2, and 3) in crude polysaccharides of L. barbarum collected from Ningxia were similar with those of Inner Mongolia, Xinjiang, and Gansu, respectively. However, significant difference was found between polysaccharides in L. barbarum collected from Ningxia and Qinghai. Moreover, the average amounts of total polysaccharide fractions (peaks 1, 2, and 3) in the raw material of L. barbarum collected from Ningxia were significantly higher than that of Qinghai. These results may contribute to the rational usage of L. barbarum produced in China, and are beneficial for the improvement of their quality control. Results suggested that HPSEC-MALLS-RID with the dn/dc method could be used as a routine method for the quality evaluation of polysaccharides from natural resources and their products. Copyright © 2016 Elsevier B.V. All rights reserved.

Generation of a large volume of clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles for cell culture studies

PubMed Central

Ingham, Eileen; Fisher, John; Tipper, Joanne L

2014-01-01

It has recently been shown that the wear of ultra-high-molecular-weight polyethylene in hip and knee prostheses leads to the generation of nanometre-sized particles, in addition to micron-sized particles. The biological activity of nanometre-sized ultra-high-molecular-weight polyethylene wear particles has not, however, previously been studied due to difficulties in generating sufficient volumes of nanometre-sized ultra-high-molecular-weight polyethylene wear particles suitable for cell culture studies. In this study, wear simulation methods were investigated to generate a large volume of endotoxin-free clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles. Both single-station and six-station multidirectional pin-on-plate wear simulators were used to generate ultra-high-molecular-weight polyethylene wear particles under sterile and non-sterile conditions. Microbial contamination and endotoxin levels in the lubricants were determined. The results indicated that microbial contamination was absent and endotoxin levels were low and within acceptable limits for the pharmaceutical industry, when a six-station pin-on-plate wear simulator was used to generate ultra-high-molecular-weight polyethylene wear particles in a non-sterile environment. Different pore-sized polycarbonate filters were investigated to isolate nanometre-sized ultra-high-molecular-weight polyethylene wear particles from the wear test lubricants. The use of the filter sequence of 10, 1, 0.1, 0.1 and 0.015 µm pore sizes allowed successful isolation of ultra-high-molecular-weight polyethylene wear particles with a size range of < 100 nm, which was suitable for cell culture studies. PMID:24658586

Generation of a large volume of clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles for cell culture studies.

PubMed

Liu, Aiqin; Ingham, Eileen; Fisher, John; Tipper, Joanne L

2014-04-01

It has recently been shown that the wear of ultra-high-molecular-weight polyethylene in hip and knee prostheses leads to the generation of nanometre-sized particles, in addition to micron-sized particles. The biological activity of nanometre-sized ultra-high-molecular-weight polyethylene wear particles has not, however, previously been studied due to difficulties in generating sufficient volumes of nanometre-sized ultra-high-molecular-weight polyethylene wear particles suitable for cell culture studies. In this study, wear simulation methods were investigated to generate a large volume of endotoxin-free clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles. Both single-station and six-station multidirectional pin-on-plate wear simulators were used to generate ultra-high-molecular-weight polyethylene wear particles under sterile and non-sterile conditions. Microbial contamination and endotoxin levels in the lubricants were determined. The results indicated that microbial contamination was absent and endotoxin levels were low and within acceptable limits for the pharmaceutical industry, when a six-station pin-on-plate wear simulator was used to generate ultra-high-molecular-weight polyethylene wear particles in a non-sterile environment. Different pore-sized polycarbonate filters were investigated to isolate nanometre-sized ultra-high-molecular-weight polyethylene wear particles from the wear test lubricants. The use of the filter sequence of 10, 1, 0.1, 0.1 and 0.015 µm pore sizes allowed successful isolation of ultra-high-molecular-weight polyethylene wear particles with a size range of < 100 nm, which was suitable for cell culture studies.

Simultaneous determination of the styrene unit content and assessment of molecular weight of triblock copolymers in adhesives by a size exclusion chromatography method.

PubMed

Wang, Mingfang; Wang, Yuerong; Luo, Pei; Zhang, Hongyang; Zhang, Min; Hu, Ping

2017-10-01

The content of styrene units in nonhydrogenated and hydrogenated styrene-butadiene-styrene and styrene-isoprene-styrene triblock copolymers significantly influences product performance. A size exclusion chromatography method was developed to determine the average styrene content of triblock copolymers blended with tackifier in adhesives. A complete separation of the triblock copolymer from the other additives was realized with size exclusion chromatography. The peak area ratio of the UV and refraction index signals of the copolymers at the same effective elution volume was correlated to the average styrene unit content using nuclear magnetic resonance spectroscopy with commercial copolymers as standards. The obtained calibration curves showed good linearity for both the hydrogenated and nonhydrogenated styrene-butadiene-styrene and styrene-isoprene-styrene triblock copolymers (r = 0.974 for styrene contents of 19.3-46.3% for nonhydrogenated ones and r = 0.970 for the styrene contents of 23-58.2% for hydrogenated ones). For copolymer blends, the developed method provided more accurate average styrene unit contents than nuclear magnetic resonance spectroscopy provided. These results were validated using two known copolymer blends consisting of either styrene-isoprene-styrene or hydrogenated styrene-butadiene-styrene and a hydrocarbon tackifying resin as well as an unknown adhesive with styrene-butadiene-styrene and an aromatic tackifying resin. The methodology can be readily applied to styrene-containing polymers in blends such as poly(acrylonitrile-butadiene styrene). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of treatment temperature on the microstructure of asphalt binders: insights on the development of dispersed domains.

PubMed

Menapace, I; Masad, E; Bhasin, A

2016-04-01

This paper offers important insights on the development of the microstructure in asphalt binders as a function of the treatment temperature. Different treatment temperatures are useful to understand how dispersed domains form when different driving energies for the mobility of molecular species are provided. Small and flat dispersed domains, with average diameter between 0.02 and 0.70 μm, were detected on the surface of two binders at room temperature, and these domains were observed to grow with an increase in treatment temperature (up to over 2 μm). Bee-like structures started to appear after treatment at or above 100°C. Moreover, the effect of the binder thickness on its microstructure at room temperature and at higher treatment temperatures was investigated and is discussed in this paper. At room temperature, the average size of the dispersed domains increased as the binder thickness decreased. A hypothesis that conciliates current theories on the origin and development of dispersed domains is proposed. Small dispersed domains (average diameter around 0.02 μm) are present in the bulk of the binder, whereas larger domains and bee-like structures develop on the surface, following heat treatment or mechanical disturbance that reduces the film thickness. Molecular mobility and association are the key factors in the development of binder microstructure. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Mucosal melanoma: correlation of clinicopathologic, prognostic, and molecular features.

PubMed

Gru, Alejandro A; Becker, Nils; Dehner, Louis P; Pfeifer, John D

2014-08-01

Although the presence of the t(12;22)(q13;q12) translocation (the defining molecular feature of malignant melanoma of soft parts/clear cell sarcoma) in cutaneous melanoma has been investigated, no large-scale studies have been performed among mucosal melanoma (MucM). In this study we assessed the prevalence of the EWSR1 rearrangement in primary MucM, and analyzed gross and microscopic features with their potential impact on diagnosis and prognosis. Overall, 132 specimens from 84 patients were included. A total of 55 cases had an intramucosal component. Survival of MucMs of the head and neck was associated with two independent factors: size and histology. Tumors more than 3 cm in greatest dimension had an average survival of 12.75 months; those 3 cm or less had an average survival of 38.3 months (P=0.035). Purely epithelioid tumors had an average worse survival of 16.8 months (P=0.028). A cut-off value of 1 mm for Breslow depth provided a statistically significant difference in survival at both 3 and 5 years (P=-0.02) by multivariate analysis in the gynecologic tract. At the molecular level three cases had a EWSR1 rearrangement by fluorescent in-situ hybridization, but only one with an intramucosal component. None of the 58 cases tested by PCR showed the presence of the EWSR1 rearrangement. With the exception of vulvar melanomas, the prognosis of mucosal-associated melanomas was poor and there was a suggestion that spindle morphology may be more favorable. Our study also showed that the EWSR1 rearrangement was very uncommon among MucM. Though 'clear cell sarcoma' is embedded in the sarcoma literature, the synonym 'melanoma of soft parts' has considerable justification in light of our evolving understanding of the molecular genetics in the family of malignant melanomas.

SCANNING NEAR-FIELD OPTICAL MICROSCOPY

PubMed Central

Vobornik, Dušan; Vobornik, Slavenka

2008-01-01

An average human eye can see details down to 0,07 mm in size. The ability to see smaller details of the matter is correlated with the development of the science and the comprehension of the nature. Today’s science needs eyes for the nano-world. Examples are easily found in biology and medical sciences. There is a great need to determine shape, size, chemical composition, molecular structure and dynamic properties of nano-structures. To do this, microscopes with high spatial, spectral and temporal resolution are required. Scanning Near-field Optical Microscopy (SNOM) is a new step in the evolution of microscopy. The conventional, lens-based microscopes have their resolution limited by diffraction. SNOM is not subject to this limitation and can offer up to 70 times better resolution. PMID:18318675

Surface plasmon enhanced cell microscopy with blocked random spatial activation

NASA Astrophysics Data System (ADS)

Son, Taehwang; Oh, Youngjin; Lee, Wonju; Yang, Heejin; Kim, Donghyun

2016-03-01

We present surface plasmon enhanced fluorescence microscopy with random spatial sampling using patterned block of silver nanoislands. Rigorous coupled wave analysis was performed to confirm near-field localization on nanoislands. Random nanoislands were fabricated in silver by temperature annealing. By analyzing random near-field distribution, average size of localized fields was found to be on the order of 135 nm. Randomly localized near-fields were used to spatially sample F-actin of J774 cells (mouse macrophage cell-line). Image deconvolution algorithm based on linear imaging theory was established for stochastic estimation of fluorescent molecular distribution. The alignment between near-field distribution and raw image was performed by the patterned block. The achieved resolution is dependent upon factors including the size of localized fields and estimated to be 100-150 nm.

Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology.

PubMed

Bulbul, Gonca; Chaves, Gepoliano; Olivier, Joseph; Ozel, Rifat Emrah; Pourmand, Nader

2018-06-06

Examining the behavior of a single cell within its natural environment is valuable for understanding both the biological processes that control the function of cells and how injury or disease lead to pathological change of their function. Single-cell analysis can reveal information regarding the causes of genetic changes, and it can contribute to studies on the molecular basis of cell transformation and proliferation. By contrast, whole tissue biopsies can only yield information on a statistical average of several processes occurring in a population of different cells. Electrowetting within a nanopipette provides a nanobiopsy platform for the extraction of cellular material from single living cells. Additionally, functionalized nanopipette sensing probes can differentiate analytes based on their size, shape or charge density, making the technology uniquely suited to sensing changes in single-cell dynamics. In this review, we highlight the potential of nanopipette technology as a non-destructive analytical tool to monitor single living cells, with particular attention to integration into applications in molecular biology.

Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

NASA Technical Reports Server (NTRS)

Frankland, S. J. V.; Gates, T. S.

2007-01-01

A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

Surface modification of carbon fibers by a polyether sulfone emulsion sizing for increased interfacial adhesion with polyether sulfone

NASA Astrophysics Data System (ADS)

Yuan, Haojie; Zhang, Shouchun; Lu, Chunxiang

2014-10-01

Interests on carbon fiber-reinforced thermoplastic composites are growing rapidly, but the challenges with poor interfacial adhesion have slowed their adoption. In this work, a polyether sulfone (PES) emulsion sizing was prepared successfully for increased interfacial adhesion of carbon fiber/PES composites. To obtain a high-quality PES emulsion sizing, the key factor, emulsifier concentration, was studied by dynamic light scattering technique. The results demonstrated that the suitable weight ratio of PES to emulsifier was 8:3, and the resulting PES emulsion sizing had an average particle diameter of 117 nm and Zeta potential of -52.6 mV. After sizing, the surface oxygen-containing functional groups, free energy and wettability of carbon fibers increased significantly, which were advantageous to promote molecular-level contact between carbon fiber and PES. Finally, short beam shear tests were performed to evaluate the interfacial adhesion of carbon fiber/PES composites. The results indicated that PES emulsion sizing played a critical role for the enhanced interfacial adhesion in carbon fiber/PES composites, and a 26% increase of interlaminar shear strength was achieved, because of the improved fiber surface wettability and interfacial compatibility between carbon fiber and PES.

Type, origin, and reservoir characteristics of dolostones of the Ordovician Majiagou Group, Ordos, North China Platform

NASA Astrophysics Data System (ADS)

Feng Zengzhao; Zhang Yongsheng; Jin Zhenkui

1998-06-01

Dolostones are well developed in the Ordovician Majiagou Group in the Ordos area, North China Platform. These dolostones can be divided into four types: mud-sized to silt-sized crystalline dolostones not associated with gypsum and halite beds (type I), mud-sized to silt-sized crystalline dolostones associated with gypsum and halite beds (type II), mottled silt-sized to very fine sand-sized crystalline dolostones (fine saccharoidal dolostones) (type III), and mottled coarse silt-sized to fine sand-sized crystalline dolostones (coarse saccharoidal dolostones) (type IV). Type I dolostones consist of mud-sized to silt-sized dolomite crystals. Laminar stromatolites, ripple marks, mud cracks and birdseyes are common. Such dolostones are not associated with gypsum and halite beds, but lath-shaped pseudomorphs after gypsum are common. The ordering of dolomites averages 0.59, and molar concentration of CaCO 3 averages 51.44%. δ13C averages -0.8‰ (PDB Standard), δ18O averages -2.9‰, δCe averages 0.83. The above characteristics suggest that type I dolostones result from penecontemporaneous dolomitization of lime mud on supratidal flat environments by hypersaline sea water. Type II dolostones mainly consist of mud-sized to silt-sized dolomite crystals. They are commonly well laminated but show no desiccation structures. Such dolostones are intercalated within laminated gypsum and halite beds or are intermixed with them. Such dolostones resulted from dolomitization of lime mud by hypersaline sea water in gypsum and halite precipitating lagoons. Type III dolostones consist of coarse silt-sized to very fine sand-sized dolomite crystals. They commonly underlie type I dolostones and grade downwards to dolomite-mottled limestones and pure limestones. The ordering of dolomites averages 0.63, and molar concentration of CaCO 3 averages 55.64%. δ13C averages -0.2‰, δ18O averages -3.3‰, δCe averages 1.24. Such dolostones resulted from reflux dolomitization by hypersaline sea water. Type IV dolostones consist of coarse-silt-sized to fine-sand-sized dolomite crystals. In such dolostones, stylolites are cut by dolomite crystals. Fluid inclusions are present, and the homogenization temperature commonly ranges from 104°C to 203°C. The ordering of dolomites averages 0.85, and molar concentration of CaCO 3 averages 50.65%. δ13C averages 0.6‰, δ18O averages -7.4‰, and δCe averages 1.16. Such dolostones resulted from deep burial dolomitization. In the Ordos area, type I and II dolostones modified by palaeokarstification are the major gas reservoir rocks of the Ordos Gas Field at present. Type IV dolostones show good reservoir characteristics and may also be potential reservoir rocks.

Relevance of nonfunctional linear polyacrylic acid for the biodegradation of superabsorbent polymer in soils.

PubMed

Bai, Mo; Wilske, Burkhard; Buegger, Franz; Esperschütz, Jürgen; Bach, Martin; Frede, Hans-Georg; Breuer, Lutz

2015-04-01

Biodegradability is a desired characteristic for synthetic soil amendments. Cross-linked polyacrylic acid (PAA) is a synthetic superabsorbent used to increase the water availability for plant growth in soils. About 4% within products of cross-linked PAA remains as linear polyacrylic acid (PAAlinear). PAAlinear has no superabsorbent function but may contribute to the apparent biodegradation of the overall product. This is the first study that shows specifically the biodegradation of PAAlinear in agricultural soil. Two (13)C-labeled PAAlinear of the average molecular weights of 530, 400, and 219,500 g mol(-1) were incubated in soil. Mineralization of PAAlinear was measured directly as the (13)CO2 efflux from incubation vessels using an automatic system, which is based on (13)C-sensitive wavelength-scanned cavity ring-down spectroscopy. After 149 days, the PAAlinear with the larger average molecular weight and chain length showed about half of the degradation (0.91% of the initial weight) of the smaller PAAlinear (1.85%). The difference in biodegradation was confirmed by the δ(13)C signature of the microbial biomass (δ(13)Cmic), which was significantly enriched in the samples with short PAAlinear (-13‰ against reference Vienna Pee Dee Belemnite,VPDB) as compared to those with long PAAlinear (-16‰ VPDB). In agreement with other polymer studies, the results suggest that the biodegradation of PAAlinear in soil is determined by the average molecular weight and occurs mainly at terminal sites. Most importantly, the study outlines that the size of PAA that escapes cross-linking can have a significant impact on the overall biodegradability of a PAA-based superabsorbent.

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain.

PubMed

Wolf, Antje; Kirschner, Karl N

2013-02-01

With improvements in computer speed and algorithm efficiency, MD simulations are sampling larger amounts of molecular and biomolecular conformations. Being able to qualitatively and quantitatively sift these conformations into meaningful groups is a difficult and important task, especially when considering the structure-activity paradigm. Here we present a study that combines two popular techniques, principal component (PC) analysis and clustering, for revealing major conformational changes that occur in molecular dynamics (MD) simulations. Specifically, we explored how clustering different PC subspaces effects the resulting clusters versus clustering the complete trajectory data. As a case example, we used the trajectory data from an explicitly solvated simulation of a bacteria's L11·23S ribosomal subdomain, which is a target of thiopeptide antibiotics. Clustering was performed, using K-means and average-linkage algorithms, on data involving the first two to the first five PC subspace dimensions. For the average-linkage algorithm we found that data-point membership, cluster shape, and cluster size depended on the selected PC subspace data. In contrast, K-means provided very consistent results regardless of the selected subspace. Since we present results on a single model system, generalization concerning the clustering of different PC subspaces of other molecular systems is currently premature. However, our hope is that this study illustrates a) the complexities in selecting the appropriate clustering algorithm, b) the complexities in interpreting and validating their results, and c) by combining PC analysis with subsequent clustering valuable dynamic and conformational information can be obtained.

Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics

PubMed Central

Wu, Xiongwu; Damjanovic, Ana; Brooks, Bernard R.

2013-01-01

This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. It has been demonstrated that with moderate parameters, SGLD can routinely cross energy barriers of 20 kT at a rate that molecular dynamics (MD) or Langevin dynamics (LD) crosses 10 kT barriers. The core of these methods is the use of local averages of forces and momenta in a direct manner that can preserve the canonical ensemble. The use of such local averages results in methods where low frequency motion “borrows” energy from high frequency degrees of freedom when a barrier is approached and then returns that excess energy after a barrier is crossed. This self-guiding effect also results in an accelerated diffusion to enhance conformational sampling efficiency. The resulting ensemble with SGLD deviates in a small way from the canonical ensemble, and that deviation can be corrected with either an on-the-fly or a post processing reweighting procedure that provides an excellent canonical ensemble for systems with a limited number of accelerated degrees of freedom. Since reweighting procedures are generally not size extensive, a newer method, SGLDfp, uses local averages of both momenta and forces to preserve the ensemble without reweighting. The SGLDfp approach is size extensive and can be used to accelerate low frequency motion in large systems, or in systems with explicit solvent where solvent diffusion is also to be enhanced. Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD. PMID:23913991

On the effective turbulence driving mode of molecular clouds formed in disc galaxies

NASA Astrophysics Data System (ADS)

Jin, Keitaro; Salim, Diane M.; Federrath, Christoph; Tasker, Elizabeth J.; Habe, Asao; Kainulainen, Jouni T.

2017-07-01

We determine the physical properties and turbulence driving mode of molecular clouds formed in numerical simulations of a Milky Way-type disc galaxy with parsec-scale resolution. The clouds form through gravitational fragmentation of the gas, leading to average values for mass, radii and velocity dispersion in good agreement with observations of Milky Way clouds. The driving parameter (b) for the turbulence within each cloud is characterized by the ratio of the density contrast (σ _{ρ /ρ _0}) to the average Mach number (M) within the cloud, b=σ _{ρ /ρ _0}/M. As shown in previous works, b ˜ 1/3 indicates solenoidal (divergence-free) driving and b ˜ 1 indicates compressive (curl-free) driving. We find that the average b value of all the clouds formed in the simulations has a lower limit of b > 0.2. Importantly, we find that b has a broad distribution, covering values from purely solenoidal to purely compressive driving. Tracking the evolution of individual clouds reveals that the b value for each cloud does not vary significantly over their lifetime. Finally, we perform a resolution study with minimum cell sizes of 8, 4, 2 and 1 pc and find that the average b value increases with increasing resolution. Therefore, we conclude that our measured b values are strictly lower limits and that a resolution better than 1 pc is required for convergence. However, regardless of the resolution, we find that b varies by factors of a few in all cases, which means that the effective driving mode alters significantly from cloud to cloud.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Quantitative atomic-scale structure characterization of ordered mesoporous carbon materials by solid state NMR

DOE PAGES

Wang, Zhuoran; Opembe, Naftali; Kobayashi, Takeshi; ...

2018-02-03

In this study, solid-state (SS)NMR techniques were applied to characterize the atomic-scale structures of ordered mesoporous carbon (OMC) materials prepared using Pluronic F127 as template with resorcinol and formaldehyde as polymerizing precursors. A rigorous quantitative analysis was developed using a combination of 13C SSNMR spectra acquired with direct polarization and cross polarization on natural abundant and selectively 13C-enriched series of samples pyrolyzed at various temperatures. These experiments identified and counted the key functional groups present in the OMCs at various stages of preparation and thermal treatment. Lastly, the chemical evolution of molecular networks, the average sizes of aromatic clusters andmore » the extended molecular structures of OMCs were then inferred by coupling this information with the elemental analysis results.« less

Quantitative atomic-scale structure characterization of ordered mesoporous carbon materials by solid state NMR

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

Wang, Zhuoran; Opembe, Naftali; Kobayashi, Takeshi

In this study, solid-state (SS)NMR techniques were applied to characterize the atomic-scale structures of ordered mesoporous carbon (OMC) materials prepared using Pluronic F127 as template with resorcinol and formaldehyde as polymerizing precursors. A rigorous quantitative analysis was developed using a combination of 13C SSNMR spectra acquired with direct polarization and cross polarization on natural abundant and selectively 13C-enriched series of samples pyrolyzed at various temperatures. These experiments identified and counted the key functional groups present in the OMCs at various stages of preparation and thermal treatment. Lastly, the chemical evolution of molecular networks, the average sizes of aromatic clusters andmore » the extended molecular structures of OMCs were then inferred by coupling this information with the elemental analysis results.« less

ENZYMATIC POLYMERIZATION OF PHENOLS IN ROOM TEMPERATURE IONIC LIQUIDS

PubMed Central

Eker, Bilge; Zagorevski, Dmitri; Zhu, Guangyu; Linhardt, Robert J.; Dordick, Jonathan S.

2009-01-01

Soybean peroxidase (SBP) was used to catalyze the polymerization of phenols in room-temperature ionic liquids (RTILs). Phenolic polymers with number average molecular weights ranging from 1200 to 4100 D were obtained depending on the composition of the reaction medium and the nature of the phenol. Specifically, SBP was highly active in methylimidazolium-containing RTILs, including 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM(BF4)), and 1-butyl-3-methylpyridinium tetrafluoroborate (BMPy(BF4)) with the ionic liquid content as high as 90% (v/v); the balance being aqueous buffer. Gel permeation chromatography and MALDI-TOF analysis indicated that higher molecular weight polymers can be synthesized in the presence of higher RTIL concentrations, with selective control over polymer size achieved by varying the RTIL concentration. The resulting polyphenols exhibited high thermostability and possessed thermosetting properties. PMID:20161409

Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents.

PubMed

Borodin, Oleg; Smith, Grant D

2006-03-30

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.

Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

DOE PAGES

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

2015-02-17

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

Effects of interaction with gene carrier polyethyleneimines on conformation and enzymatic activity of pig heart lactate dehydrogenase.

PubMed

Wang, Fan; Mo, Junyong; Huang, Aimin; Zhang, Min; Ma, Lin

2018-06-15

Polyethyleneimine (PEI) has long been considered as "golden standard" for polymeric gene delivery carrier, however also induces cytotoxicity. To make a further insight into the molecular basis of PEI cytotoxicity, fluorescence, absorption and circular dichroism spectroscopy were conducted to investigate the influence of PEI (average molecular weight 25,000 and 1800 Da) on the conformation of pig heart lactate dehydrogenase (LDH) and its catalytic efficiency. Zeta-potential measurement and isothermal titration calorimetry were used to reveal the interaction between PEI and LDH. PEI was found to bind onto the surface of LDH predominantly via hydrophobic interaction, inducing a more compact conformation and an increased surface hydrophobicity of the enzyme. The conformational change of LDH induced by PEI binding had little influence on the complex formation between LDH and reduced nicotinamide adenine dinucleotide (NADH, the co-enzyme). However, the nonspecific binding of PEI on the surface of LDH retarded the turnover of the enzyme. Meanwhile, the large quantity of amine groups on the polymer chain made PEI subject to form complexes with NADH and pyruvate (the substrate) via hydrogen bond and electrostatic interaction, which greatly reduced the binding efficient of LDH. The polymer size played an important role in PEI-LDH interaction. The smaller size of lower molecular weight PEI facilitated the close contact with LDH and consequential reduction of the turnover number of the enzyme. However, higher molecular weight PEI was more favorable for competitive binding with NADH and pyruvate and generally decreased the catalytic efficient of LDH. Copyright © 2018. Published by Elsevier B.V.

77 FR 72766 - Small Business Size Standards: Support Activities for Mining

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-06

... its entirety for parties who have an interest in SBA's overall approach to establishing, evaluating....gov , Docket ID: SBA-2009- 0008. SBA continues to welcome comments on its methodology from interested.... Average firm size. SBA computes two measures of average firm size: simple average and weighted average...

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Waif goodbye! Average-size female models promote positive body image and appeal to consumers.

PubMed

Diedrichs, Phillippa C; Lee, Christina

2011-10-01

Despite consensus that exposure to media images of thin fashion models is associated with poor body image and disordered eating behaviours, few attempts have been made to enact change in the media. This study sought to investigate an effective alternative to current media imagery, by exploring the advertising effectiveness of average-size female fashion models, and their impact on the body image of both women and men. A sample of 171 women and 120 men were assigned to one of three advertisement conditions: no models, thin models and average-size models. Women and men rated average-size models as equally effective in advertisements as thin and no models. For women with average and high levels of internalisation of cultural beauty ideals, exposure to average-size female models was associated with a significantly more positive body image state in comparison to exposure to thin models and no models. For men reporting high levels of internalisation, exposure to average-size models was also associated with a more positive body image state in comparison to viewing thin models. These findings suggest that average-size female models can promote positive body image and appeal to consumers.

Interactions between sodium dodecyl sulphate and non-ionic cellulose derivatives studied by size exclusion chromatography with online multi-angle light scattering and refractometric detection.

PubMed

Wittgren, Bengt; Stefansson, Morgan; Porsch, Bedrich

2005-08-05

The novel approach described allows to characterise the surfactant-polymer interaction under several sodium dodecyl sulphate (SDS) concentrations (0-20 mM) using size exclusion chromatography (SEC) with online multi-angle light scattering (MALS) and refractometric (RI) detection. Three different cellulose derivatives, hydroxypropyl cellulose (HPC), hydroxypropyl methyl cellulose (HPMC) and hydroxyethyl cellulose (HEC), have been studied in solution containing 10 mM NaCl and various concentrations of sodium dodecyl sulphate. It is shown that this approach is well suited for successful application of both Hummel-Dreyer and multi-component light scattering principles and yields reliable molecular masses of both the polymer complex and the polymer itself within the complex, the amount of surfactant bound into the complex as well as appropriate values of the refractive index increment (dn/dc)micro, of both the complex and the polymer in question. The more hydrophobic derivatives HPC and HPMC adsorbed significantly more SDS than HEC. The inter-chain interactions close to critical aggregation concentration (cac) were clearly seen for HPC and HPMC as an almost two-fold average increase in polymer molecular mass contained in the complex.

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

Wang, Wenwen; Wang, Weiyu; Li, Hui

In this study, high molecular weight “comb-shaped” graft copolymers, poly(isoprene-g-styrene), with polyisoprene as the backbone and polystyrene as side chains, were synthesized via free radical emulsion polymerization by copolymerization of isoprene with a polystyrene macromonomer synthesized using anionic polymerization. A small amount of toluene was used in order to successfully disperse the macromonomer. Both a redox and thermal initiation system were used in the emulsion polymerization, and the latex particle size and distribution were investigated by dynamic light scattering. The structural characteristics of the macromonomer and comb graft copolymers were investigated through use of size exclusion chromatography, spectroscopy, microscopy, thermalmore » analysis, and rheology. While the macromonomer was successfully copolymerized to obtain the desired multigraft copolymers, small amounts of unreacted macromonomer remained in the products, reflecting its reduced reactivity due to steric effects. Nevertheless, the multigraft copolymers obtained were very high in molecular weight (5–12 × 10 5 g/mol) and up to 10 branches per chain, on average, could be incorporated. A material incorporating 29 wt% polystyrene exhibits a disordered microphase separated morphology and elastomeric properties. As a result, these materials show promise as new, highly tunable, and potentially low cost thermoplastic elastomers.« less

Supercritical fluid molecular spray thin films and fine powders

DOEpatents

Smith, Richard D.

1988-01-01

Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. The solvent is vaporized and pumped away. Solution pressure is varied to determine, together with flow rate, the rate of deposition and to control in part whether a film or powder is produced and the granularity of each. Solution temperature is varied in relation to formation of a two-phase system during expansion to control porosity of the film or powder. A wide variety of film textures and powder shapes are produced of both organic and inorganic compounds. Films are produced with regular textural feature dimensions of 1.0-2.0 .mu.m down to a range of 0.01 to 0.1 .mu.m. Powders are formed in very narrow size distributions, with average sizes in the range of 0.02 to 5 .mu.m.

Advanced bioanalytics for precision medicine.

PubMed

Roda, Aldo; Michelini, Elisa; Caliceti, Cristiana; Guardigli, Massimo; Mirasoli, Mara; Simoni, Patrizia

2018-01-01

Precision medicine is a new paradigm that combines diagnostic, imaging, and analytical tools to produce accurate diagnoses and therapeutic interventions tailored to the individual patient. This approach stands in contrast to the traditional "one size fits all" concept, according to which researchers develop disease treatments and preventions for an "average" patient without considering individual differences. The "one size fits all" concept has led to many ineffective or inappropriate treatments, especially for pathologies such as Alzheimer's disease and cancer. Now, precision medicine is receiving massive funding in many countries, thanks to its social and economic potential in terms of improved disease prevention, diagnosis, and therapy. Bioanalytical chemistry is critical to precision medicine. This is because identifying an appropriate tailored therapy requires researchers to collect and analyze information on each patient's specific molecular biomarkers (e.g., proteins, nucleic acids, and metabolites). In other words, precision diagnostics is not possible without precise bioanalytical chemistry. This Trend article highlights some of the most recent advances, including massive analysis of multilayer omics, and new imaging technique applications suitable for implementing precision medicine. Graphical abstract Precision medicine combines bioanalytical chemistry, molecular diagnostics, and imaging tools for performing accurate diagnoses and selecting optimal therapies for each patient.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines.

PubMed

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P; Bolgiano, Barbara

2015-03-10

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8×10(6) g/mol to larger than 20×10(6) g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines

PubMed Central

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P.; Bolgiano, Barbara

2015-01-01

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8 × 106 g/mol to larger than 20 × 106 g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. PMID:25640334

One pot synthesis of gold nanoparticles using chitosan with varying degree of deacetylation and molecular weight.

PubMed

Sun, Lijun; Li, Jin; Cai, Jun; Zhong, Lian; Ren, Guohui; Ma, Qimin

2017-12-15

Gold nanoparticles (AuNPs) were synthesized in one-step by reducing gold salt using nontoxic and biodegradable chitosan as dual roles of reducing agent and stabilizer. The obtained AuNPs were characterized with UV-vis spectroscopy and transmission electron microscopy. The results indicated that control over the size and shape of AuNPs is achieved through the careful selection of experimental conditions, such as reaction temperature, reaction time, concentration of gold salt and chitosan, and chitosan molecular parameters, i.e., degree of deacetylation (DD) and molecular weight (MW). At low chitosan concentration (0.005% and 0.01% (w/v)), individual spherical AuNPs with average particle size around 10nm were obtained regardless of chitosan DD and MW, while anisotropic AuNPs were obtained at concentration above 0.05% (w/v) for all investigated chitosan at the optimum condition (1mL of 1mmol/L HAuCl 4 added to 3mL of chitosan solution reacted for 120min at 70°C). The growth of larger polygonal AuNPs was promoted as the higher concentration and lower DD chitosan was used as reducing agent and stabilizer. Au nanoplate was synthesized by water-soluble chitosan (M v 566kDa, DD 53%) at concentration above 0.15% (w/v). Chitooligomers (M v 2.4kDa, DD 94%) showed the highest reduction ability for Au 3+ and the synthesized AuNPs exhibited aggregation on morphology. It was considered that chitosan DD and concentration played a more important role than MW in the size and shape of AuNPs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Perception of the average size of multiple objects in chimpanzees (Pan troglodytes).

PubMed

Imura, Tomoko; Kawakami, Fumito; Shirai, Nobu; Tomonaga, Masaki

2017-08-30

Humans can extract statistical information, such as the average size of a group of objects or the general emotion of faces in a crowd without paying attention to any individual object or face. To determine whether summary perception is unique to humans, we investigated the evolutional origins of this ability by assessing whether chimpanzees, which are closely related to humans, can also determine the average size of multiple visual objects. Five chimpanzees and 18 humans were able to choose the array in which the average size was larger, when presented with a pair of arrays, each containing 12 circles of different or the same sizes. Furthermore, both species were more accurate in judging the average size of arrays consisting of 12 circles of different or the same sizes than they were in judging the average size of arrays consisting of a single circle. Our findings could not be explained by the use of a strategy in which the chimpanzee detected the largest or smallest circle among those in the array. Our study provides the first evidence that chimpanzees can perceive the average size of multiple visual objects. This indicates that the ability to compute the statistical properties of a complex visual scene is not unique to humans, but is shared between both species. © 2017 The Authors.

Perception of the average size of multiple objects in chimpanzees (Pan troglodytes)

PubMed Central

Kawakami, Fumito; Shirai, Nobu; Tomonaga, Masaki

2017-01-01

Humans can extract statistical information, such as the average size of a group of objects or the general emotion of faces in a crowd without paying attention to any individual object or face. To determine whether summary perception is unique to humans, we investigated the evolutional origins of this ability by assessing whether chimpanzees, which are closely related to humans, can also determine the average size of multiple visual objects. Five chimpanzees and 18 humans were able to choose the array in which the average size was larger, when presented with a pair of arrays, each containing 12 circles of different or the same sizes. Furthermore, both species were more accurate in judging the average size of arrays consisting of 12 circles of different or the same sizes than they were in judging the average size of arrays consisting of a single circle. Our findings could not be explained by the use of a strategy in which the chimpanzee detected the largest or smallest circle among those in the array. Our study provides the first evidence that chimpanzees can perceive the average size of multiple visual objects. This indicates that the ability to compute the statistical properties of a complex visual scene is not unique to humans, but is shared between both species. PMID:28835550

Recent progress in cell-free solubilization of coal

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

Cohen, M.S.; Aronson, H.; Feldman, K.

1988-01-01

Low rank coal has been solubilized using cell-free filtrates separated from cultures of Polyporus versicolor. Solubilization has been obtained with neat filtrates and with fractions collected from the neat filtrates after gel permeation chromatography. The coal solubilizing enzymes have been collected in enriched fractions with gpc. This increased relative purity has allowed the determination of the average molecular weight of this enzyme by gel permeation chromatography and by polyacrylamide gel electrophoresis. Rates of coal solubilization are dependent on the size of coal particles, mass of coal, temperature, pH, concentration of the cell-free filtrate, and the concentration of several inorganic ions.

Modelling CO emission - II. The physical characteristics that determine the X factor in Galactic molecular clouds

NASA Astrophysics Data System (ADS)

Shetty, Rahul; Glover, Simon C.; Dullemond, Cornelis P.; Ostriker, Eve C.; Harris, Andrew I.; Klessen, Ralf S.

2011-08-01

We investigate how the X factor, the ratio of the molecular hydrogen column density (?) to velocity-integrated CO intensity (W), is determined by the physical properties of gas in model molecular clouds (MCs). The synthetic MCs are results of magnetohydrodynamic simulations, including a treatment of chemistry. We perform radiative transfer calculations to determine the emergent CO intensity, using the large velocity gradient approximation for estimating the CO population levels. In order to understand why observations generally find cloud-averaged values of X = XGal˜ 2 × 1020 cm-2 K-1 km-1 s, we focus on a model representing a typical Milky Way MC. Using globally integrated ? and W reproduces the limited range in X found in observations and a mean value X = XGal= 2.2 × 1020 cm-2 K-1 km-1 s. However, we show that when considering limited velocity intervals, X can take on a much larger range of values due to CO line saturation. Thus, the X factor strongly depends on both the range in gas velocities and the volume densities. The temperature variations within individual MCs do not strongly affect X, as dense gas contributes most to setting the X factor. For fixed velocity and density structure, gas with higher temperatures T has higher W, yielding X ∝ T-1/2 for T ˜ 20-100 K. We demonstrate that the linewidth-size scaling relationship does not influence the X factor - only the range in velocities is important. Clouds with larger linewidths σ, regardless of the linewidth-size relationship, have a higher W, corresponding to a lower value of X, scaling roughly as X ∝σ-1/2. The 'mist' model, often invoked to explain a constant XGal consisting of optically thick cloudlets with well-separated velocities, does not accurately reflect the conditions in a turbulent MC. We propose that the observed cloud-averaged values of X ˜ XGal are simply a result of the limited range in ?, temperatures and velocities found in Galactic MCs - a nearly constant value of X therefore does not require any linewidth-size relationship, or that MCs are virialized objects. Since gas properties likely differ (albeit even slightly) from cloud to cloud, masses derived through a standard value of the X factor should only be considered as a rough first estimate. For temperatures T ˜ 10-20 K, velocity dispersions σ˜ 1-6 km s-1and ? cm-2, we find cloud-averaged values X ˜ 2-4 × 1020 cm-2 K-1 km-1 s for solar-metallicity models.

Fermentation pH Modulates the Size Distributions and Functional Properties of Gluconobacter albidus TMW 2.1191 Levan

PubMed Central

Ua-Arak, Tharalinee; Jakob, Frank; Vogel, Rudi F.

2017-01-01

Bacterial levan has gained an increasing interest over the last decades due to its unique characteristics and multiple possible applications. Levan and other exopolysaccharides (EPSs) production are usually optimized to obtain the highest concentration or yield while a possible change of the molecular size and mass during the production process is mostly neglected. In this study, the molar mass and radius of levan samples were monitored during fermentations with the food-grade, levan-producing acetic acid bacterium Gluconobacter (G.) albidus TMW 2.1191 in shake flasks (without pH control) and bioreactors (with pH control at 4.5, 5.5 and 6.5, respectively). In uncontrolled fermentations, the levan size/molar mass continuously decreased concomitantly with the continuous acidification of the nutrient medium. On the contrary, the amount, molar mass and size of levan could be directly influenced by controlling the pH during fermentation. Using equal initial substrate amounts, the largest weight average molar mass and geometric radius of levan were observed at constant pH 6.5, while the highest levan concentration was obtained at constant pH 4.5. Since there is a special demand to find suitable hydrocolloids from food-grade bacteria to develop novel gluten-free (GF) products, these differently produced levans were used for baking of GF breads, and the best quality improvement was obtained by addition of levan with the highest mass and radius. This work, therefore, demonstrates for the first time that one bacterial strain can produce specific high molecular weight fractions of one EPS type, which differ in properties and sizes among each other in dependence of the controllable production conditions. PMID:28522999

GI Joe or Average Joe? The impact of average-size and muscular male fashion models on men's and women's body image and advertisement effectiveness.

PubMed

Diedrichs, Phillippa C; Lee, Christina

2010-06-01

Increasing body size and shape diversity in media imagery may promote positive body image. While research has largely focused on female models and women's body image, men may also be affected by unrealistic images. We examined the impact of average-size and muscular male fashion models on men's and women's body image and perceived advertisement effectiveness. A sample of 330 men and 289 women viewed one of four advertisement conditions: no models, muscular, average-slim or average-large models. Men and women rated average-size models as equally effective in advertisements as muscular models. For men, exposure to average-size models was associated with more positive body image in comparison to viewing no models, but no difference was found in comparison to muscular models. Similar results were found for women. Internalisation of beauty ideals did not moderate these effects. These findings suggest that average-size male models can promote positive body image and appeal to consumers. 2010 Elsevier Ltd. All rights reserved.

Elastic constants from microscopic strain fluctuations

PubMed

Sengupta; Nielaba; Rao; Binder

2000-02-01

Fluctuations of the instantaneous local Lagrangian strain epsilon(ij)(r,t), measured with respect to a static "reference" lattice, are used to obtain accurate estimates of the elastic constants of model solids from atomistic computer simulations. The measured strains are systematically coarse-grained by averaging them within subsystems (of size L(b)) of a system (of total size L) in the canonical ensemble. Using a simple finite size scaling theory we predict the behavior of the fluctuations as a function of L(b)/L and extract elastic constants of the system in the thermodynamic limit at nonzero temperature. Our method is simple to implement, efficient, and general enough to be able to handle a wide class of model systems, including those with singular potentials without any essential modification. We illustrate the technique by computing isothermal elastic constants of "hard" and "soft" disk triangular solids in two dimensions from Monte Carlo and molecular dynamics simulations. We compare our results with those from earlier simulations and theory.

High efficiency and low cost preparation of size controlled starch nanoparticles through ultrasonic treatment and precipitation.

PubMed

Chang, Yanjiao; Yan, Xiaoxia; Wang, Qian; Ren, Lili; Tong, Jin; Zhou, Jiang

2017-07-15

The purpose of this work was to develop an approach to produce size controlled starch nanoparticles (SNPs), via precipitation with high efficiency and low cost. High concentration starch aqueous pastes (up to 5wt.%) were treated by ultrasound. Viscosity measurements and size exclusion chromatography characterization revealed that, after 30min ultrasonic treatment, viscosity of the starch pastes decreased two orders of magnitude and the weight average molecular weight of the starch decreased from 8.4×10 7 to 2.7×10 6 g/mol. Dynamic light scattering measurements and scanning electron microscopy observations showed that the SNPs prepared from the starch pastes with ultrasonic treatments were smaller (∼75nm) and more uniform. Moreover, SNPs could be obtained using less non-solvents. X-ray diffraction results indicated that effect of the ultrasonic treatment on crystalline structure of the SNPs was negligible. Ultrasound can be utilized to prepare smaller SNPs through nanoprecipitation with higher efficiency and lower cost. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Micro vs. macro: structural-functional organization of avian micro- and macrochromosomes].

PubMed

Rodionov, A V

1996-05-01

Karyotypes of lower vertebrates mainly consist of microchromosomes. In higher vertebrates, microchromosomes are present in each class of the most primitive orders. Birds have more microchromosomes in their karyotype than other vertebrates. Accumulation of microchromosomes in the avian karyotype probably occurred after separation of birds from reptilians in Triassic, but prior to radiation of ancestors of the modern orders (late Cretaceous-early Jurassic). In this review, the structural, molecular, and functional organization of avian macro- and microchromosomes and their participation in genetic processes are discussed. The average size of an avian microchromosome is about 12.4 Mb, which is ten times less than the size of an average macrochromosome. In contrast to macrochromosomes, medium and small avian chromosomes lack the highest level of chromosomal organization: their chromonemes do not have spiral coiling. Microchromosomal euchromatin largely consists of GC-rich R regions. More than half of the mapped avian genes are located on microchromosomes. Crossing-over frequency in microchromosomes is approximately threefold higher than in macrochromosomes. This may be caused by high GC content and recombination hot spots, which are present on each microchromosome. High recombination frequency in microchromosomes increases the probability of their correct meiotic segregation.

Surface morphology and molecular bonding of CaCO3 nanocrystallites by gas diffusion method

NASA Astrophysics Data System (ADS)

Sulimai, N. H.; Rani, Rozina Abdul; Khusaimi, Z.; Abdullah, S.; Salifairus, M. J.; Alrokayan, Salman; Khan, Haseeb; Rusop, M.

2018-05-01

Calcium carbonate with the chemical formula of (CaCO3) is the most abundant element in the world. Its usage on certain applications is largely affected by its properties. The best means to control its properties is through controlled preparation of CaCO3. This study uses diffusion method between the precursors Calcium Chloride and Ammonium Carbonate. Instead of using water, ethanol was used to prepare the salt. Reaction was done in room temperature (RT) for 6h-24h. Smallest average crystallite size measured by FESEM micrograph is 500nm produced by synthesis of CaCO3 reacted for 168 hours. From energy-dispersive X-ray spectrum also indicated the smallest particle size is by CaCO3 reacted for 168 hours. Changes was seen for element Ca at 3.7keV.

Structural and Dynamical Properties of Alkaline Earth Metal Halides in Supercritical Water: Effect of Ion Size and Concentration.

PubMed

Keshri, Sonanki; Tembe, B L

2017-11-22

Constant temperature-constant pressure molecular dynamics simulations have been performed for aqueous alkaline earth metal chloride [M 2+ -Cl - (M = Mg, Ca, Sr, and Ba)] solutions over a wide range of concentrations (0.27-5.55 m) in supercritical (SC) and ambient conditions to investigate their structural and dynamical properties. A strong influence of the salt concentration is observed on the ion-ion pair correlation functions in both ambient and SC conditions. In SC conditions, significant clustering is observed in the 0.27 m solution, whereas the reverse situation is observed at room temperature and this is also supported by the residence times of the clusters. The concentration and ion size (cation size) seem to have opposite effects on the average number of hydrogen bonds. The simulation results show that the self-diffusion coefficients of water, cations, and the chloride ion increase with increasing temperature, whereas they decrease with increasing salt concentration. The cluster size distribution shows a strong density dependence in both ambient and SC conditions. In SC conditions, cluster sizes display a near-Gaussian distribution, whereas the distribution decays monotonically in ambient conditions.

A study on size effect of carboxymethyl starch nanogel crosslinked by electron beam radiation

NASA Astrophysics Data System (ADS)

Binh, Doan; Pham Thi Thu Hong; Nguyen Ngoc Duy; Nguyen Thanh Duoc; Nguyen Nguyet Dieu

2012-07-01

The formation of carboxymethyl starch (CMS) nanogel with 50 nm less particle size was carried out through a radiation crosslinked process on the electron beam (EB) linear accelerator. Changes of intrinsic viscosities and weight averaged molecular weight in the CMS concentration, which ranged from 3 to 10 mg ml-1 in absorbed doses were investigated. There were some new peaks in the 1H NMR spectra of CMS nanogel compared with those of CMS polymer. These results were anticipated that the predominant intramolecular crosslinking of dilute CMS aqueous solution occurred while being exposed to a short intense pulse of ionizing radiation. Hydrodynamic radius (often called particle size, Rh) and distribution of particle size were measured by a dynamic light scattering technique. The radiation yield of intermolecular crosslinking of CMS solution was calculated from the expression of Gx (Charlesby, 1960; Jung-Chul, 2010). The influence of the "size effect" was demonstrated by testing culture of Lactobacillus bacteria on MRS agar culture medium containing CMS nanogel and polymer. Results showed that the number of Lactobacillus bacteria growing on nanogel containing culture medium is about 170 cfu/ml and on polymer containing culture medium is only 6 cfu/ml.

Extending rule-based methods to model molecular geometry and 3D model resolution.

PubMed

Hoard, Brittany; Jacobson, Bruna; Manavi, Kasra; Tapia, Lydia

2016-08-01

Computational modeling is an important tool for the study of complex biochemical processes associated with cell signaling networks. However, it is challenging to simulate processes that involve hundreds of large molecules due to the high computational cost of such simulations. Rule-based modeling is a method that can be used to simulate these processes with reasonably low computational cost, but traditional rule-based modeling approaches do not include details of molecular geometry. The incorporation of geometry into biochemical models can more accurately capture details of these processes, and may lead to insights into how geometry affects the products that form. Furthermore, geometric rule-based modeling can be used to complement other computational methods that explicitly represent molecular geometry in order to quantify binding site accessibility and steric effects. We propose a novel implementation of rule-based modeling that encodes details of molecular geometry into the rules and binding rates. We demonstrate how rules are constructed according to the molecular curvature. We then perform a study of antigen-antibody aggregation using our proposed method. We simulate the binding of antibody complexes to binding regions of the shrimp allergen Pen a 1 using a previously developed 3D rigid-body Monte Carlo simulation, and we analyze the aggregate sizes. Then, using our novel approach, we optimize a rule-based model according to the geometry of the Pen a 1 molecule and the data from the Monte Carlo simulation. We use the distances between the binding regions of Pen a 1 to optimize the rules and binding rates. We perform this procedure for multiple conformations of Pen a 1 and analyze the impact of conformation and resolution on the optimal rule-based model. We find that the optimized rule-based models provide information about the average steric hindrance between binding regions and the probability that antibodies will bind to these regions. These optimized models quantify the variation in aggregate size that results from differences in molecular geometry and from model resolution.

Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion.

PubMed

Freed, Karl F

2014-10-14

A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, "The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition" [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.

Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion

NASA Astrophysics Data System (ADS)

Freed, Karl F.

2014-10-01

A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, "The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition" [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.

Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion

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

Freed, Karl F., E-mail: freed@uchicago.edu

A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, “The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition” [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic naturemore » of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.« less

Extraction of hyaluronic acid (HA) from rooster comb and characterization using flow field-flow fractionation (FlFFF) coupled with multiangle light scattering (MALS).

PubMed

Kang, Dong Young; Kim, Won-Suk; Heo, In Sook; Park, Young Hun; Lee, Seungho

2010-11-01

Hyaluronic acid (HA) was extracted in a relatively large scale from rooster comb using a method similar to that reported previously. The extraction method was modified to simplify and to reduce time and cost in order to accommodate a large-scale extraction. Five hundred grams of frozen rooster combs yielded about 500 mg of dried HA. Extracted HA was characterized using asymmetrical flow field-flow fractionation (AsFlFFF) coupled online to a multiangle light scattering detector and a refractive index detector to determine the molecular size, molecular weight (MW) distribution, and molecular conformation of HA. For characterization of HA, AsFlFFF was operated by a simplified two-step procedure, instead of the conventional three-step procedure, where the first two steps (sample loading and focusing) were combined into one to avoid the adsorption of viscous HA onto the channel membrane. The simplified two-step AsFlFFF yielded reasonably good separations of HA molecules based on their MWs. The weight average MW (M(w) ) and the average root-mean-square (RMS) radius of HA extracted from rooster comb were 1.20×10(6) and 94.7 nm, respectively. When the sample solution was filtered through a 0.45 μm disposable syringe filter, they were reduced down to 3.8×10(5) and 50.1 nm, respectively. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Degradation of chitosan by gamma ray with presence of hydrogen peroxide

NASA Astrophysics Data System (ADS)

Mahmud, Maznah; Naziri, Muhammad Ihsan; Yacob, Norzita; Talip, Norhashidah; Abdullah, Zahid

2014-02-01

The radiation degraded chitosan samples were prepared by swelling the chitosan powder in water and exposed for gamma irradiation. The ratio chitosan to water was 1:6 with the presence of hydrogen peroxide (H2O2), 1%-5%. These chitosan-water mixtures were irradiated at 6kGy, which is the lowest irradiation dose that facility can offered. All samples were purified and proceed with characterization. The molecular weight (MW) study was monitored by size exclusion chromatography-multi angle laser light scattering (SEC-MALLS). Results showed that MW of chitosan reduced as the dose increased. Application of H2O2 enhanced the degradation rate of chitosan even at very low irradiation dose. Homogenous degradation also occurred during treatment with H2O2based on the polydispersity index (PDI) derived from the calculation of weight average molecular weight over number average molecular weight (Mw/Mn). Mechanism of chitosan radiation degradation with and without hydrogen peroxide was also discussed in this paper. Structure of degraded products was characterized with Fourier-transform infrared spectra. The degree of deacetylation (DDA) values of the samples was determined by acid-base titration. Solubility test results showed that, chitosan powder even at low Mw was insoluble in water even at low pH water. Chitosan as well as irradiated chitosan powder are soluble in strong and weak acid solution. Further discussion on behaviours of radiation degraded chitosan will be elaborated more in this paper.

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

Mahmud, Maznah; Yacob, Norzita; Talip, Norhashidah

The radiation degraded chitosan samples were prepared by swelling the chitosan powder in water and exposed for gamma irradiation. The ratio chitosan to water was 1:6 with the presence of hydrogen peroxide (H{sub 2}O{sub 2}), 1%–5%. These chitosan-water mixtures were irradiated at 6kGy, which is the lowest irradiation dose that facility can offered. All samples were purified and proceed with characterization. The molecular weight (MW) study was monitored by size exclusion chromatography-multi angle laser light scattering (SEC-MALLS). Results showed that MW of chitosan reduced as the dose increased. Application of H{sub 2}O{sub 2} enhanced the degradation rate of chitosan evenmore » at very low irradiation dose. Homogenous degradation also occurred during treatment with H{sub 2}O{sub 2}based on the polydispersity index (PDI) derived from the calculation of weight average molecular weight over number average molecular weight (Mw/Mn). Mechanism of chitosan radiation degradation with and without hydrogen peroxide was also discussed in this paper. Structure of degraded products was characterized with Fourier-transform infrared spectra. The degree of deacetylation (DDA) values of the samples was determined by acid-base titration. Solubility test results showed that, chitosan powder even at low Mw was insoluble in water even at low pH water. Chitosan as well as irradiated chitosan powder are soluble in strong and weak acid solution. Further discussion on behaviours of radiation degraded chitosan will be elaborated more in this paper.« less

The fundamentally different dynamics of dust and gas in molecular clouds

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Lee, Hyunseok

2016-03-01

We study the behaviour of large dust grains in turbulent molecular clouds (MCs). In primarily neutral regions, dust grains move as aerodynamic particles, not necessarily with the gas. We therefore directly simulate, for the first time, the behaviour of aerodynamic grains in highly supersonic, magnetohydrodynamic turbulence typical of MCs. We show that, under these conditions, grains with sizes a ≳ 0.01 micron exhibit dramatic (exceeding factor ˜1000) fluctuations in the local dust-to-gas ratio (implying large small-scale variations in abundances, dust cooling rates, and dynamics). The dust can form highly filamentary structures (which would be observed in both dust emission and extinction), which can be much thinner than the characteristic width of gas filaments. Sometimes, the dust and gas filaments are not even in the same location. The `clumping factor' < n_dust2 > / < n_dust > 2 of the dust (critical for dust growth/coagulation/shattering) can reach ˜100, for grains in the ideal size range. The dust clustering is maximized around scales ˜ 0.2 pc (a/μm) (ngas/100 cm- 3)- 1, and is `averaged out' on larger scales. However, because the density varies widely in supersonic turbulence, the dynamic range of scales (and interesting grain sizes) for these fluctuations is much broader than in the subsonic case. Our results are applicable to MCs of essentially all sizes and densities, but we note how Lorentz forces and other physics (neglected here) may change them in some regimes. We discuss the potentially dramatic consequences for star formation, dust growth and destruction, and dust-based observations of MCs.

The Association between Penis Size and Sexual Health among Men Who Have Sex with Men

PubMed Central

Grov, Christian; Parsons, Jeffrey T.; Bimbi, David S.

2010-01-01

Larger penis size has been equated with a symbol of power, stamina, masculinity, and social status. Yet, there has been little research among men who have sex with men assessing the association between penis size and social-sexual health. Survey data from a diverse sample of 1,065 men who have sex with men were used to explore the association between perceived penis size and a variety of psychosocial outcomes. Seven percent of men felt their penis was “below average,” 53.9% “average,” and 35.5% “above average.” Penis size was positively related to satisfaction with size and inversely related to lying about penis size (all p < .01). Size was unrelated to condom use, frequency of sex partners, HIV status, or recent diagnoses of HBV, HCV, gonorrhea/Chlamydia/urinary tract infections, and syphilis. Men with above average penises were more likely to report HPV and HSV-2 (Fisher’s exact p ≤ .05). Men with below average penises were significantly more likely to identify as “bottoms” (anal receptive) and men with above average penises were significantly more likely to identify as tops (anal insertive). Finally, men with below average penises fared significantly worse than other men on three measures of psychosocial adjustment. Though most men felt their penis size was average, many fell outside this “norm.” The disproportionate number of viral skin-to-skin STIs (HSV-2 and HPV) suggest size may play a role in condom slippage/breakage. Further, size played a significant role in sexual positioning and psychosocial adjustment. These data highlight the need to better understand the real individual-level consequences of living in a penis-centered society. PMID:19139986

The global star formation law of galaxies revisited in the radio continuum

NASA Astrophysics Data System (ADS)

Liu, LiJie; Gao, Yu

2012-02-01

We study the global star formation law, the relation between the gas and star formation rate (SFR) in a sample of 130 local galaxies with infrared (IR) luminosities spanning over three orders of magnitude (109-1012 L⊙), which includes 91 normal spiral galaxies and 39 (ultra)luminous IR galaxies [(U)LIRGs]. We derive their total (atomic and molecular) gas and dense molecular gas masses using newly available HI, CO and HCN data from the literature. The SFR of galaxies is determined from total IR (8-1000 μm) and 1.4 GHz radio continuum (RC) luminosities. The galaxy disk sizes are defined by the de-convolved elliptical Gaussian FWHM of the RC maps. We derive the galaxy disk-averaged SFRs and various gas surface densities, and investigate their relationships. We find that the galaxy disk-averaged surface density of dense molecular gas mass has the tightest correlation with that of SFR (scatter ˜0.26 dex), and is linear in log-log space (power-law slope of N=1.03±0.02) across the full galaxy sample. The correlation between the total gas and SFR surface densities for the full sample has a somewhat larger scatter (˜0.48 dex), and is best fit by a power-law with slope 1.45±0.02. However, the slope changes from ˜1 when only normal spirals are considered, to ˜1.5 when more and more (U)LIRGs are included in the fitting. When different CO-to-H2 conversion factors are used to infer molecular gas masses for normal galaxies and (U)LIRGs, the bi-modal relations claimed recently in CO observations of high-redshift galaxies appear to also exist in local populations of star-forming galaxies.

Alignment-independent technique for 3D QSAR analysis

NASA Astrophysics Data System (ADS)

Wilkes, Jon G.; Stoyanova-Slavova, Iva B.; Buzatu, Dan A.

2016-04-01

Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test 2 = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test 2 = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test 2 = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.

PubMed

Nilofer, Christina; Sukhwal, Anshul; Mohanapriya, Arumugam; Kangueane, Pandjassarame

2017-01-01

Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Several interface features have been documented using known X-ray structures of protein complexes since 1975. This has improved our understanding of the interface using structural features such as interface area, binding energy, hydrophobicity, relative hydrophobicity, salt bridges and hydrogen bonds. The strength of binding between two proteins is dependent on interface size (number of residues at the interface) and thus its corresponding interface area. It is known that large interfaces have high binding energy (sum of (van der Waals) vdW, H-bonds, electrostatics). However, the selective role played by each of these energy components and more especially that of vdW is not explicitly known. Therefore, it is important to document their individual role in known protein-protein structural complexes. It is of interest to relate interface size with vdW, H-bonds and electrostatic interactions at the interfaces of protein structural complexes with known function using statistical and multiple linear regression analysis methods to identify the prominent force. We used the manually curated non-redundant dataset of 278 hetero-dimeric protein structural complexes grouped using known functions by Sowmya et al. (2015) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (Anshul and Sowdhamini, 2015). This dataset consists of obligatory (enzymes, regulator, biological assembly), immune and nonobligatory (enzyme and regulator inhibitors) complexes. Results show that the total binding energy is more for large interfaces. However, this is not true for its individual energy factors. Analysis shows that vdW energies contribute to about 75% ± 11% on average among all complexes and it also increases with interface size (r2 ranging from 0.67 to 0.89 with p<0.01) at 95% confidence limit irrespective of molecular function. Thus, vdW is both dominant and proportional at the interface independent of molecular function. Nevertheless, H bond energy contributes to 15% ± 6.5% on average in these complexes. It also moderately increases with interface size (r2 ranging from 0.43 to 0.61 with p<0.01) only among obligatory and immune complexes. Moreover, there is about 11.3% ± 8.7% contribution by electrostatic energy. It increases with interface size specifically among non-obligatory regulator-inhibitors (r2 = 0.44). It is implied that both H-bonds and electrostatics are neither dominant nor proportional at the interface. Nonetheless, their presence cannot be ignored in binding. Therefore, H-bonds and (or) electrostatic energy having specific role for improved stability in complexes is implied. Thus, vdW is common at the interface stabilized further with selective H-bonds and (or) electrostatic interactions at an atomic level in almost all complexes. Comparison of this observation with residue level analysis of the interface is compelling. The role by H-bonds (14.83% ± 6.5% and r2 = 0.61 with p<0.01) among obligatory and electrostatic energy (8.8% ± 4.77% and r2 = 0.63 with p <0.01) among non-obligatory complexes within interfaces (class A) having more non-polar residues than surface is influencing our inference. However, interfaces (class B) having less non-polar residues than surface show 1.5 fold more electrostatic energy on average. The interpretation of the interface using inter-atomic (vdW, H-bonds, electrostatic) interactions combined with inter-residue predominance (class A and class B) in relation to known function is the key to reveal its molecular principles with new challenges.

Morphology, directed self-assembly and pattern transfer from a high molecular weight polystyrene-block-poly(dimethylsiloxane) block copolymer film

NASA Astrophysics Data System (ADS)

Cheng, Li-Chen; Bai, Wubin; Fernandez Martin, Eduardo; Tu, Kun-Hua; Ntetsikas, Konstantinos; Liontos, George; Avgeropoulos, Apostolos; Ross, C. A.

2017-04-01

The self-assembly of block copolymers with large feature sizes is inherently challenging as the large kinetic barrier arising from chain entanglement of high molecular weight (MW) polymers limits the extent over which long-range ordered microdomains can be achieved. Here, we illustrate the evolution of thin film morphology from a diblock copolymer of polystyrene-block-poly(dimethylsiloxane) exhibiting total number average MW of 123 kg mol-1, and demonstrate the formation of layers of well-ordered cylindrical microdomains under appropriate conditions of binary solvent mix ratio, commensurate film thickness, and solvent vapor annealing time. Directed self-assembly of the block copolymer within lithographically patterned trenches occurs with alignment of cylinders parallel to the sidewalls. Fabrication of ordered cobalt nanowire arrays by pattern transfer was also implemented, and their magnetic properties and domain wall behavior were characterized.

Premelting, fluctuations, and coarse-graining of water-ice interfaces.

PubMed

Limmer, David T; Chandler, David

2014-11-14

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Premelting, fluctuations, and coarse-graining of water-ice interfaces

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2014-11-01

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Calculation of a solid/liquid surface tension: A methodological study

NASA Astrophysics Data System (ADS)

Dreher, T.; Lemarchand, C.; Soulard, L.; Bourasseau, E.; Malfreyt, P.; Pineau, N.

2018-01-01

The surface tension of a model solid/liquid interface constituted of a graphene sheet surrounded by liquid methane has been computed using molecular dynamics in the Kirkwood-Buff formalism. We show that contrary to the fluid/fluid case, the solid/liquid case can lead to different structurations of the first fluid layer, leading to significantly different values of surface tension. Therefore we present a statistical approach that consists in running a series of molecular simulations of similar systems with different initial conditions, leading to a distribution of surface tensions from which an average value and uncertainty can be extracted. Our results suggest that these distributions converge as the system size increases. Besides we show that surface tension is not particularly sensitive to the choice of the potential energy cutoff and that long-range corrections can be neglected contrary to what we observed in the liquid/vapour interfaces. We have not observed the previously reported commensurability effect.

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.

PubMed

Luginbühl, P; Güntert, P; Billeter, M; Wüthrich, K

1996-09-01

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

Evaluating Activated Carbon Adsorption of Dissolved Organic Matter and Micropollutants Using Fluorescence Spectroscopy.

PubMed

Shimabuku, Kyle K; Kennedy, Anthony M; Mulhern, Riley E; Summers, R Scott

2017-03-07

Dissolved organic matter (DOM) negatively impacts granular activated carbon (GAC) adsorption of micropollutants and is a disinfection byproduct precursor. DOM from surface waters, wastewater effluent, and 1 kDa size fractions were adsorbed by GAC and characterized using fluorescence spectroscopy, UV-absorption, and size exclusion chromatography (SEC). Fluorescing DOM was preferentially adsorbed relative to UV-absorbing DOM. Humic-like fluorescence (peaks A and C) was selectively adsorbed relative to polyphenol-like fluorescence (peaks T and B) potentially due to size exclusion effects. In the surface waters and size fractions, peak C was preferentially removed relative to peak A, whereas the reverse was found in wastewater effluent, indicating that humic-like fluorescence is associated with different compounds depending on DOM source. Based on specific UV-absorption (SUVA), aromatic DOM was preferentially adsorbed. The fluorescence index (FI), if interpreted as an indicator of aromaticity, indicated the opposite but exhibited a strong relationship with average molecular weight, suggesting that FI might be a better indicator of DOM size than aromaticity. The influence of DOM intermolecular interactions on adsorption were minimal based on SEC analysis. Fluorescence parameters captured the impact of DOM size on the fouling of 2-methylisoborneol and warfarin adsorption and correlated with direct competition and pore blockage indicators.

Adsorption of Poly(methyl methacrylate) on Concave Al2O3 Surfaces in Nanoporous Membranes

PubMed Central

Nunnery, Grady; Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, Rina

2009-01-01

The objective of this study was to determine the influence of polymer molecular weight and surface curvature on the adsorption of polymers onto concave surfaces. Poly(methyl methacrylate) (PMMA) of various molecular weights was adsorbed onto porous aluminum oxide membranes having various pore sizes, ranging from 32 to 220 nm. The surface coverage, expressed as repeat units per unit surface area, was observed to vary linearly with molecular weight for molecular weights below ~120 000 g/mol. The coverage was independent of molecular weight above this critical molar mass, as was previously reported for the adsorption of PMMA on convex surfaces. Furthermore, the coverage varied linearly with pore size. A theoretical model was developed to describe curvature-dependent adsorption by considering the density gradient that exists between the surface and the edge of the adsorption layer. According to this model, the density gradient of the adsorbed polymer segments scales inversely with particle size, while the total coverage scales linearly with particle size, in good agreement with experiment. These results show that the details of the adsorption of polymers onto concave surfaces with cylindrical geometries can be used to calculate molecular weight (below a critical molecular weight) if pore size is known. Conversely, pore size can also be determined with similar adsorption experiments. Most significantly, for polymers above a critical molecular weight, the precise molecular weight need not be known in order to determine pore size. Moreover, the adsorption developed and validated in this work can be used to predict coverage also onto surfaces with different geometries. PMID:19415910

Resolved Giant Molecular Clouds in Nearby Spiral Galaxies: Insights from the CANON CO (1-0) Survey

NASA Astrophysics Data System (ADS)

Donovan Meyer, Jennifer; Koda, Jin; Momose, Rieko; Mooney, Thomas; Egusa, Fumi; Carty, Misty; Kennicutt, Robert; Kuno, Nario; Rebolledo, David; Sawada, Tsuyoshi; Scoville, Nick; Wong, Tony

2013-08-01

We resolve 182 individual giant molecular clouds (GMCs) larger than 2.5 × 105 M ⊙ in the inner disks of 5 large nearby spiral galaxies (NGC 2403, NGC 3031, NGC 4736, NGC 4826, and NGC 6946) to create the largest such sample of extragalactic GMCs within galaxies analogous to the Milky Way. Using a conservatively chosen sample of GMCs most likely to adhere to the virial assumption, we measure cloud sizes, velocity dispersions, and 12CO (J = 1-0) luminosities and calculate cloud virial masses. The average conversion factor from CO flux to H2 mass (or X CO) for each galaxy is 1-2 × 1020 cm-2 (K km s-1)-1, all within a factor of two of the Milky Way disk value (~2 × 1020 cm-2 (K km s-1)-1). We find GMCs to be generally consistent within our errors between the galaxies and with Milky Way disk GMCs; the intrinsic scatter between clouds is of order a factor of two. Consistent with previous studies in the Local Group, we find a linear relationship between cloud virial mass and CO luminosity, supporting the assumption that the clouds in this GMC sample are gravitationally bound. We do not detect a significant population of GMCs with elevated velocity dispersions for their sizes, as has been detected in the Galactic center. Though the range of metallicities probed in this study is narrow, the average conversion factors of these galaxies will serve to anchor the high metallicity end of metallicity-X CO trends measured using conversion factors in resolved clouds; this has been previously possible primarily with Milky Way measurements.

Fabrication of antibody-loaded microgels using microfluidics and thiol-ene photoclick chemistry.

PubMed

Gregoritza, Manuel; Abstiens, Kathrin; Graf, Moritz; Goepferich, Achim M

2018-06-01

Reducing burst effects, providing controlled release, and safeguarding biologics against degradation are a few of several highly attractive applications for microgels in the field of controlled release. However, the incorporation of proteins into microgels without impairing stability is highly challenging. In this proof of concept study, the combination of microfluidics and thiol-ene photoclick chemistry was evaluated for the fabrication of antibody-loaded microgels with narrow size distribution. Norbornene-modified eight-armed poly(ethylene glycol) with an average molecular mass of 10,000 Da, 20,000 Da, or 40,000 Da were prepared as macromonomers for microgel formation. For functionalization, either hydrolytically cleavable ester or stable amide bonds were used. A microfluidic system was employed to generate precursor solution droplets containing macromonomers, the cross-linker dithiothreitol and the initiator Eosin-Y. Irradiation with visible light was used to trigger thiol-ene reactions which covalently cross-linked the droplets. For all bond-types, molecular masses, and concentrations gelation was very rapid (<20 s) and a plateau for the complex shear modulus was reached after only 5 min. The generated microgels had a rod-like shape and did not show considerable cellular toxicity. Stress conditions during the fabrication process were simulated and it could be shown that fabrication did not impair the activity of the model proteins lysozyme and bevacizumab. It was confirmed that the average hydrogel network mesh size was similar or smaller than the hydrodynamic diameter of bevacizumab which is a crucial factor for restricting diffusion and delaying release. Finally, microgels were loaded with bevacizumab and a sustained release over a period of 30 ± 4 and 47 ± 7 days could be achieved in vitro. Copyright © 2018 Elsevier B.V. All rights reserved.

Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

PubMed

Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

2016-09-02

The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

Composition and Antioxidant Activity of Water-Soluble Polysaccharides from Tuber indicum

PubMed Central

Luo, Qiang; Zhang, Jie; Yan, Liang; Tang, Yuanlin; Ding, Xiang; Yang, Zhirong

2011-01-01

Abstract Crude water-soluble Chinese truffle Tuber indicum polysaccharide (TIP) was extracted from the fruiting bodies with water and then successively purified by DEAE–cellulose 52 and Sephadex G-100 column chromatography, yielding two major polysaccharide fractions: TIP1-1 and TIP2-1. High-performance gel permeation chromatography analysis showed that the average molecular sizes of TIP1-1 and TIP2-1 were approximately 1.75×104 Da and 5.73×103 Da, respectively. Monosaccharide component analysis by gas chromatography indicated that TIP1-1 was composed of mannose, glucose, galactose, and rhamannose in the respective molar ratio of 3.93:1.24:0.75:1.26 and that TIP2-1 contained mannose, glucose, and arabinose in the respective molar ratio of 5.27:1.44:0.43. The antioxidant activity analyses revealed that TIP1-1 and TIP2-1 possessed considerable antioxidant activity. Compared with TIP1-1, which has a higher molecular weight and contains no uronic acid, TIP2-1 exhibited a protective effect on PC12 cells injured by H2O2 and a higher scavenging activity against free radicals. The relative effects of the lower molecular size, the presence of uronic acid, and the antioxidant activity of TIP2-1 appear to be significant. Accordingly, the Chinese truffle T. indicum might serve as an effective antioxidative healthcare food and source of natural antioxidants. PMID:21877953

Visualization of the collective vortex-like motions in liquid argon and water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Anikeenko, A. V.; Malenkov, G. G.; Naberukhin, Yu. I.

2018-03-01

We propose a new measure of collectivity of molecular motion in the liquid: the average vector of displacement of the particles, ⟨ΔR⟩, which initially have been localized within a sphere of radius Rsph and then have executed the diffusive motion during a time interval Δt. The more correlated the motion of the particles is, the longer will be the vector ⟨ΔR⟩. We visualize the picture of collective motions in molecular dynamics (MD) models of liquids by constructing the ⟨ΔR⟩ vectors and pinning them to the sites of the uniform grid which divides each of the edges of the model box into equal parts. MD models of liquid argon and water have been studied by this method. Qualitatively, the patterns of ⟨ΔR⟩ vectors are similar for these two liquids but differ in minor details. The most important result of our research is the revealing of the aggregates of ⟨ΔR⟩ vectors which have the form of extended flows which sometimes look like the parts of vortices. These vortex-like clusters of ⟨ΔR⟩ vectors have the mesoscopic size (of the order of 10 nm) and persist for tens of picoseconds. Dependence of the ⟨ΔR⟩ vector field on parameters Rsph, Δt, and on the model size has been investigated. This field in the models of liquids differs essentially from that in a random-walk model.

Iterative divergent/convergent doubling approach to linear conjugated oligomers. A rapid route to a 128 A long potential molecular wire

NASA Astrophysics Data System (ADS)

Tour, James M.; Schumm, Jeffrey S.; Pearson, Darren L.

1994-06-01

Described is the synthesis of oligo (2-ethylphenylene ethynylene)s and oligo (2-(3'ethylheptyl) phenylene ethynylene)s via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, and octamer of the ethyl derivative and the monomer, dimer, tetramer, octamer, and 16-mer of the ethylheptyl derivative. The 16-mer is 128 A long. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers verses the random coils of polystyrene. These differences become quite apparent at the octamer stage. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

PubMed

Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

2018-03-06

Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Continuously Adjustable, Molecular-Sieving “Gate” on 5A Zeolite for Distinguishing Small Organic Molecules by Size

PubMed Central

Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

2015-01-01

Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. This novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation. PMID:26358480

Continuously adjustable, molecular-sieving “gate” on 5A zeolite for distinguishing small organic molecules by size

DOE PAGES

Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; ...

2015-09-11

Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences weremore » effectively distinguished via appropriate misalignment. Lastly, this novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation.« less

A Kolmogorov-Smirnov test for the molecular clock based on Bayesian ensembles of phylogenies

PubMed Central

Antoneli, Fernando; Passos, Fernando M.; Lopes, Luciano R.

2018-01-01

Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter λ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides a gain of power. PMID:29300759

A novel microfluidic platform for size and deformability based separation and the subsequent molecular characterization of viable circulating tumor cells.

PubMed

Hvichia, G E; Parveen, Z; Wagner, C; Janning, M; Quidde, J; Stein, A; Müller, V; Loges, S; Neves, R P L; Stoecklein, N H; Wikman, H; Riethdorf, S; Pantel, K; Gorges, T M

2016-06-15

Circulating tumor cells (CTCs) were introduced as biomarkers more than 10 years ago, but capture of viable CTCs at high purity from peripheral blood of cancer patients is still a major technical challenge. Here, we report a novel microfluidic platform designed for marker independent capture of CTCs. The Parsortix™ cell separation system provides size and deformability-based enrichment with automated staining for cell identification, and subsequent recovery (harvesting) of cells from the device. Using the Parsortix™ system, average cell capture inside the device ranged between 42% and 70%. Subsequent harvest of cells from the device ranged between 54% and 69% of cells captured. Most importantly, 99% of the isolated tumor cells were viable after processing in spiking experiments as well as after harvesting from patient samples and still functional for downstream molecular analysis as demonstrated by mRNA characterization and array-based comparative genomic hybridization. Analyzing clinical blood samples from metastatic (n = 20) and nonmetastatic (n = 6) cancer patients in parallel with CellSearch(®) system, we found that there was no statistically significant difference between the quantitative behavior of the two systems in this set of twenty six paired separations. In conclusion, the epitope independent Parsortix™ system enables the isolation of viable CTCs at a very high purity. Using this system, viable tumor cells are easily accessible and ready for molecular and functional analysis. The system's ability for enumeration and molecular characterization of EpCAM-negative CTCs will help to broaden research into the mechanisms of cancer as well as facilitating the use of CTCs as "liquid biopsies." © 2016 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

The 27-28 October 1986 FIRE IFO Cirrus Case Study: Cloud Optical Properties Determined by High Spectral Resolution Lidar

NASA Technical Reports Server (NTRS)

Grund, C. J.; Eloranta, E. W.

1996-01-01

During the First ISCCP Region Experiment (FIRE) cirrus intensive field observation (IFO) the High Spectral Resolution Lidar was operated from a roof top site on the University of Wisconsin-Madison campus. Because the HSRL technique separately measures the molecular and cloud particle backscatter components of the lidar return, the optical thickness is determined independent of particle backscatter. This is accomplished by comparing the known molecular density distribution to the observed decrease in molecular backscatter signal with altitude. The particle to molecular backscatter ratio yields calibrated measurements of backscatter cross sections that can be plotted ro reveal cloud morphology without distortion due to attenuation. Changes in cloud particle size, shape, and phase affect the backscatter to extinction ratio (backscatter-phase function). The HSRL independently measures cloud particle backscatter phase function. This paper presents a quantitative analysis of the HSRL cirrus cloud data acquired over an approximate 33 hour period of continuous near zenith observations. Correlations between small scale wind structure and cirrus cloud morphology have been observed. These correlations can bias the range averaging inherent in wind profiling lidars of modest vertical resolution, leading to increased measurement errors at cirrus altitudes. Extended periods of low intensity backscatter were noted between more strongly organized cirrus cloud activity. Optical thicknesses ranging from 0.01-1.4, backscatter phase functions between 0.02-0.065 sr (exp -1) and backscatter cross sections spanning 4 orders of magnitude were observed. the altitude relationship between cloud top and bottom boundaries and the cloud optical center altitude was dependent on the type of formation observed Cirrus features were observed with characteristic wind drift estimated horizontal sizes of 5-400 km. The clouds frequently exhibited cellular structure with vertical to horizontal dimension ratios of 1:5-1:1.

Fluorophore-assisted carbohydrate electrophoresis for the determination of molecular mass of heparins and low-molecular-weight (LMW) heparins.

PubMed

Buzzega, Dania; Maccari, Francesca; Volpi, Nicola

2008-11-01

We report the use of fluorophore-assisted carbohydrate electrophoresis (FACE) to determine the molecular mass (M) values of heparins (Heps) and low-molecular-weight (LMW)-Hep derivatives. Hep are labeled with 8-aminonaphthalene-1,3,6-trisulfonic acid and FACE is able to resolve each fraction as a discrete band depending on their M. After densitometric acquisition, the migration distance of each Hep standard is acquired and the third-grade polynomial calibration standard curve is determined by plotting the logarithms of the M values as a function of migration ratio. Purified Hep samples having different properties, pharmaceutical Heps and various LMW-Heps were analyzed by both FACE and conventional high-performance size-exclusion liquid chromatography (HPSEC) methods. The molecular weight value on the top of the chromatographic peak (Mp), the number-average Mn, weight-average Mw and polydispersity (Mw/Mn) were examined by both techniques and found to be similar. This approach offers certain advantages over the HPSEC method. The derivatization process with 8-aminonaphthalene-1,3,6-trisulfonic acid is complete after 4 h so that many samples may be analyzed in a day also considering that multiple samples can be run simultaneously and in parallel and that a single FACE analysis requires approx. 15 min. Furthermore, FACE is a very sensitive method as it requires approx. 5-10 microg of Heps, about 10-100-fold lower than samples and standards used in HPSEC evaluation. Finally, the utilization of mini-gels allows the use of very low amounts of reagents with neither expensive equipment nor any complicated procedures having to be applied. This study demonstrates that FACE analysis is a sensitive method for the determination of the M values of Heps and LMW-Heps with possible utilization in virtually any kind of research and development such as quality control laboratories due to its rapid, parallel analysis of multiple samples by means of common and simple largely used analytical laboratory equipment.

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

DOE PAGES

Stewart, James A.; Brookman, G.; Price, Patrick Michael; ...

2018-04-25

In this study, the evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage productionmore » and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. Finally, this characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.« less

Molecular Dynamics Investigation of Each Bubble Behavior in Coarsening of Cavitation Bubbles in a Finite Space

NASA Astrophysics Data System (ADS)

Tsuda, Shin-Ichi; Nakano, Yuta; Watanabe, Satoshi

2017-11-01

Recently, several studies using Molecular Dynamics (MD) simulation have been conducted for investigation of Ostwald ripening of cavitation bubbles in a finite space. The previous studies focused a characteristic length of bubbles as one of the spatially-averaged quantities, but each bubble behavior was not been investigated in detail. The objective of this study is clarification of the characteristics of each bubble behavior in Ostwald ripening, and we conducted MD simulation of a Lennard-Jones fluid in a semi-confined space. As a result, the time dependency of the characteristic length of bubbles as a spatially-averaged quantity suggested that the driving force of the Ostwald ripening is Evaporation/Condensation (EC) across liquid-vapor surface, which is the same result as the previous works. The radius change of the relatively larger bubbles also showed the same tendency to a classical EC model. However, the sufficiently smaller bubbles than the critical size, e.g., the bubbles just before collapsing, showed a different characteristic from the classical EC model. Those smaller bubbles has a tendency to be limited by mechanical non-equilibrium in which viscosity of liquid is dominant rather than by EC across liquid-vapor surface. This work was supported by JSPS KAKENHI Grant Number JP16K06085.

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

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

Stewart, James A.; Brookman, G.; Price, Patrick Michael

In this study, the evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage productionmore » and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. Finally, this characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.« less

Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods

NASA Astrophysics Data System (ADS)

Stewart, J. A.; Brookman, G.; Price, P.; Franco, M.; Ji, W.; Hattar, K.; Dingreville, R.

2018-04-01

The evolution and characterization of single-isolated-ion-strikes are investigated by combining atomistic simulations with selected-area electron diffraction (SAED) patterns generated from these simulations. Five molecular dynamics simulations are performed for a single 20 keV primary knock-on atom in bulk crystalline Si. The resulting cascade damage is characterized in two complementary ways. First, the individual cascade events are conventionally quantified through the evolution of the number of defects and the atomic (volumetric) strain associated with these defect structures. These results show that (i) the radiation damage produced is consistent with the Norgett, Robinson, and Torrens model of damage production and (ii) there is a net positive volumetric strain associated with the cascade structures. Second, virtual SAED patterns are generated for the resulting cascade-damaged structures along several zone axes. The analysis of the corresponding diffraction patterns shows the SAED spots approximately doubling in size, on average, due to broadening induced by the defect structures. Furthermore, the SAED spots are observed to exhibit an average radial outward shift between 0.33% and 0.87% depending on the zone axis. This characterization approach, as utilized here, is a preliminary investigation in developing methodologies and opportunities to link experimental observations with atomistic simulations to elucidate microstructural damage states.

Amphiphilic conjunct of methyl cellulose and well-defined polyvinyl acetate.

PubMed

Xiao, Congming; Xia, Cunping

2013-01-01

Tailor-made conjunct of methyl cellulose (MC) and polyvinyl acetate (PVAc) was synthesized through the combination of reversible addition-fragmentation chain transfer (RAFT) polymerization and thiol-ene click reaction. MC was firstly transferred into unsaturated MC (UMC), and then covalently connected with well-defined PVAc obtained by RAFT polymerization of vinyl acetate. The structure of the conjunct polymer (MCV) was confirmed with Fourier transform infrared spectra (FTIR) and proton nuclear magnetic resonance ((1)H NMR). Well-defined MCV was amphiphilic and able to self-assemble into size controllable micelles, which was verified with transmission electron microscopy (TEM) and size distribution analysis. It was found that the mean diameters of the micelles in aqueous solution were 105.6, 96.0 and 75.9 nm when the number average molecular weights of PVAc segments of MCV were 49,300, 32,500 and 18,200, respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Food photography. I: The perception of food portion size from photographs.

PubMed

Nelson, M; Atkinson, M; Darbyshire, S

1994-11-01

Fifty-one male and female volunteers aged 18-90 years from a wide variety of social and occupational backgrounds completed 7284 assessments of portion size in relation to food photographs. Subjects were shown six portion sizes (two small, two medium and two large) for each of six foods, and asked to compare the amount on the plate in front of them to (a) a series of eight photographs showing weights of portions from the 5th to the 95th centile of portion size (British Adult Dietary Survey), or (b) a single photograph of the average (median) portion size. Photographs were prepared either in colour or in black and white, and in two different sizes. The order of presentation of foods; use of black and white or colour; the size of photographs; and presentation of eight or average photographs were each randomized independently. On average, the mean differences between the portion size presented and the estimate of portion size using the photographs varied from -8 to +6 g (-4 to +5%) for the series of eight photographs, and from -34 to -1 g (-23 to +9%) for the single average photograph. Large portion sizes tended to be underestimated more than medium or small portion sizes, especially when using the average photograph (from -79 to -14 g, -37 to -13%). Being female, 65 years and over, or retired, or seeing photographs in colour, were all associated with small but statistically significant overestimations of portion size. Having a body mass index > or = 30 kg/m2 was associated with an 8% underestimate of portion size. We conclude that use of a series of eight photographs is associated with relatively small errors in portion size perception, whereas use of an average photograph is consistently associated with substantial underestimation across a variety of foods.

Branched chain amino acids maintain the molecular weight of poly(γ-glutamic acid) of Bacillus licheniformis ATCC 9945 during the fermentation.

PubMed

Mitsunaga, Hitoshi; Meissner, Lena; Büchs, Jochen; Fukusaki, Eiichiro

2016-10-01

Poly(γ-glutamic acid) mainly produced by Bacillus spp. is an industrially important compound due to several useful features. Among them, molecular weight is an important characteristic affecting on the physical properties such as viscosities and negative charge densities. However, it is difficult to control the molecular size of PGA since it decreases during fermentation. Previous study reported that PGA produced in the media containing different carbon sources such as glucose and glycerol showed differences in molecular weight. Therefore in this study, the effect of carbon source on the PGA molecular weight was examined; with the aim of developing a strategy to maintain the high molecular weight of PGA during fermentation. Our result showed that the weight average molecular weight (Mw) of PGA of Bacillus licheniformis ATCC 9945 cultivated in the media containing PTS-sugars were higher than the medium containing glycerol (non-PTS). The result of metabolome analysis indicated the possibility of CodY (a global regulator protein) activation in the cells cultivated in the media containing PTS-sugars. To mimic this effect, branched-chain amino acids (BCAAs), which are activators of CodY, were added to a medium containing glycerol. As the result, the Mw of PGA in the BCAAs-supplemented media were maintained and high during the early production phase compared to the non BCAAs-supplemented medium. These results indicate that BCAAs can repress the PGA molecular weight reduction during fermentation in B. licheniformis ATCC 9945. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Calculating the surface tension of binary solutions of simple fluids of comparable size

NASA Astrophysics Data System (ADS)

Zaitseva, E. S.; Tovbin, Yu. K.

2017-11-01

A molecular theory based on the lattice gas model (LGM) is used to calculate the surface tension of one- and two-component planar vapor-liquid interfaces of simple fluids. Interaction between nearest neighbors is considered in the calculations. LGM is applied as a tool of interpolation: the parameters of the model are corrected using experimental surface tension data. It is found that the average accuracy of describing the surface tension of pure substances (Ar, N2, O2, CH4) and their mixtures (Ar-O2, Ar-N2, Ar-CH4, N2-CH4) does not exceed 2%.

Note: Nonpolar solute partial molar volume response to attractive interactions with water.

PubMed

Williams, Steven M; Ashbaugh, Henry S

2014-01-07

The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

Note: Nonpolar solute partial molar volume response to attractive interactions with water

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

Williams, Steven M.; Ashbaugh, Henry S., E-mail: hanka@tulane.edu

2014-01-07

The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

Characterization of nanoporous shales with gas sorption

NASA Astrophysics Data System (ADS)

Joewondo, N.; Prasad, M.

2017-12-01

The understanding of the fluid flow in porous media requires the knowledge of the pore system involved. Fluid flow in fine grained shales falls under different regime than transport regime in conventional reservoir due to the different average pore sizes in the two materials; the average pore diameter of conventional sandstones is on the micrometer scale, while of shales can be as small as several nanometers. Mercury intrusion porosimetry is normally used to characterize the pores of conventional reservoir, however with increasingly small pores, the injection pressure required to imbibe the pores becomes infinitely large due to surface tension. Characterization of pores can be expressed by a pore size distribution (PSD) plot, which reflects distribution of pore volume or surface area with respect to pore size. For the case of nanoporous materials, the surface area, which serves as the interface between the rock matrix and fluid, becomes increasingly large and important. Physisorption of gas has been extensively studied as a method of nanoporous solid characterization (particularly for the application of catalysis, metal organic frameworks, etc). The PSD is obtained by matching the experimental result to the calculated theoretical result (using Density Functional Theory (DFT), a quantum mechanics based modelling method for molecular scale interactions). We present the challenges and experimental result of Nitrogen and CO2 gas sorption on shales with various mineralogy and the interpreted PSD obtained by DFT method. Our result shows significant surface area contributed by the nanopores of shales, hence the importance of surface area measurements for the characterization of shales.

Influence of Natural Organic Matter (NOM) Character on the Distribution of Chlorinated and Chloraminated Disinfection By-Products (DBPs) at Rand Water

NASA Astrophysics Data System (ADS)

Marais, Savia S.; Ncube, Esper J.; Haarhoff, Johannes; Msagati, Titus AM; Mamba, Bhekie B.; Nkambule, Thabo I.

2016-04-01

Certain disinfection by-products (DBPs) are likely human carcinogens or present mutagenic effects while many DBPs are unidentified. Considering the possibility of DBPs being harmful to human health and the fact that trihalomethanes (THMs) are the only regulated DBP in the South African National Standard (SANS:241) for drinking water, special interest in the precursors to these DBPs' formation is created. It is essential to understand the reactivity and character of the precursors responsible for the formation of DBPs in order to enhance precursor removal strategies during the treatment of drinking water. In this study the character of NOM within surface water and the subsequent distribution of THMs formed in the drinking water from Rand Waters' full scale treatment plant were investigated. Molecular size distribution (MSD) of NOM within the surface water was determined by high performance size exclusion chromatography (HPSEC). Specific ultraviolet absorbance (SUVA) and UV254 measurements formed part of the NOM character study as they provide an indication of the aromaticity of organic matter. The four THMs; bromoform, chloroform, dibromochloromethane (DBCM) and bromodichloromethane (BDCM)were measured by gas chromatography. The sum of these four THMs was expressed as total trihalomethane (TTHM). On average the chloroform constituted 76.2% of the total TTHM, BDCM 22.5% while DBCM and bromoform measured below the detection limit. THM speciation after chlorination and chloramination concentrations increased in the sequence bromoform < DBCM < BDCM < chloroform. Results of the MSD showed a significant correlation between NOM of high molecular size (peak I) and TTHM formation specifically during the summer months (R2= 0.971, p < 0.05). High molecular weight (HMW) NOM also related well to chloroform formation (R2 = 0.963, p < 0.05) however, the formation of BDCM was not due to HWM fraction as indicated by weak regression coefficient. A positive correlation existed between SUVA and UV254 removal percentage (R2 = 0.937, p < 0.05). Seasonal variability in NOM character was evident in the source water in summer when high temperatures and rainfall occurred. The results displayed are an indication that aromatic NOM were the main precursor to TTHM formation, more prominently during summer. Keywords: disinfection by-products, molecular size distribution, natural organic matter, UV254

Micropore analysis of polymer networks by gas sorption and 129Xe NMR spectroscopy: toward a better understanding of intrinsic microporosity.

PubMed

Weber, Jens; Schmidt, Johannes; Thomas, Arne; Böhlmann, Winfried

2010-10-05

The microporosity of two microporous polymer networks is investigated in detail. Both networks are based on a central spirobifluorene motif but have different linker groups, namely, imide and thiophene units. The microporosity of the networks is based on the "polymers of intrinsic microporosity (PIM)" design strategy. Nitrogen, argon, and carbon dioxide were used as sorbates in order to analyze the microporosity in greater detail. The gas sorption data was analyzed with respect to important parameters such as specific surface area, pore volume, and pore size (distribution). It is shown that the results can be strongly model dependent and swelling effects have to be regarded. (129)Xe NMR was used as an independent technique for the estimation of the average pore size of the polymer networks. The results indicate that both networks are mainly ultramicroporous (pore sizes < 0.8 nm) in the dry state, which was not expected based on the molecular design. Phase separation and network defects might influence the overall network morphology strongly. Finally, the observed swelling indicates that this "soft" microporous matter might have a different micropore size in the solvent swollen/filled state that in the dry state.

Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size.

PubMed

Pathak, Ashish K; Singh, Sudhir P; Gupta, Yogesh; Gurjar, Anoop K S; Mantri, Shrikant S; Tuli, Rakesh

2016-11-08

Litchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.

A Kennicutt-Schmidt relation at molecular cloud scales and beyond

NASA Astrophysics Data System (ADS)

Khoperskov, Sergey A.; Vasiliev, Evgenii O.

2017-06-01

Using N-body/gasdynamic simulations of a Milky Way-like galaxy, we analyse a Kennicutt-Schmidt (KS) relation, Σ _SFR ∝ Σ _gas^N, at different spatial scales. We simulate synthetic observations in CO lines and ultraviolet (UV) band. We adopt the star formation rate (SFR) defined in two ways: based on free fall collapse of a molecular cloud - ΣSFR, cl, and calculated by using a UV flux calibration - ΣSFR,UV. We study a KS relation for spatially smoothed maps with effective spatial resolution from molecular cloud scales to several hundred parsecs. We find that for spatially and kinematically resolved molecular clouds the Σ _{SFR, cl} ∝ σ _{gas}^N relation follows the power law with index N ≈ 1.4. Using UV flux as SFR calibrator, we confirm a systematic offset between the ΣSFR,UV and Σgas distributions on scales compared to molecular cloud sizes. Degrading resolution of our simulated maps for surface densities of gas and SFRs, we establish that there is no relation ΣSFR,UV -Σgas below the resolution ˜50 pc. We find a transition range around scales ˜50-120 pc, where the power-law index N increases from 0 to 1-1.8 and saturates for scales larger ˜120 pc. A value of the index saturated depends on a surface gas density threshold and it becomes steeper for higher Σgas threshold. Averaging over scales with size of ≳ 150 pc the power-law index N equals 1.3-1.4 for surface gas density threshold ˜5 M⊙ pc-2. At scales ≳ 120 pc surface SFR densities determined by using CO data and UV flux, ΣSFR,UV/SFR, cl, demonstrate a discrepancy about a factor of 3. We argue that this may be originated from overestimating (constant) values of conversion factor, star formation efficiency or UV calibration used in our analysis.

A molecular dynamics study of water nucleation using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Pérez, Alejandro; Rubio, Angel

2011-12-01

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

Characterization of organic aerosol in fine particles in a mega-city of South China: Molecular composition, seasonal variation, and size distribution

NASA Astrophysics Data System (ADS)

Huang, Xiao-Feng; Chen, Dong-Lei; Lan, Zi-Juan; Feng, Ning; He, Ling-Yan; Yu, Guang-He; Luan, Sheng-Ji

2012-10-01

A one-year-long observation on major organic compounds in PM2.5 was performed in a coastal mega-city in South China, Shenzhen, in order to gain information of their ambient concentration levels and the implications for sources. The compounds identified included alkanes, PAHs, hopanes, fatty acids and dicarboxylic acids, whose annual average concentrations during the year were 56.0, 14.8, 2.51, 253, and 25.2 ng m- 3, respectively. The seasonal molecular distributions of these organic compounds were discussed to explore their contributing sources in Shenzhen. Conclusively, alkanes and PAHs had the dominant source of fossil fuel combustion, although alkanes also had significant contribution from plant wax (~ 16%). The hopane series distributions further indicated that vehicle emissions were the dominant fossil fuel combustion source for PM2.5 in Shenzhen. Cooking emissions were inferred to be the most possible main source for fatty acids, while both primary and secondary origins were implied for azelaic acid, the dominant one in the dicarboxylic acids identified. Most of the organic compounds analyzed showed a size distribution pattern peaking at 0.32-0.56 or 0.56-1 μm in the accumulation mode, except that the cooking-related organic acids showed implication of a coarse mode-dominated pattern.

Homogeneous SPC/E water nucleation in large molecular dynamics simulations.

PubMed

Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K; Tanaka, Hidekazu

2015-08-14

We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10(6) molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10(19) cm(-3) s(-1), helping close the gap between experimentally measured rates ∼ 10(17) cm(-3) s(-1). We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.

Effect of thermal treatment on potato starch evidenced by EPR, XRD and molecular weight distribution.

PubMed

Bidzińska, Ewa; Michalec, Marek; Pawcenis, Dominika

2015-12-01

Effect of heating of the potato starch on damages of its structure was investigated by quantitative electron paramagnetic resonance (EPR) spectroscopy, X-ray diffraction and determination of the molecular weight distribution. The measurements were performed in the temperature range commonly used for starch modifications optimizing properties important for industrial applications. Upon thermal treatment, because of breaking of the polymer chains, diminishing of the average molecular weights occurred, which significantly influences generation of radicals, evidenced by EPR. For the relatively mild conditions, with heating parameters not exceeding temperature 230 °C and time of heating equal to 30 min a moderate changes of both the number of thermally generated radicals and the mean molecular weight of the starch were observed. After more drastic thermal treatment (e.g. 2 h at 230 °C), a rapid increase in the radical amount occurred, which was accompanied by significant reduction of the starch molecular size and crystallinity. Experimentally established threshold values of heating parameters should not be exceeded in order to avoid excessive damages of the starch structure accompanied by the formation of the redundant amount of radicals. This requirement is important for industrial applications, because significant destruction of the starch matrix might annihilate the positive influence of the previously performed intentional starch modification. Copyright © 2015 John Wiley & Sons, Ltd.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

PubMed

Wang, Junmei; Hou, Tingjun

2011-12-01

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. Copyright © 2011 Wiley Periodicals, Inc.

Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses.

PubMed

Sharma, Deepali; Ashaduzzaman, Md; Golabi, Mohsen; Shriwastav, Amritanshu; Bisetty, Krishna; Tiwari, Ashutosh

2015-11-04

Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80-125 nm, surface area 20.27 m(2)/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antibacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antibacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electron spectroscopy (SEM) observation showed that the ZnO NHs ruptured the cell wall of bacteria and internalized into the cell. The molecular docking studies were carried out using binding proteins present in the gram negative bacteria (lipopolysaccharide and lipocalin Blc) and gram positive bacteria (Staphylococcal Protein A, SpA). It was envisaged that the proteins present in the bacterial cell wall were found to interact and adsorb on the surface of SIZnO NHs thereby blocking the active sites of the proteins used for cell wall synthesis. The binding affinity and interaction energies were higher in the case of binding proteins present in gram negative bacteria as compared to that of gram positive bacteria. In addition, a kinetic mathematical model (KMM) was developed in MATLAB to predict the internalization in the bacterial cellular uptake of the ZnO NHs for better understanding of their controlled toxicity. The results obtained from KMM exhibited a good agreement with the experimental data. Exploration of mechanistic interactions, as well as the formation of bioconjugate of proteins and ZnO NHs would play a key role to interpret more complex biological systems in nature.

Optical-NIR dust extinction towards Galactic O stars

NASA Astrophysics Data System (ADS)

Maíz Apellániz, J.; Barbá, R. H.

2018-05-01

Context. O stars are excellent tracers of the intervening ISM because of their high luminosity, blue intrinsic SED, and relatively featureless spectra. We are currently conducting the Galactic O-Star Spectroscopic Survey (GOSSS), which is generating a large sample of O stars with accurate spectral types within several kpc of the Sun. Aims: We aim to obtain a global picture of the properties of dust extinction in the solar neighborhood based on optical-NIR photometry of O stars with accurate spectral types. Methods: We have processed a carefully selected photometric set with the CHORIZOS code to measure the amount [E(4405 - 5495)] and type [R5495] of extinction towards 562 O-type stellar systems. We have tested three different families of extinction laws and analyzed our results with the help of additional archival data. Results: The Maíz Apellániz et al. (2014, A&A, 564, A63) family of extinction laws provides a better description of Galactic dust that either the Cardelli et al. (1989, ApJ, 345, 245) or Fitzpatrick (1999, PASP, 111, 63) families, so it should be preferentially used when analysing samples similar to the one in this paper. In many cases O stars and late-type stars experience similar amounts of extinction at similar distances but some O stars are located close to the molecular clouds left over from their births and have larger extinctions than the average for nearby late-type populations. In qualitative terms, O stars experience a more diverse extinction than late-type stars, as some are affected by the small-grain-size, low-R5495 effect of molecular clouds and others by the large-grain-size, high-R5495 effect of H II regions. Late-type stars experience a narrower range of grain sizes or R5495, as their extinction is predominantly caused by the average, diffuse ISM. We propose that the reason for the existence of large-grain-size, high-R5495 regions in the ISM in the form of H II regions and hot-gas bubbles is the selective destruction of small dust grains by EUV photons and possibly by thermal sputtering by atoms or ions. Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/613/A9

Statistical errors in molecular dynamics averages

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

Schiferl, S.K.; Wallace, D.C.

1985-11-15

A molecular dynamics calculation produces a time-dependent fluctuating signal whose average is a thermodynamic quantity of interest. The average of the kinetic energy, for example, is proportional to the temperature. A procedure is described for determining when the molecular dynamics system is in equilibrium with respect to a given variable, according to the condition that the mean and the bandwidth of the signal should be sensibly constant in time. Confidence limits for the mean are obtained from an analysis of a finite length of the equilibrium signal. The role of serial correlation in this analysis is discussed. The occurence ofmore » unstable behavior in molecular dynamics data is noted, and a statistical test for a level shift is described.« less

Synthesis and Characterisation of Photocrosslinked poly(ethylene glycol) diacrylate Implants for Sustained Ocular Drug Delivery.

PubMed

McAvoy, Kathryn; Jones, David; Thakur, Raghu Raj Singh

2018-01-16

To investigate the sustained ocular delivery of small and large drug molecules from photocrosslinked poly(ethylene glycol) diacrylate (PEGDA) implants with varying pore forming agents. Triamcinolone acetonide and ovalbumin loaded photocrosslinked PEGDA implants, with or without pore-forming agents, were fabricated and characterised for chemical, mechanical, swelling, network parameters, as well as drug release and biocompatibility. HPLC-based analytical methods were employed for analysis of two molecules; ELISA was used to demonstrate bioactivity of ovalbumin. Regardless of PEGDA molecular weight or pore former composition all implants loaded with triamcinolone acetonide released significantly faster than those loaded with ovalbumin. Higher molecular weight PEGDA systems (700 Da) resulted in faster drug release of triamcinolone acetonide than their 250 Da counterpart. All ovalbumin released over the 56-day time period was found to be bioactive. Increasing PEGDA molecular weight resulted in increased system swelling, decreased crosslink density (Ve), increased polymer-water interaction parameter (χ), increased average molecular weight between crosslinks (Mc) and increased mesh size (ε). SEM studies showed the porosity of implants increased with increasing PEGDA molecular weight. Biocompatibility showed both PEGDA molecular weight implants were non-toxic when exposed to retinal epithelial cells over a 7-day period. Photocrosslinked PEGDA implant based systems are capable of controlled drug release of both small and large drug molecules through adaptations in the polymer system network. We are currently continuing evaluation of these systems as potential sustained drug delivery devices.

Neurological and endocrine phenotypes of fragile X carrier women.

PubMed

Hall, D; Todorova-Koteva, K; Pandya, S; Bernard, B; Ouyang, B; Walsh, M; Pounardjian, T; Deburghraeve, C; Zhou, L; Losh, M; Leehey, M; Berry-Kravis, E

2016-01-01

Women who carry fragile X mental retardation 1 (FMR1)gene premutation expansions frequently report neurological or endocrine symptoms and prior studies have predominantly focused on questionnaire report of medical issues. Premutation carrier (PMC) women (n = 33) and non-carrier controls (n = 13) were recruited and evaluated by a neurologist, neuropsychologist, and endocrinologist. Blood and skin biopsies were collected for molecular measures. Scales for movement disorders, neuropathy, cognitive function, psychiatric symptoms, sleep, and quality of life were completed. The average age of the women was 51 years (n = 46) and average CGG repeat size was 91 ± 24.9 in the FMR1 PMC women. Seventy percent of the PMC women had an abnormal neurological examination. PMC women had significantly higher scores on the Fragile X-Associated Tremor Ataxia Syndrome (FXTAS) rating scale, more neuropathy, and difficulty with tandem gait compared to controls. Central sensitivity syndromes, a neuroticism profile on the NEO Personality Profile, and sleep disorders were also prevalent. Discrepancies between subject report and examination findings were also seen. This pilot study suggests that women with the FMR1 premutation may have a phenotype that overlaps with that seen in FXTAS. Additional research with larger sample sizes is warranted to better delineate the clinical features. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Solubility Enhancement of a Poorly Water Soluble Drug by Forming Solid Dispersions using Mechanochemical Activation

PubMed Central

Rojas-Oviedo, I.; Retchkiman-Corona, B.; Quirino-Barreda, C. T.; Cárdenas, J.; Schabes-Retchkiman, P. S.

2012-01-01

Mechanochemical activation is a practical cogrinding operation used to obtain a solid dispersion of a poorly water soluble drug through changes in the solid state molecular aggregation of drug-carrier mixtures and the formation of noncovalent interactions (hydrogen bonds) between two crystalline solids such as a soluble carrier, lactose, and a poorly soluble drug, indomethacin, in order to improve its solubility and dissolution rate. Samples of indomethacin and a physical mixture with a weight ratio of 1:1 of indomethacin and lactose were ground using a high speed vibrating ball mill. Particle size was determined by electron microscopy, the reduction of crystallinity was determined by calorimetry and transmission electron microscopy, infrared spectroscopy was used to find evidence of any interactions between the drug and the carrier and the determination of apparent solubility allowed for the corroboration of changes in solubility. Before grinding, scanning electron microscopy showed the drug and lactose to have an average particle size of around 50 and 30 μm, respectively. After high speed grinding, indomethacin and the mixture had a reduced average particle size of around 5 and 2 μm, respectively, showing a morphological change. The ground mixture produced a solid dispersion that had a loss of crystallinity that reached 81% after 30 min of grinding while the drug solubility of indomethacin within the solid dispersion increased by 2.76 fold as compared to the pure drug. Drug activation due to hydrogen bonds between the carboxylic group of the drug and the hydroxyl group of lactose as well as the decrease in crystallinity of the solid dispersion and the reduction of the particle size led to a better water solubility of indomethacin. PMID:23798775

Biosynthesis and characterization of zinc, magnesium and titanium nanoparticles: an eco-friendly approach

NASA Astrophysics Data System (ADS)

Raliya, Ramesh; Tarafdar, J. C.

2014-02-01

In the present study, zinc (Zn), magnesium (Mg) and titanium (Ti) nanoparticles synthesized using fungus by employing various precursor salts of sulfate salts, nitrate salts, chloride salts and oxide salts. To access the nanoparticle production potential, over a hundreds of fungi were isolated from the soil and tested with precursor salts of the Zn, Mg and Ti. Out of which, only 14 fungal isolates were identified, having potential to reduce metal salt into metal nanoparticles. Upon molecular identification, six were identified as Aspergillus flavus, two each as Aspergillus terreus and Aspergillus tubingensis and one each as Aspergillus niger, Rhizoctonia bataticola, Aspergillus fumigatus, and Aspergillus oryzae. Factors responsible for more production of monodispersed Zn, Mg and Ti nanoparticles were optimized. It was concluded that 0.01 mM precursor salt concentration, 72 h of incubation at pH 5.5 and temperature 28 °C resulted smaller nanoparticles obtained. The biosynthesized functional Zn and Ti nanoparticles can be stored up to 90 days and Mg nanoparticles up to 105 days in its nanoform. Bio-transformed products were analyzed using valid characterization technique i.e. dynamic light scattering, transmission electron microscopy, atomic force microscopy, energy dispersive X-ray spectroscopy to confirm size, shape, surface morphology and elemental composition. It was found that the average size of developed nano Zn was 8.2 nm, with surface charge of -5.70 mV and 98 % particles were of Zn metal only. Similarly, the average size of Mg nanoparticles was 6.4 nm with surface charge of -6.66 and 97.4 % Mg metal yield, whereas, Ti nanoparticles size were found in the ranges between 1.5 and 30 nm with surface charge of -6.25 mV and 98.6 % Ti metal yield.

Transport of dissolved organic matter in Boom Clay: Size effects

NASA Astrophysics Data System (ADS)

Durce, D.; Aertsens, M.; Jacques, D.; Maes, N.; Van Gompel, M.

2018-01-01

A coupled experimental-modelling approach was developed to evaluate the effects of molecular weight (MW) of dissolved organic matter (DOM) on its transport through intact Boom Clay (BC) samples. Natural DOM was sampled in-situ in the BC layer. Transport was investigated with percolation experiments on 1.5 cm BC samples by measuring the outflow MW distribution (MWD) by size exclusion chromatography (SEC). A one-dimensional reactive transport model was developed to account for retardation, diffusion and entrapment (attachment and/or straining) of DOM. These parameters were determined along the MWD by implementing a discretisation of DOM into several MW points and modelling the breakthrough of each point. The pore throat diameter of BC was determined as 6.6-7.6 nm. Below this critical size, transport of DOM is MW dependent and two major types of transport were identified. Below MW of 2 kDa, DOM was neither strongly trapped nor strongly retarded. This fraction had an averaged capacity factor of 1.19 ± 0.24 and an apparent dispersion coefficient ranging from 7.5 × 10- 11 to 1.7 × 10- 11 m2/s with increasing MW. DOM with MW > 2 kDa was affected by both retardation and straining that increased significantly with increasing MW while apparent dispersion coefficients decreased. Values ranging from 1.36 to 19.6 were determined for the capacity factor and 3.2 × 10- 11 to 1.0 × 10- 11 m2/s for the apparent dispersion coefficient for species with 2.2 kDa < MW < 9.3 kDa. Straining resulted in an immobilisation of in average 49 ± 6% of the injected 9.3 kDa species. Our findings show that an accurate description of DOM transport requires the consideration of the size effects.

Nano-fabrication of molecular electronic junctions by targeted modification of metal-molecule bonds

NASA Astrophysics Data System (ADS)

Jafri, S. Hassan M.; Löfås, Henrik; Blom, Tobias; Wallner, Andreas; Grigoriev, Anton; Ahuja, Rajeev; Ottosson, Henrik; Leifer, Klaus

2015-09-01

Reproducibility, stability and the coupling between electrical and molecular properties are central challenges in the field of molecular electronics. The field not only needs devices that fulfill these criteria but they also need to be up-scalable to application size. In this work, few-molecule based electronics devices with reproducible electrical characteristics are demonstrated. Our previously reported 5 nm gold nanoparticles (AuNP) coated with ω-triphenylmethyl (trityl) protected 1,8-octanedithiol molecules are trapped in between sub-20 nm gap spacing gold nanoelectrodes forming AuNP-molecule network. When the trityl groups are removed, reproducible devices and stable Au-thiol junctions are established on both ends of the alkane segment. The resistance of more than 50 devices is reduced by orders of magnitude as well as a reduction of the spread in the resistance histogram is observed. By density functional theory calculations the orders of magnitude decrease in resistance can be explained and supported by TEM observations thus indicating that the resistance changes and strongly improved resistance spread are related to the establishment of reproducible and stable metal-molecule bonds. The same experimental sequence is carried out using 1,6-hexanedithiol functionalized AuNPs. The average resistances as a function of molecular length, demonstrated herein, are comparable to the one found in single molecule devices.

Mesoporous Polymer Frameworks from End-Reactive Bottlebrush Copolymers

DOE PAGES

Altay, Esra; Nykypanchuk, Dmytro; Rzayev, Javid

2017-08-07

Reticulated nanoporous materials generated by versatile molecular framework approaches are limited to pore dimensions on the scale of the utilized rigid molecular building blocks (<5 nm). The inherent flexibility of linear polymers precludes their utilization as long framework connectors for the extension of this strategy to larger length scales. We report a method for the fabrication of mesoporous frameworks by using bottlebrush copolymers with reactive end blocks serving as rigid macromolecular interconnectors with directional reactivity. End-reactive bottlebrush copolymers with pendant alkene functionalities were synthesized by a combination of controlled radical polymerization and polymer modification protocols. Ru-catalyzed cross-metathesis cross-linking of bottlebrushmore » copolymers with two reactive end blocks resulted in the formation of polymer frameworks where isolated cross-linked domains were interconnected with bottlebrush copolymer bridges. The resulting materials were characterized by a continuous network pore structure with average pore sizes of 9–50 nm, conveniently tunable by the length of the utilized bottlebrush copolymer building blocks. As a result, the materials fabrication strategy described in this work expands the length scale of molecular framework materials and provides access to mesoporous polymers with a molecularly tunable reticulated pore structure without the need for templating, sacrificial component etching, or supercritical fluid drying.« less

Biodegradability enhancement and detoxification of cork processing wastewater molecular size fractions by ozone.

PubMed

Santos, Diana C; Silva, Lúcia; Albuquerque, António; Simões, Rogério; Gomes, Arlindo C

2013-11-01

Cork boiling wastewater pollutants were fractionated by sequential use of four ultrafiltration membranes and five fractions were obtained: four retentates (>100, 50-100, 20-50 and 10-20 kDa) and one permeate (<10 kDa); which were used to study the correlation of molecular size with biodegradability and toxicity before and after ozonation. The results show that molecular size is correlated with organic load and restrains biodegradability. The fraction with >100 kDa corresponds to 56% of the organic load and the one with <10 kDa only 8%. The biodegradability of fractions increased 182% with fractions molecular size reduction from >100 to <10 kDa and the chemical oxygen demand (COD) was from 3436 to 386 mg L(-1). For biodegradability enhancement the best outcome of ozonation was obtained with compounds having molecular size >20 kDa and range from 5% up to 175% for applied ozone doses to COD ratios between 0.15 and 0.38. Copyright © 2013 Elsevier Ltd. All rights reserved.

The macroevolution of size and complexity in insect male genitalia

PubMed Central

Rudoy, Andrey

2016-01-01

The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables. PMID:27114865

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

PubMed

Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

2016-07-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

Molecular weight of Escherichia coli β-galactosidase in concentrated solutions of guanidine hydrochloride

PubMed Central

Erickson, Robert P.

1970-01-01

The molecular weight of Escherichia coli β-galactosidase was determined in 6m- and 8m-guanidine hydrochloride by meniscus-depletion sedimentation equilibrium, sedimentation velocity and viscosity. Sedimentation equilibrium revealed heterogeneity with the smallest component having a molecular weight of about 50000. At lower speeds, the apparent weight-average molecular weight is about 80000. By use of a calculation based on an empirical correlation for proteins that are random coils in 6m-guanidine hydrochloride, sedimentation velocity gave a molecular weight of 91000, and the intrinsic viscosity indicated a viscosity-average molecular weight of 84000. Heating in 6m-guanidine hydrochloride lowered the viscosity of β-galactosidase in a variable manner. PMID:4924171

Strategies to indium nitride and gallium nitride nanoparticles: Low-temperature, solution-phase and precursor routes

NASA Astrophysics Data System (ADS)

Dingman, Sean Douglas

I present new strategies to low-temperature solution-phase synthesis of indium and gallium nitride (InN and GaN) ceramic materials. The strategies include: direct conversion of precursor molecules to InN by pyrolysis, solution-phase synthesis of nanostructured InN fibers via molecular precursors and co-reactants, and synthesis of powders through reactions derived from molten-salt chemistry. Indium nitride powders are prepared by pyrolysis of the precursors R 2InN3 (R = t-Bu (1), i-Amyl(2), Et(3), i-Pr( 4)). The precursors are synthesized via azide-alkoxide exchange of R2InOMe with Me3SiN3. The precursors are coordination polymers containing five-coordinate indium centers. Pyrolysis of 1 and 2 under N2 at 400°C yields powders consisting primarily of InN with average crystal sizes of 15--35 nm. 1 yields nanocrystalline InN with average particle sizes of 7 nm at 250°C. 3 and 4 yield primarily In metal from pyrolysis. Refluxing 1 in diisopropylbenzene (203°C) in the presence of primary amines yields InN nanofibers 10--100 nm in length. InN nanofibers of up to 1 mum can be synthesized by treating 1 with 1,1-dimethylhydrazine (DMHy) The DMHy appears to control the fiber length by acting as a secondary source of active nitrogen in order to sustain fiber growth. The resulting fibers are attached to droplets of indium metal implying a solution-liquid-solid growth mechanism. Precursor 4 yields crystalline InN whiskers when reacted with DMHy. Reactions of 4 with reducing agents such as HSnBu3, yield InN nanoparticles with an average crystallite size of 16 nm. Gallium precursors R2GaN3 (R = t-Bu( 5), Me3SiCH2(6) and i-Pr( 7)), synthesized by azide-alkoxide exchange, are found to be inert toward solution decomposition and do not yield GaN. These compounds are molecular dimers and trimers unlike the indium analogs. Compound 6 displays a monomer-dimer equilibrium in benzene solution, but exists as a solid-state trimer. InN powders are also synthesized by reactions of InCl3 and LiNH2 in a molten alkali-halide eutectic, KBr: Liar (60:40), at 400°C. The molten salt acts as an appropriate recrystallization medium for InN. Large InN platelets up to 500 nm could be synthesized. This is a significant step in finding mild reaction conditions that yield large InN crystals.

Structural distributions from single-molecule measurements as a tool for molecular mechanics

PubMed Central

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2011-01-01

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ~190 Å, ~67 Å, ~51 Å, and ~76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules. PMID:22661822

Convergence and approximate calculation of average degree under different network sizes for decreasing random birth-and-death networks

NASA Astrophysics Data System (ADS)

Long, Yin; Zhang, Xiao-Jun; Wang, Kui

2018-05-01

In this paper, convergence and approximate calculation of average degree under different network sizes for decreasing random birth-and-death networks (RBDNs) are studied. First, we find and demonstrate that the average degree is convergent in the form of power law. Meanwhile, we discover that the ratios of the back items to front items of convergent reminder are independent of network link number for large network size, and we theoretically prove that the limit of the ratio is a constant. Moreover, since it is difficult to calculate the analytical solution of the average degree for large network sizes, we adopt numerical method to obtain approximate expression of the average degree to approximate its analytical solution. Finally, simulations are presented to verify our theoretical results.

Molecular Weight Cut-Off and Structural Analysis of Vacuum-Assisted Titania Membranes for Water Processing

PubMed Central

Abd Jalil, Siti Nurehan; Wang, David K.; Yacou, Christelle; Motuzas, Julius; Smart, Simon; Diniz da Costa, João C.

2016-01-01

This work investigates the structural formation and analyses of titania membranes (TM) prepared using different vacuum exposure times for molecular weight (MW) cut-off performance and oil/water separation. Titania membranes were synthesized via a sol-gel method and coated on macroporous alumina tubes followed by exposure to a vacuum between 30 and 1200 s and then calcined at 400 °C. X-ray diffraction and nitrogen adsorption analyses showed that the crystallite size and particle size of titania increased as a function of vacuum time. All the TM membranes were mesoporous with an average pore diameter of ~3.6 nm with an anatase crystal morphology. Water, glucose, sucrose, and polyvinylpyrrolidone with 40 and 360 kDa (PVP-40 kDa and PVP-360 kDa) were used as feed solutions for MW cut-off and hexadecane solution for oil filtration investigation. The TM membranes were not able to separate glucose and sucrose, thus indicating the membrane pore sizes are larger than the kinetic diameter of sucrose of 0.9 nm, irrespective of vacuum exposure time. They also showed only moderate rejection (20%) of the smaller PVP-40 kDa, however, all the membranes were able to obtain an excellent rejection of near 100% for the larger PVP-360 kDa molecule. Furthermore, the TM membranes were tested for the separation of oil emulsions with a high concentration of oil (3000 ppm), reaching high oil rejections of more than 90% of oil. In general, the water fluxes increased with the vacuum exposure time indicating a pore structural tailoring effect. It is therefore proposed that a mechanism of pore size tailoring was formed by an interconnected network of Ti–O–Ti nanoparticles with inter-particle voids, which increased as TiO2 nanoparticle size increased as a function of vacuum exposure time, and thus reduced the water transport resistance through the TM membranes. PMID:28774057

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis.

PubMed

Estoup, Arnaud; Jarne, Philippe; Cornuet, Jean-Marie

2002-09-01

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

MC3T3-E1 osteoblast attachment and proliferation on porous hydroxyapatite scaffolds fabricated with nanophase powder

PubMed Central

Smith, Ian O; McCabe, Laura R; Baumann, Melissa J

2006-01-01

Porous bone tissue engineering scaffolds were fabricated using both nano hydroxyapatite (nano HA) powder (20 nm average particle size) and micro HA powder (10 μm average particle size), resulting in sintered scaffolds of 59 vol% porosity and 8.6±1.9 μm average grain size and 72 vol% porosity and 588±55 nm average grain size, respectively. Scanning electron microscopy was used to measure both the grain size and pore size. MC3T3-E1 osteoblast (OB) attachment and proliferation on both nano HA and micro HA porous scaffolds were quantified. As expected, OB cell number was greater on nano HA scaffolds compared with similarly processed micro HA scaffolds 5 days after seeding, while OB attachment did not appear greater on the nano HA scaffolds (p<0.05). PMID:17722535

Hydration shell parameters of aqueous alcohols: THz excess absorption and packing density.

PubMed

Matvejev, V; Zizi, M; Stiens, J

2012-12-06

Solvation in water requires minimizing the perturbations in its hydrogen bonded network. Hence solutes distort water molecular motions in a surrounding domain, forming a molecule-specific hydration shell. The properties of those hydration shells impact the structure and function of the solubilized molecules, both at the single molecule and at higher order levels. The size of the hydration shell and the picoseconds time-scale water dynamics retardation are revealed by terahertz (THz) absorption coefficient measurements. Room-temperature absorption coefficient at f = 0.28 [THz] is measured as a function of alcohol concentration in aqueous methanol, ethanol, 1,2-propanol, and 1-butanol solutions. Highly diluted alcohol measurements and enhanced overall measurement accuracy are achieved with a THz absorption measurement technique of nL-volume liquids in a capillary tube. In the absorption analysis, bulk and interfacial molecular domains of water and alcohol are considered. THz ideal and excess absorption coefficients are defined in accordance with thermodynamics mixing formulations. The parameter extraction method is developed based on a THz excess absorption model and hydrated solute molecule packing density representation. First, the hydration shell size is deduced from the hydrated solute packing densities at two specific THz excess absorption nonlinearity points: at infinite alcohol dilution (IAD) and at the THz excess absorption extremum (EAE). Consequently, interfacial water and alcohol molecular domain absorptions are deduced from the THz excess absorption model. The hydration shell sizes obtained at the THz excess absorption extremum are in excellent agreement with other reports. The hydration shells of methanol, ethanol, 1- and 2-propanol consist of 13.97, 22.94, 22.99, and 31.10 water molecules, respectively. The hydration shell water absorption is on average 0.774 ± 0.028 times the bulk water absorption. The hydration shell parameters might shed light on hydration dynamics of biomolecules.

A Phase Field Study of the Effect of Microstructure Grain Size Heterogeneity on Grain Growth

NASA Astrophysics Data System (ADS)

Crist, David J. D.

Recent studies conducted with sharp-interface models suggest a link between the spatial distribution of grain size variance and average grain growth rate. This relationship and its effect on grain growth rate was examined using the diffuse-interface Phase Field Method on a series of microstructures with different degrees of grain size gradation. Results from this work indicate that the average grain growth rate has a positive correlation with the average grain size dispersion for phase field simulations, confirming previous observations. It is also shown that the grain growth rate in microstructures with skewed grain size distributions is better measured through the change in the volume-weighted average grain size than statistical mean grain size. This material is based upon work supported by the National Science Foundation under Grant No. 1334283. The NSF project title is "DMREF: Real Time Control of Grain Growth in Metals" and was awarded by the Civil, Mechanical and Manufacturing Innovation division under the Designing Materials to Revolutionize and Engineer our Future (DMREF) program.

Effect of heterogeneity on the characterization of cell membrane compartments: I. Uniform size and permeability.

PubMed

Hall, Damien

2010-03-15

Observations of the motion of individual molecules in the membrane of a number of different cell types have led to the suggestion that the outer membrane of many eukaryotic cells may be effectively partitioned into microdomains. A major cause of this suggested partitioning is believed to be due to the direct/indirect association of the cytosolic face of the cell membrane with the cortical cytoskeleton. Such intimate association is thought to introduce effective hydrodynamic barriers into the membrane that are capable of frustrating molecular Brownian motion over distance scales greater than the average size of the compartment. To date, the standard analytical method for deducing compartment characteristics has relied on observing the random walk behavior of a labeled lipid or protein at various temporal frequencies and different total lengths of time. Simple theoretical arguments suggest that the presence of restrictive barriers imparts a characteristic turnover to a plot of mean squared displacement versus sampling period that can be interpreted to yield the average dimensions of the compartment expressed as the respective side lengths of a rectangle. In the following series of articles, we used computer simulation methods to investigate how well the conventional analytical strategy coped with heterogeneity in size, shape, and barrier permeability of the cell membrane compartments. We also explored questions relating to the necessary extent of sampling required (with regard to both the recorded time of a single trajectory and the number of trajectories included in the measurement bin) for faithful representation of the actual distribution of compartment sizes found using the SPT technique. In the current investigation, we turned our attention to the analytical characterization of diffusion through cell membrane compartments having both a uniform size and permeability. For this ideal case, we found that (i) an optimum sampling time interval existed for the analysis and (ii) the total length of time for which a trajectory was recorded was a key factor. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Prediction of boiling points of organic compounds by QSPR tools.

PubMed

Dai, Yi-min; Zhu, Zhi-ping; Cao, Zhong; Zhang, Yue-fei; Zeng, Ju-lan; Li, Xun

2013-07-01

The novel electro-negativity topological descriptors of YC, WC were derived from molecular structure by equilibrium electro-negativity of atom and relative bond length of molecule. The quantitative structure-property relationships (QSPR) between descriptors of YC, WC as well as path number parameter P3 and the normal boiling points of 80 alkanes, 65 unsaturated hydrocarbons and 70 alcohols were obtained separately. The high-quality prediction models were evidenced by coefficient of determination (R(2)), the standard error (S), average absolute errors (AAE) and predictive parameters (Qext(2),RCV(2),Rm(2)). According to the regression equations, the influences of the length of carbon backbone, the size, the degree of branching of a molecule and the role of functional groups on the normal boiling point were analyzed. Comparison results with reference models demonstrated that novel topological descriptors based on the equilibrium electro-negativity of atom and the relative bond length were useful molecular descriptors for predicting the normal boiling points of organic compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular simulation of fluid adsorption in buckytubes and MCM-41

NASA Astrophysics Data System (ADS)

Maddox, M. W.; Gubbins, K. E.

1994-11-01

We report grand canonical Monte Carlo (GCMC) molecular-simulation studies of argon and nitrogen in models of two novel adsorbents, buckytubes and MCM-41. Buckytubes are monodisperse carbon tubes with internal diameters of 1 5 nm and a regular pore structure. MCM-41 is one member of a new family of highly uniform mesoporous aluminosilicates produced by Mobil. The pore size of MCM-41 can be accurately controlled within the range 1.5-I.0 nm. The adsorption of argon in a buckytube and the adsorption of nitrogen in two different MCM-41 pores are studied at 77 K. Both fluids are modeled as Lennard-Jones spheres. and an averaged fluid-wall potential, dependent only on the distance of the adsorbed molecule from the center of the tube or pore is used. Isotherms and isosteric heats are calculated. Layering transitions and a hysteresis loop are observed for the buckytube and good agreement is found between simulated and experimental isotherms for the MCM-41 systems.

Photo-enhanced performance and photo-tunable degradation in LC ecopolymers

NASA Astrophysics Data System (ADS)

Kaneko, Tatsuo

2007-05-01

Photosensitive, liquid crystalline (LC) polymers were prepared by in-bulk polymerization of phytomonomers such as cinnamic acid derivatives. The p-coumaric acid (4HCA) homopolymer showed a thermotropic LC phase where a photoreaction of [2+2] cycloaddition occurred by ultraviolet irradiation. LC phase was exhibited only in a low molecular weight state but the polymer was too brittle to materialize. Then we copolymerized 4HCA with multifunctional cinnamate, 3,4 dihydroxycinnamic acid (caffeic acid; DHCA), to prepare the hyperbranching architecture. Many branches increased the apparent size of the polymer chain but kept the low number-average molecular weight. P(4HCA-co-DHCA)s showed high performances which may be attained through the entanglement by in-bulk formation of hyperbranching, rigid structures. P(4HCA-co-DHCA)s showed a smooth hydrolysis, an in-soil degradation and a photoreaction cross-linking from conjugated cinnamate esters to aliphatic esters. The change in photoconversion degree tuned the polymer performance and chain hydrolysis.

Purification and partial elucidation of the structure of an antioxidant carbohydrate biopolymer from the probiotic bacterium Bacillus coagulans RK-02.

PubMed

Kodali, Vidya P; Perali, Ramu S; Sen, R

2011-08-26

An exopolysaccharide (EPS) was isolated from Bacillus coagulans RK-02 and purified by size exclusion chromatography. The purified, homogeneous EPS had an average molecular weight of ∼3 × 10⁴ Da by comparison with FITC-labeled dextran standards. In vivo evaluations showed that, like other reported polysaccharides, this EPS displayed significant antioxidant activity. FTIR spectroscopy analysis showed the presence of hydroxy, carboxy, and α-glycosidic linkages and a mannose residue. GC analysis indicated that the EPS was a heteropolymer composed of glucose, mannose, galactose, glucosamine, and fucose as monomeric constituent units. Partial elucidation of the structure of the carbohydrate biopolymer based on GC-MS and NMR analysis showed the presence of two unique sets of tetrasaccharide repeating units that have 1→3 and 1→6 glycosidic linkages. This is also the first report of a Gram-positive bacterial polysaccharide with both fucose as a sugar monomer and 1→3 and 1→6 glycosidic linkages in the molecular backbone.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

3D-liquid chromatography as a complex mixture characterization tool for knowledge-based downstream process development.

PubMed

Hanke, Alexander T; Tsintavi, Eleni; Ramirez Vazquez, Maria Del Pilar; van der Wielen, Luuk A M; Verhaert, Peter D E M; Eppink, Michel H M; van de Sandt, Emile J A X; Ottens, Marcel

2016-09-01

Knowledge-based development of chromatographic separation processes requires efficient techniques to determine the physicochemical properties of the product and the impurities to be removed. These characterization techniques are usually divided into approaches that determine molecular properties, such as charge, hydrophobicity and size, or molecular interactions with auxiliary materials, commonly in the form of adsorption isotherms. In this study we demonstrate the application of a three-dimensional liquid chromatography approach to a clarified cell homogenate containing a therapeutic enzyme. Each separation dimension determines a molecular property relevant to the chromatographic behavior of each component. Matching of the peaks across the different separation dimensions and against a high-resolution reference chromatogram allows to assign the determined parameters to pseudo-components, allowing to determine the most promising technique for the removal of each impurity. More detailed process design using mechanistic models requires isotherm parameters. For this purpose, the second dimension consists of multiple linear gradient separations on columns in a high-throughput screening compatible format, that allow regression of isotherm parameters with an average standard error of 8%. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1283-1291, 2016. © 2016 American Institute of Chemical Engineers.

Chitin and Cellulose Processing in Low-Temperature Electron Beam Plasma.

PubMed

Vasilieva, Tatiana; Chuhchin, Dmitry; Lopatin, Sergey; Varlamov, Valery; Sigarev, Andrey; Vasiliev, Michael

2017-11-06

Polysaccharide processing by means of low-temperature Electron Beam Plasma (EBP) is a promising alternative to the time-consuming and environmentally hazardous chemical hydrolysis in oligosaccharide production. The present paper considers mechanisms of the EBP-stimulated destruction of crab shell chitin, cellulose sulfate, and microcrystalline cellulose, as well as characterization of the produced oligosaccharides. The polysaccharide powders were treated in oxygen EBP for 1-20 min at 40 °C in a mixing reactor placed in the zone of the EBP generation. The chemical structure and molecular mass of the oligosaccharides were analyzed by size exclusion and the reversed phase chromatography, FTIR-spectroscopy, XRD-, and NMR-techniques. The EBP action on original polysaccharides reduces their crystallinity index and polymerization degree. Water-soluble products with lower molecular weight chitooligosaccharides (weight-average molecular mass, M w = 1000-2000 Da and polydispersity index 2.2) and cellulose oligosaccharides with polymerization degrees 3-10 were obtained. The ¹H-NMR analysis revealed 25-40% deacetylation of the EBP-treated chitin and FTIR-spectroscopy detected an increase of carbonyl- and carboxyl-groups in the oligosaccharides produced. Possible reactions of β-1,4-glycosidic bonds' destruction due to active oxygen species and high-energy electrons are given.

Particles Growing in Solutions: Depletion Forces and Instability of Homogeneous Particle Distribution

NASA Technical Reports Server (NTRS)

Chernov, A. A.

2004-01-01

Crystallites, droplets and amorphous precipitates growing from supersaturated solution are surrounded by zones, which are depleted with respect to the molecules they are built of. If two such particles of colloidal size are separated by a distance comparable to their diameters, then the depletion within the gap between particles is deeper than that at the outer portion of the particles. This will cause depletion attraction between the particles should appear. It may cause particle coagulation and decay of the originally homogeneous particle distribution into a system of clouds within which the particle number density is higher, separated by the region of the lower number density. Stability criterion, Q = 4 pi R(exp 3)c/3 >> 1, was analytically found along with typical particle density distribution wavevector q = (Q/I)(exp 1/2)(a/R)(exp 1/4). Here, R and a are the particle and molecular radii, respectively, c is the average molecular number density in solution and I is the squared diffusion length covered by a molecule during a typical time characterizing decay of molecular concentration in solution due to consumption of the molecules by the growing particles.

Preferred Molecular Orientation of Coumarin 343 on TiO 2 Surfaces: Application to Dye-Sensitized Solar Cells

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

McCree-Grey, Jonathan; Cole, Jacqueline M.; Evans, Peter J.

2015-07-21

The dye…TiO2 interfacial structure in working electrodes of dye-sensitized solar cells (DSCs) is known to influence its photovoltaic device performance. Despite this, direct and quantitative reports of such structure remain sparse. This case study presents the application of X-ray reflectometry to determine the preferred structural orientation and molecular packing of the organic dye, coumarin 343, adsorbed onto amorphous TiO2. Results show that the dye molecules are, on average, tilted by 61.1° relative to the TiO2 surface, and are separated from each other by 8.2 Å. These findings emulate the molecular packing arrangement of a monolayer of coumarin 343 within itsmore » crystal structure. This suggests that the dye adsorbs onto TiO2 in one of its lowest energy configurations, i.e. dye…TiO2 self assembly is driven more by thermodynamic rather than kinetic means. Complementary DSC device tests illustrate that this interfacial structure compromises photovoltaic performance, unless a suitably sized co-adsorbant is interdispersed between the coumarin 343 chromophores on the TiO2 surface.« less

Molecular gas in elliptical galaxies with dust lanes

NASA Technical Reports Server (NTRS)

Wang, Zhong; Kenney, Jeffrey D. P.; Ishizuki, Sumio

1992-01-01

We have searched for CO(1-0) line emission in eight dust lane elliptical and lenticular galaxies using the Nobeyama 45 m telescope. Five of the eight galaxies, including the well-studied elliptical NGC 1052, have CO emission at above the 5-sigma level, with inferred molecular gas masses ranging from 10 exp 8 to a few times 10 exp 9 solar masses. Our selection criterion differs from previous surveys in that it does not depend on the FIR fluxes, and thus is less sensitive to the sizes and distances of the host galaxies or to the degree to which dust is heated. The relatively high detection rate of CO in these ellipticals suggests a close correlation between molecular mass and cold dust. Compared with previously studied samples of FIR selected early-type galaxies, our sample has on average four times more CO emission per unit FIR (40-120 microns) luminosity. If the intrinsic gas-to-dust ratio of these galaxies as similar to that of the Milky Way, then only about 5 percent of the dust mass in dust lane ellipticals radiates substantially at 60 and 100 microns, and the remaining dust must be colder than about 30 K.

Molecular Subtypes of Indonesian Breast Carcinomas - Lack of Association with Patient Age and Tumor Size

PubMed Central

Rahmawati, Yeni; Setyawati, Yunita; Widodo, Irianiwati; Ghozali, Ahmad; Purnomosari, Dewajani

2018-01-01

Objective: Breast carcinoma (BC) is a heterogeneous disease that exhibits variation in biological behaviour, prognosis and response to therapy. Molecular classification is generally into Luminal A, Luminal B, HER2+ and triple negative/basal-like, depending on receptor characteristics. Clinical factors that determined the BC prognosis are age and tumor size. Since information on molecular subtypes of Indonesian BCs is limited, the present study was conducted, with attention to subtypes in relation to age and tumor size. Methods: A retrospective cross-sectional study of 247 paraffin-embedded samples of invasive BC from Dr. Sardjito General Hospital Yogyakarta in the year 2012- 2015 was performed. Immunohistochemical staining using anti- ER, PR, HER2, Ki-67 and CK 5/6 antibodies was applied to classify molecular subtypes. Associations with age and tumor size were analyzed using the Chi Square Test. Results: The Luminal A was the most common subtype of Indonesian BC (41.3%), followed by triple negative (25.5%), HER2 (19.4%) and luminal B (13.8%). Among the triple negative lesions, the basal-like subtype was more frequent than the non basal-like (58.8 % vs 41.2%). Luminal B accounted for the highest percentage of younger age cases (< 40 years old) while HER2+ was most common in older age (> 50 years old) patients. Triple negative/basal-like were commonly large in size. Age (p = 0.080) and tumor size (p = 0.462) were not significantly associated with molecular subtypes of BC. Conclusion: The most common molecular subtype of Indonesian BC is luminal A, followed by triple-negative, HER2+ and luminal B. The majority of triple-negative lesions are basal-like. There are no association between age and tumor size with molecular subtypes of Indonesian BCs. PMID:29373908

Molecular Subtypes of Indonesian Breast Carcinomas - Lack of Association with Patient Age and Tumor Size

PubMed

Rahmawati, Yeni; Setyawati, Yunita; Widodo, Irianiwati; Ghozali, Ahmad; Purnomosari, Dewajani

2018-01-27

Objective: Breast carcinoma (BC) is a heterogeneous disease that exhibits variation in biological behaviour, prognosis and response to therapy. Molecular classification is generally into Luminal A, Luminal B, HER2+ and triple negative/basal-like, depending on receptor characteristics. Clinical factors that determined the BC prognosis are age and tumor size. Since information on molecular subtypes of Indonesian BCs is limited, the present study was conducted, with attention to subtypes in relation to age and tumor size. Methods: A retrospective cross-sectional study of 247 paraffin-embedded samples of invasive BC from Dr. Sardjito General Hospital Yogyakarta in the year 2012- 2015 was performed. Immunohistochemical staining using anti- ER, PR, HER2, Ki-67 and CK 5/6 antibodies was applied to classify molecular subtypes. Associations with age and tumor size were analyzed using the Chi Square Test. Results: The Luminal A was the most common subtype of Indonesian BC (41.3%), followed by triple negative (25.5%), HER2 (19.4%) and luminal B (13.8%). Among the triple negative lesions, the basal-like subtype was more frequent than the non basal-like (58.8 % vs 41.2%). Luminal B accounted for the highest percentage of younger age cases (< 40 years old) while HER2+ was most common in older age (> 50 years old) patients. Triple negative/basal-like were commonly large in size. Age (p = 0.080) and tumor size (p = 0.462) were not significantly associated with molecular subtypes of BC. Conclusion: The most common molecular subtype of Indonesian BC is luminal A, followed by triple-negative, HER2+ and luminal B. The majority of triple-negative lesions are basal-like. There are no association between age and tumor size with molecular subtypes of Indonesian BCs. Creative Commons Attribution License

Localized surface plasmon enhanced cellular imaging using random metallic structures

NASA Astrophysics Data System (ADS)

Son, Taehwang; Lee, Wonju; Kim, Donghyun

2017-02-01

We have studied fluorescence cellular imaging with randomly distributed localized near-field induced by silver nano-islands. For the fabrication of nano-islands, a 10-nm silver thin film evaporated on a BK7 glass substrate with an adhesion layer of 2-nm thick chromium. Micrometer sized silver square pattern was defined using e-beam lithography and then the film was annealed at 200°C. Raw images were restored using electric field distribution produced on the surface of random nano-islands. Nano-islands were modeled from SEM images. 488-nm p-polarized light source was set to be incident at 60°. Simulation results show that localized electric fields were created among nano-islands and that their average size was found to be 135 nm. The feasibility was tested using conventional total internal reflection fluorescence microscopy while the angle of incidence was adjusted to maximize field enhancement. Mouse microphage cells were cultured on nano-islands, and actin filaments were selectively stained with FITC-conjugated phalloidin. Acquired images were deconvolved based on linear imaging theory, in which molecular distribution was sampled by randomly distributed localized near-field and blurred by point spread function of far-field optics. The optimum fluorophore distribution was probabilistically estimated by repetitively matching a raw image. The deconvolved images are estimated to have a resolution in the range of 100-150 nm largely determined by the size of localized near-fields. We also discuss and compare the results with images acquired with periodic nano-aperture arrays in various optical configurations to excite localized plasmonic fields and to produce super-resolved molecular images.

Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

DOE PAGES

Gordiz, Kiarash; Singh, David J.; Henry, Asegun

2015-01-29

In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

Constraints on Fluctuations in Sparsely Characterized Biological Systems.

PubMed

Hilfinger, Andreas; Norman, Thomas M; Vinnicombe, Glenn; Paulsson, Johan

2016-02-05

Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.

Constraints on Fluctuations in Sparsely Characterized Biological Systems

NASA Astrophysics Data System (ADS)

Hilfinger, Andreas; Norman, Thomas M.; Vinnicombe, Glenn; Paulsson, Johan

2016-02-01

Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.

Emission characteristics for gaseous- and size-segregated particulate PAHs in coal combustion flue gas from circulating fluidized bed (CFB) boiler.

PubMed

Wang, Ruwei; Liu, Guijian; Sun, Ruoyu; Yousaf, Balal; Wang, Jizhong; Liu, Rongqiong; Zhang, Hong

2018-07-01

The partitioning behavior of polycyclic aromatic hydrocarbons (PAHs) between gaseous and particulate phases from coal-fired power plants (CFPPs) is critically important to predict PAH removal by dust control devices. In this study, 16 US-EPA priority PAHs in gaseous and size-segregated particulate phases at the inlet and outlet of the fabric filter unit (FFs) of a circulating fluidized bed (CFB) boiler were analyzed. The partitioning mechanisms of PAHs between gaseous and particulate phases and in particles of different size classes were investigated. We found that the removal efficiencies of PAHs are 45.59% and 70.67-89.06% for gaseous and particulate phases, respectively. The gaseous phase mainly contains low molecular weight (LMW) PAHs (2- and 3-ring PAHs), which is quite different from the particulate phase that mainly contains medium and high molecular weight (MMW and HMW) PAHs (4- to 6-ring PAHs). The fractions of LMW PAHs show a declining trend with the decrease of particle size. The gas-particle partitioning of PAHs is primarily controlled by organic carbon absorption, in addition, it has a clear dependence on the particle sizes. Plot of log (TPAH/PM) against logD p shows that all slope values were below -1, suggesting that PAHs were mainly adsorbed to particulates. The adsorption effect of PAHs in size-segregated PMs for HMW PAHs is more evident than LMW PAHs. The particle size distributions (PSDs) of individual PAHs show that most of PAHs exhibit bi-model structures, with one mode peaking in the accumulation size range (2.1-1.1 μm) and another mode peaking in coarse size range (5.8-4.7 μm). The intensities of these two peaks vary in function of ring number of PAHs, which is likely attributed to Kelvin effect that the less volatile HMW PAH species preferentially condense onto the finer particulates. The emission factor of PAHs was calculated as 3.53 mg/kg of coal burned, with overall mean EF PAH of 0.55 and 2.98 mg/kg for gaseous and particulate phase, respectively. Moreover, the average emission amount of PAHs for the investigated CFPP was 1016.6 g/day and 371073.6 g/y, respectively. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dual-targeted and pH-sensitive Doxorubicin Prodrug-Microbubble Complex with Ultrasound for Tumor Treatment

PubMed Central

Luo, Wanxian; Wen, Ge; Yang, Li; Tang, Jiao; Wang, Jianguo; Wang, Jihui; Zhang, Shiyu; Zhang, Li; Ma, Fei; Xiao, Liling; Wang, Ying; Li, Yingjia

2017-01-01

In this study, we investigated the potential of a dual-targeted pH-sensitive doxorubicin prodrug-microbubble complex (DPMC) in ultrasound (US)-assisted antitumor therapy. The doxorubicin prodrug (DP) consists of a succinylated-heparin carrier conjugated with doxorubicin (DOX) via hydrazone linkage and decorated with dual targeting ligands, folate and cRGD peptide. Combination of microbubble (MB) and DP, generated via avidin-biotin binding, promoted intracellular accumulation and improved therapeutic efficiency assisted by US cavitation and sonoporation. Aggregates of prepared DP were observed with an inhomogeneous size distribution (average diameters: 149.6±29.8 nm and 1036.2±38.8 nm, PDI: 1.0) while DPMC exhibited a uniform distribution (average diameter: 5.804±2.1 μm), facilitating its usage for drug delivery. Notably, upon US exposure, DPMC was disrupted and aggregated DP dispersed into homogeneous small-sized nanoparticles (average diameter: 128.6±42.3 nm, PDI: 0.21). DPMC could target to angiogenic endothelial cells in tumor region via αvβ3-mediated recognition and subsequently facilitate its specific binding to tumor cells mediated via recognition of folate receptor (FR) after US exposure. In vitro experiments showed higher tumor specificity and killing ability of DPMC with US than free DOX and DP for breast cancer MCF-7 cells. Furthermore, significant accumulation and specificity for tumor tissues of DPMC with US were detected using in vivo fluorescence and ultrasound molecular imaging, indicating its potential to integrate tumor imaging and therapy. In particular, through inducing apoptosis, inhibiting cell proliferation and antagonizing angiogenesis, DPMC with US produced higher tumor inhibition rates than DOX or DPMC without US in MCF-7 xenograft tumor-bearing mice while inducing no obvious body weight loss. Our strategy provides an effective platform for the delivery of large-sized or aggregated particles to tumor sites, thereby extending their therapeutic applications in vivo. PMID:28255342

2D Size Distribution of Chondrules and Chondritic Fragments of an Ordinary Chondrite from Lut Desert (Iran)

NASA Astrophysics Data System (ADS)

Pourkhorsandi, H.; Mirnejad, H.

2014-09-01

2D size measurement of chondrules and chondiritic fragments of a meteorite from Lut desert of Iran is conducted. Chondrules exhibit a size range of 55-1800 µm (average 437 µm). Chondiritic fragments show a size range of 46-1220 µm (average 261 µm).

Brief communication: Preoperative anticoagulant activity after bridging low-molecular-weight heparin for temporary interruption of warfarin.

PubMed

O'Donnell, Martin J; Kearon, Clive; Johnson, Judy; Robinson, Marlene; Zondag, Michelle; Turpie, Irene; Turpie, Alexander G

2007-02-06

Preoperative low-molecular-weight heparin (LMWH) is often used when warfarin therapy is interrupted for surgery. To determine the preoperative anticoagulant activity of LMWH following a standardized "bridging" regimen. Prospective cohort study. Single university hospital. Consecutive patients who had warfarin therapy interrupted before an invasive procedure. Enoxaparin, 1 mg/kg of body weight, twice daily. The last dose was administered the evening before surgery. Blood anti-factor Xa heparin levels measured shortly before surgery. Preoperative anti-Xa heparin levels were obtained in 80 patients at an average of 14 hours after the last dose of enoxaparin was administered. The average anti-Xa heparin level was 0.6 U/mL. The anti-Xa heparin level, measured shortly before surgery, was 0.5 U/mL or greater in 54 (68%) patients and 1.0 U/mL or greater in 13 (16%) patients. A shorter interval since the last dose (P < 0.001) and a higher body mass index (P = 0.001) were associated with higher preoperative anti-Xa heparin levels. The small sample size limits accurate estimates of the frequency of the clinical outcomes. A single regimen of LMWH was evaluated. Anti-Xa heparin levels often remain high at the time of surgery if a last dose of a twice-daily regimen of LMWH is given the evening before surgery.

A Theory of the von Weimarn Rules Governing the Average Size of Crystals Precipitated from a Supersaturated Solution

NASA Technical Reports Server (NTRS)

Barlow, Douglas A.; Baird, James K.; Su, Ching-Hua

2003-01-01

More than 75 years ago, von Weimarn summarized his observations of the dependence of the average crystal size on the initial relative concentration supersaturation prevailing in a solution from which crystals were growing. Since then, his empirically derived rules have become part of the lore of crystal growth. The first of these rules asserts that the average crystal size measured at the end of a crystallization increases as the initial value of the relative supersaturation decreases. The second rule states that for a given crystallization time, the average crystal size passes through a maximum as a function of the initial relative supersaturation. Using a theory of nucleation and growth due to Buyevich and Mansurov, we calculate the average crystal size as a function of the initial relative supersaturation. We confirm the von Weimarn rules for the case where the nucleation rate is proportional to the third power or higher of the relative supersaturation.

Line-by-line transport calculations for Jupiter entry probes. [of radiative transfer

NASA Technical Reports Server (NTRS)

Arnold, J. O.; Cooper, D. M.; Park, C.; Prakash, S. G.

1979-01-01

Line-by-line calculations of the radiative transport for a condition near peak heating for entry of the Galileo probe into the Jovian atmosphere are described. The discussion includes a thorough specification of the atomic and molecular input data used in the calculations that could be useful to others working in the field. The results show that the use of spectrally averaged cross sections for diatomic absorbers such as CO and C2 in the boundary layer can lead to an underestimation (by as much as 29%) of the spectral flux at the stagnation point. On the other hand, for the turbulent region near the cone frustum on the probe, the flow tends to be optically thin, and the spectrally averaged results commonly used in coupled radiative transport-flow field calculations are in good agreement with the present line-by-line results. It is recommended that these results be taken into account in sizing the final thickness of the Galileo's heat shield.

Increasing molecular weight parameters of a helical polymer through polymerization in a chiral solvent.

PubMed

Holder, Simon J; Achilleos, Mariliz; Jones, Richard G

2006-09-27

In this communication, we will demonstrate that polymerization in a chiral solvent can affect the molecular weight distribution of the product by perturbing the balance of the P and M helical screw senses of the growing chains. Specifically, for the Wurtz-type synthesis of polymethylphenylsilane (PMPS) in either (R) or (S)-limonene, the weight-average molecular weight of the products (average Mw = 80 000) was twice that of PMPS synthesized in (R/S)-limonene (average Mw = 39 200). Peturbation of the helical segmentation along the polymer chains leads to a reduction in the rate of occurrence of a key termination step. This the first time that a chiral solvent has been demonstrated to have such an effect on a polymerization process in affecting molecular weight parameters in contrast to affecting tacticity.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

PubMed Central

Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

2016-01-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

Using pulse field gradient NMR diffusion measurements to define molecular size distributions in glycan preparations.

PubMed

Miller, Michelle C; Klyosov, Anatole; Platt, David; Mayo, Kevin H

2009-07-06

Glycans comprise perhaps the largest biomass in nature, and more and more glycans are used in a number of applications, including those as pharmaceutical agents in the clinic. However, defining glycan molecular weight distributions during and after their preparation is not always straightforward. Here, we use pulse field gradient (PFG) (1)H NMR self-diffusion measurements to assess molecular weight distributions in various glycan preparations. Initially, we derived diffusion coefficients, D, on a series of dextrans with reported weight-average molecular weights from about 5 kDa to 150 kDa. For each dextran sample, we analyzed 15 diffusion decay curves, one from each of the 15 major (1)H resonance envelopes, to provide diffusion coefficients. By measuring D as a function of dextran concentration, we determined D at infinite dilution, D(inf), which allowed estimation of the hydrodynamic radius, R(h), using the Stokes-Einstein relationship. A plot of log D(inf) versus log R(h) was linear and provided a standard calibration curve from which R(h) is estimated for other glycans. We then applied this methodology to investigate two other glycans, an alpha-(1-->2)-L-rhamnosyl-alpha-(1-->4)-D-galacturonosyl with quasi-randomly distributed, mostly terminal beta(1-->4)-linked galactose side-chains (GRG) and an alpha(1-->6)-D-galacto-beta(1-->4)-D-mannan (Davanat), which is presently being tested against cancer in the clinic. Using the dextran-derived calibration curve, we find that average R(h) values for GRG and Davanat are 76+/-6 x 10(-10) m and 56+/-3 x 10(-10) m, with GRG being more polydispersed than Davanat. Results from this study will be useful to investigators requiring knowledge of polysaccharide dispersity, needing to study polysaccharides under various solution conditions, or wanting to follow degradation of polysaccharides during production.

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

Khezri, Khezrollah, E-mail: kh.khezri@ut.ac.ir; Roghani-Mamaqani, Hossein

Graphical abstract: Effect of mesoporous silica nanoparticles (MCM-41) on the activator generated by electron transfer for atom transfer radical polymerization (AGET ATRP) is investigated. Decrement of conversion and number average molecular weight and also increment of polydispersity index (PDI) values are three main results of addition of MCM-41 nanoparticles. Incorporation of MCM-41 nanoparticles in the polystyrene matrix can clearly increase thermal stability and decrease glass transition temperature of the nanocomposites. - Highlights: • Spherical morphology, hexagonal structure, and high surface area with regular pore diameters of the synthesized MCM-41 nanoparticles are examined. • AGET ATRP of styrene in the presencemore » of MCM-41 nanoparticles is performed. • Effect of MCM-41 nanoparticles addition on the polymerization rate, conversion and molecular weights of the products are discussed. • Improvement in thermal stability of the nanocomposites and decreasing T{sub g} values was also observed by incorporation of MCM-41 nanoparticles. - Abstract: Activator generated by electron transfer for atom transfer radical polymerization was employed to synthesize well-defined mesoporous silica nanoparticles/polystyrene composites. Inherent features of spherical mesoporous silica nanoparticles were evaluated by nitrogen adsorption/desorption isotherm, X-ray diffraction and scanning electron microscopy analysis techniques. Conversion and molecular weight evaluations were carried out using gas and size exclusion chromatography respectively. By the addition of only 3 wt% mesoporous silica nanoparticles, conversion decreases from 81 to 58%. Similarly, number average molecular weight decreases from 17,116 to 12,798 g mol{sup −1}. However, polydispersity index (PDI) values increases from 1.24 to 1.58. A peak around 4.1–4.2 ppm at proton nuclear magnetic resonance spectroscopy results clearly confirms the living nature of the polymerization. Thermogravimetric analysis shows that thermal stability of the nanocomposites increases by adding nanoparticles content. Decrease of glass transition temperature is also demonstrated by the addition of 3 wt% of silica nanoparticles according to the differential scanning calorimetry results.« less

Factors that affect molecular weight distribution of Suwannee river fulvic acid as determined by electrospray ionization/mass spectrometry

USGS Publications Warehouse

Rostad, Colleen E.; Leenheer, Jerry A.

2004-01-01

Effects of methylation, molar response, multiple charging, solvents, and positive and negative ionization on molecular weight distributions of aquatic fulvic acid were investigated by electrospray ionization/mass spectrometry. After preliminary analysis by positive and negative modes, samples and mixtures of standards were derivatized by methylation to minimize ionization sites and reanalyzed.Positive ionization was less effective and produced more complex spectra than negative ionization. Ionization in methanol/water produced greater response than in acetonitrile/water. Molar response varied widely for the selected free acid standards when analyzed individually and in a mixture, but after methylation this range decreased. After methylation, the number average molecular weight of the Suwannee River fulvic acid remained the same while the weight average molecular weight decreased. These differences are probably indicative of disaggregation of large aggregated ions during methylation. Since the weight average molecular weight decreased, it is likely that aggregate formation in the fulvic acid was present prior to derivatization, rather than multiple charging in the mass spectra.

Comparing methods to estimate Reineke’s maximum size-density relationship species boundary line slope

Treesearch

Curtis L. VanderSchaaf; Harold E. Burkhart

2010-01-01

Maximum size-density relationships (MSDR) provide natural resource managers useful information about the relationship between tree density and average tree size. Obtaining a valid estimate of how maximum tree density changes as average tree size changes is necessary to accurately describe these relationships. This paper examines three methods to estimate the slope of...

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker.

PubMed

Allio, Remi; Donega, Stefano; Galtier, Nicolas; Nabholz, Benoit

2017-11-01

It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Study design requirements for RNA sequencing-based breast cancer diagnostics.

PubMed

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

Quantum Theory of Atoms in Molecules Charge-Charge Transfer-Dipolar Polarization Classification of Infrared Intensities.

PubMed

Duarte, Leonardo J; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E

2017-10-26

Fundamental infrared vibrational transition intensities of gas-phase molecules are sensitive probes of changes in electronic structure accompanying small molecular distortions. Models containing charge, charge transfer, and dipolar polarization effects are necessary for a successful classification of the C-H, C-F, and C-Cl stretching and bending intensities. C-H stretching and in-plane bending vibrations involving sp 3 carbon atoms have small equilibrium charge contributions and are accurately modeled by the charge transfer-counterpolarization contribution and its interaction with equilibrium charge movement. Large C-F and C═O stretching intensities have dominant equilibrium charge movement contributions compared to their charge transfer-dipolar polarization ones and are accurately estimated by equilibrium charge and the interaction contribution. The C-F and C-Cl bending modes have charge and charge transfer-dipolar polarization contribution sums that are of similar size but opposite sign to their interaction values resulting in small intensities. Experimental in-plane C-H bends have small average intensities of 12.6 ± 10.4 km mol -1 owing to negligible charge contributions and charge transfer-counterpolarization cancellations, whereas their average out-of-plane experimental intensities are much larger, 65.7 ± 20.0 km mol -1 , as charge transfer is zero and only dipolar polarization takes place. The C-F bending intensities have large charge contributions but very small intensities. Their average experimental out-of-plane intensity of 9.9 ± 12.6 km mol -1 arises from the cancellation of large charge contributions by dipolar polarization contributions. The experimental average in-plane C-F bending intensity, 5.8 ± 7.3 km mol -1 , is also small owing to charge and charge transfer-counterpolarization sums being canceled by their interaction contributions. Models containing only atomic charges and their fluxes are incapable of describing electronic structure changes for simple molecular distortions that are of interest in classifying infrared intensities. One can expect dipolar polarization effects to also be important for larger distortions of chemical interest.

Sample Size Bias in Judgments of Perceptual Averages

ERIC Educational Resources Information Center

Price, Paul C.; Kimura, Nicole M.; Smith, Andrew R.; Marshall, Lindsay D.

2014-01-01

Previous research has shown that people exhibit a sample size bias when judging the average of a set of stimuli on a single dimension. The more stimuli there are in the set, the greater people judge the average to be. This effect has been demonstrated reliably for judgments of the average likelihood that groups of people will experience negative,…

On the Importance of Cycle Minimum in Sunspot Cycle Prediction

NASA Technical Reports Server (NTRS)

Wilson, Robert M.; Hathaway, David H.; Reichmann, Edwin J.

1996-01-01

The characteristics of the minima between sunspot cycles are found to provide important information for predicting the amplitude and timing of the following cycle. For example, the time of the occurrence of sunspot minimum sets the length of the previous cycle, which is correlated by the amplitude-period effect to the amplitude of the next cycle, with cycles of shorter (longer) than average length usually being followed by cycles of larger (smaller) than average size (true for 16 of 21 sunspot cycles). Likewise, the size of the minimum at cycle onset is correlated with the size of the cycle's maximum amplitude, with cycles of larger (smaller) than average size minima usually being associated with larger (smaller) than average size maxima (true for 16 of 22 sunspot cycles). Also, it was found that the size of the previous cycle's minimum and maximum relates to the size of the following cycle's minimum and maximum with an even-odd cycle number dependency. The latter effect suggests that cycle 23 will have a minimum and maximum amplitude probably larger than average in size (in particular, minimum smoothed sunspot number Rm = 12.3 +/- 7.5 and maximum smoothed sunspot number RM = 198.8 +/- 36.5, at the 95-percent level of confidence), further suggesting (by the Waldmeier effect) that it will have a faster than average rise to maximum (fast-rising cycles have ascent durations of about 41 +/- 7 months). Thus, if, as expected, onset for cycle 23 will be December 1996 +/- 3 months, based on smoothed sunspot number, then the length of cycle 22 will be about 123 +/- 3 months, inferring that it is a short-period cycle and that cycle 23 maximum amplitude probably will be larger than average in size (from the amplitude-period effect), having an RM of about 133 +/- 39 (based on the usual +/- 30 percent spread that has been seen between observed and predicted values), with maximum amplitude occurrence likely sometime between July 1999 and October 2000.

Size and emotion averaging: costs of dividing attention after all.

PubMed

Brand, John; Oriet, Chris; Tottenham, Laurie Sykes

2012-03-01

Perceptual averaging is a process by which sets of similar items are represented by summary statistics such as their average size, luminance, or orientation. Researchers have argued that this process is automatic, able to be carried out without interference from concurrent processing. Here, we challenge this conclusion and demonstrate a reliable cost of computing the mean size of circles distinguished by colour (Experiments 1 and 2) and the mean emotionality of faces distinguished by sex (Experiment 3). We also test the viability of two strategies that could have allowed observers to guess the correct response without computing the average size or emotionality of both sets concurrently. We conclude that although two means can be computed concurrently, doing so incurs a cost of dividing attention.

Genome size analyses of Pucciniales reveal the largest fungal genomes.

PubMed

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Genome size analyses of Pucciniales reveal the largest fungal genomes

PubMed Central

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G.; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T.; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research. PMID:25206357

Professional hazards? The impact of models' body size on advertising effectiveness and women's body-focused anxiety in professions that do and do not emphasize the cultural ideal of thinness.

PubMed

Dittmar, Helga; Howard, Sarah

2004-12-01

Previous experimental research indicates that the use of average-size women models in advertising prevents the well-documented negative effect of thin models on women's body image, while such adverts are perceived as equally effective (Halliwell & Dittmar, 2004). The current study extends this work by: (a) seeking to replicate the finding of no difference in advertising effectiveness between average-size and thin models (b) examining level of ideal-body internalization as an individual, internal factor that moderates women's vulnerability to thin media models, in the context of (c) comparing women in professions that differ radically in their focus on, and promotion of, the sociocultural ideal of thinness for women--employees in fashion advertising (n = 75) and teachers in secondary schools (n = 75). Adverts showing thin, average-size and no models were perceived as equally effective. High internalizers in both groups of women felt worse about their body image after exposure to thin models compared to other images. Profession affected responses to average-size models. Teachers reported significantly less body-focused anxiety after seeing average-size models compared to no models, while there was no difference for fashion advertisers. This suggests that women in professional environments with less focus on appearance-related ideals can experience increased body-esteem when exposed to average-size models, whereas women in appearance-focused professions report no such relief.

Void initiation from interfacial debonding of spherical silicon particles inside a silicon-copper nanocomposite: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Cui, Yi; Chen, Zengtao

2017-02-01

Silicon particles with diameters from 1.9 nm to 30 nm are embedded in a face-centered-cubic copper matrix to form nanocomposite specimens for simulation. The interfacial debonding of silicon particles from the copper matrix and the subsequent growth of nucleated voids are studied via molecular dynamics (MD). The MD results are examined from several different perspectives. The overall mechanical performance is monitored by the average stress-strain response and the accumulated porosity. The ‘relatively farthest-traveled’ atoms are identified to characterize the onset of interfacial debonding. The relative displacement field is plotted to illustrate both subsequent interfacial debonding and the growth of a nucleated void facilitated by a dislocation network. Our results indicate that the initiation of interfacial debonding is due to the accumulated surface stress if the matrix is initially dislocation-free. However, pre-existing dislocations can make a considerable difference. In either case, the dislocation emission also contributes to the subsequent debonding process. As for the size effect, the debonding of relatively larger particles causes a drop in the stress-strain curve. The volume fraction of second-phase particles is found to be more influential than the size of the simulation box on the onset of interfacial debonding. The volume fraction of second-phase particles also affects the shape of the nucleated void and, therefore, influences the stress response of the composite.

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

Bradley, R.H.; Rand, B.

The physical adsorption of nonpolar and polar vapors by active carbons is discussed in relation to pore structure and pore wall chemistry. For nonpolar vapors the Dubinin-Radushkevich equation is used to derive micropore volumes (W[sub 0]), average adsorption energies (E[sub 0]), and micropore widths (L) for a number of systems. These parameters are used to interpret the adsorption behavior of nitrogen which, because it is a relatively small molecule, is frequently used at 77 K to probe porosity and surface area. Results are presented for three carbons from differing precursors, namely, coal, coconut shells, and polyvinylidene chloride (PVDC) to illustratemore » the applicability of the technique. For the latter carbon increases in micropore size, induced by activation in carbon dioxide, and reductions in accessible pore volume caused by heat treatment in argon are also characterized and related to structural changes. The approach is then extended to the adsorption of larger hydrogen vapors, where the resulting W[sub 0] values may require correction for molecular packing effects which occur in the lower relative pressure regions of the isotherms, i.e., during the filling of ultramicropores. These packing effects are shown to limit the use of the Polanyi characteristic curve for correlating isotherm data for several vapors, of differing molecular size, by one adsorbent. Data for the adsorption of water, which is a strongly polar liquid, have been interpreted using the Dubinin-Serpinsky equation.« less

Multistate Evaluation of an Ultrafiltration-Based Procedure for Simultaneous Recovery of Enteric Microbes in 100-Liter Tap Water Samples▿

PubMed Central

Hill, Vincent R.; Kahler, Amy M.; Jothikumar, Narayanan; Johnson, Trisha B.; Hahn, Donghyun; Cromeans, Theresa L.

2007-01-01

Ultrafiltration (UF) is increasingly being recognized as a potentially effective procedure for concentrating and recovering microbes from large volumes of water and treated wastewater. Because of their very small pore sizes, UF membranes are capable of simultaneously concentrating viruses, bacteria, and parasites based on size exclusion. In this study, a UF-based water sampling procedure was used to simultaneously recover representatives of these three microbial classes seeded into 100-liter samples of tap water collected from eight cities covering six hydrologic areas of the United States. The UF-based procedure included hollow-fiber UF as the primary step for concentrating microbes and then used membrane filtration for bacterial culture assays, immunomagnetic separation for parasite recovery and quantification, and centrifugal UF for secondary concentration of viruses. Water samples were tested for nine water quality parameters to investigate whether water quality data correlated with measured recovery efficiencies and molecular detection levels. Average total method recovery efficiencies were 71, 97, 120, 110, and 91% for φX174 bacteriophage, MS2 bacteriophage, Enterococcus faecalis, Clostridium perfringens spores, and Cryptosporidium parvum oocysts, respectively. Real-time PCR and reverse transcription-PCR (RT-PCR) for seeded microbes and controls indicated that tap water quality could affect the analytical performance of molecular amplification assays, although no specific water quality parameter was found to correlate with reduced PCR or RT-PCR performance. PMID:17483281

Synthesis of Aluminium Nanoparticles in A Water/Polyethylene Glycol Mixed Solvent using μ-EDM

NASA Astrophysics Data System (ADS)

Sahu, R. K.; Hiremath, Somashekhar S.

2017-08-01

Nanoparticles present a practical way of retaining the results of the property at the atomic or molecular level. Due to the recent use of nanoparticles in scientific, industrial and medical applications, synthesis of nanoparticles and their characterization have become considerably important. Currently, aluminium nanoparticles have attracted significant research attention because of their reasonable cost, unique properties and interdisciplinary emerging applications. The present paper reports the synthesis of aluminium nanoparticles in the mixture of Deionized water (DI water) and Polyethylene Glycol (PEG) using a developed micro-Electrical Discharge Machining (μ-EDM) method. PEG was used as a stabilizer to prevent nanoparticles from agglomeration produced during the μ -EDM process. The synthesized aluminium nanoparticles were examined by Transmission Electron Microscopy (TEM), Energy Dispersive Analysis by X-rays (EDAX) and Selected Area Electron Diffraction (SAED) pattern to determine their size, shape, chemical nature and crystal structure. The average size of the polyhedral aluminium nanoparticles is found to be 196 nm.

Principles of Considering the Effect of the Limited Volume of a System on Its Thermodynamic State

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.

2018-01-01

The features of a system with a finite volume that affect its thermodynamic state are considered in comparison to describing small bodies in macroscopic phases. Equations for unary and pair distribution functions are obtained using difference derivatives of a discrete statistical sum. The structure of the equation for the free energy of a system consisting of an ensemble of volume-limited regions with different sizes and a full set of equations describing a macroscopic polydisperse system are discussed. It is found that the equations can be applied to molecular adsorption on small faces of microcrystals, to bound and isolated pores of a polydisperse material, and to describe the spinodal decomposition of a fluid in brief periods of time and high supersaturations of the bulk phase when each local region functions the same on average. It is shown that as the size of a system diminishes, corrections must be introduced for the finiteness of the system volume and fluctuations of the unary and pair distribution functions.

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

Fath, L., E-mail: lukas.fath@kit.edu; Hochbruck, M., E-mail: marlis.hochbruck@kit.edu; Singh, C.V., E-mail: chandraveer.singh@utoronto.ca

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementationmore » in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.« less

Theory of molecular crowding in Brownian hard-sphere liquids.

PubMed

Zaccone, Alessio; Terentjev, Eugene M

2012-06-01

We derive an analytical pair potential of mean force for Brownian molecules in the liquid state. Our approach accounts for many-particle correlations of crowding particles of the liquid and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Focusing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential and to a much stronger attraction (by a factor of ≈4 at average volume fraction of crowders φ{0}=0.25) than in the standard depletion interaction where the diffusive effects are neglected. As an illustration of the theory, we use it to study the size of a polymer chain in a solution of inert crowders. Even in the case of an athermal background solvent, when a classical chain should be fully swollen, we find a sharp coil-globule transition of the ideal chain collapsing at a critical value of the crowder volume fraction φ{c}≈0.145.

Self-association of urea in aqueous solutions: a Voronoi polyhedron analysis study.

PubMed

Idrissi, Abdenacer; Damay, Pierre; Yukichi, Kitamura; Jedlovszky, Pal

2008-10-28

Molecular dynamics simulation of the aqueous solutions of urea of seven different concentrations (including neat water as a reference system) has been performed on the isothermal-isobaric (N,p,T) ensemble. The ability of the urea molecules of self-association is investigated by means of the method of Voronoi polyhedra. For this purpose, all the analyses are repeated by removing one of the two components from the sample configurations and considering only the other one. In this way, the analysis of self-aggregation is reduced to the analysis of voids, a problem that can routinely be addressed by means of Voronoi analysis. The obtained results show that the urea molecules exhibit self-association behavior, which is found to be the strongest at the urea mole fraction of 0.23. However, the size of these urea aggregates is found to be rather limited; on average, they are built up by 3-4 molecules, and never exceed the size of 20-25 molecules.

Molecular-Size-Separated Brown Carbon Absorption for Biomass-Burning Aerosol at Multiple Field Sites.

PubMed

Di Lorenzo, Robert A; Washenfelder, Rebecca A; Attwood, Alexis R; Guo, Hongyu; Xu, Lu; Ng, Nga L; Weber, Rodney J; Baumann, Karsten; Edgerton, Eric; Young, Cora J

2017-03-21

Biomass burning is a known source of brown carbon aerosol in the atmosphere. We collected filter samples of biomass-burning emissions at three locations in Canada and the United States with transport times of 10 h to >3 days. We analyzed the samples with size-exclusion chromatography coupled to molecular absorbance spectroscopy to determine absorbance as a function of molecular size. The majority of absorption was due to molecules >500 Da, and these contributed an increasing fraction of absorption as the biomass-burning aerosol aged. This suggests that the smallest molecular weight fraction is more susceptible to processes that lead to reduced light absorption, while larger-molecular-weight species may represent recalcitrant brown carbon. We calculate that these large-molecular-weight species are composed of more than 20 carbons with as few as two oxygens and would be classified as extremely low volatility organic compounds (ELVOCs).

Method to grow carbon thin films consisting entirely of diamond grains 3-5 nm in size and high-energy grain boundaries

DOEpatents

Carlisle, John A.; Auciello, Orlando; Birrell, James

2006-10-31

An ultrananocrystalline diamond (UNCD) having an average grain size between 3 and 5 nanometers (nm) with not more than about 8% by volume diamond having an average grain size larger than 10 nm. A method of manufacturing UNCD film is also disclosed in which a vapor of acetylene and hydrogen in an inert gas other than He wherein the volume ratio of acetylene to hydrogen is greater than 0.35 and less than 0.85, with the balance being an inert gas, is subjected to a suitable amount of energy to fragment at least some of the acetylene to form a UNCD film having an average grain size of 3 to 5 nm with not more than about 8% by volume diamond having an average grain size larger than 10 nm.

Improving Sensitivity in Ultrasound Molecular Imaging by Tailoring Contrast Agent Size Distribution: In Vivo Studies

PubMed Central

Streeter, Jason E.; Gessner, Ryan; Miles, Iman; Dayton, Paul A.

2010-01-01

Molecular imaging with ultrasound relies on microbubble contrast agents (MCAs) selectively adhering to a ligand-specific target. Prior studies have shown that only small quantities of microbubbles are retained at their target sites, therefore, enhancing contrast sensitivity to low concentrations of microbubbles is essential to improve molecular imaging techniques. In order to assess the effect of MCA diameter on imaging sensitivity, perfusion and molecular imaging studies were performed with microbubbles of varying size distributions. To assess signal improvement and MCA circulation time as a function of size and concentration, blood perfusion was imaged in rat kidneys using nontargeted size-sorted MCAs with a Siemens Sequoia ultrasound system (Siemans, Mountain View, CA) in cadence pulse sequencing (CPS) mode. Molecular imaging sensitivity improvements were studied with size-sorted αvβ3-targeted bubbles in both fibrosarcoma and R3230 rat tumor models. In perfusion imaging studies, video intensity and contrast persistence was ≈8 times and ≈3 times greater respectively, for “sorted 3-micron” MCAs (diameter, 3.3 ± 1.95 μm) when compared to “unsorted” MCAs (diameter, 0.9 ± 0.45 μm) at low concentrations. In targeted experiments, application of sorted 3-micron MCAs resulted in a ≈20 times video intensity increase over unsorted populations. Tailoring size-distributions results in substantial imaging sensitivity improvement over unsorted populations, which is essential in maximizing sensitivity to small numbers of MCAs for molecular imaging. PMID:20236606

Removal of haloacetic acids from swimming pool water by reverse osmosis and nanofiltration.

PubMed

Yang, Linyan; She, Qianhong; Wan, Man Pun; Wang, Rong; Chang, Victor W-C; Tang, Chuyang Y

2017-06-01

Recent studies report high concentrations of haloacetic acids (HAAs), a prevalent class of toxic disinfection by-products, in swimming pool water (SPW). We investigated the removal of 9 HAAs by four commercial reverse osmosis (RO) and nanofiltration (NF) membranes. Under typical SPW conditions (pH 7.5 and 50 mM ionic strength), HAA rejections were >60% for NF270 with molecular weight cut-off (MWCO) equal to 266 Da and equal or higher than 90% for XLE, NF90 and SB50 with MWCOs of 96, 118 and 152 Da, respectively, as a result of the combined effects of size exclusion and charge repulsion. We further included 7 neutral hydrophilic surrogates as molecular probes to resolve the rejection mechanisms. In the absence of strong electrostatic interaction (e.g., pH 3.5), the rejection data of HAAs and surrogates by various membranes fall onto an identical size-exclusion (SE) curve when plotted against the relative-size parameter, i.e., the ratio of molecular radius over membrane pore radius. The independence of this SE curve on molecular structures and membrane properties reveals that the relative-size parameter is a more fundamental SE descriptor compared to molecular weight. An effective molecular size with the Stokes radius accounting for size exclusion and the Debye length accounting for electrostatic interaction was further used to evaluate the rejection. The current study provides valuable insights on the rejection of trace contaminants by RO/NF membranes. Copyright © 2017. Published by Elsevier Ltd.

RESOLVED GIANT MOLECULAR CLOUDS IN NEARBY SPIRAL GALAXIES: INSIGHTS FROM THE CANON CO (1-0) SURVEY

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

Donovan Meyer, Jennifer; Koda, Jin; Mooney, Thomas

We resolve 182 individual giant molecular clouds (GMCs) larger than 2.5 Multiplication-Sign 10{sup 5} M{sub Sun} in the inner disks of 5 large nearby spiral galaxies (NGC 2403, NGC 3031, NGC 4736, NGC 4826, and NGC 6946) to create the largest such sample of extragalactic GMCs within galaxies analogous to the Milky Way. Using a conservatively chosen sample of GMCs most likely to adhere to the virial assumption, we measure cloud sizes, velocity dispersions, and {sup 12}CO (J = 1-0) luminosities and calculate cloud virial masses. The average conversion factor from CO flux to H{sub 2} mass (or X{sub CO})more » for each galaxy is 1-2 Multiplication-Sign 10{sup 20} cm{sup -2} (K km s{sup -1}){sup -1}, all within a factor of two of the Milky Way disk value ({approx}2 Multiplication-Sign 10{sup 20} cm{sup -2} (K km s{sup -1}){sup -1}). We find GMCs to be generally consistent within our errors between the galaxies and with Milky Way disk GMCs; the intrinsic scatter between clouds is of order a factor of two. Consistent with previous studies in the Local Group, we find a linear relationship between cloud virial mass and CO luminosity, supporting the assumption that the clouds in this GMC sample are gravitationally bound. We do not detect a significant population of GMCs with elevated velocity dispersions for their sizes, as has been detected in the Galactic center. Though the range of metallicities probed in this study is narrow, the average conversion factors of these galaxies will serve to anchor the high metallicity end of metallicity-X{sub CO} trends measured using conversion factors in resolved clouds; this has been previously possible primarily with Milky Way measurements.« less

MALT90 Kinematic Distances to Dense Molecular Clumps

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

Whitaker, J. Scott; Jackson, James M.; Sanhueza, Patricio

Using molecular-line data from the Millimetre Astronomy Legacy Team 90 GHz Survey (MALT90), we have estimated kinematic distances to 1905 molecular clumps identified in the ATLASGAL 870 μ m continuum survey over the longitude range 295° <  l  < 350°. The clump velocities were determined using a flux-weighted average of the velocities obtained from Gaussian fits to the HCO{sup +}, HNC, and N{sub 2}H{sup +} (1–0) transitions. The near/far kinematic distance ambiguity was addressed by searching for the presence or absence of absorption or self-absorption features in 21 cm atomic hydrogen spectra from the Southern Galactic Plane Survey. Our algorithm provides anmore » estimation of the reliability of the ambiguity resolution. The Galactic distribution of the clumps indicates positions where the clumps are bunched together, and these locations probably trace the locations of spiral arms. Several clumps fall at the predicted location of the far side of the Scutum–Centaurus arm. Moreover, a number of clumps with positive radial velocities are unambiguously located on the far side of the Milky Way at galactocentric radii beyond the solar circle. The measurement of these kinematic distances, in combination with continuum or molecular-line data, now enables the determination of fundamental parameters such as mass, size, and luminosity for each clump.« less

Human skeletal muscle biochemical diversity.

PubMed

Tirrell, Timothy F; Cook, Mark S; Carr, J Austin; Lin, Evie; Ward, Samuel R; Lieber, Richard L

2012-08-01

The molecular components largely responsible for muscle attributes such as passive tension development (titin and collagen), active tension development (myosin heavy chain, MHC) and mechanosensitive signaling (titin) have been well studied in animals but less is known about their roles in humans. The purpose of this study was to perform a comprehensive analysis of titin, collagen and MHC isoform distributions in a large number of human muscles, to search for common themes and trends in the muscular organization of the human body. In this study, 599 biopsies were obtained from six human cadaveric donors (mean age 83 years). Three assays were performed on each biopsy - titin molecular mass determination, hydroxyproline content (a surrogate for collagen content) and MHC isoform distribution. Titin molecular mass was increased in more distal muscles of the upper and lower limbs. This trend was also observed for collagen. Percentage MHC-1 data followed a pattern similar to collagen in muscles of the upper extremity but this trend was reversed in the lower extremity. Titin molecular mass was the best predictor of anatomical region and muscle functional group. On average, human muscles had more slow myosin than other mammals. Also, larger titins were generally associated with faster muscles. These trends suggest that distal muscles should have higher passive tension than proximal ones, and that titin size variability may potentially act to 'tune' the protein's mechanotransduction capability.

Human skeletal muscle biochemical diversity

PubMed Central

Tirrell, Timothy F.; Cook, Mark S.; Carr, J. Austin; Lin, Evie; Ward, Samuel R.; Lieber, Richard L.

2012-01-01

SUMMARY The molecular components largely responsible for muscle attributes such as passive tension development (titin and collagen), active tension development (myosin heavy chain, MHC) and mechanosensitive signaling (titin) have been well studied in animals but less is known about their roles in humans. The purpose of this study was to perform a comprehensive analysis of titin, collagen and MHC isoform distributions in a large number of human muscles, to search for common themes and trends in the muscular organization of the human body. In this study, 599 biopsies were obtained from six human cadaveric donors (mean age 83 years). Three assays were performed on each biopsy – titin molecular mass determination, hydroxyproline content (a surrogate for collagen content) and MHC isoform distribution. Titin molecular mass was increased in more distal muscles of the upper and lower limbs. This trend was also observed for collagen. Percentage MHC-1 data followed a pattern similar to collagen in muscles of the upper extremity but this trend was reversed in the lower extremity. Titin molecular mass was the best predictor of anatomical region and muscle functional group. On average, human muscles had more slow myosin than other mammals. Also, larger titins were generally associated with faster muscles. These trends suggest that distal muscles should have higher passive tension than proximal ones, and that titin size variability may potentially act to ‘tune’ the protein's mechanotransduction capability. PMID:22786631

Nano-fabrication of molecular electronic junctions by targeted modification of metal-molecule bonds

PubMed Central

Jafri, S. Hassan M.; Löfås, Henrik; Blom, Tobias; Wallner, Andreas; Grigoriev, Anton; Ahuja, Rajeev; Ottosson, Henrik; Leifer, Klaus

2015-01-01

Reproducibility, stability and the coupling between electrical and molecular properties are central challenges in the field of molecular electronics. The field not only needs devices that fulfill these criteria but they also need to be up-scalable to application size. In this work, few-molecule based electronics devices with reproducible electrical characteristics are demonstrated. Our previously reported 5 nm gold nanoparticles (AuNP) coated with ω-triphenylmethyl (trityl) protected 1,8-octanedithiol molecules are trapped in between sub-20 nm gap spacing gold nanoelectrodes forming AuNP-molecule network. When the trityl groups are removed, reproducible devices and stable Au-thiol junctions are established on both ends of the alkane segment. The resistance of more than 50 devices is reduced by orders of magnitude as well as a reduction of the spread in the resistance histogram is observed. By density functional theory calculations the orders of magnitude decrease in resistance can be explained and supported by TEM observations thus indicating that the resistance changes and strongly improved resistance spread are related to the establishment of reproducible and stable metal-molecule bonds. The same experimental sequence is carried out using 1,6-hexanedithiol functionalized AuNPs. The average resistances as a function of molecular length, demonstrated herein, are comparable to the one found in single molecule devices. PMID:26395225

Understanding gas-surface interactions from direct force measurements using a specialized torsion balance

NASA Technical Reports Server (NTRS)

Cook, S. R.; Hoffbauer, M. A.

1996-01-01

The first comprehensive measurements of the magnitude and direction of the forces exerted on surfaces by molecular beams are discussed and used to obtain information about the microscopic properties of the gas-surface interactions. This unique approach is not based on microscopic measurements of the scattered molecules. The reduced force coefficients are introduced as a new set of parameters that completely describe the macroscopic average momentum transfer to a surface by an incident molecular beam. By using a specialized torsion balance and molecular beams of N2, CO, CO2, and H2, the reduced force coefficients are determined from direct measurements of the force components exerted on surface of a solar panel array material, Kapton, SiO2-coated Kapton, and Z-93 as a function of the angle of incidence ranging from 0 degrees to 85 degrees. The absolute flux densities of the molecular beams were measured using a different torsion balance with a beam-stop that nullified the force of the scattered molecules. Standard time-of-flight techniques were used to determine the flux-weighted average velocities of the various molecular beams ranging from 1600 m/s to 4600 m/s. The reduced force coefficients can be used to directly obtain macroscopic average properties of the scattered molecules, such as the flux-weighted average velocity and translational energy, that can then be used to determine microscopic details concerning gas-surface interactions without the complications associated with averaging microscopic measurements.

Enhanced pulsed magneto-motive ultrasound imaging using superparamagnetic nanoclusters

PubMed Central

Mehrmohammadi, M; Yoon, KY; Qu, M; Johnston, KP; Emelianov, SY

2011-01-01

Recently, pulsed magneto-motive ultrasound (pMMUS) imaging augmented with ultra-small magnetic nanoparticles has been introduced as a tool capable of imaging events at molecular and cellular levels. The sensitivity of a pMMUS system depends on several parameters, including the size, geometry and magnetic properties of the nanoparticles. Under the same magnetic field, larger magnetic nanostructures experience a stronger magnetic force and produce larger displacement, thus improving the sensitivity and signal-to-noise ratio (SNR) of pMMUS imaging. Unfortunately, large magnetic iron-oxide nanoparticles are typically ferromagnetic and thus are very difficult to stabilize against colloidal aggregation. In the current study we demonstrate improvement of pMMUS image quality by using large size superparamagnetic nanoclusters characterized by strong magnetization per particle. Water-soluble magnetic nanoclusters of two sizes (15 and 55 nm average size) were synthesized from 3 nm iron precursors in the presence of citrate capping ligand. The size distribution of synthesized nanoclusters and individual nanoparticles was characterized using dynamic light scattering (DLS) analysis and transmission electron microscopy (TEM). Tissue mimicking phantoms containing single nanoparticles and two sizes of nanoclusters were imaged using a custom-built pMMUS imaging system. While the magnetic properties of citrate-coated nanoclusters are identical to those of superparamagnetic nanoparticles, the magneto-motive signal detected from nanoclusters is larger, i.e. the same magnetic field produced larger magnetically induced displacement. Therefore, our study demonstrates that clusters of superparamagnetic nanoparticles result in pMMUS images with higher contrast and SNR. PMID:21157009

The Impact of the Polymer Chain Length on the Catalytic Activity of Poly(N-vinyl-2-pyrrolidone)-supported Gold Nanoclusters.

PubMed

Haesuwannakij, Setsiri; Kimura, Tetsunari; Furutani, Yuji; Okumura, Kazu; Kokubo, Ken; Sakata, Takao; Yasuda, Hidehiro; Yakiyama, Yumi; Sakurai, Hidehiro

2017-08-29

Poly(N-vinyl-2-pyrrolidone) (PVP) of varying molecular weight (M w  = 40-360 kDa) were employed to stabilize gold nanoclusters of varying size. The resulting Au:PVP clusters were subsequently used as catalysts for a kinetic study on the sized-dependent aerobic oxidation of 1-indanol, which was monitored by time-resolved in situ infrared spectroscopy. The obtained results suggest that the catalytic behaviour is intimately correlated to the size of the clusters, which in turn depends on the molecular weight of the PVPs. The highest catalytic activity was observed for clusters with a core size of ~7 nm, and the size of the cluster should increase with the molecular weight of the polymer in order to maintain optimal catalytic activity. Studies on the electronic and colloid structure of these clusters revealed that the negative charge density on the cluster surface also strongly depends on the molecular weight of the stabilizing polymers.

Volatilization of organic compounds from streams

USGS Publications Warehouse

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

1982-01-01

Mass-transfer coefficients for the volatilization of ethylene and propane were correlated with the hydraulic and geometric properties of seven streams, and predictive equations were developed. The equations were evaluated using a normalized root-mean-square error as the criterion of comparison. The two best equations were a two-variable equation containing the energy dissipated per unit mass per unit time and the average depth of flow and a three-variable equation containing the average velocity, the average depth of flow, and the slope of the stream. Procedures for adjusting the ethylene and propane coefficients for other organic compounds were evaluated. These procedures are based on molecular diffusivity, molecular diameter, or molecular weight. Because of limited data, none of these procedures have been extensively verified. Therefore, until additional data become available, it is suggested that the mass-transfer coefficient be assumed to be inversely proportional to the square root of the molecular weight.

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.

PubMed

Ramírez-Sánchez, Obed; Pérez-Rodríguez, Paulino; Delaye, Luis; Tiessen, Axel

2016-12-01

Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Averaging processes in granular flows driven by gravity

NASA Astrophysics Data System (ADS)

Rossi, Giulia; Armanini, Aronne

2016-04-01

One of the more promising theoretical frames to analyse the two-phase granular flows is offered by the similarity of their rheology with the kinetic theory of gases [1]. Granular flows can be considered a macroscopic equivalent of the molecular case: the collisions among molecules are compared to the collisions among grains at a macroscopic scale [2,3]. However there are important statistical differences in dealing with the two applications. In the two-phase fluid mechanics, there are two main types of average: the phasic average and the mass weighed average [4]. The kinetic theories assume that the size of atoms is so small, that the number of molecules in a control volume is infinite. With this assumption, the concentration (number of particles n) doesn't change during the averaging process and the two definitions of average coincide. This hypothesis is no more true in granular flows: contrary to gases, the dimension of a single particle becomes comparable to that of the control volume. For this reason, in a single realization the number of grain is constant and the two averages coincide; on the contrary, for more than one realization, n is no more constant and the two types of average lead to different results. Therefore, the ensamble average used in the standard kinetic theory (which usually is the phasic average) is suitable for the single realization, but not for several realization, as already pointed out in [5,6]. In the literature, three main length scales have been identified [7]: the smallest is the particles size, the intermediate consists in the local averaging (in order to describe some instability phenomena or secondary circulation) and the largest arises from phenomena such as large eddies in turbulence. Our aim is to solve the intermediate scale, by applying the mass weighted average, when dealing with more than one realizations. This statistical approach leads to additional diffusive terms in the continuity equation: starting from experimental results, we aim to define the scales governing the diffusive phenomenon, introducing the diffusive terms following the Boussinesq model. The diffusive coefficient will be experimentally defined; it will be probably proportional to the square root of the granular temperature θ and the diameter of the particles d or, alternatively, the flow height h. REFERENCES 1 Chapman S., Cowling T.G., 1971. Cambridge University Press, Cambridge, England. 2 Jenkins J.T., Savage S.B., 1983 J. Fluid.Mech., 130: 187-202 3 Savage S.B.,1984. J. Fluid.Mech., 24: 289-366 4 D.A.Drew, 1983. Annu. Rev. Fluid Mech. 15:261-291 5 I. Goldhirsch, 2003. Annu. Rev. Fluid Mech., 35:267-293. 6 I. Goldhirsch, 2008. Powder Technology, 182: 130-136. 7 T.J. Hsu, J.T. Jenkins, P.L. Liu 2004. Proc. Royal Soc.

Perceptual Averaging in Individuals with Autism Spectrum Disorder.

PubMed

Corbett, Jennifer E; Venuti, Paola; Melcher, David

2016-01-01

There is mounting evidence that observers rely on statistical summaries of visual information to maintain stable and coherent perception. Sensitivity to the mean (or other prototypical value) of a visual feature (e.g., mean size) appears to be a pervasive process in human visual perception. Previous studies in individuals diagnosed with Autism Spectrum Disorder (ASD) have uncovered characteristic patterns of visual processing that suggest they may rely more on enhanced local representations of individual objects instead of computing such perceptual averages. To further explore the fundamental nature of abstract statistical representation in visual perception, we investigated perceptual averaging of mean size in a group of 12 high-functioning individuals diagnosed with ASD using simplified versions of two identification and adaptation tasks that elicited characteristic perceptual averaging effects in a control group of neurotypical participants. In Experiment 1, participants performed with above chance accuracy in recalling the mean size of a set of circles ( mean task ) despite poor accuracy in recalling individual circle sizes ( member task ). In Experiment 2, their judgments of single circle size were biased by mean size adaptation. Overall, these results suggest that individuals with ASD perceptually average information about sets of objects in the surrounding environment. Our results underscore the fundamental nature of perceptual averaging in vision, and further our understanding of how autistic individuals make sense of the external environment.

Tunable separations based on a molecular size effect for biomolecules by poly(ethylene glycol) gel-based capillary electrophoresis.

PubMed

Kubo, Takuya; Nishimura, Naoki; Furuta, Hayato; Kubota, Kei; Naito, Toyohiro; Otsuka, Koji

2017-11-10

We report novel capillary gel electrophoresis (CGE) with poly(ethylene glycol) (PEG)-based hydrogels for the effective separations of biomolecules containing sugars and DNAs based on a molecular size effect. The gel capillaries were prepared in a fused silica capillary modified with 3-(trimethoxysilyl)propylmethacrylate using a variety of the PEG-based hydrogels. After the fundamental evaluations in CGE regarding the separation based on the molecular size effect depending on the crosslinking density, the optimized capillary provided the efficient separation of glucose ladder (G1 to G20). In addition, another capillary showed the successful separation of DNA ladder in the range of 10-1100 base pair, which is superior to an authentic acrylamide-based gel capillary. For both glucose and DNA ladders, the separation ranges against the molecular size were simply controllable by alteration of the concentration and/or units of ethylene oxide in the PEG-based crosslinker. Finally, we demonstrated the separations of real samples, which included sugars carved out from monoclonal antibodies, mAbs, and then the efficient separations based on the molecular size effect were achieved. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular gas in low-metallicity starburst galaxies:. Scaling relations and the CO-to-H2 conversion factor

NASA Astrophysics Data System (ADS)

Amorín, R.; Muñoz-Tuñón, C.; Aguerri, J. A. L.; Planesas, P.

2016-04-01

Context. Tracing the molecular gas-phase in low-mass star-forming galaxies becomes extremely challenging due to significant UV photo-dissociation of CO molecules in their low-dust, low-metallicity ISM environments. Aims: We aim to study the molecular content and the star-formation efficiency of a representative sample of 21 blue compact dwarf galaxies (BCDs), previously characterized on the basis of their spectrophotometric properties. Methods: We present CO (1-0) and (2-1) observations conducted at the IRAM-30m telescope. These data are further supplemented with additional CO measurements and multiwavelength ancillary data from the literature. We explore correlations between the derived CO luminosities and several galaxy-averaged properties. Results: We detect CO emission in seven out of ten BCDs observed. For two galaxies these are the first CO detections reported so far. We find the molecular content traced by CO to be correlated with the stellar and Hi masses, star formation rate (SFR) tracers, the projected size of the starburst, and its gas-phase metallicity. BCDs appear to be systematically offset from the Schmidt-Kennicutt (SK) law, showing lower average gas surface densities for a given ΣSFR, and therefore showing extremely low (≲0.1 Gyr) H2 and H2 +Hi depletion timescales. The departure from the SK law is smaller when considering H2 +Hi rather than H2 only, and is larger for BCDs with lower metallicity and higher specific SFR. Thus, the molecular fraction (ΣH2/ ΣHI) and CO depletion timescale (ΣH2/ ΣSFR) of BCDs is found to be strongly correlated with metallicity. Using this, and assuming that the empirical correlation found between the specific SFR and galaxy-averaged H2 depletion timescale of more metal-rich galaxies extends to lower masses, we derive a metallicity-dependent CO-to-H2 conversion factor αCO,Z ∝ (Z/Z⊙)- y, with y = 1.5(±0.3)in qualitative agreement with previous determinations, dust-based measurements, and recent model predictions. Consequently, our results suggest that in vigorously star-forming dwarfs the fraction of H2 traced by CO decreases by a factor of about 40 from Z ~ Z⊙ to Z ~ 0.1 Z⊙, leading to a strong underestimation of the H2 mass in metal-poor systems when a Galactic αCO,MW is considered. Adopting our metallicity-dependent conversion factor αCO,Z we find that departures from the SK law are partially resolved. Conclusions: Our results suggest that starbursting dwarfs have shorter depletion gas timescales and lower molecular fractions compared to normal late-type disc galaxies, even accounting for the molecular gas not traced by CO emission in metal-poor environments, raising additional constraints to model predictions. Based on observations carried out with the IRAM 30m Telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany) and IGN (Spain).

The X CO Conversion Factor from Galactic Multiphase ISM Simulations

NASA Astrophysics Data System (ADS)

Gong, Munan; Ostriker, Eve C.; Kim, Chang-Goo

2018-05-01

{CO}(J=1{--}0) line emission is a widely used observational tracer of molecular gas, rendering essential the X CO factor, which is applied to convert CO luminosity to {{{H}}}2 mass. We use numerical simulations to study how X CO depends on numerical resolution, non-steady-state chemistry, physical environment, and observational beam size. Our study employs 3D magnetohydrodynamics (MHD) simulations of galactic disks with solar neighborhood conditions, where star formation and the three-phase interstellar medium (ISM) are self-consistently regulated by gravity and stellar feedback. Synthetic CO maps are obtained by postprocessing the MHD simulations with chemistry and radiation transfer. We find that CO is only an approximate tracer of {{{H}}}2. On parsec scales, W CO is more fundamentally a measure of mass-weighted volume density, rather than {{{H}}}2 column density. Nevertheless, < {X}{{CO}} > =(0.7{\\textstyle {--}}1.0)× {10}20 {{{cm}}}-2 {{{K}}}-1 {{{km}}}-1 {{s}}, which is consistent with observations and insensitive to the evolutionary ISM state or radiation field strength if steady-state chemistry is assumed. Due to non-steady-state chemistry, younger molecular clouds have slightly lower < {X}CO}> and flatter profiles of X CO versus extinction than older ones. The {CO}-dark {{{H}}}2 fraction is 26%–79%, anticorrelated with the average extinction. As the observational beam size increases from 1 to 100 pc, < {X}CO}> increases by a factor of ∼2. Under solar neighborhood conditions, < {X}CO}> in molecular clouds is converged at a numerical resolution of 2 pc. However, the total CO abundance and luminosity are not converged even at the numerical resolution of 1 pc. Our simulations successfully reproduce the observed variations of X CO on parsec scales, as well as the dependence of X CO on extinction and the CO excitation temperature.

Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association.

PubMed

Lindström, Fredrick; Williamson, Philip T F; Gröbner, Gerhard

2005-05-11

Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic potential present at the surface of biological model membranes, the electrostatic charge distribution across the membrane interface, and changes that occur upon peptide association. The spectral resolution in (31)P and (14)N MAS NMR spectra is sufficient to probe directly the negatively charged phosphate and positively charged choline segment of the electrostatic P(-)-O-CH(2)-CH(2)-N(+)(CH(3))(3) headgroup dipole of zwitterionic DMPC (dimyristoylphosphatidylcholine) in mixed-lipid systems. The isotropic shifts report on the size of the potential existing at the phosphate and ammonium group within the lipid headgroup while the chemical shielding anisotropy ((31)P) and anisotropic quadrupolar interaction ((14)N) characterize changes in headgroup orientation in response to surface potential. The (31)P/(14)N isotropic chemical shifts for DMPC show opposing systematic changes in response to changing membrane potential, reflecting the size of the electrostatic potential at opposing ends of the P(-)-N(+) dipole. The orientational response of the DMPC lipid headgroup to electrostatic surface variations is visible in the anisotropic features of (14)N and (31)P NMR spectra. These features are analyzed in terms of a modified "molecular voltmeter" model, with changes in dynamic averaging reflecting the tilt of the C(beta)-N(+)(CH)(3) choline and PO(4)(-) segment. These properties have been exploited to characterize the changes in surface potential upon the binding of nociceptin to negatively charged membranes, a process assumed to proceed its agonistic binding to its opoid G-protein coupled receptor.

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

Experiments for the Undergraduate Laboratory that Illustrate the Size-Exclusion Properties of Zeolite Molecular Sieves

ERIC Educational Resources Information Center

Cooke, Jason; Henderson, Eric J.

2009-01-01

Experiments are presented that demonstrate the size-exclusion properties of zeolites and reveal the reason for naming zeolites "molecular sieves". If an IR spectrometer is available, the adsorption or exclusion of alcohols of varying sizes from dichloromethane or chloroform solutions can be readily demonstrated by monitoring changes in the…

Ultrahigh molecular weight aromatic siloxane polymers

NASA Technical Reports Server (NTRS)

Ludwick, L. M.

1982-01-01

The condensation of a diol with a silane in toluene yields a silphenylene-siloxane polymer. The reaction of stiochiometric amounts of the diol and silane produced products with molecular weights in the range 2.0 - 6.0 x 10 to the 5th power. The molecular weight of the product was greatly increased by a multistep technique. The methodology for synthesis of high molecular weight polymers using a two step procedure was refined. Polymers with weight average molecular weights in excess of 1.0 x 10 to the 6th power produced by this method. Two more reactive silanes, bis(pyrrolidinyl)dimethylsilane and bis(gamma butyrolactam)dimethylsilane, are compared with the dimethyleminodimethylsilane in ability to advance the molecular weight of the prepolymer. The polymers produced are characterized by intrinsic viscosity in tetrahydrofuran. Weight and number average molecular weights and polydispersity are determined by gel permeation chromatography.

Spin polarization of two-dimensional electron system in parabolic potential

NASA Astrophysics Data System (ADS)

Miyake, Takashi; Totsuji, Chieko; Nakanishi, Kenta; Tsuruta, Kenji; Totsuji, Hiroo

2008-09-01

We analyze the ground state of the two-dimensional quantum system of electrons confined in a parabolic potential with the system size around 100 at 0 K. We map the system onto a classical system on the basis of the classical-map hypernetted-chain (CHNC) method which has been proven to work in the integral-equation-based analyses of uniform systems and apply classical Monte Carlo and molecular dynamics simulations. We find that, when we decrease the strength of confinement keeping the number of confined electrons fixed, the energy of the spin-polarized state with somewhat lower average density becomes smaller than that of the spin-unpolarized state with somewhat higher average density. This system thus undergoes the transition from the spin-unpolarized state to the spin polarized state and the corresponding critical value of r estimated from the average density is as low as r∼0.4 which is much smaller than the r value for the Wigner lattice formation. When we compare the energies of spin-unpolarized and spin-polarized states for given average density, our data give the critical r value for the transition between unpolarized and polarized states around 10 which is close to but still smaller than the known possibility of polarization at r∼27. The advantage of our method is a direct applicability to geometrically complex systems which are difficult to analyze by integral equations and this is an example.

Sulphur hexaflouride: low energy (e,2e) experiments and molecular three-body distorted wave theory

NASA Astrophysics Data System (ADS)

Nixon, Kate L.; Murray, Andrew J.; Chaluvadi, H.; Ning, C. G.; Colgan, James; Madison, Don H.

2016-10-01

Experimental and theoretical triple differential ionisation cross-sections (TDCSs) are presented for the highest occupied molecular orbital of sulphur hexafluoride. These measurements were performed in the low energy regime, with outgoing electron energies ranging from 5 to 40 eV in a coplanar geometry, and with energies of 10 and 20 eV in a perpendicular geometry. Complementary theoretical predictions of the TDCS were calculated using the molecular three-body distorted wave formalism. Calculations were performed using a proper average over molecular orientations as well as the orientation-averaged molecular orbital approximation. This more sophisticated model was found to be in closer agreement with the experimental data, however neither model accurately predicts the TDCS over all geometries and energies.

Ensemble representations: effects of set size and item heterogeneity on average size perception.

PubMed

Marchant, Alexander P; Simons, Daniel J; de Fockert, Jan W

2013-02-01

Observers can accurately perceive and evaluate the statistical properties of a set of objects, forming what is now known as an ensemble representation. The accuracy and speed with which people can judge the mean size of a set of objects have led to the proposal that ensemble representations of average size can be computed in parallel when attention is distributed across the display. Consistent with this idea, judgments of mean size show little or no decrement in accuracy when the number of objects in the set increases. However, the lack of a set size effect might result from the regularity of the item sizes used in previous studies. Here, we replicate these previous findings, but show that judgments of mean set size become less accurate when set size increases and the heterogeneity of the item sizes increases. This pattern can be explained by assuming that average size judgments are computed using a limited capacity sampling strategy, and it does not necessitate an ensemble representation computed in parallel across all items in a display. Copyright © 2012 Elsevier B.V. All rights reserved.

Weighting by Inverse Variance or by Sample Size in Random-Effects Meta-Analysis

ERIC Educational Resources Information Center

Marin-Martinez, Fulgencio; Sanchez-Meca, Julio

2010-01-01

Most of the statistical procedures in meta-analysis are based on the estimation of average effect sizes from a set of primary studies. The optimal weight for averaging a set of independent effect sizes is the inverse variance of each effect size, but in practice these weights have to be estimated, being affected by sampling error. When assuming a…

Toward an organ based dose prescription method for the improved accuracy of murine dose in orthovoltage x-ray irradiators.

PubMed

Belley, Matthew D; Wang, Chu; Nguyen, Giao; Gunasingha, Rathnayaka; Chao, Nelson J; Chen, Benny J; Dewhirst, Mark W; Yoshizumi, Terry T

2014-03-01

Accurate dosimetry is essential when irradiating mice to ensure that functional and molecular endpoints are well understood for the radiation dose delivered. Conventional methods of prescribing dose in mice involve the use of a single dose rate measurement and assume a uniform average dose throughout all organs of the entire mouse. Here, the authors report the individual average organ dose values for the irradiation of a 12, 23, and 33 g mouse on a 320 kVp x-ray irradiator and calculate the resulting error from using conventional dose prescription methods. Organ doses were simulated in the Geant4 application for tomographic emission toolkit using the MOBY mouse whole-body phantom. Dosimetry was performed for three beams utilizing filters A (1.65 mm Al), B (2.0 mm Al), and C (0.1 mm Cu + 2.5 mm Al), respectively. In addition, simulated x-ray spectra were validated with physical half-value layer measurements. Average doses in soft-tissue organs were found to vary by as much as 23%-32% depending on the filter. Compared to filters A and B, filter C provided the hardest beam and had the lowest variation in soft-tissue average organ doses across all mouse sizes, with a difference of 23% for the median mouse size of 23 g. This work suggests a new dose prescription method in small animal dosimetry: it presents a departure from the conventional approach of assigninga single dose value for irradiation of mice to a more comprehensive approach of characterizing individual organ doses to minimize the error and uncertainty. In human radiation therapy, clinical treatment planning establishes the target dose as well as the dose distribution, however, this has generally not been done in small animal research. These results suggest that organ dose errors will be minimized by calibrating the dose rates for all filters, and using different dose rates for different organs.

Toward an organ based dose prescription method for the improved accuracy of murine dose in orthovoltage x-ray irradiators

PubMed Central

Belley, Matthew D.; Wang, Chu; Nguyen, Giao; Gunasingha, Rathnayaka; Chao, Nelson J.; Chen, Benny J.; Dewhirst, Mark W.; Yoshizumi, Terry T.

2014-01-01

Purpose: Accurate dosimetry is essential when irradiating mice to ensure that functional and molecular endpoints are well understood for the radiation dose delivered. Conventional methods of prescribing dose in mice involve the use of a single dose rate measurement and assume a uniform average dose throughout all organs of the entire mouse. Here, the authors report the individual average organ dose values for the irradiation of a 12, 23, and 33 g mouse on a 320 kVp x-ray irradiator and calculate the resulting error from using conventional dose prescription methods. Methods: Organ doses were simulated in the Geant4 application for tomographic emission toolkit using the MOBY mouse whole-body phantom. Dosimetry was performed for three beams utilizing filters A (1.65 mm Al), B (2.0 mm Al), and C (0.1 mm Cu + 2.5 mm Al), respectively. In addition, simulated x-ray spectra were validated with physical half-value layer measurements. Results: Average doses in soft-tissue organs were found to vary by as much as 23%–32% depending on the filter. Compared to filters A and B, filter C provided the hardest beam and had the lowest variation in soft-tissue average organ doses across all mouse sizes, with a difference of 23% for the median mouse size of 23 g. Conclusions: This work suggests a new dose prescription method in small animal dosimetry: it presents a departure from the conventional approach of assigning a single dose value for irradiation of mice to a more comprehensive approach of characterizing individual organ doses to minimize the error and uncertainty. In human radiation therapy, clinical treatment planning establishes the target dose as well as the dose distribution, however, this has generally not been done in small animal research. These results suggest that organ dose errors will be minimized by calibrating the dose rates for all filters, and using different dose rates for different organs. PMID:24593746

Toward an organ based dose prescription method for the improved accuracy of murine dose in orthovoltage x-ray irradiators

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

Belley, Matthew D.; Wang, Chu; Nguyen, Giao

2014-03-15

Purpose: Accurate dosimetry is essential when irradiating mice to ensure that functional and molecular endpoints are well understood for the radiation dose delivered. Conventional methods of prescribing dose in mice involve the use of a single dose rate measurement and assume a uniform average dose throughout all organs of the entire mouse. Here, the authors report the individual average organ dose values for the irradiation of a 12, 23, and 33 g mouse on a 320 kVp x-ray irradiator and calculate the resulting error from using conventional dose prescription methods. Methods: Organ doses were simulated in the Geant4 application formore » tomographic emission toolkit using the MOBY mouse whole-body phantom. Dosimetry was performed for three beams utilizing filters A (1.65 mm Al), B (2.0 mm Al), and C (0.1 mm Cu + 2.5 mm Al), respectively. In addition, simulated x-ray spectra were validated with physical half-value layer measurements. Results: Average doses in soft-tissue organs were found to vary by as much as 23%–32% depending on the filter. Compared to filters A and B, filter C provided the hardest beam and had the lowest variation in soft-tissue average organ doses across all mouse sizes, with a difference of 23% for the median mouse size of 23 g. Conclusions: This work suggests a new dose prescription method in small animal dosimetry: it presents a departure from the conventional approach of assigninga single dose value for irradiation of mice to a more comprehensive approach of characterizing individual organ doses to minimize the error and uncertainty. In human radiation therapy, clinical treatment planning establishes the target dose as well as the dose distribution, however, this has generally not been done in small animal research. These results suggest that organ dose errors will be minimized by calibrating the dose rates for all filters, and using different dose rates for different organs.« less

Aggregation of Lens Crystallins in an In Vivo Hyperbaric Oxygen Guinea Pig Model of Nuclear Cataract: Dynamic Light-Scattering and HPLC Analysis

PubMed Central

Simpanya, M. Francis; Ansari, Rafat R.; Suh, Kwang I.; Leverenz, Victor R.; Giblin, Frank J.

2006-01-01

Purpose The role of oxygen in the formation of lens high-molecular-weight (HMW) protein aggregates during the development of human nuclear cataract is not well understood. The purpose of this study was to investigate lens crystallin aggregate formation in hyperbaric oxygen (HBO)–treated guinea pigs by using in vivo and in vitro methods. Methods Guinea pigs were treated three times weekly for 7 months with HBO, and lens crystallin aggregation was investigated in vivo with the use of dynamic light-scattering (DLS) and in vitro by HPLC analysis of water-insoluble (WI) proteins. DLS measurements were made every 0.1 mm across the 4.5- to 5.0-mm optical axis of the guinea pig lens. Results The average apparent diameter of proteins in the nucleus (the central region) of lenses of HBO-treated animals was nearly twice that of the control animals (P < 0.001). Size distribution analysis conducted at one selected point in the nucleus and cortex (the outer periphery of the lens) after dividing the proteins into small-diameter and large-diameter groups, showed in the O2-treated nucleus a threefold increase in intensity (P < 0.001) and a doubling in apparent size (P = 0.03) of large-diameter aggregate proteins, compared with the same control group. No significant changes in apparent protein diameter were detected in the O2-treated cortex, compared with the control. The average diameter of protein aggregates at the single selected location in the O2-treated nucleus was estimated to be 150 nm, a size capable of scattering light and similar to the size of aggregates found in human nuclear cataracts. HPLC analysis indicated that one half of the experimental nuclear WI protein fraction (that had been dissolved in guanidine) consisted of disulfide cross-linked 150- to 1000-kDa aggregates, not present in the control. HPLC-isolated aggregates contained αA-, β-, γ-, and ζ-crystallins, but not αB-crystallin, which is devoid of −SH groups and thus does not participate in disulfide cross-linking. All ζ-crystallin present in the nuclear WI fraction appeared to be there as a result of disulfide cross-linking. Conclusions The results indicate that molecular oxygen in vivo can induce the cross-linking of guinea pig lens nuclear crystallins into large disulfide-bonded aggregates capable of scattering light. A similar process may be involved in the formation of human nuclear cataract. PMID:16303961

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

PubMed Central

Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

2016-01-01

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

Characterization of rubber particles and rubber chain elongation in Taraxacum koksaghyz

PubMed Central

2010-01-01

Background Natural rubber is a biopolymer with exceptional qualities that cannot be completely replaced using synthetic alternatives. Although several key enzymes in the rubber biosynthetic pathway have been isolated, mainly from plants such as Hevea brasiliensis, Ficus spec. and the desert shrub Parthenium argentatum, there have been no in planta functional studies, e.g. by RNA interference, due to the absence of efficient and reproducible protocols for genetic engineering. In contrast, the Russian dandelion Taraxacum koksaghyz, which has long been considered as a potential alternative source of low-cost natural rubber, has a rapid life cycle and can be genetically transformed using a simple and reliable procedure. However, there is very little molecular data available for either the rubber polymer itself or its biosynthesis in T. koksaghyz. Results We established a method for the purification of rubber particles - the active sites of rubber biosynthesis - from T. koksaghyz latex. Photon correlation spectroscopy and transmission electron microscopy revealed an average particle size of 320 nm, and 13C nuclear magnetic resonance (NMR) spectroscopy confirmed that isolated rubber particles contain poly(cis-1,4-isoprene) with a purity >95%. Size exclusion chromatography indicated that the weight average molecular mass (w) of T. koksaghyz natural rubber is 4,000-5,000 kDa. Rubber particles showed rubber transferase activity of 0.2 pmol min-1 mg-1. Ex vivo rubber biosynthesis experiments resulted in a skewed unimodal distribution of [1-14C]isopentenyl pyrophosphate (IPP) incorporation at a w of 2,500 kDa. Characterization of recently isolated cis-prenyltransferases (CPTs) from T. koksaghyz revealed that these enzymes are associated with rubber particles and are able to produce long-chain polyprenols in yeast. Conclusions T. koksaghyz rubber particles are similar to those described for H. brasiliensis. They contain very pure, high molecular mass poly(cis-1,4-isoprene) and the chain elongation process can be studied ex vivo. Because of their localization on rubber particles and their activity in yeast, we propose that the recently described T. koksaghyz CPTs are the major rubber chain elongating enzymes in this species. T. koksaghyz is amenable to genetic analysis and modification, and therefore could be used as a model species for the investigation and comparison of rubber biosynthesis. PMID:20170509

Effects of electronic excitation in 150 keV Ni ion irradiation of metallic systems

NASA Astrophysics Data System (ADS)

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2018-01-01

We use the two-temperature model in molecular dynamic simulations of 150 keV Ni ion cascades in nickel and nickel-based alloys to investigate the effect of the energy exchange between the atomic and the electronic systems during the primary stages of radiation damage. We find that the electron-phonon interactions result in a smaller amount of defects and affect the cluster formation, resulting in smaller clusters. These results indicate that ignoring the local heating due to the electrons results in the overestimation of the amount of damage and the size of the defect clusters. A comparison of the average defect production to the Norgett-Robinson-Torrens (NRT) prediction over a range of energies is provided.

Robot Towed Shortwave Infrared Camera for Specific Surface Area Retrieval of Surface Snow

NASA Astrophysics Data System (ADS)

Elliott, J.; Lines, A.; Ray, L.; Albert, M. R.

2017-12-01

Optical grain size and specific surface area are key parameters for measuring the atmospheric interactions of snow, as well as tracking metamorphosis and allowing for the ground truthing of remote sensing data. We describe a device using a shortwave infrared camera with changeable optical bandpass filters (centered at 1300 nm and 1550 nm) that can be used to quickly measure the average SSA over an area of 0.25 m^2. The device and method are compared with calculations made from measurements taken with a field spectral radiometer. The instrument is designed to be towed by a small autonomous ground vehicle, and therefore rides above the snow surface on ultra high molecular weight polyethylene (UHMW) skis.

3D RISM theory with fast reciprocal-space electrostatics.

PubMed

Heil, Jochen; Kast, Stefan M

2015-03-21

The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

Molecular characterization of branched polysaccharides from Tremella fuciformis by asymmetrical flow field-flow fractionation and size exclusion chromatography.

PubMed

Wu, Ding-Tao; Deng, Yong; Zhao, Jing; Li, Shao-Ping

2017-11-01

To accurately characterize branched polysaccharides with high molecular weights from medicinal and edible mushrooms and identify the limitations of size exclusion chromatography, molecular characteristics of polysaccharides from Tremella fuciformis were determined and compared by asymmetrical flow field-flow fractionation coupled with multiangle laser light scattering and refractive index detection, and size exclusion chromatography coupled with multiangle laser light scattering and refractive index detection, respectively. Results showed that molecular weights of three batches of T. fuciformis polysaccharides were determined as 2.167 × 10 6 (TF1), 2.334 × 10 6 (TF2), and 2.435 × 10 6  Da (TF3) by size exclusion chromatography, and 3.432 × 10 6 (TF1), 3.739 × 10 6 (TF2), and 3.742 × 10 6  Da (TF3) by asymmetrical flow field-flow fractionation, as well as 3.469 × 10 6  Da (TF1) by off-line multiangle laser light scattering, respectively. Results suggested that size exclusion chromatography was unable to accurately characterize T. fuciformis polysaccharides, which may be due to its limitations such as shear degradation and abnormal coelution. Compared to size exclusion chromatography, asymmetrical flow field-flow fractionation could be a better technique for the molecular characterization of branched polysaccharides with high molecular weights from medicinal and edible mushrooms, as well as from other natural resources. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Factors that affect molecular weight distribution of Suwannee river fulvic acid as determined by electrospray ionization/mass spectrometry

USGS Publications Warehouse

Rostad, C.E.; Leenheer, J.A.

2004-01-01

Effects of methylation, molar response, multiple charging, solvents, and positive and negative ionization on molecular weight distributions of aquatic fulvic acid were investigated by electrospray ionization/mass spectrometry. After preliminary analysis by positive and negative modes, samples and mixtures of standards were derivatized by methylation to minimize ionization sites and reanalyzed.Positive ionization was less effective and produced more complex spectra than negative ionization. Ionization in methanol/water produced greater response than in acetonitrile/water. Molar response varied widely for the selected free acid standards when analyzed individually and in a mixture, but after methylation this range decreased. After methylation, the number average molecular weight of the Suwannee River fulvic acid remained the same while the weight average molecular weight decreased. These differences are probably indicative of disaggregation of large aggregated ions during methylation. Since the weight average molecular weight decreased, it is likely that aggregate formation in the fulvic acid was present prior to derivatization, rather than multiple charging in the mass spectra. ?? 2004 Elsevier B.V. All rights reserved.

Epidemiologic and Molecular Relationship Between Vaccine Manufacture and Autism Spectrum Disorder Prevalence.

PubMed

Deisher, Theresa A; Doan, Ngoc V; Koyama, Kumiko; Bwabye, Sarah

2015-01-01

To assess the public health consequences of fetal cell line manufactured vaccines that contain residual human fetal DNA fragments utilizing laboratory and ecological approaches including statistics, molecular biology and genomics. MMR coverage and autism disorder or autism spectrum disorder prevalence data for Norway, Sweden and the UK were obtained from public and government websites as well as peer reviewed published articles. Biologically, the size and quantity of the contaminating fetal DNA in Meruvax II and Havrix as well as the propensity of various cell lines for cellular and nuclear uptake of primitive human DNA fragments were measured and quantified using gel electrophoresis, fluorescence microscopy and fluorometry. Lastly, genomic analysis identified the specific sites where fetal DNA fragment integration into a child's genome is most likely to occur. The average MMR coverage for the three countries fell below 90% after Dr. Wakefield's infamous 1998 publication but started to recover slowly after 2001 until reaching over 90% coverage again by 2004. During the same time period, the average autism spectrum disorder prevalence in the United Kingdom, Norway and Sweden dropped substantially after birth year 1998 and gradually increased again after birth year 2000. Average single stranded DNA and double stranded DNA in Meruvax II were 142.05 ng/vial and 35.00 ng/vial, respectively, and 276.00 ng/vial and 35.74 ng/vial in Havrix respectively. The size of the fetal DNA fragments in Meruvax II was approximately 215 base pairs. There was spontaneous cellular and nuclear DNA uptake in HFF1 and NCCIT cells. Genes that have been linked to autism (autism associated genes; AAGs) have a more concentrated susceptibility for insults to genomic stability in comparison to the group of all genes contained within the human genome. Of the X chromosome AAGs, 15 of 19 have double strand break motifs less than 100 kilobases away from the center of a meiotic recombination hotspot located within an exon. Vaccines manufactured in human fetal cell lines contain unacceptably high levels of fetal DNA fragment contaminants. The human genome naturally contains regions that are susceptible to double strand break formation and DNA insertional mutagenesis. The "Wakefield Scare" created a natural experiment that may demonstrate a causal relationship between fetal cell-line manufactured vaccines and ASD prevalence.

Identification of early indicators of altered metabolism in normal development using a rodent model system.

PubMed

Prabakaran, Ashok Daniel; Karakkat, Jimsheena Valiyakath; Vijayan, Ranjit; Chalissery, Jisha; Ibrahim, Marwa F; Kaimala, Suneesh; Adeghate, Ernest A; Al-Marzouqi, Ahmed Hassan; Ansari, Suraiya Anjum; Mensah-Brown, Eric; Emerald, Bright Starling

2018-03-01

Although the existence of a close relationship between the early maternal developmental environment, fetal size at birth and the risk of developing disease in adulthood has been suggested, most studies, however, employed experimentally induced intrauterine growth restriction as a model to link this with later adult disease. Because embryonic size variation also occurs under normal growth and differentiation, elucidating the molecular mechanisms underlying these changes and their relevance to later adult disease risk becomes important. The birth weight of rat pups vary according to the uterine horn positions. Using birth weight as a marker, we compared two groups of rat pups - lower birth weight (LBW, 5th to 25th percentile) and average birth weight (ABW, 50th to 75th percentile) - using morphological, biochemical and molecular biology, and genetic techniques. Our results show that insulin metabolism, Pi3k/Akt and Pparγ signaling and the genes regulating growth and metabolism are significantly different in these groups. Methylation at the promoter of the InsII ( Ins2 ) gene and DNA methyltransferase 1 in LBW pups are both increased. Additionally, the Dnmt1 repressor complex, which includes Hdac1, Rb (Rb1) and E2f1, was also upregulated in LBW pups. We conclude that the Dnmt1 repressor complex, which regulates the restriction point of the cell cycle, retards the rate at which cells traverse the G1 or G0 phase of the cell cycle in LBW pups, thereby slowing down growth. This regulatory mechanism mediated by Dnmt1 might contribute to the production of small-size pups and altered physiology and pathology in adult life. © 2018. Published by The Company of Biologists Ltd.

Identification of early indicators of altered metabolism in normal development using a rodent model system

PubMed Central

Prabakaran, Ashok Daniel; Karakkat, Jimsheena Valiyakath; Chalissery, Jisha; Ibrahim, Marwa F.; Kaimala, Suneesh; Adeghate, Ernest A.; Al-Marzouqi, Ahmed Hassan; Ansari, Suraiya Anjum

2018-01-01

ABSTRACT Although the existence of a close relationship between the early maternal developmental environment, fetal size at birth and the risk of developing disease in adulthood has been suggested, most studies, however, employed experimentally induced intrauterine growth restriction as a model to link this with later adult disease. Because embryonic size variation also occurs under normal growth and differentiation, elucidating the molecular mechanisms underlying these changes and their relevance to later adult disease risk becomes important. The birth weight of rat pups vary according to the uterine horn positions. Using birth weight as a marker, we compared two groups of rat pups – lower birth weight (LBW, 5th to 25th percentile) and average birth weight (ABW, 50th to 75th percentile) – using morphological, biochemical and molecular biology, and genetic techniques. Our results show that insulin metabolism, Pi3k/Akt and Pparγ signaling and the genes regulating growth and metabolism are significantly different in these groups. Methylation at the promoter of the InsII (Ins2) gene and DNA methyltransferase 1 in LBW pups are both increased. Additionally, the Dnmt1 repressor complex, which includes Hdac1, Rb (Rb1) and E2f1, was also upregulated in LBW pups. We conclude that the Dnmt1 repressor complex, which regulates the restriction point of the cell cycle, retards the rate at which cells traverse the G1 or G0 phase of the cell cycle in LBW pups, thereby slowing down growth. This regulatory mechanism mediated by Dnmt1 might contribute to the production of small-size pups and altered physiology and pathology in adult life. PMID:29434026

Improved drug loading and antibacterial activity of minocycline-loaded PLGA nanoparticles prepared by solid/oil/water ion pairing method.

PubMed

Kashi, Tahereh Sadat Jafarzadeh; Eskandarion, Solmaz; Esfandyari-Manesh, Mehdi; Marashi, Seyyed Mahmoud Amin; Samadi, Nasrin; Fatemi, Seyyed Mostafa; Atyabi, Fatemeh; Eshraghi, Saeed; Dinarvand, Rassoul

2012-01-01

Low drug entrapment efficiency of hydrophilic drugs into poly(lactic-co-glycolic acid) (PLGA) nanoparticles is a major drawback. The objective of this work was to investigate different methods of producing PLGA nanoparticles containing minocycline, a drug suitable for periodontal infections. Different methods, such as single and double solvent evaporation emulsion, ion pairing, and nanoprecipitation were used to prepare both PLGA and PEGylated PLGA nanoparticles. The resulting nanoparticles were analyzed for their morphology, particle size and size distribution, drug loading and entrapment efficiency, thermal properties, and antibacterial activity. The nanoparticles prepared in this study were spherical, with an average particle size of 85-424 nm. The entrapment efficiency of the nanoparticles prepared using different methods was as follows: solid/oil/water ion pairing (29.9%) > oil/oil (5.5%) > water/oil/water (4.7%) > modified oil/water (4.1%) > nano precipitation (0.8%). Addition of dextran sulfate as an ion pairing agent, acting as an ionic spacer between PEGylated PLGA and minocycline, decreased the water solubility of minocycline, hence increasing the drug entrapment efficiency. Entrapment efficiency was also increased when low molecular weight PLGA and high molecular weight dextran sulfate was used. Drug release studies performed in phosphate buffer at pH 7.4 indicated slow release of minocycline from 3 days to several weeks. On antibacterial analysis, the minimum inhibitory concentration and minimum bactericidal concentration of nanoparticles was at least two times lower than that of the free drug. Novel minocycline-PEGylated PLGA nanoparticles prepared by the ion pairing method had the best drug loading and entrapment efficiency compared with other prepared nanoparticles. They also showed higher in vitro antibacterial activity than the free drug.

Improved drug loading and antibacterial activity of minocycline-loaded PLGA nanoparticles prepared by solid/oil/water ion pairing method

PubMed Central

Kashi, Tahereh Sadat Jafarzadeh; Eskandarion, Solmaz; Esfandyari-Manesh, Mehdi; Marashi, Seyyed Mahmoud Amin; Samadi, Nasrin; Fatemi, Seyyed Mostafa; Atyabi, Fatemeh; Eshraghi, Saeed; Dinarvand, Rassoul

2012-01-01

Background Low drug entrapment efficiency of hydrophilic drugs into poly(lactic-co-glycolic acid) (PLGA) nanoparticles is a major drawback. The objective of this work was to investigate different methods of producing PLGA nanoparticles containing minocycline, a drug suitable for periodontal infections. Methods Different methods, such as single and double solvent evaporation emulsion, ion pairing, and nanoprecipitation were used to prepare both PLGA and PEGylated PLGA nanoparticles. The resulting nanoparticles were analyzed for their morphology, particle size and size distribution, drug loading and entrapment efficiency, thermal properties, and antibacterial activity. Results The nanoparticles prepared in this study were spherical, with an average particle size of 85–424 nm. The entrapment efficiency of the nanoparticles prepared using different methods was as follows: solid/oil/water ion pairing (29.9%) > oil/oil (5.5%) > water/oil/water (4.7%) > modified oil/water (4.1%) > nano precipitation (0.8%). Addition of dextran sulfate as an ion pairing agent, acting as an ionic spacer between PEGylated PLGA and minocycline, decreased the water solubility of minocycline, hence increasing the drug entrapment efficiency. Entrapment efficiency was also increased when low molecular weight PLGA and high molecular weight dextran sulfate was used. Drug release studies performed in phosphate buffer at pH 7.4 indicated slow release of minocycline from 3 days to several weeks. On antibacterial analysis, the minimum inhibitory concentration and minimum bactericidal concentration of nanoparticles was at least two times lower than that of the free drug. Conclusion Novel minocycline-PEGylated PLGA nanoparticles prepared by the ion pairing method had the best drug loading and entrapment efficiency compared with other prepared nanoparticles. They also showed higher in vitro antibacterial activity than the free drug. PMID:22275837

Nanopores creation in boron and nitrogen doped polycrystalline graphene: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Izadifar, Mohammadreza; Abadi, Rouzbeh; Nezhad Shirazi, Ali Hossein; Alajlan, Naif; Rabczuk, Timon

2018-05-01

In the present paper, molecular dynamic simulations have been conducted to investigate the nanopores creation on 10% of boron and nitrogen doped polycrystalline graphene by silicon and diamond nanoclusters. Two types of nanoclusters based on silicon and diamond are used to investigate their effect for the fabrication of nanopores. Therefore, three different diameter sizes of the clusters with five kinetic energies of 10, 50, 100, 300 and 500 eV/atom at four different locations in boron or nitrogen doped polycrystalline graphene nanosheets have been perused. We also study the effect of 3% and 6% of boron doped polycrystalline graphene with the best outcome from 10% of doping. Our results reveal that the diamond cluster with diameter of 2 and 2.5 nm fabricates the largest nanopore areas on boron and nitrogen doped polycrystalline graphene, respectively. Furthermore, the kinetic energies of 10 and 50 eV/atom can not fabricate nanopores in some cases for silicon and diamond clusters on boron doped polycrystalline graphene nanosheets. On the other hand, silicon and diamond clusters fabricate nanopores for all locations and all tested energies on nitrogen doped polycrystalline graphene. The area sizes of nanopores fabricated by silicon and diamond clusters with diameter of 2 and 2.5 nm are close to the actual area size of the related clusters for the kinetic energy of 300 eV/atom in all locations on boron doped polycrystalline graphene. The maximum area and the average maximum area of nanopores are fabricated by the kinetic energy of 500 eV/atom inside the grain boundary at the center of the nanosheet and in the corner of nanosheet with diameters of 2 and 3 nm for silicon and diamond clusters on boron and nitrogen doped polycrystalline graphene.

Molecular-Sized DNA or RNA Sequencing Machine | NCI Technology Transfer Center | TTC

Cancer.gov

The National Cancer Institute's Gene Regulation and Chromosome Biology Laboratory is seeking statements of capability or interest from parties interested in collaborative research to co-develop a molecular-sized DNA or RNA sequencing machine.

The role of size polydispersity in magnetic fluid hyperthermia: average vs. local infra/over-heating effects.

PubMed

Munoz-Menendez, Cristina; Conde-Leboran, Ivan; Baldomir, Daniel; Chubykalo-Fesenko, Oksana; Serantes, David

2015-11-07

An efficient and safe hyperthermia cancer treatment requires the accurate control of the heating performance of magnetic nanoparticles, which is directly related to their size. However, in any particle system the existence of some size polydispersity is experimentally unavoidable, which results in a different local heating output and consequently a different hyperthermia performance depending on the size of each particle. With the aim to shed some light on this significant issue, we have used a Monte Carlo technique to study the role of size polydispersity in heat dissipation at both the local (single particle) and global (macroscopic average) levels. We have systematically varied size polydispersity, temperature and interparticle dipolar interaction conditions, and evaluated local heating as a function of these parameters. Our results provide a simple guide on how to choose, for a given polydispersity degree, the more adequate average particle size so that the local variation in the released heat is kept within some limits that correspond to safety boundaries for the average-system hyperthermia performance. All together we believe that our results may help in the design of more effective magnetic hyperthermia applications.

Factors determining the average body size of geographically separated Arctodiaptomus salinus (Daday, 1885) populations

PubMed Central

Anufriieva, Elena V.; Shadrin, Nickolai V.

2014-01-01

Arctodiaptomus salinus inhabits water bodies across Eurasia and North Africa. Based on our own data and that from the literature, we analyzed the influences of several factors on the intra- and inter-population variability of this species. A strong negative linear correlation between temperature and average body size in the Crimean and African populations was found, in which the parameters might be influenced by salinity. Meanwhile, asignificant negative correlation between female body size and the altitude of habitats was found by comparing body size in populations from different regions. Individuals from environments with highly varying abiotic parameters, e.g. temporary reservoirs, had a larger body size than individuals from permanent water bodies. The changes in average body mass in populations were at 11.4 times, whereas, those in individual metabolic activities were at 6.2 times. Moreover, two size groups of A. salinus in the Crimean and the Siberian lakes were observed. The ratio of female length to male length fluctuatedbetween 1.02 and 1.30. The average size of A. salinus in populations and its variations were determined by both genetic and environmental factors. However, the paritiesof these factors were unequal in either spatial or temporal scales. PMID:24668656

Factors determining the average body size of geographically separated Arctodiaptomus salinus (Daday, 1885) populations.

PubMed

Anufriieva, Elena V; Shadrin, Nickolai V

2014-03-01

Arctodiaptomus salinus inhabits water bodies across Eurasia and North Africa. Based on our own data and that from the literature, we analyzed the influences of several factors on the intra- and inter-population variability of this species. A strong negative linear correlation between temperature and average body size in the Crimean and African populations was found, in which the parameters might be influenced by salinity. Meanwhile, a significant negative correlation between female body size and the altitude of habitats was found by comparing body size in populations from different regions. Individuals from environments with highly varying abiotic parameters, e.g. temporary reservoirs, had a larger body size than individuals from permanent water bodies. The changes in average body mass in populations were at 11.4 times, whereas, those in individual metabolic activities were at 6.2 times. Moreover, two size groups of A. salinus in the Crimean and the Siberian lakes were observed. The ratio of female length to male length fluctuated between 1.02 and 1.30. The average size of A. salinus in populations and its variations were determined by both genetic and environmental factors. However, the parities of these factors were unequal in either spatial or temporal scales.

Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries

PubMed Central

Kerrigan, Elizabeth A.; Irwin, Andrew J.

2015-01-01

Climate change over the last two centuries has been associated with significant shifts in diatom community structure in lakes from the high arctic to temperate latitudes. To test the hypotheses that recent climate warming selects for species of smaller size within communities and a decrease in the average size of species within populations, we quantified the size of individual diatom valves from 10 depths in a sediment core covering the last ∼200 years from a pristine subarctic lake. Over the last ∼200 years, changes in the relative abundance of species of different average size and changes in the average valve size of populations of species contribute equally to the changes in community size structure, but are often opposite in sign, compensating for one another and moderating temporal changes in community size structure. In the surface sediments that correspond to the recent decades when air temperatures have warmed, the mean size of valves in the diatom community has significantly decreased due to an increase in the proportion of smaller-sized planktonic diatom species. PMID:26157637

Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects.

PubMed

Ho, Po-Yi; Lin, Jie; Amir, Ariel

2018-05-20

Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its molecular implementations, protein number regulation, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation.

Creating Cost-Effective DNA Size Standards for Use in Teaching and Research Laboratories

ERIC Educational Resources Information Center

Shultz, Jeff

2011-01-01

I have devised a method with which a molecular size standard can be readily manufactured using Lambda DNA and PCR. This method allows the production of specific sized DNA fragments and is easily performed in a standard molecular biology laboratory. The material required to create these markers can also be used to provide a highly robust and…

Hindered transport of macromolecules in isolated glomeruli. II. Convection and pressure effects in basement membrane.

PubMed

Edwards, A; Daniels, B S; Deen, W M

1997-01-01

The filtration rates for water and a polydisperse mixture of Ficoll across films of isolated glomerular basement membrane (GBM) were measured to characterize convective transport across this part of the glomerular capillary wall. Glomeruli were isolated from rat kidneys and the cells were removed by detergent lysis, leaving a preparation containing almost pure GBM that could be consolidated into a layer at the base of a small ultrafiltration cell. A Ficoll mixture with Stokes-Einstein radii ranging from about 2.0 to 7.0 nm was labeled with fluorescein, providing a set of rigid, spherical test macromolecules with little molecular charge. Filtration experiments were performed at two physiologically relevant hydraulic pressure differences (delta P), 35 and 60 mmHg. The sieving coefficient (filtrate-to-retentate concentration ratio) for a given size of Ficoll tended to be larger at 35 than at 60 mmHg, the changes being greater for the smaller molecules. The Darcy permeability also varied inversely with pressure, averaging 1.48 +/- 0.10 nm2 at 35 mmHg and 0.82 +/- 0.07 nm2 at 60 mmHg. Both effects could be explained most simply by postulating that the intrinsic permeability properties of the GBM change in response to compression. The sieving data were consistent with linear declines in the hindrance factors for convection and diffusion with increasing pressure, and correlations were derived to relate those hindrance factors to molecular size and delta P. Comparisons with previous Ficoll sieving data for rats in vivo suggest that the GBM is less size-restrictive than the cell layers, but that its contribution to the overall size selectivity of the barrier is not negligible. Theoretical predictions of the Darcy permeability based on a model in which the GBM is a random fibrous network consisting of two populations of fibers were in excellent agreement with the present data and with ultrastructural observations in the literature.

Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions

PubMed Central

Mester, Dávid

2017-01-01

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller–Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as the evaluation of the MP2 and CIS(D) density matrices. All in all, an average speedup of more than an order of magnitude can be achieved at the expense of a mean absolute error of 0.02 eV in the calculated excitation energies compared to the canonical CC2 results. Our benchmark calculations demonstrate that the new approach enables the efficient computation of CC2 excitation energies for excited states of all types of medium-sized molecules composed of up to 100 atoms with triple-zeta quality basis sets. PMID:28527453

Size-controlled synthesis and formation mechanism of manganese oxide OMS-2 nanowires under reflux conditions with KMnO4 and inorganic acids

NASA Astrophysics Data System (ADS)

Zhang, Qin; Cheng, Xiaodi; Qiu, Guohong; Liu, Fan; Feng, Xionghan

2016-05-01

This study presents a simplified approach for size-controlled synthesis of manganese oxide octahedral molecular sieve (OMS-2) nanowires using potassium permanganate (KMnO4) and different inorganic acids (HCl, HNO3, and H2SO4) under reflux conditions. The morphology and nanostructure of the synthesized products are characterized by X-ray diffraction, Ar adsorption, and electron microscopy analysis, in order to elucidate the controlling effects of acid concentration and type as well as the formation mechanism of OMS-2 nanowires. The concentration of inorganic acid is a crucial factor controlling the phase of the synthesized products. OMS-2 nanowires are obtained with HCl at the concentration ≥0.96 mol/L or with HNO3 and H2SO4 at the concentrations ≥0.72 mol/L. Differently, the type of inorganic acid effectively determines the particle size of OMS-2 nanowires. When the acid is changed from HCl to HNO3 and H2SO4 in the reflux system, the average length of OMS-2 declines significantly by 60-70% (1104-442 and 339 nm), with minor decreased in the average width (43-39 and 34 nm). The formation of OMS-2 nanowires under reflux conditions with KMnO4 and inorganic acids involves a two-step process, i.e., the initial formation of layered manganese oxides, and subsequent transformation to OMS-2 via a dissolution-recrystallization process under acidic conditions. The proposed reflux route provides an alternative approach for synthesizing OMS-2 nanowires as well as other porous nano-crystalline OMS materials.

Optimal size for heating efficiency of superparamagnetic dextran-coated magnetite nanoparticles for application in magnetic fluid hyperthermia

NASA Astrophysics Data System (ADS)

Shaterabadi, Zhila; Nabiyouni, Gholamreza; Soleymani, Meysam

2018-06-01

Dextran-coated magnetite (Fe3O4) nanoparticles with average particle sizes of 4 and 19 nm were synthesized through in situ and semi-two-step co-precipitation methods, respectively. The experimental results confirm the formation of pure phase of magnetite as well as the presence of dextran layer on the surface of modified magnetite nanoparticles. The results also reveal that both samples have the superparamagnetic behavior. Furthermore, calorimetric measurements show that the dextran-coated Fe3O4 nanoparticles with an average size of 4 nm cannot produce any appreciable heat under a biologically safe alternating magnetic field used in hyperthermia therapy; whereas, the larger ones (average size of 19 nm) are able to increase the temperature of their surrounding medium up to above therapeutic range. In addition, measured specific absorption rate (SAR) values confirm that magnetite nanoparticles with an average size of 19 nm are very excellent candidates for application in magnetic hyperthermia therapy.

Size of Human Figure Drawings as Influenced by Instructions for "Sexy" versus "Average" Drawings and by the Status of the Experimenter.

ERIC Educational Resources Information Center

Duffy, Karen G.; And Others

1982-01-01

Investigated the effects of experimenter status and sex and instructional set on the size of "sexy" and "average" human figure drawings by students. Results showed no effects for experimenter status or sex. "Sexy" drawings were consistently drawn larger than "average" drawings and male figures were drawn…

Use of gold nanoparticles as crosslink agent to form chitosan nanocapsules: study of the direct interaction in aqueous solutions.

PubMed

Prado-Gotor, R; López-Pérez, G; Martín, M J; Cabrera-Escribano, F; Franconetti, A

2014-06-01

A systematic study of the interaction between free anionic gold nanoparticles and chitosan in a solution is presented. A spectroscopic study of the interaction between 10nm gold nanoparticles and low molecular weight chitosan is reported as a function of the concentration and pH of the polymer in a solution. Zeta potential measurements and TEM images indicate the effective aggregation of the nanoparticles in the presence of chitosan. At the same time, anionic gold nanoparticles act as crosslink agents to form chitosan nanocapsules with an average molecular size of 260nm. The changes of the surface plasmon band due to the adsorption of the polymer on the nanoparticle surface allow using of the citrate gold nanoparticles as sensors of the polymer for analytical purposes. The limit of detection for chitosan biopolymer is 69nM. The optimum pH for the interaction between the biopolymer and the nanoparticles is found at a value of 6.4, obtained from spectrophotometric measurements and applying a deconvolution analysis of the experimental data. A simple model based on molecular surface electrostatic interactions is proposed to understand the pH dependence of the investigated system. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition

DOE PAGES

Bergsman, David S.; Closser, Richard G.; Tassone, Christopher J.; ...

2017-01-01

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on themore » monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ~25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. In conclusion, these results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.« less

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

CO line ratios in molecular clouds: the impact of environment

NASA Astrophysics Data System (ADS)

Peñaloza, Camilo H.; Clark, Paul C.; Glover, Simon C. O.; Klessen, Ralf S.

2018-04-01

Line emission is strongly dependent on the local environmental conditions in which the emitting tracers reside. In this work, we focus on modelling the CO emission from simulated giant molecular clouds (GMCs), and study the variations in the resulting line ratios arising from the emission from the J = 1-0, J = 2-1, and J = 3-2 transitions. We perform a set of smoothed particle hydrodynamics simulations with time-dependent chemistry, in which environmental conditions - including total cloud mass, density, size, velocity dispersion, metallicity, interstellar radiation field (ISRF), and the cosmic ray ionization rate (CRIR) - were systematically varied. The simulations were then post-processed using radiative transfer to produce synthetic emission maps in the three transitions quoted above. We find that the cloud-averaged values of the line ratios can vary by up to ±0.3 dex, triggered by changes in the environmental conditions. Changes in the ISRF and/or in the CRIR have the largest impact on line ratios since they directly affect the abundance, temperature, and distribution of CO-rich gas within the clouds. We show that the standard methods used to convert CO emission to H2 column density can underestimate the total H2 molecular gas in GMCs by factors of 2 or 3, depending on the environmental conditions in the clouds.

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

DOE PAGES

Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

2016-06-06

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

Charge transport properties of carbazole dendrimers in organic field-effect transistors

NASA Astrophysics Data System (ADS)

Mutkins, Karyn; Chen, Simon S. Y.; Aljada, Muhsen; Powell, Ben J.; Olsen, Seth; Burn, Paul L.; Meredith, Paul

2011-10-01

We report three generations of p-type dendrimer semiconductors comprised of spirobifluorene cores, carbazole branching units and fluorene surface groups for use in organic field-effect transistors (OFETs). The group of dendrimers are defined by their generation and noted as SBF-(Gx)2, where x is the generation. Top contact-bottom gate OFETs were fabricated by spin-coating the dendrimers onto an n-octyltrichlorosilane (OTS) passivated silicon dioxide surface. The dendrimer films were found to be amorphous. The highest mobility was measured for the first generation dendrimer (SBF-(G1)2), which had an average mobility of (6.6 +/- 0.2) × 10-5 cm2/V s and an ON/OFF ratio of 3.0 × 104. As the generation of the dendrimer was increased there was only a slight decrease in the measured mobility in spite of the significantly different molecular sizes of the dendrimers. The mobility of SBF-(G3)2, which had a hydrodynamic radius almost twice of SBF-(G1)2, still had an average mobility of (4.7 +/- 0.6) × 10-5 cm2/V s and an ON/OFF ratio of 2.7 × 103. Density functional theory calculations showed that the highest occupied molecular orbital was distributed over the core and carbazole units meaning that both intra- and intermolecular charge transfer could occur enabling the hole mobility to remain essentially constant even though the dendrimers would pack differently in the solid-state.

Morphology and molecular phylogeny of Apoterritricha lutea n. g., n. sp. (Ciliophora, Spirotrichea, Hypotrichia): a putative missing link connecting Cyrtohymena and Afrokeronopsis.

PubMed

Kim, Ji Hye; Vďačný, Peter; Shazib, Shahed Uddin Ahmed; Shin, Mann Kyoon

2014-01-01

A new hypotrichous ciliate, Apoterritricha lutea n. g., n. sp., was discovered in a sample of a terrestrial liverwort from Korea. Its morphology was studied using detailed in vivo observation and protargol impregnation. Its phylogenetic relationships were revealed by analyses of the 18S rRNA gene. This new taxon is characterized by a combination of the following traits: (i) ellipsoidal to narrowly ellipsoidal body with an average size of 230 × 85 μm; (ii) two macronuclear nodules and two to five micronuclei; (iii) golden yellow cortical granules, forming small groups along the microtubular appendages of cirri, adoral membranelles, and dorsal kineties; (iv) typically three frontal cirri, one buccal cirrus, four frontoventral cirri, seven midventral cirri, two pretransverse cirri, seven transverse cirri, ca. 38 left, and ca. 36 right marginal cirri; and (v) on average six dorsal kineties, three dorsomarginal kineties, and three caudal cirri. In molecular phylogenies, A. lutea clusters with strong support within a clade containing Afrokeronopsis aurea and several "typical" oxytrichids having golden yellow to brown cortical granules. In this light we propose a hypothesis that is not unambiguously rejected by the present phylogenetic analyses, which shows how the Afrokeronopsis-like pattern could have evolved from a Rubrioxytricha-like ancestor via an Apoterritricha-like stage by cirri-multiplication. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2007-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Accuracy of theory for calculating electron impact ionization of molecules

NASA Astrophysics Data System (ADS)

Chaluvadi, Hari Hara Kumar

The study of electron impact single ionization of atoms and molecules has provided valuable information about fundamental collisions. The most detailed information is obtained from triple differential cross sections (TDCS) in which the energy and momentum of all three final state particles are determined. These cross sections are much more difficult for theory since the detailed kinematics of the experiment become important. There are many theoretical approximations for ionization of molecules. One of the successful methods is the molecular 3-body distorted wave (M3DW) approximation. One of the strengths of the DW approximation is that it can be applied for any energy and any size molecule. One of the approximations that has been made to significantly reduce the required computer time is the OAMO (orientation averaged molecular orbital) approximation. In this dissertation, the accuracy of the M3DW-OAMO is tested for different molecules. Surprisingly, the M3DW-OAMO approximation yields reasonably good agreement with experiment for ionization of H2 and N2. On the other hand, the M3DW-OAMO results for ionization of CH4, NH3 and DNA derivative molecules did not agree very well with experiment. Consequently, we proposed the M3DW with a proper average (PA) calculation. In this dissertation, it is shown that the M3DW-PA calculations for CH4 and SF6 are in much better agreement with experimental data than the M3DW-OAMO results.

Atomic-scale dynamics of a model glass-forming metallic liquid: Dynamical crossover, dynamical decoupling, and dynamical clustering

DOE PAGES

Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang

2015-04-01

The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu 40Zr 51Al 9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T x ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T m ~ 900K),more » and the crossover temperature is roughly twice of the glass-transition temperature (T g). Below T x, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a non-parametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below T x and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter and the four-point correlation function.« less

Application of Molecular Dynamics Simulations in Molecular Property Prediction II: Diffusion Coefficient

PubMed Central

Wang, Junmei; Hou, Tingjun

2011-01-01

In this work, we have evaluated how well the General AMBER force field (GAFF) performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, 5 organic compounds in aqueous solutions, 4 proteins in aqueous solutions, and 9 organic compounds in non-aqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned error (AUE) and the root-mean-square error (RMSE) are 0.137 and 0.171 ×10−5 cm−2s−1, respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for 8 organic solvents with experimental data (R2 = 0.784), 4 proteins in aqueous solutions (R2 = 0.996) and 9 organic compounds in non-aqueous solutions (R2 = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide (DMSO) and cyclohexane have been studied. The major MD settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement (MSD) collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. PMID:21953689

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

Sabin, Charles; Plevka, Pavel, E-mail: pavel.plevka@ceitec.muni.cz

Molecular replacement and noncrystallographic symmetry averaging were used to detwin a data set affected by perfect hemihedral twinning. The noncrystallographic symmetry averaging of the electron-density map corrected errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of themore » domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C{sup α} atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.« less

Potential of mean force between identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte

NASA Astrophysics Data System (ADS)

Guerrero-García, Guillermo Iván; González-Mozuelos, Pedro; de la Cruz, Mónica Olvera

2011-10-01

In a previous theoretical and simulation study [G. I. Guerrero-García, E. González-Tovar, and M. Olvera de la Cruz, Soft Matter 6, 2056 (2010)], it has been shown that an asymmetric charge neutralization and electrostatic screening depending on the charge polarity of a single nanoparticle occurs in the presence of a size-asymmetric monovalent electrolyte. This effect should also impact the effective potential between two macroions suspended in such a solution. Thus, in this work we study the mean force and the potential of mean force between two identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte, showing that these results go beyond the standard description provided by the well-known Derjaguin-Landau-Verwey-Overbeek theory. To include consistently the ion-size effects, molecular dynamics (MD) simulations and liquid theory calculations are performed at the McMillan-Mayer level of description in which the solvent is taken into account implicitly as a background continuum with the suitable dielectric constant. Long-range electrostatic interactions are handled properly in the simulations via the well established Ewald sums method and the pre-averaged Ewald sums approach, originally proposed for homogeneous ionic fluids. An asymmetric behavior with respect to the colloidal charge polarity is found for the effective interactions between two identical nanoparticles. In particular, short-range attractions are observed between two equally charged nanoparticles, even though our model does not include specific interactions; these attractions are greatly enhanced for anionic nanoparticles immersed in standard electrolytes where cations are smaller than anions. Practical implications of some of the presented results are also briefly discussed. A good accord between the standard Ewald method and the pre-averaged Ewald approach is attained, despite the fact that the ionic system studied here is certainly inhomogeneous. In general, good agreement between the liquid theory approach and MD simulations is also found.

A high-dispersion molecular gas component in nearby galaxies

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

Caldú-Primo, Anahi; Walter, Fabian; Sandstrom, Karin

2013-12-01

We present a comprehensive study of the velocity dispersion of the atomic (H I) and molecular (H{sub 2}) gas components in the disks (R ≲ R {sub 25}) of a sample of 12 nearby spiral galaxies with moderate inclinations. Our analysis is based on sensitive high-resolution data from the THINGS (atomic gas) and HERACLES (molecular gas) surveys. To obtain reliable measurements of the velocity dispersion, we stack regions several kiloparsecs in size, after accounting for intrinsic velocity shifts due to galactic rotation and large-scale motions. We stack using various parameters: the galactocentric distance, star formation rate surface density, H Imore » surface density, H{sub 2} surface density, and total gas surface density. We fit single Gaussian components to the stacked spectra and measure median velocity dispersions for H I of 11.9 ± 3.1 km s{sup –1} and for CO of 12.0 ± 3.9 km s{sup –1}. The CO velocity dispersions are thus, surprisingly, very similar to the corresponding ones of H I, with an average ratio of σ{sub HI}/σ{sub CO}= 1.0 ± 0.2 irrespective of the stacking parameter. The measured CO velocity dispersions are significantly higher (factor of ∼2) than the traditional picture of a cold molecular gas disk associated with star formation. The high dispersion implies an additional thick molecular gas disk (possibly as thick as the H I disk). Our finding is in agreement with recent sensitive measurements in individual edge-on and face-on galaxies and points toward the general existence of a thick disk of molecular gas, in addition to the well-known thin disk in nearby spiral galaxies.« less

Chemical composition and molecular structure of polysaccharide-protein biopolymer from Durio zibethinus seed: extraction and purification process

PubMed Central

2012-01-01

Background The biological functions of natural biopolymers from plant sources depend on their chemical composition and molecular structure. In addition, the extraction and further processing conditions significantly influence the chemical and molecular structure of the plant biopolymer. The main objective of the present study was to characterize the chemical and molecular structure of a natural biopolymer from Durio zibethinus seed. A size-exclusion chromatography coupled to multi angle laser light-scattering (SEC-MALS) was applied to analyze the molecular weight (Mw), number average molecular weight (Mn), and polydispersity index (Mw/Mn). Results The most abundant monosaccharide in the carbohydrate composition of durian seed gum were galactose (48.6-59.9%), glucose (37.1-45.1%), arabinose (0.58-3.41%), and xylose (0.3-3.21%). The predominant fatty acid of the lipid fraction from the durian seed gum were palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid (C18:2). The most abundant amino acids of durian seed gum were: leucine (30.9-37.3%), lysine (6.04-8.36%), aspartic acid (6.10-7.19%), glycine (6.07-7.42%), alanine (5.24-6.14%), glutamic acid (5.57-7.09%), valine (4.5-5.50%), proline (3.87-4.81%), serine (4.39-5.18%), threonine (3.44-6.50%), isoleucine (3.30-4.07%), and phenylalanine (3.11-9.04%). Conclusion The presence of essential amino acids in the chemical structure of durian seed gum reinforces its nutritional value. PMID:23062269

How ABA block polymers activate cytochrome c in toluene: molecular dynamics simulation and experimental observation.

PubMed

Chen, Gong; Kong, Xian; Zhu, Jingying; Lu, Diannan; Liu, Zheng

2015-04-28

While the conjugation of enzymes with ABA copolymers has resulted in increased enzymatic activities in organic solvents, by several orders of magnitude, the underpinning mechanism has not been fully uncovered, particularly at the molecular level. In the present work, a coarse-grained molecular dynamics simulation of cytochrome c (Cyt c) conjugated with a PEO-PPO-PEO block copolymer (ABA) in toluene was simulated with Cyt c as a control. It is shown that the hydrophilic segments (PEO) of the conjugated block copolymer molecules tend to entangle around the hydrophilic patch of Cyt c, while the hydrophobic segments (PPO) extend into the toluene. At a lower temperature, the PEO tails tend to form a hairpin structure outside the conjugated protein, whereas the Cyt c-ABA conjugates tend to form larger aggregates. At a higher temperature, however, the PEO tails tend to adsorb onto the hydrophilic protein surface, thus improving the suspension of the Cyt c-ABA conjugates and, consequently, the contact with the substrate. Moreover, the temperature increase drives the conformational transition of the active site of Cyt c-ABA from an "inactive state" to an "activated state" and thus results in an enhanced activity. To validate the above simulations, Cyt c was conjugated to F127, an extensively used ABA copolymer. By elevating the temperature, a decrease in the average size of the Cyt c-F127 conjugates along with a great increase in the apparent activity in toluene was observed, as can be predicted from the molecular dynamics simulation. The above mentioned molecular simulations offer a molecular insight into the temperature-responsive behaviour of protein-ABA copolymers, which is helpful for the design and application of enzyme-polymer conjugates for industrial biocatalysis.

Effect of nucleoside analogue antimetabolites on the structure of PEO–PPO–PEO micelles investigated by SANS

DOE PAGES

Han, Youngkyu; Zhang, Zhe; Smith, Gregory S.; ...

2017-04-19

In this work, the effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strengthmore » of the effect was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.« less

Effect of nucleoside analogue antimetabolites on the structure of PEO–PPO–PEO micelles investigated by SANS

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

Han, Youngkyu; Zhang, Zhe; Smith, Gregory S.

2017-01-01

The effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strength of the effectmore » was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.« less

Characterization of deuterium clusters mixed with helium gas for an application in beam-target-fusion experiments

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

Bang, W.; Quevedo, H. J.; Bernstein, A. C.

We measured the average deuterium cluster size within a mixture of deuterium clusters and helium gas by detecting Rayleigh scattering signals. The average cluster size from the gas mixture was comparable to that from a pure deuterium gas when the total backing pressure and temperature of the gas mixture were the same as those of the pure deuterium gas. According to these measurements, the average size of deuterium clusters depends on the total pressure and not the partial pressure of deuterium in the gas mixture. To characterize the cluster source size further, a Faraday cup was used to measure themore » average kinetic energy of the ions resulting from Coulomb explosion of deuterium clusters upon irradiation by an intense ultrashort pulse. The deuterium ions indeed acquired a similar amount of energy from the mixture target, corroborating our measurements of the average cluster size. As the addition of helium atoms did not reduce the resulting ion kinetic energies, the reported results confirm the utility of using a known cluster source for beam-target-fusion experiments by introducing a secondary target gas.« less

Improving La0.6Sr0.4Co0.8Fe0.2O3-δ infiltrated solid oxide fuel cell cathode performance through precursor solution desiccation

NASA Astrophysics Data System (ADS)

Burye, Theodore E.; Nicholas, Jason D.

2015-02-01

Here, for the first time, the average size of solid oxide fuel cell (SOFC) electrode nano-particles was reduced through the chemical desiccation of infiltrated precursor nitrate solutions. Specifically, after firing at 700 °C, CaCl2-desiccated La0.6Sr0.4Co0.8Fe0.2O3-δ (LSCF) - Ce0.9Gd0.1O1.95 (GDC) cathodes contained LSCF infiltrate particles with an average size of 22 nm. This is in contrast to comparable, undesiccated LSCF-GDC cathodes which contained LSCF infiltrate particles with an average size of 48 nm. X-ray diffraction, scanning electron microscopy, and controlled atmosphere electrochemical impedance spectroscopy revealed that desiccation reduced the average infiltrate particle size without altering the infiltrate phase purity, the cathode concentration polarization resistance, or the cathode electronic resistance. Compared to undesiccated LSCF-GDC cathodes achieving polarization resistances of 0.10 Ωcm2 at 640 °C, comparable CaCl2-dessicated LSCF-GDC cathodes achieved 0.10 Ωcm2 at 575 °C. Mathematical modeling suggested that these performance improvements resulted solely from average infiltrate particle size reductions.

Characterization of deuterium clusters mixed with helium gas for an application in beam-target-fusion experiments

DOE PAGES

Bang, W.; Quevedo, H. J.; Bernstein, A. C.; ...

2014-12-10

We measured the average deuterium cluster size within a mixture of deuterium clusters and helium gas by detecting Rayleigh scattering signals. The average cluster size from the gas mixture was comparable to that from a pure deuterium gas when the total backing pressure and temperature of the gas mixture were the same as those of the pure deuterium gas. According to these measurements, the average size of deuterium clusters depends on the total pressure and not the partial pressure of deuterium in the gas mixture. To characterize the cluster source size further, a Faraday cup was used to measure themore » average kinetic energy of the ions resulting from Coulomb explosion of deuterium clusters upon irradiation by an intense ultrashort pulse. The deuterium ions indeed acquired a similar amount of energy from the mixture target, corroborating our measurements of the average cluster size. As the addition of helium atoms did not reduce the resulting ion kinetic energies, the reported results confirm the utility of using a known cluster source for beam-target-fusion experiments by introducing a secondary target gas.« less

Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

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

Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik

2016-05-14

We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less

Determination of the linear coefficient of thermal expansion in polymer films at the nanoscale: influence of the composition of EVA copolymers and the molecular weight of PMMA.

PubMed

González-Benito, J; Castillo, E; Cruz-Caldito, J F

2015-07-28

Nanothermal-expansion of poly(ethylene-co-vinylacetate), EVA, and poly(methyl methacrylate), PMMA, in the form of films was measured to finally obtain linear coefficients of thermal expansion, CTEs. The simple deflection of a cantilever in an atomic force microscope, AFM, was used to monitor thermal expansions at the nanoscale. The influences of: (a) the structure of EVA in terms of its composition (vinylacetate content) and (b) the size of PMMA chains in terms of the molecular weight were studied. To carry out this, several polymer samples were used, EVA copolymers with different weight percents of the vinylacetate comonomer (12, 18, 25 and 40%) and PMMA polymers with different weight average molecular weights (33.9, 64.8, 75.600 and 360.0 kg mol(-1)). The dependencies of the vinyl acetate weight fraction of EVA and the molecular weight of PMMA on their corresponding CTEs were analyzed to finally explain them using new, intuitive and very simple models based on the rule of mixtures. In the case of EVA copolymers a simple equation considering the weighted contributions of each comonomer was enough to estimate the final CTE above the glass transition temperature. On the other hand, when the molecular weight dependence is considered the free volume concept was used as novelty. The expansion of PMMA, at least at the nanoscale, was well and easily described by the sum of the weighted contributions of the occupied and free volumes, respectively.

Comparison of selected analytical techniques for protein sizing, quantitation and molecular weight determination.

PubMed

Goetz, H; Kuschel, M; Wulff, T; Sauber, C; Miller, C; Fisher, S; Woodward, C

2004-09-30

Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. In the present paper we compare selected techniques, which are used for protein sizing, quantitation and molecular weight determination: sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip or microfluidics technology (LoaC), size exclusion chromatography (SEC) and mass spectrometry (MS). We compare advantages and limitations of each technique in respect to different application areas, analysis time, protein sizing and quantitation performance.

Role of SiO2 coating in multiferroic CoCr2O4 nanoparticles

NASA Astrophysics Data System (ADS)

Kamran, M.; Ullah, Asmat; Mehmood, Y.; Nadeem, K.; Krenn, H.

2017-02-01

Effect of silica (SiO2) coating concentration on structural and magnetic properties of multiferroic cobalt chromite (CoCr2O4) nanoparticles have been studied. The nanoparticles with average crystallite size in the range 19 to 28 nm were synthesised by sol-gel method. X-ray diffraction (XRD) analysis has verified the composition of single-phase cubic normal spinel structure of CoCr2O4 nanoparticles. The average crystallite size and cell parameter decreased with increasing SiO2 concentration. TEM image revealed that the shape of nanoparticles was non-spherical. Zero field cooled/field cooled (ZFC/FC) curves revealed that nanoparticles underwent a transition from paramagnetic (PM) state to collinear short-range ferrimagnetic (FiM) state, and this PM-FiM transition temperature decreased from 101 to 95 K with increasing SiO2 concentration or decreasing crystallite size. A conical spin state at Ts = 27 K was also observed for all the samples which decreased with decreasing average crystallite size. Low temperature lock-in transition was also observed in these nanoparticles at 12 K for uncoated nanoparticles which slightly shifted towards low temperature with decreasing average crystallite size. Saturation magnetization (Ms) showed decreasing trend with increasing SiO2 concentration, which was due to decrease in average crystallite size of nanoparticles and enhanced surface disorder in smaller nanoparticles. The temperature dependent AC-susceptibility also showed the decrease in the transition temperature (Tc), broadening of the Tc peak and decrease in magnetization with increasing SiO2 concentration or decreasing average crystallite size. In summary, the concentration of SiO2 has significantly affected the structural and magnetic properties of CoCr2O4 nanoparticles.

A geometrical optics approach for modeling aperture averaging in free space optical communication applications

NASA Astrophysics Data System (ADS)

Yuksel, Heba; Davis, Christopher C.

2006-09-01

Intensity fluctuations at the receiver in free space optical (FSO) communication links lead to a received power variance that depends on the size of the receiver aperture. Increasing the size of the receiver aperture reduces the power variance. This effect of the receiver size on power variance is called aperture averaging. If there were no aperture size limitation at the receiver, then there would be no turbulence-induced scintillation. In practice, there is always a tradeoff between aperture size, transceiver weight, and potential transceiver agility for pointing, acquisition and tracking (PAT) of FSO communication links. We have developed a geometrical simulation model to predict the aperture averaging factor. This model is used to simulate the aperture averaging effect at given range by using a large number of rays, Gaussian as well as uniformly distributed, propagating through simulated turbulence into a circular receiver of varying aperture size. Turbulence is simulated by filling the propagation path with spherical bubbles of varying sizes and refractive index discontinuities statistically distributed according to various models. For each statistical representation of the atmosphere, the three-dimensional trajectory of each ray is analyzed using geometrical optics. These Monte Carlo techniques have proved capable of assessing the aperture averaging effect, in particular, the quantitative expected reduction in intensity fluctuations with increasing aperture diameter. In addition, beam wander results have demonstrated the range-cubed dependence of mean-squared beam wander. An effective turbulence parameter can also be determined by correlating beam wander behavior with the path length.

SEDFIT-MSTAR: Molecular weight and molecular weight distribution analysis of polymers by sedimentation equilibrium in the ultracentrifuge

PubMed Central

Schuck, Peter; Gillis, Richard B.; Besong, Tabot M.D.; Almutairi, Fahad; Adams, Gary G.; Rowe, Arthur J.; Harding, Stephen E.

2014-01-01

Sedimentation equilibrium (analytical ultracentrifugation) is one of the most inherently suitable methods for the determination of average molecular weights and molecular weight distributions of polymers, because of its absolute basis (no conformation assumptions) and inherent fractionation ability (without the need for columns or membranes and associated assumptions over inertness). With modern instrumentation it is also possible to run up to 21 samples simultaneously in a single run. Its application has been severely hampered because of difficulties in terms of baseline determination (incorporating estimation of the concentration at the air/solution meniscus) and complexity of the analysis procedures. We describe a new method for baseline determination based on a smart-smoothing principle and built into the highly popular platform SEDFIT for the analysis of the sedimentation behavior of natural and synthetic polymer materials. The SEDFIT-MSTAR procedure – which takes only a few minutes to perform - is tested with four synthetic data sets (including a significantly non-ideal system) a naturally occurring protein (human IgG1) and two naturally occurring carbohydrate polymers (pullulan and λ–carrageenan) in terms of (i) weight average molecular weight for the whole distribution of species in the sample (ii) the variation in “point” average molecular weight with local concentration in the ultracentrifuge cell and (iii) molecular weight distribution. PMID:24244936

Novel method for the determination of average molecular weight of natural polymers based on 2D DOSY NMR and chemometrics: Example of heparin.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Do, Tung X; Schulze, Margit; Witzleben, Steffen

2018-02-05

Apart from the characterization of impurities, the full characterization of heparin and low molecular weight heparin (LMWH) also requires the determination of average molecular weight, which is closely related to the pharmaceutical properties of anticoagulant drugs. To determine average molecular weight of these animal-derived polymer products, partial least squares regression (PLS) was utilized for modelling of diffused-ordered spectroscopy NMR data (DOSY) of a representative set of heparin (n=32) and LMWH (n=30) samples. The same sets of samples were measured by gel permeation chromatography (GPC) to obtain reference data. The application of PLS to the data led to calibration models with root mean square error of prediction of 498Da and 179Da for heparin and LMWH, respectively. The average coefficients of variation (CVs) did not exceed 2.1% excluding sample preparation (by successive measuring one solution, n=5) and 2.5% including sample preparation (by preparing and analyzing separate samples, n=5). An advantage of the method is that the sample after standard 1D NMR characterization can be used for the molecular weight determination without further manipulation. The accuracy of multivariate models is better than the previous results for other matrices employing internal standards. Therefore, DOSY experiment is recommended to be employed for the calculation of molecular weight of heparin products as a complementary measurement to standard 1D NMR quality control. The method can be easily transferred to other matrices as well. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomolecule-loaded chitosan nanoparticles induce apoptosis and molecular changes in cancer cell line (SiHa).

PubMed

Sujima Anbu, Anbu; Velmurugan, Palanivel; Lee, Jeong-Ho; Oh, Byung-Taek; Venkatachalam, Perumal

2016-07-01

The present study reports on the synthesis of chitosan nanoparticles (CNPs) using methanol extracts of Gymnema sylvestre (GS) leaves and Cinnamomum zeylanicum (CZ) bark. Biomolecule-loaded nanoparticles induced apoptosis in a human cervical cancer (SiHa) cell line, and experiments were carried out to elucidate the underlying molecular mechanisms. FT-IR and XRD showed possible functional groups of the biomolecules and the crystalline nature of CNPs, respectively. Transmission electron microscopy images revealed that synthesized GSCNPs and CZCNPs had a smooth spherical shape with average sizes of about 58-80 and 60-120nm, respectively. Dynamic light scattering studies indicated that both GSCNPs and CZCNs were structurally stable with homogenous and heterogeneous natures, respectively. Furthermore, synthesized GSCNPs and CZCNPs exhibited dose-dependent cytotoxicity against the SiHa cancer cell line, with inhibitory concentration (IC50) values of 102.17μg/ml, 87.75μg/ml, 132.74μg/ml and 90.35μg/ml for GS leaf extract, GSCNPs, CZBE and CZCNPs, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystalline ricin D, a toxic anti-tumor lectin from seeds of Ricinus communis

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

Wei, C.H.; Koh, C.

1978-03-25

A toxic lectin, ricin D, present in the seeds of Ricinus communis has been purified and crystallized in a form suitable for high resolution crystallographic structure studies. This protein is different from a previously found form of ricin (also present in the same seeds), the only ricin for which a preliminary x-ray investigation has been reported so far. Ricin D crystallizes from an aqueous solution in an orthorhombic unit cell of symmetry P2/sub 1/2/sub 1/2/sub 1/ and a = 79.0, b = 114.7, and c = 72.8 A. The asymmetric unit contains one molecule with an average molecular weight ofmore » 62,400. The crystal is fairly stable to x-radiation and has a water content of approximately 54% by volume. It appears to comprise two closely related species of proteins, the major species corresponding to ricin D and the other presumably corresponding to a deamidation product of ricin D. The two species have nearly identical molecular size and amino acid compositions, but different charges.« less

[cDNA library construction from panicle meristem of finger millet].

PubMed

Radchuk, V; Pirko, Ia V; Isaenkov, S V; Emets, A I; Blium, Ia B

2014-01-01

The protocol for production of full-size cDNA using SuperScript Full-Length cDNA Library Construction Kit II (Invitrogen) was tested and high quality cDNA library from meristematic tissue of finger millet panicle (Eleusine coracana (L.) Gaertn) was created. The titer of obtained cDNA library comprised 3.01 x 10(5) CFU/ml in avarage. In average the length of cDNA insertion consisted about 1070 base pairs, the effectivity of cDNA fragment insertions--99.5%. The selective sequencing of cDNA clones from created library was performed. The sequences of cDNA clones were identified with usage of BLAST-search. The results of cDNA library analysis and selective sequencing represents prove good functionality and full length character of inserted cDNA clones. Obtained cDNA library from meristematic tissue of finger millet panicle represents good and valuable source for isolation and identification of key genes regulating metabolism and meristematic development and for mining of new molecular markers to conduct out high quality genetic investigations and molecular breeding as well.

Mixed Matrix Carbon Molecular Sieve and Alumina (CMS-Al2O3) Membranes

NASA Astrophysics Data System (ADS)

Song, Yingjun; Wang, David K.; Birkett, Greg; Martens, Wayde; Duke, Mikel C.; Smart, Simon; Diniz da Costa, João C.

2016-07-01

This work shows mixed matrix inorganic membranes prepared by the vacuum-assisted impregnation method, where phenolic resin precursors filled the pore of α-alumina substrates. Upon carbonisation, the phenolic resin decomposed into several fragments derived from the backbone of the resin matrix. The final stages of decomposition (>650 °C) led to a formation of carbon molecular sieve (CMS) structures, reaching the lowest average pore sizes of ~5 Å at carbonisation temperatures of 700 °C. The combination of vacuum-assisted impregnation and carbonisation led to the formation of mixed matrix of CMS and α-alumina particles (CMS-Al2O3) in a single membrane. These membranes were tested for pervaporative desalination and gave very high water fluxes of up to 25 kg m-2 h-1 for seawater (NaCl 3.5 wt%) at 75 °C. Salt rejection was also very high varying between 93-99% depending on temperature and feed salt concentration. Interestingly, the water fluxes remained almost constant and were not affected as feed salt concentration increased from 0.3, 1 and 3.5 wt%.

Molecular dynamics study of the isotropic-nematic quench.

PubMed

Bradac, Z; Kralj, S; Zumer, S

2002-02-01

Effects of cylindrical and spherical confinement on the kinetics of the isotropic-nematic quench is studied numerically. The nematic liquid crystal structure was modeled by a modified induced-dipole--induced-dipole interaction. Molecules were allowed to wander around points of a hexagonal lattice. Brownian molecular dynamics was used in order to access macroscopic time scales. In the bulk we distinguish between the early, domain, and late stage regime. The early regime is characterized by the exponential growth of the nematic uniaxial order parameter. In the domain regime domains are clearly visible and the average nematic domain size xi(d) obeys the dynamical scaling law xi(d)-t(gamma). The late stage evolution is dominated by dynamics of individual defects. In a confined system the qualitative change of the scaling behavior appears when xi(d) becomes comparable to a typical linear dimension R of the confinement. In the confining regime (xi(d)>or=R) the scaling coefficient gamma depends on the details of the confinement and also the final equilibrium nematic structure. The domain growth is well described with the Kibble-Zurek mechanism.

Molecular dynamic simulations of the high-speed copper nanoparticles collision with the aluminum surface

NASA Astrophysics Data System (ADS)

Pogorelko, V. V.; Mayer, A. E.

2016-11-01

With the use of the molecular dynamic simulations, we investigated the effect of the high-speed (500 m/s, 1000 m/s) copper nanoparticle impact on the mechanical properties of an aluminum surface. Dislocation analysis shows that a large number of dislocations are formed in the impact area; the total length of dislocations is determined not only by the speed and size of the incoming copper nanoparticle (kinetic energy of the nanoparticle), but by a temperature of the system as well. The dislocations occupy the whole area of the aluminum single crystal at high kinetic energy of the nanoparticle. With the decrease of the nanoparticle kinetic energy, the dislocation structures are formed in the near-surface layer; formation of the dislocation loops takes place. Temperature rise of the system (aluminum substrate + nanoparticle) reduces the total dislocation length in the single crystal of aluminum; there is deeper penetration of the copper atoms in the aluminum at high temperatures. Average energy of the nanoparticles and room temperature of the system are optimal for production of high-quality layers of copper on the aluminum surface.

Mixed Matrix Carbon Molecular Sieve and Alumina (CMS-Al2O3) Membranes.

PubMed

Song, Yingjun; Wang, David K; Birkett, Greg; Martens, Wayde; Duke, Mikel C; Smart, Simon; Diniz da Costa, João C

2016-07-29

This work shows mixed matrix inorganic membranes prepared by the vacuum-assisted impregnation method, where phenolic resin precursors filled the pore of α-alumina substrates. Upon carbonisation, the phenolic resin decomposed into several fragments derived from the backbone of the resin matrix. The final stages of decomposition (>650 °C) led to a formation of carbon molecular sieve (CMS) structures, reaching the lowest average pore sizes of ~5 Å at carbonisation temperatures of 700 °C. The combination of vacuum-assisted impregnation and carbonisation led to the formation of mixed matrix of CMS and α-alumina particles (CMS-Al2O3) in a single membrane. These membranes were tested for pervaporative desalination and gave very high water fluxes of up to 25 kg m(-2) h(-1) for seawater (NaCl 3.5 wt%) at 75 °C. Salt rejection was also very high varying between 93-99% depending on temperature and feed salt concentration. Interestingly, the water fluxes remained almost constant and were not affected as feed salt concentration increased from 0.3, 1 and 3.5 wt%.

Magnetic behavior in Cr{sub 2}@Ge{sub n} (1≤n≤12) clusters: A density functional investigation

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

Dhaka, Kapil, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in; Trivedi, Ravi, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in; Bandyopadhyay, Debashis, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in

2014-04-24

With a goal to produce magnetic moment in Cr{sub 2} Doped Ge{sub n} clusters which will be useful for practical applications, we have considered the structure and magnetic properties of Pure Germanium clusters and substitutionally doped it with Cr dimer to produce Cr{sub 2}@Ge{sub n} clusters. As the first step of calculation, geometrical optimizations of the nanoclusters have been done. These optimized geometries have been used in calculate the average binding energy per atom (BE), HOMO-LUMO gap and hence the relative stability of the clusters. These parameters have been demonstrated as structural and electronic properties of the clusters. Gap betweenmore » highest occupied molecular orbital and lowest unoccupied molecular orbital indicate cluster to be a potential motif for generating magnetic cluster assembled materials. Based on these values a comparative study on different sized clusters has been done in order to understand the origin of structures, electronic and magnetic properties of Cr{sub 2}@Ge{sub n} nanoclusters.« less

Edge localized mode characteristics during edge localized mode mitigation by supersonic molecular beam injection in Korea Superconducting Tokamak Advanced Research

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

Lee, H. Y.; Hong, J. H.; Jang, J. H.

It has been reported that supersonic molecular beam injection (SMBI) is an effective means of edge localized mode (ELM) mitigation. This paper newly reports the changes in the ELM, plasma profiles, and fluctuation characteristics during ELM mitigation by SMBI in Korea Superconducting Tokamak Advanced Research. During the mitigated ELM phase, the ELM frequency increased by a factor of 2–3 and the ELM size, which was estimated from the D{sub α} amplitude, the fractional changes in the plasma-stored energy and the line-averaged electron density, and divertor heat flux during an ELM burst, decreased by a factor of 0.34–0.43. Reductions in themore » electron and ion temperatures rather than in the electron density were observed during the mitigated ELM phase. In the natural ELM phase, frequency chirping of the plasma fluctuations was observed before the ELM bursts; however, the ELM bursts occurred without changes in the plasma fluctuation frequency in the mitigated ELM phase.« less

Implications of grain size variation in magnetic field alignment of block copolymer blends

DOE PAGES

Rokhlenko, Yekaterina; Majewski, Pawel W.; Larson, Steven R.; ...

2017-03-28

Recent experiments have highlighted the intrinsic magnetic anisotropy in coil–coil diblock copolymers, specifically in poly(styrene- block-4-vinylpyridine) (PS- b-P4VP), that enables magnetic field alignment at field strengths of a few tesla. We consider here the alignment response of two low molecular weight (MW) lamallae-forming PS- b-P4VP systems. Cooling across the disorder–order transition temperature (T odt) results in strong alignment for the higher MW sample (5.5K), whereas little alignment is discernible for the lower MW system (3.6K). This disparity under otherwise identical conditions of field strength and cooling rate suggests that different average grain sizes are produced during slow cooling of thesemore » materials, with larger grains formed in the higher MW material. Blending the block copolymers results in homogeneous samples which display T odt, d-spacings, and grain sizes that are intermediate between the two neat diblocks. Similarly, the alignment quality displays a smooth variation with the concentration of the higher MW diblock in the blends, and the size of grains likewise interpolates between limits set by the neat diblocks, with a factor of 3.5× difference in the grain size observed in high vs low MW neat diblocks. Finally, these results highlight the importance of grain growth kinetics in dictating the field response in block copolymers and suggests an unconventional route for the manipulation of such kinetics.« less

Limited genomic consequences of mixed mating in the recently derived sister species pair, Collinsia concolor and Collinsia parryi.

PubMed

Salcedo, A; Kalisz, S; Wright, S I

2014-07-01

Highly selfing species often show reduced effective population sizes and reduced selection efficacy. Whether mixed mating species, which produce both self and outcross progeny, show similar patterns of diversity and selection remains less clear. Examination of patterns of molecular evolution and levels of diversity in species with mixed mating systems can be particularly useful for investigating the relative importance of linked selection and demographic effects on diversity and the efficacy of selection, as the effects of linked selection should be minimal in mixed mating populations, although severe bottlenecks tied to founder events could still be frequent. To begin to address this gap, we assembled and analysed the transcriptomes of individuals from a recently diverged mixed mating sister species pair in the self-compatible genus, Collinsia. The de novo assembly of 52 and 37 Mbp C. concolor and C. parryi transcriptomes resulted in ~40 000 and ~55 000 contigs, respectively, both with an average contig size ~945. We observed a high ratio of shared polymorphisms to fixed differences in the species pair and minimal differences between species in the ratio of synonymous to replacement substitutions or codon usage bias implying comparable effective population sizes throughout species divergence. Our results suggest that differences in effective population size and selection efficacy in mixed mating taxa shortly after their divergence may be minimal and are likely influenced by fluctuating mating systems and population sizes. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event.

PubMed

Schneider, Kevin; Resl, Philipp; Spribille, Toby

2016-07-01

Large, architecturally complex lichen symbioses arose only a few times in evolution, increasing thallus size by orders of magnitude over those from which they evolved. The innovations that enabled symbiotic assemblages to acquire and maintain large sizes are unknown. We mapped morphometric data against an eight-locus fungal phylogeny across one of the best-sampled thallus size transition events, the origins of the Placopsis lichen symbiosis, and used a phylogenetic comparative framework to explore the role of nitrogen-fixing cyanobacteria in size differences. Thallus thickness increased by >150% and fruiting body core volume increased ninefold on average after acquisition of cyanobacteria. Volume of cyanobacteria-containing structures (cephalodia), once acquired, correlates with thallus thickness in both phylogenetic generalized least squares and phylogenetic generalized linear mixed-effects analyses. Our results suggest that the availability of nitrogen is an important factor in the formation of large thalli. Cyanobacterial symbiosis appears to have enabled lichens to overcome size constraints in oligotrophic environments such as acidic, rain-washed rock surfaces. In the case of the Placopsis fungal symbiont, this has led to an adaptive radiation of more than 60 recognized species from related crustose members of the genus Trapelia. Our data suggest that precyanobacterial symbiotic lineages were constrained to forming a narrow range of phenotypes, so-called cryptic species, leading systematists until now to recognize only six of the 13 species clusters we identified in Trapelia. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Implications of grain size variation in magnetic field alignment of block copolymer blends

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

Rokhlenko, Yekaterina; Majewski, Pawel W.; Larson, Steven R.

Recent experiments have highlighted the intrinsic magnetic anisotropy in coil–coil diblock copolymers, specifically in poly(styrene- block-4-vinylpyridine) (PS- b-P4VP), that enables magnetic field alignment at field strengths of a few tesla. We consider here the alignment response of two low molecular weight (MW) lamallae-forming PS- b-P4VP systems. Cooling across the disorder–order transition temperature (T odt) results in strong alignment for the higher MW sample (5.5K), whereas little alignment is discernible for the lower MW system (3.6K). This disparity under otherwise identical conditions of field strength and cooling rate suggests that different average grain sizes are produced during slow cooling of thesemore » materials, with larger grains formed in the higher MW material. Blending the block copolymers results in homogeneous samples which display T odt, d-spacings, and grain sizes that are intermediate between the two neat diblocks. Similarly, the alignment quality displays a smooth variation with the concentration of the higher MW diblock in the blends, and the size of grains likewise interpolates between limits set by the neat diblocks, with a factor of 3.5× difference in the grain size observed in high vs low MW neat diblocks. Finally, these results highlight the importance of grain growth kinetics in dictating the field response in block copolymers and suggests an unconventional route for the manipulation of such kinetics.« less

Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

DTIC Science & Technology

2017-05-05

dependent density functional theory (TD-DFT). The size of the clusters considered is relatively large compared to those considered in previous studies...are characterized by many different geometries, which potentially can be optimized with respect to specific materials design criteria, i.e., molecular...SixOy molecular clusters using density functional theory (DFT). The size of the clusters considered, however, is relatively large compared to those

Electron and nuclear dynamics of molecular clusters in ultraintense laser fields. III. Coulomb explosion of deuterium clusters.

PubMed

Last, Isidore; Jortner, Joshua

2004-08-15

In this paper we present a theoretical and computational study of the energetics and temporal dynamics of Coulomb explosion of molecular clusters of deuterium (D2)n/2 (n = 480 - 7.6 x 10(4), cluster radius R0 = 13.1 - 70 A) in ultraintense laser fields (laser peak intensity I = 10(15) - 10(20)W cm(-2)). The energetics of Coulomb explosion was inferred from the dependence of the maximal energy EM and the average energy Eav of the product D+ ions on the laser intensity, the laser pulse shape, the cluster radius, and the laser frequency. Electron dynamics of outer cluster ionization and nuclear dynamics of Coulomb explosion were investigated by molecular dynamics simulations. Several distinct laser pulse shape envelopes, involving a rectangular field, a Gaussian field, and a truncated Gaussian field, were employed to determine the validity range of the cluster vertical ionization (CVI) approximation. The CVI predicts that Eav, EM proportional to R0(2) and that the energy distribution is P(E) proportional to E1/2. For a rectangular laser pulse the CVI conditions are satisfied when complete outer ionization is obtained, with the outer ionization time toi being shorter than both the pulse width and the cluster radius doubling time tau2. By increasing toi, due to the increase of R0 or the decrease of I, we have shown that the deviation of Eav from the corresponding CVI value (Eav(CVI)) is (Eav(CVI) - Eav)/Eav(CVI) approximately (toi/2.91tau2)2. The Gaussian pulses trigger outer ionization induced by adiabatic following of the laser field and of the cluster size, providing a pseudo-CVI behavior at sufficiently large laser fields. The energetics manifest the existence of a finite range of CVI size dependence, with the validity range for the applicability of the CVI being R0 < or = (R0)I, with (R0)I representing an intensity dependent boundary radius. Relating electron dynamics of outer ionization to nuclear dynamics for Coulomb explosion induced by a Gaussian pulse, the boundary radius (R0)I and the corresponding ion average energy (Eav)I were inferred from simulations and described in terms of an electrostatic model. Two independent estimates of (R0)I, which involve the cluster size where the CVI relation breaks down and the cluster size for the attainment of complete outer ionization, are in good agreement with each other, as well as with the electrostatic model for cluster barrier suppression. The relation (Eav)I proportional to (R0)I(2) provides the validity range of the pseudo-CVI domain for the cluster sizes and laser intensities, where the energetics of D+ ions produced by Coulomb explosion of (D)n clusters is optimized. The currently available experimental data [Madison et al., Phys. Plasmas 11, 1 (2004)] for the energetics of Coulomb explosion of (D)n clusters (Eav = 5 - 7 keV at I = 2 x 10(18) W cm(-2)), together with our simulation data, lead to the estimates of R0 = 51 - 60 A, which exceed the experimental estimate of R0 = 45 A. The predicted anisotropy of the D+ ion energies in the Coulomb explosion at I = 10(18) W cm(-2) is in accord with experiment. We also explored the laser frequency dependence of the energetics of Coulomb explosion in the range nu = 0.1 - 2.1 fs(-1) (lambda = 3000 - 140 nm), which can be rationalized in terms of the electrostatic model. (c) 2004 American Institute of Physics.

The Molecular Weight Distribution of Polymer Samples

ERIC Educational Resources Information Center

Horta, Arturo; Pastoriza, M. Alejandra

2007-01-01

Various methods for the determination of the molecular weight distribution (MWD) of different polymer samples are presented. The study shows that the molecular weight averages and distribution of a polymerization completely depend on the characteristics of the reaction itself.

On violations of Le Chatelier's principle for a temperature change in small systems observed for short times

NASA Astrophysics Data System (ADS)

Dasmeh, Pouria; Searles, Debra J.; Ajloo, Davood; Evans, Denis J.; Williams, Stephen R.

2009-12-01

Le Chatelier's principle states that when a system is disturbed, it will shift its equilibrium to counteract the disturbance. However for a chemical reaction in a small, confined system, the probability of observing it proceed in the opposite direction to that predicted by Le Chatelier's principle, can be significant. This work gives a molecular level proof of Le Chatelier's principle for the case of a temperature change. Moreover, a new, exact mathematical expression is derived that is valid for arbitrary system sizes and gives the relative probability that a single experiment will proceed in the endothermic or exothermic direction, in terms of a microscopic phase function. We show that the average of the time integral of this function is the maximum possible value of the purely irreversible entropy production for the thermal relaxation process. Our result is tested against computer simulations of the unfolding of a polypeptide. We prove that any equilibrium reaction mixture on average responds to a temperature increase by shifting its point of equilibrium in the endothermic direction.

Organic matter in central California radiation fogs.

PubMed

Herckes, Pierre; Lee, Taehyoung; Trenary, Laurie; Kang, Gongunn; Chang, Hui; Collett, Jeffrey L

2002-11-15

Organic matter was studied in radiation fogs in the San Joaquin Valley of California during the California Regional Particulate Air Quality Study (CRPAQS). Total organic carbon (TOC) concentrations ranged from 2 to 40 ppm of C. While most organic carbon was found in solution as dissolved organic carbon (DOC), 23% on average was not dissolved inside the fog drops. We observe a clear variation of organic matter concentration with droplet size. TOC concentrations in small fog drops (<17 microm) were a factor of 3, on average, higher than TOC concentrations in larger drops. As much as half of the dissolved organic matter was determined to have a molecular weight higher than 500 Da. Deposition fluxes of organic matter in fog drops were high (0.5-4.3 microg of C m(-2) min(-1)), indicating the importance of fog processing as a vector for removal of organic matter from the atmosphere. Deposition velocities of organic matter, however, were usually found to be lower than deposition velocities for fogwater, consistent with the enrichment of the organic matter in smaller fog drops with lower terminal settling velocities.

Investigating the effect of sputtering conditions on the physical properties of aluminum thin film and the resulting alumina template

NASA Astrophysics Data System (ADS)

Taheriniya, Shabnam; Parhizgar, Sara Sadat; Sari, Amir Hossein

2018-06-01

To study the alumina template pore size distribution as a function of Al thin film grain size distribution, porous alumina templates were prepared by anodizing sputtered aluminum thin films. To control the grain size the aluminum samples were sputtered with the rate of 0.5, 1 and 2 Å/s and the substrate temperature was either 25, 75 or 125 °C. All samples were anodized for 120 s in 1 M sulfuric acid solution kept at 1 °C while a 15 V potential was being applied. The standard deviation value for samples deposited at room temperature but with different rates is roughly 2 nm in both thin film and porous template form but it rises to approximately 4 nm with substrate temperature. Samples with the average grain size of 13, 14, 18.5 and 21 nm respectively produce alumina templates with an average pore size of 8.5, 10, 15 and 16 nm in that order which shows the average grain size limits the average pore diameter in the resulting template. Lateral correlation length and grain boundary effect are other factors that affect the pore formation process and pore size distribution by limiting the initial current density.

Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo Temperature Basin Paving and Molecular Tailoring Approaches benchmarked by full MP2 calculations

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

Sahu, Nityananda; Gadre, Shridhar R.; Bandyopadhyay, Pradipta

We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving (MCTBP) sampling of the cluster’s Potential Energy Surface (PES) with the Effective Fragment Potential (EFP), subsequent geometry optimization using the Molecular Tailoring fragmentation Approach (MTA) and final refinement at the second order Møller Plesset perturbation (MP2) level of theory. The MTA geometry optimizations usedmore » between 14 and 18 main fragments with maximum sizes between 11 and 14 water molecules and average size of 10 water molecules, whose energies and gradients were computed at the MP2 level. The MTA-MP2 optimized geometries were found to be quite close (within < 0.5 kcal/mol) to the ones obtained from the MP2 optimization of the whole cluster. The grafting of the MTA-MP2 energies yields electronic energies that are within < 5×10-4 a.u. from the MP2 results for the whole cluster while preserving their energy order. The MTA-MP2 method was also found to reproduce the MP2 harmonic vibrational frequencies in both the HOH bending and the OH stretching regions.« less

Decorin and biglycan of normal and pathologic human corneas

NASA Technical Reports Server (NTRS)

Funderburgh, J. L.; Hevelone, N. D.; Roth, M. R.; Funderburgh, M. L.; Rodrigues, M. R.; Nirankari, V. S.; Conrad, G. W.

1998-01-01

PURPOSE: Corneas with scars and certain chronic pathologic conditions contain highly sulfated dermatan sulfate, but little is known of the core proteins that carry these atypical glycosaminoglycans. In this study the proteoglycan proteins attached to dermatan sulfate in normal and pathologic human corneas were examined to identify primary genes involved in the pathobiology of corneal scarring. METHODS: Proteoglycans from human corneas with chronic edema, bullous keratopathy, and keratoconus and from normal corneas were analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative immunoblotting, and immunohistology with peptide antibodies to decorin and biglycan. RESULTS: Proteoglycans from pathologic corneas exhibit increased size heterogeneity and binding of the cationic dye alcian blue compared with those in normal corneas. Decorin and biglycan extracted from normal and diseased corneas exhibited similar molecular size distribution patterns. In approximately half of the pathologic corneas, the level of biglycan was elevated an average of seven times above normal, and decorin was elevated approximately three times above normal. The increases were associated with highly charged molecular forms of decorin and biglycan, indicating modification of the proteins with dermatan sulfate chains of increased sulfation. Immunostaining of corneal sections showed an abnormal stromal localization of biglycan in pathologic corneas. CONCLUSIONS: The increased dermatan sulfate associated with chronic corneal pathologic conditions results from stromal accumulation of decorin and particularly of biglycan in the affected corneas. These proteins bear dermatan sulfate chains with increased sulfation compared with normal stromal proteoglycans.

Polycyclic Aromatic Hydrocarbon Far-infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Boersma, C.; Bauschlicher, C. W., Jr.; Ricca, A.; Mattioda, A. L.; Peeters, E.; Tielens, A. G. G. M.; Allamandola, L. J.

2011-03-01

The far-IR characteristics of astrophysically relevant polycyclic aromatic hydrocarbons (PAHs) averaging in size around 100 carbon atoms have been studied using the theoretical spectra in the NASA Ames PAH IR Spectroscopic Database. These spectra were calculated using density functional theory. Selections of PAH species are made, grouped together by common characteristics or trends, such as size, shape, charge, and composition, and their far-IR spectra compared. The out-of-plane modes involving the entire molecule are explored in detail, astronomical relevance is assessed, and an observing strategy is discussed. It is shown that PAHs produce richer far-IR spectra with increasing size. PAHs also produce richer far-IR spectra with increasing number of irregularities. However, series of irregular-shaped PAHs with the same compact core have common "Jumping-Jack" modes that "pile up" at specific frequencies in their average spectrum. For the PAHs studied here, around 100 carbon atoms in size, this band falls near 50 μm. PAH charge and nitrogen inclusion affect band intensities but have little effect on far-IR band positions. Detailed analysis of the two-dimensional, out-of-plane bending "drumhead" modes in the coronene and pyrene "families" and the one-dimensional, out-of-plane bending "bar" modes in the acene "family" show that these molecular vibrations can be treated as classical vibrating sheets and bars of graphene, respectively. The analysis also shows that the peak position of these modes is very sensitive to the area of the emitting PAH and does not depend on the particular geometry. Thus, these longest wavelength PAH bands could provide a unique handle on the size of the largest species in the interstellar PAH family. However, these bands are weak. Observing highly excited regions showing the mid-IR bands in which the emission from classical dust peaks at short wavelengths offers the best chance of detecting PAH emission in the far-IR. For these regions sensitivity is not an issue, spectral contrast is maximized and the PAH population is only comprised of highly stable, compact symmetric PAHs, such as the members of the pyrene and coronene "families" discussed in detail here.

In vitro and in vivo gene delivery using chitosan/hyaluronic acid nanoparticles: Influences of molecular mass of hyaluronic acid and lyophilization on transfection efficiency.

PubMed

Sato, Toshinori; Nakata, Mitsuhiro; Yang, Zhihong; Torizuka, Yu; Kishimoto, Satoko; Ishihara, Masayuki

2017-08-01

Lyophilization is an effective method for preserving nonviral gene vectors. To improve the stability and transgene expression of lyophilized plasmid DNA (pDNA) complexes, we coated the surfaces of pDNA/chitosan complexes with hyaluronic acid (HA) of varying molecular masses. The transgene expression of pDNA/chitosan/HA ternary complexes was characterized in vitro and in vivo. pDNA complexes were lyophilized overnight and the resultant products with spongy, porous consistencies were stored at -30, 4 or 25°C for 2 weeks. Rehydrated complexes were characterized using gel retardation assays, aiming to confirm complex formation, measure particle size and evaluate zeta potential, as well as conduct luciferase gene reporter assays. The anti-tumor effects of pDNA ternary complexes were evaluated using suicide gene (pTK) coding thymidine kinase in Huh7-implanted mice. Transfection efficiencies of pDNA/chitosan/HA ternary complexes were dependent on the average molecular masses of HA. The coating of pDNA/chitosan complexes with HA maintained the cellular transfection efficiencies of lyophilized pDNA ternary complexes. Furthermore, intratumoral injection of lyophilized, rehydrated pDNA ternary complexes into tumor-bearing mice showed a significant suppression of tumor growth. The coating of pDNA/chitosan complexes with high-molecular-weight HA augmented the stability and cellular transfection ability of the complexes after lyophilization-rehydration. Copyright © 2017 John Wiley & Sons, Ltd.

Molecularly imprinted polymer for glutathione by modified precipitation polymerization and its application to determination of glutathione in supplements.

PubMed

Nakamura, Yukari; Masumoto, Shizuka; Matsunaga, Hisami; Haginaka, Jun

2017-09-10

Molecularly imprinted polymers (MIP) particles for glutathione (GSH) with a narrow particle size distribution were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer, divinylbenzene as a crosslinker and water as a co-solvent. The particle diameters of the MIP and non-imprinted polymer (NIP) prepared under the optimum conditions were 3.81±0.95 (average±standard deviation) and 3.39±1.22μm, respectively. The retention and molecular-recognition properties of the prepared MIP were evaluated using a mixture of acetonitrile and water as a mobile phase in hydrophilic interaction chromatography. With an increase of acetonitrile content, the retention factor of GSH was increased on the MIP. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of GSH on the MIP. The MIP had a specific molecular-recognition ability for GSH, while glutathione disulfide, l-Glu, l-Cys, Gly-Gly and l-Cys-Gly could not be retained or recognized on the MIP. The effect of column temperature revealed that the separation of GSH on the MIP was entropically driven. Binding experiments and Scatchard analyses revealed that one binding sites were formed on both the MIP and NIP, while the MIP gave higher affinity and capacity for GSH than the NIP. Furthermore, the MIP was successfully applied for determination of GSH in the supplements. Copyright © 2016 Elsevier B.V. All rights reserved.

An ensemble predictive modeling framework for breast cancer classification.

PubMed

Nagarajan, Radhakrishnan; Upreti, Meenakshi

2017-12-01

Molecular changes often precede clinical presentation of diseases and can be useful surrogates with potential to assist in informed clinical decision making. Recent studies have demonstrated the usefulness of modeling approaches such as classification that can predict the clinical outcomes from molecular expression profiles. While useful, a majority of these approaches implicitly use all molecular markers as features in the classification process often resulting in sparse high-dimensional projection of the samples often comparable to that of the sample size. In this study, a variant of the recently proposed ensemble classification approach is used for predicting good and poor-prognosis breast cancer samples from their molecular expression profiles. In contrast to traditional single and ensemble classifiers, the proposed approach uses multiple base classifiers with varying feature sets obtained from two-dimensional projection of the samples in conjunction with a majority voting strategy for predicting the class labels. In contrast to our earlier implementation, base classifiers in the ensembles are chosen based on maximal sensitivity and minimal redundancy by choosing only those with low average cosine distance. The resulting ensemble sets are subsequently modeled as undirected graphs. Performance of four different classification algorithms is shown to be better within the proposed ensemble framework in contrast to using them as traditional single classifier systems. Significance of a subset of genes with high-degree centrality in the network abstractions across the poor-prognosis samples is also discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

The Effect of Game-Assisted Mathematics Education on Academic Achievement in Turkey: A Meta-Analysis Study

ERIC Educational Resources Information Center

Turgut, Sedat; Temur, Özlem Dogan

2017-01-01

In this research, the effects of using game in mathematics teaching process on academic achievement in Turkey were examined by metaanalysis method. For this purpose, the average effect size value and the average effect size values of the moderator variables (education level, the field of education, game type, implementation period and sample size)…

Effects of epidemic threshold definition on disease spread statistics

NASA Astrophysics Data System (ADS)

Lagorio, C.; Migueles, M. V.; Braunstein, L. A.; López, E.; Macri, P. A.

2009-03-01

We study the statistical properties of SIR epidemics in random networks, when an epidemic is defined as only those SIR propagations that reach or exceed a minimum size sc. Using percolation theory to calculate the average fractional size of an epidemic, we find that the strength of the spanning link percolation cluster P∞ is an upper bound to . For small values of sc, P∞ is no longer a good approximation, and the average fractional size has to be computed directly. We find that the choice of sc is generally (but not always) guided by the network structure and the value of T of the disease in question. If the goal is to always obtain P∞ as the average epidemic size, one should choose sc to be the typical size of the largest percolation cluster at the critical percolation threshold for the transmissibility. We also study Q, the probability that an SIR propagation reaches the epidemic mass sc, and find that it is well characterized by percolation theory. We apply our results to real networks (DIMES and Tracerouter) to measure the consequences of the choice sc on predictions of average outcome sizes of computer failure epidemics.

Controlling chitosan-based encapsulation for protein and vaccine delivery

PubMed Central

Koppolu, Bhanu prasanth; Smith, Sean G.; Ravindranathan, Sruthi; Jayanthi, Srinivas; Kumar, Thallapuranam K.S.; Zaharoff, David A.

2014-01-01

Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, was inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters. PMID:24560459

Vapor-pressure osmometric study of the molecular weight and aggregation tendency of a reference-soil fulvic acid

USGS Publications Warehouse

Marinsky, J.A.; Reddy, M.M.

1990-01-01

The molecular weight and aggregation tendency of a reference-soil fulvic acid in Armadale horizon Bh were determined by vapor-pressure osmometry using tetrahydrofuran and water as solvents. With tetrahydrofuran, number-average molecular weight values of 767 ?? 34 and 699 ?? 8 daltons were obtained from two separate sets of measurements. Two sets of measurements with water also yielded values within this range (754 ?? 70 daltons) provided that the fulvic acid concentration in water did not exceed 7 mg ml-1; at higher concentrations (9.1-13.7 mg ml-1) a number-average molecular weight of 956 ?? 25 daltons was resolved, providing evidence of molecular aggregation. Extension of these studies to 80% neutralized fulvic acid showed that a sizeable fraction of the sodium counter ion is not osmotically active.

Separation of both fibrous and globular proteins on the basis of molecular weight using high-performance size exclusion chromatography.

PubMed

Barden, J A

1983-11-01

A high-performance size exclusion liquid chromatographic system has been used to separate proteins with different shapes solely on the basis of their molecular weights. After the effects of ionic and hydrophobic interactions with the stationary phase have been overcome, protein elution is normally governed by their effective size in solution. Conditions are described under which proteins, with isoelectric points within the normal operating pH range of the columns, are eluted independent of their Stokes' radii. Even fibrous proteins with axial ratios of 50 elute according to their known molecular weights over the range 2000-2,000,000.

Genome size variation in the genus Avena.

PubMed

Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

2016-03-01

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

The geometry of proliferating dicot cells.

PubMed

Korn, R W

2001-02-01

The distributions of cell size and cell cycle duration were studied in two-dimensional expanding plant tissues. Plastic imprints of the leaf epidermis of three dicot plants, jade (Crassula argentae), impatiens (Impatiens wallerana), and the common begonia (Begonia semperflorens) were made and cell outlines analysed. The average, standard deviation and coefficient of variance (CV = 100 x standard deviation/average) of cell size were determined with the CV of mother cells less than the CV for daughter cells and both are less than that for all cells. An equation was devised as a simple description of the probability distribution of sizes for all cells of a tissue. Cell cycle durations as measured in arbitrary time units were determined by reconstructing the initial and final sizes of cells and they collectively give the expected asymmetric bell-shaped probability distribution. Given the features of unequal cell division (an average of 11.6% difference in size of daughter cells) and the size variation of dividing cells, it appears that the range of cell size is more critically regulated than the size of a cell at any particular time.

Estimation After a Group Sequential Trial.

PubMed

Milanzi, Elasma; Molenberghs, Geert; Alonso, Ariel; Kenward, Michael G; Tsiatis, Anastasios A; Davidian, Marie; Verbeke, Geert

2015-10-01

Group sequential trials are one important instance of studies for which the sample size is not fixed a priori but rather takes one of a finite set of pre-specified values, dependent on the observed data. Much work has been devoted to the inferential consequences of this design feature. Molenberghs et al (2012) and Milanzi et al (2012) reviewed and extended the existing literature, focusing on a collection of seemingly disparate, but related, settings, namely completely random sample sizes, group sequential studies with deterministic and random stopping rules, incomplete data, and random cluster sizes. They showed that the ordinary sample average is a viable option for estimation following a group sequential trial, for a wide class of stopping rules and for random outcomes with a distribution in the exponential family. Their results are somewhat surprising in the sense that the sample average is not optimal, and further, there does not exist an optimal, or even, unbiased linear estimator. However, the sample average is asymptotically unbiased, both conditionally upon the observed sample size as well as marginalized over it. By exploiting ignorability they showed that the sample average is the conventional maximum likelihood estimator. They also showed that a conditional maximum likelihood estimator is finite sample unbiased, but is less efficient than the sample average and has the larger mean squared error. Asymptotically, the sample average and the conditional maximum likelihood estimator are equivalent. This previous work is restricted, however, to the situation in which the the random sample size can take only two values, N = n or N = 2 n . In this paper, we consider the more practically useful setting of sample sizes in a the finite set { n 1 , n 2 , …, n L }. It is shown that the sample average is then a justifiable estimator , in the sense that it follows from joint likelihood estimation, and it is consistent and asymptotically unbiased. We also show why simulations can give the false impression of bias in the sample average when considered conditional upon the sample size. The consequence is that no corrections need to be made to estimators following sequential trials. When small-sample bias is of concern, the conditional likelihood estimator provides a relatively straightforward modification to the sample average. Finally, it is shown that classical likelihood-based standard errors and confidence intervals can be applied, obviating the need for technical corrections.

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.

PubMed

Feinstein, Wei P; Brylinski, Michal

2015-01-01

Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. This fully automated procedure can be used to optimize docking protocols in order to improve the ranking accuracy in production virtual screening simulations. Importantly, the optimized search space systematically yields better results than the default method not only for experimental pockets, but also for those predicted from protein structures. A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size. Graphical AbstractWe developed a procedure to optimize the box size in molecular docking calculations. Left panel shows the predicted binding pose of NADP (green sticks) compared to the experimental complex structure of human aldose reductase (blue sticks) using a default protocol. Right panel shows the docking accuracy using an optimized box size.

Action of polysaccharides of similar average mass but differing molecular volume and charge on fluid drainage through synovial interstitium in rabbit knees

PubMed Central

Scott, D; Coleman, P J; Mason, R M; Levick, J R

2000-01-01

Hyaluronan (HA), an anionic polysaccharide of synovial fluid, attenuates fluid loss from joints as joint pressure is raised (‘outflow buffering’). The buffering is thought to depend on the expanded molecular domain of the polymer, which causes reflection by synovial extracellular matrix, leading to flow-dependent concentration polarization. We therefore assessed the effects of polysaccharides of differing average molecular volume and charge. Trans-synovial fluid drainage(Q̇s) was measured at controlled joint fluid pressure (Pj) in knees of anaesthetized rabbits. The joints were infused with polydisperse HA of weight-average mass 2100 kDa (4 mg ml−1, n = 17), with polydisperse neutral dextran of similar average mass (2000 kDa; n = 7) or with Ringer solution vehicle (n = 2). The role of polymer charge was assessed by infusions of neutral or sulphated dextran of average molecular mass 500 kDa (n = 6). When HA was present, Q̇s increased little with pressure, forming a virtual plateau of ∼4 μl min−1 from 10 to 25 cmH2O. Neutral dextran 2000 failed to replicate this effect. Instead, Q̇s increased steeply with Pj, reaching eight times the HA value by 20 cmH2O (P = 0.0001, ANOVA). Dextran 2000 reduced flows in comparison with Ringer solution. Analysis of the aspirated joint fluid showed that 31 ± 0.07 % (s.e.m.) of dextran 2000 in the filtrand was reflected by synovium, compared with ≥ 79 % for HA. The viscometric molecular radius of the dextran, ∼31 nm, was smaller than that of HA (101–181 nm), as was its osmotic pressure. Anionic dextran 500 failed to buffer fluid drainage, but it reduced fluid escape and synovial conductance dQ̇s/dPj more than neutral dextran 500 (P < 0.0001, ANOVA). The anionic charge increased the molecular volume and viscosity of dextran 500. The results support the hypothesis that polymer molecular volume influences its reflection by interstitial matrix and outflow buffering. Polymer charge influences flow through an effect on viscosity and possibly electrostatic interactions with negatively charged interstitial matrix. PMID:11060134

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

PubMed

Barrera-Redondo, Josué; Ramírez-Barahona, Santiago; Eguiarte, Luis E

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Preparation and screening of an arrayed human genomic library generated with the P1 cloning system.

PubMed Central

Shepherd, N S; Pfrogner, B D; Coulby, J N; Ackerman, S L; Vaidyanathan, G; Sauer, R H; Balkenhol, T C; Sternberg, N

1994-01-01

We describe here the construction and initial characterization of a 3-fold coverage genomic library of the human haploid genome that was prepared using the bacteriophage P1 cloning system. The cloned DNA inserts were produced by size fractionation of a Sau3AI partial digest of high molecular weight genomic DNA isolated from primary cells of human foreskin fibroblasts. The inserts were cloned into the pAd10sacBII vector and packaged in vitro into P1 phage. These were used to generate recombinant bacterial clones, each of which was picked robotically from an agar plate into a well of a 96-well microtiter dish, grown overnight, and stored at -70 degrees C. The resulting library, designated DMPC-HFF#1 series A, consists of approximately 130,000-140,000 recombinant clones that were stored in 1500 microtiter dishes. To screen the library, clones were combined in a pooling strategy and specific loci were identified by PCR analysis. On average, the library contains two or three different clones for each locus screened. To date we have identified a total of 17 clones containing the hypoxanthine-guanine phosphoribosyltransferase, human serum albumin-human alpha-fetoprotein, p53, cyclooxygenase I, human apurinic endonuclease, beta-polymerase, and DNA ligase I genes. The cloned inserts average 80 kb in size and range from 70 to 95 kb, with one 49-kb insert and one 62-kb insert. Images PMID:8146166

Acid Hydrolysis and Molecular Density of Phytoglycogen and Liver Glycogen Helps Understand the Bonding in Glycogen α (Composite) Particles

PubMed Central

Powell, Prudence O.; Sullivan, Mitchell A.; Sheehy, Joshua J.; Schulz, Benjamin L.; Warren, Frederick J.; Gilbert, Robert G.

2015-01-01

Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired. PMID:25799321

Accurate Size and Size-Distribution Determination of Polystyrene Latex Nanoparticles in Aqueous Medium Using Dynamic Light Scattering and Asymmetrical Flow Field Flow Fractionation with Multi-Angle Light Scattering

PubMed Central

Kato, Haruhisa; Nakamura, Ayako; Takahashi, Kayori; Kinugasa, Shinichi

2012-01-01

Accurate determination of the intensity-average diameter of polystyrene latex (PS-latex) by dynamic light scattering (DLS) was carried out through extrapolation of both the concentration of PS-latex and the observed scattering angle. Intensity-average diameter and size distribution were reliably determined by asymmetric flow field flow fractionation (AFFFF) using multi-angle light scattering (MALS) with consideration of band broadening in AFFFF separation. The intensity-average diameter determined by DLS and AFFFF-MALS agreed well within the estimated uncertainties, although the size distribution of PS-latex determined by DLS was less reliable in comparison with that determined by AFFFF-MALS. PMID:28348293

Effect of polyoxyethylene sorbitan esters and sodium caseinate on physicochemical properties of palm-based functional lipid nanodispersions.

PubMed

Cheong, Jean Ne; Mirhosseini, Hamed; Tan, Chin Ping

2010-06-01

The main objective of the present study was to investigate the effect of polyoxyethylene sorbitan esters and sodium caseinate on physicochemical properties of palm-based functional lipid nanodispersions prepared by the emulsification-evaporation technique. The results indicated that the average droplet size increased significantly (P < 0.05) by increasing the chain length of fatty acids and also by increasing the hydrophile-lipophile balance value. Among the prepared nanodispersions, the nanoemulsion containing Polysorbate 20 showed the smallest average droplet size (202 nm) and narrowest size distribution for tocopherol-tocotrienol nanodispersions, while sodium caseinate-stabilized nanodispersions containing carotenoids had the largest average droplet size (386 nm), thus indicating a greater emulsifying role for Polysorbate 20 compared with sodium caseinate.

Molecular-dynamics study on characteristics of energy and tangential momentum accommodation coefficients

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroki; Matsuda, Yu; Niimi, Tomohide

2017-07-01

Gas-surface interaction is studied by the molecular dynamics method to investigate qualitatively characteristics of accommodation coefficients. A large number of trajectories of gas molecules colliding to and scattering from a surface are statistically analyzed to calculate the energy (thermal) accommodation coefficient (EAC) and the tangential momentum accommodation coefficient (TMAC). Considering experimental measurements of the accommodation coefficients, the incident velocities are stochastically sampled to represent a bulk condition. The accommodation coefficients for noble gases show qualitative coincidence with experimental values. To investigate characteristics of these accommodation coefficients in detail, the gas-surface interaction is parametrically studied by varying the molecular mass of gas, the gas-surface interaction strength, and the molecular size of gas, one by one. EAC increases with increasing every parameter, while TMAC increases with increasing the interaction strength, but decreases with increasing the molecular mass and the molecular size. Thus, contradictory results in experimentally measured TMAC for noble gases could result from the difference between the surface conditions employed in the measurements in the balance among the effective parameters of molecular mass, interaction strength, and molecular size, due to surface roughness and/or adsorbed molecules. The accommodation coefficients for a thermo-fluid dynamics field with a temperature difference between gas and surface and a bulk flow at the same time are also investigated.

Undergraduate research studies program at participating institutions of the HBCU Fossil Energy Consortium

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

Bhatia, S.C.; Cardelino, B.H.; Hall, J.H. Jr.

1990-07-31

The objectives of this research program are to expose students in minority institutions of energy and fossil fuels research, to stimulate their interest in the sciences and engineering, and to encourage them to pursue graduate studies, thereby ensuring the necessary supply of manpower for the industrial and energy sectors of the national economy. Two projects are discussed here. The first is focused on the surface chemical properties of coal and their influence on the adsorption of aqueous soluble catalyst metals. The objective of the second project is to characterize coal derived liquids for distribution of oxygen, nitrogen and sulfur heteroatomsmore » relative to the average molecular weight distribution of the coal liquid. The technique of size exclusion chromatography will be used. 2 refs., 2 figs.« less

Formation and photopatterning of nanoporous titania thin films

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

Park, Oun-Ho; Cheng, Joy Y.; Kim, Hyun Suk

2007-06-04

Photopatternable nanoporous titania thin films were generated from mixtures of an organic diblock copolymer, poly(styrene-b-ethylene oxide) (PS-b-PEO), and an oligomeric titanate (OT) prepared from a chelated titanium isopropoxide. The PS-b-PEO templates well-defined microdomains in thin films of the mixtures, which upon thermal treatment at 450 deg. C, become nanopores in titania. Average pore size and porosity are controlled by the molecular weight and loading level of the PS-b-PEO, respectively. Patterns of nanoporous titania were created by selectively exposing UV light on the mixture films. The UV irradiation destroys the chelating bond and induces the cross-linking reaction of the OT. Subsequentmore » wet development followed by thermal treatment gives patterned nanoporous films of anatase phase titania.« less

Effects of electronic excitation in 150 keV Ni ion irradiation of metallic systems

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

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

We use the two-temperature model in molecular dynamic simulations of 150 keV Ni ion cascades in nickel and nickel-based alloys to investigate the effect of the energy exchange between the atomic and the electronic systems during the primary stages of radiation damage. We find that the electron-phonon interactions result in a smaller amount of defects and affect the cluster formation, resulting in smaller clusters. These results indicate that ignoring the local heating due to the electrons results in the overestimation of the amount of damage and the size of the defect clusters. A comparison of the average defect production tomore » the Norgett-Robinson-Torrens (NRT) prediction over a range of energies is provided.« less

Membranes for nanometer-scale mass fast transport

DOEpatents

Bakajin, Olgica [San Leandro, CA; Holt, Jason [Berkeley, CA; Noy, Aleksandr [Belmont, CA; Park, Hyung Gyu [Oakland, CA

2011-10-18

Nanoporous membranes comprising single walled, double walled, and multiwalled carbon nanotubes embedded in a matrix material were fabricated for fluid mechanics and mass transfer studies on the nanometer scale and commercial applications. Average pore size can be 2 nm to 20 nm, or seven nm or less, or two nanometers or less. The membrane can be free of large voids spanning the membrane such that transport of material such as gas or liquid occurs exclusively through the tubes. Fast fluid, vapor, and liquid transport are observed. Versatile micromachining methods can be used for membrane fabrication. A single chip can comprise multiple membranes. These membranes are a robust platform for the study of confined molecular transport, with applications in liquid and gas separations and chemical sensing including desalination, dialysis, and fabric formation.

Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains

NASA Technical Reports Server (NTRS)

Glaessgen, E. H.; Saether, E.; Yamakov, V.

2008-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

PubMed

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Synthesis, characterization and evaluation of uniformly sized core-shell imprinted microspheres for the separation trans-resveratrol from giant knotweed

NASA Astrophysics Data System (ADS)

Zhang, Zhaohui; Liu, Li; Li, Hui; Yao, Shouzhuo

2009-09-01

A novel core-shell molecularly imprinting microspheres (MIMs) with trans-resveratrol as the template molecule; acrylamide (AA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker, was prepared based on SiO 2 microspheres with surface imprinting technique. These core-shell trans-resveratrol imprinted microspheres were characterized by infrared spectra (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and high performance liquid chromatography (HPLC). The results showed that these core-shell imprinted microspheres, which take on perfect spherical shape with average shell thickness of 150 nm, exhibit especially selective recognition for trans-resveratrol. These imprinted microspheres were applied as solid-phase extraction materials for selective extraction of trans-resveratrol from giant knotweed extracting solution successfully.

Effects of electronic excitation in 150 keV Ni ion irradiation of metallic systems

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2018-01-18

We use the two-temperature model in molecular dynamic simulations of 150 keV Ni ion cascades in nickel and nickel-based alloys to investigate the effect of the energy exchange between the atomic and the electronic systems during the primary stages of radiation damage. We find that the electron-phonon interactions result in a smaller amount of defects and affect the cluster formation, resulting in smaller clusters. These results indicate that ignoring the local heating due to the electrons results in the overestimation of the amount of damage and the size of the defect clusters. A comparison of the average defect production tomore » the Norgett-Robinson-Torrens (NRT) prediction over a range of energies is provided.« less

Laboratory Experiments to Evaluate Matrix Diffusion of Dissolved Organic Carbon Carbon-14 in Southern Nevada Fractured-rock Aquifers

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

Hershey, Ronald L.; Fereday, Wyatt

Dissolved inorganic carbon (DIC) carbon-14 ( 14C) is used to estimate groundwater ages by comparing the DIC 14C content in groundwater in the recharge area to the DIC 14C content in the downgradient sampling point. However, because of chemical reactions and physical processes between groundwater and aquifer rocks, the amount of DIC 14C in groundwater can change and result in 14C loss that is not because of radioactive decay. This loss of DIC 14C results in groundwater ages that are older than the actual groundwater ages. Alternatively, dissolved organic carbon (DOC) 14C in groundwater does not react chemically with aquifermore » rocks, so DOC 14C ages are generally younger than DIC 14C ages. In addition to chemical reactions, 14C ages may also be altered by the physical process of matrix diffusion. The net effect of a continuous loss of 14C to the aquifer matrix by matrix diffusion and then radioactive decay is that groundwater appears to be older than it actually is. Laboratory experiments were conducted to measure matrix diffusion coefficients for DOC 14C in volcanic and carbonate aquifer rocks from southern Nevada. Experiments were conducted using bromide (Br-) as a conservative tracer and 14C-labeled trimesic acid (TMA) as a surrogate for groundwater DOC. Outcrop samples from six volcanic aquifers and five carbonate aquifers in southern Nevada were used. The average DOC 14C matrix diffusion coefficient for volcanic rocks was 2.9 x 10 -7 cm 2/s, whereas the average for carbonate rocks was approximately the same at 1.7 x 10 -7 cm 2/s. The average Br- matrix diffusion coefficient for volcanic rocks was 10.4 x 10 -7 cm 2/s, whereas the average for carbonate rocks was less at 6.5 x 10 -7 cm 2/s. Carbonate rocks exhibited greater variability in DOC 14C and Br- matrix diffusion coefficients than volcanic rocks. These results confirmed, at the laboratory scale, that the diffusion of DOC 14C into southern Nevada volcanic and carbonate aquifers is slower than DIC 14C. Because of the apparent sorption of 14C-labeled TMA in the experiments, matrix diffusion coefficients are likely even lower. The reasons for the higher than expected Br-/ 14C-labeled TMA are unknown. Because the molecular size of TMA is on the low end of the range in molecular size for typical humic substances, the matrix diffusion coefficients for the 14C-labeled TMA likely represent close to the maximum diffusion rates for DOC 14C in the volcanic and carbonate aquifers in southern Nevada.« less

Preparation and characterization of nanocrystalline cellulose/Eucommia ulmoides gum nanocomposite film.

PubMed

Sun, Qianqian; Zhao, Xinkun; Wang, Dongmei; Dong, Juane; She, Diao; Peng, Pai

2018-02-01

The nanocomposite films were prepared using Eucommia ulmoides gum (EUG) matrix reinforced with nanocrystalline cellulose (NCC) at different concentrations. Subsequently, the obtained films were characterized by Raman spectra, AFM, XRD, TGA, and DSC. Meanwhile, the wettability, mechanical, and water vapor barrier properties of these films were analyzed. AFM noticed that the average sizes of NCC were 81.95×50.17×13.06nm, while the size of molecular chain for EUG was 2530×57.33×1.28nm. In comparison with control film, a certain amount of NCC obviously improved elongation at break and enhanced their crystallinity and ΔH m . More importantly, NCC/EUG nanocomposite films presented lower thermal stability, glass transition temperature (T g ), melting temperature (T m ), and water vapor permeability (WVP) values, especially the WVP values of 4% NCC film were the lowest as 0.28×10 -9 , 0.30×10 -9 , and 0.58×10 -9 g/m/h/Pa at RH 34%, 55%, and 76%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Results of Simulation Studies

NASA Technical Reports Server (NTRS)

2003-01-01

Lattice Monte Carlo and off-lattice molecular dynamics simulations of h(sub 1)t(sub 4) and h(sub 4)t(sub l) (head/tail) amphiphile solutions have been performed as a function of surfactant concentration and temperature. The lattice and off-lattice systems exhibit quite different self-assembly behavior at equivalent thermodynamic conditions. We found that in the weakly aggregating regime (no preferred-size micelles), all models yield similar micelle size distributions at the same average aggregation number, albeit at different thermodynamic conditions (temperatures). In the strongly aggregating regime, this mapping between models (through temperature adjustment) fails, and the models exhibit qualitatively different micellization behavior. Incipient micellization in a model self-associating telechelic polymer solution results in a network with a transient elastic response that decays by a two-step relaxation: the first is due to a heterogeneous jump-diffusion process involving entrapment of end-groups within well-defined clusters and this is followed by rapid diffusion to neighboring clusters and a decay (terminal relaxation) due to cluster disintegration. The viscoelastic response of the solution manifests characteristics of a glass transition and entangled polymer network.

Study of the ammonia ice cloud layer in the north tropical zone of Jupiter from the infrared interferometric experiment on Voyager

NASA Technical Reports Server (NTRS)

Shaffer, William A.; Samuelson, Robert E.; Conrath, Barney J.

1986-01-01

An average of 51 Voyager 1 IRIS spectra of Jupiter's North Tropical Zone was analyzed to infer the abundance, vertical extent, and size distribution of the particles making up the ammonia cloud in this region. It is assumed that the cloud base coincides with the level at which 100% saturation of ammonia vapor occurs. The vertical distribution of particulates above this level is determined by assuming a constant total ammonia mixing ratio and adjusting the two phases so that the vapor is saturated throughout the cloud. A constant scaling factor then adjusts the base number density. A radiative transfer program is used that includes the effects of absorption and emission of all relevant gases as well as anisotropic scattering by cloud particles. Mie scattering from a gaussian particle size distribution is assumed. The vertical thermal structure is inferred from a temperature retrieval program that utilizes the collision induced S(0) and S(1) molecular hydrogen lines between 300 and 700.cm, and the 1304.cm methane band.

Gene expression analysis in rat lungs after intratracheal exposure to nanoparticles doped with cadmium

NASA Astrophysics Data System (ADS)

Coccini, Teresa; Fabbri, Marco; Roda, Elisa; Grazia Sacco, Maria; Manzo, Luigi; Gribaldo, Laura

2011-07-01

Silica nanoparticles (NPs) incorporating cadmium (Cd) have been developed for a range of potential application including drug delivery devices. Occupational Cd inhalation has been associated with emphysema, pulmonary fibrosis and lung tumours. Mechanistically, Cd can induce oxidative stress and mediate cell-signalling pathways that are involved in inflammation.This in vivo study aimed at investigating pulmonary molecular effects of NPs doped with Cd (NP-Cd, 1 mg/animal) compared to soluble CdCl2 (400 μg/animal), in Sprague Dawley rats treated intra-tracheally, 7 and 30 days after administration. NPs of silica containing Cd salt were prepared starting from commercial nano-size silica powder (HiSil™ T700 Degussa) with average pore size of 20 nm and surface area of 240 m2/g. Toxicogenomic analysis was performed by the DNA microarray technology (using Agilent Whole Rat Genome Microarray 4×44K) to evaluate changes in gene expression of the entire genome. These findings indicate that the whole genome analysis may represent a valuable approach to assess the whole spectrum of biological responses to cadmium containing nanomaterials.

Compatibilizing Bulk Polymer Blends by Using Organoclays

NASA Astrophysics Data System (ADS)

Si, Mayu; Gersappe, Dilip; Zhang, Wenhua; Ade, Harald; Rafailovich, Miriam; Sokolov, Jonathan; Rudomen, Gregory; Schwartz, Bradley; Fisher, Robert

2004-03-01

We investigated the compatiblizing performance of organoclays on melt mixed binary and tertiary polymer blends, such as, PS/PMMA, PC/SAN, PS/PMMA/PVC and PS/PMMA/PE. These polymer blends were characterized by TEM, STXM, DSC and DMA. TEM and STXM photographs show that the addition of organoclays into polymer blends drastically reduces the average domain size of the component phases. And the organoclay goes to the interfacial region between the different polymers and effectively slows down the domain size increasing during high temperature annealing. DMA and DSC results show the effect of organoclays on the mechanical properties and glass transitions temperature, which indicates the compatibilization on the molecular level. The generalized compatibilization induced by the nanoscale fillers for blends can be explained in terms of mean field models where the reduction of interfacial tension induced by in-situ grafting is counterbalanced by the increased bending energy due to the rigidity of the filler. This in turn can be shown to be a function of the degree of exfoliation, aspect ratio, and polymer filler interactions. Supported by NSF funded MRSEC at Stony Brook

Time-dependent gas-liquid interaction in molecular-sized nanopores.

PubMed

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

2014-10-08

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

The Micromechanics of the Moving Contact Line

NASA Technical Reports Server (NTRS)

Han, Minsub; Lichter, Seth; Lin, Chih-Yu; Perng, Yeong-Yan

1996-01-01

The proposed research is divided into three components concerned with molecular structure, molecular orientation, and continuum averages of discrete systems. In the experimental program, we propose exploring how changes in interfacial molecular structure generate contact line motion. Rather than rely on the electrostatic and electrokinetic fields arising from the molecules themselves, we augment their interactions by an imposed field at the solid/liquid interface. By controling the field, we can manipulate the molecular structure at the solid/liquid interface. In response to controlled changes in molecular structure, we observe the resultant contact line motion. In the analytical portion of the proposed research we seek to formulate a system of equations governing fluid motion which accounts for the orientation of fluid molecules. In preliminary work, we have focused on describing how molecular orientation affects the forces generated at the moving contact line. Ideally, as assumed above, the discrete behavior of molecules can be averaged into a continuum theory. In the numerical portion of the proposed research, we inquire whether the contact line region is, in fact, large enough to possess a well-defined average. Additionally, we ask what types of behavior distinguish discrete systems from continuum systems. Might the smallness of the contact line region, in itself, lead to behavior different from that in the bulk? Taken together, our proposed research seeks to identify and accurately account for some of the molecular dynamics of the moving contact line, and attempts to formulate a description from which one can compute the forces at the moving contact line.

Mechanical properties of silk of the Australian golden orb weavers Nephila pilipes and Nephilaplumipes.

PubMed

Kerr, Genevieve G; Nahrung, Helen F; Wiegand, Aaron; Kristoffersen, Joanna; Killen, Peter; Brown, Cameron; Macdonald, Joanne

2018-02-22

Silks from orb-weaving spiders are exceptionally tough, producing a model polymer for biomimetic fibre development. The mechanical properties of naturally spun silk threads from two species of Australian orb-weavers, Nephila pilipes and Nephila plumipes , were examined here in relation to overall thread diameter, the size and number of fibres within threads, and spider size. N. pilipes , the larger of the two species, had significantly tougher silk with higher strain capacity than its smaller congener, producing threads with average toughness of 150 MJ m -3 , despite thread diameter, mean fibre diameter and number of fibres per thread not differing significantly between the two species. Within N. pilipes , smaller silk fibres were produced by larger spiders, yielding tougher threads. In contrast, while spider size was correlated with thread diameter in N. plumipes , there were no clear patterns relating to silk toughness, which suggests that the differences in properties between the silk of the two species arise through differing molecular structure. Our results support previous studies that found that the mechanical properties of silk differ between distantly related spider species, and extends on that work to show that the mechanical and physical properties of silk from more closely related species can also differ remarkably. © 2018. Published by The Company of Biologists Ltd.

Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.).

PubMed

Diekmann, Kerstin; Hodkinson, Trevor R; Wolfe, Kenneth H; van den Bekerom, Rob; Dix, Philip J; Barth, Susanne

2009-06-01

Lolium perenne L. (perennial ryegrass) is globally one of the most important forage and grassland crops. We sequenced the chloroplast (cp) genome of Lolium perenne cultivar Cashel. The L. perenne cp genome is 135 282 bp with a typical quadripartite structure. It contains genes for 76 unique proteins, 30 tRNAs and four rRNAs. As in other grasses, the genes accD, ycf1 and ycf2 are absent. The genome is of average size within its subfamily Pooideae and of medium size within the Poaceae. Genome size differences are mainly due to length variations in non-coding regions. However, considerable length differences of 1-27 codons in comparison of L. perenne to other Poaceae and 1-68 codons among all Poaceae were also detected. Within the cp genome of this outcrossing cultivar, 10 insertion/deletion polymorphisms and 40 single nucleotide polymorphisms were detected. Two of the polymorphisms involve tiny inversions within hairpin structures. By comparing the genome sequence with RT-PCR products of transcripts for 33 genes, 31 mRNA editing sites were identified, five of them unique to Lolium. The cp genome sequence of L. perenne is available under Accession number AM777385 at the European Molecular Biology Laboratory, National Center for Biotechnology Information and DNA DataBank of Japan.

Characterization and analysis of the molecular weight of lignin for biorefining studies

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

Tolbert, Allison; Akinosho, Hannah; Khunsupat, Ratayakorn

2014-06-04

The molecular weight of lignin is a fundamental property that infl uences the recalcitrance of biomass and the valorization of lignin. The determination of the molecular weight of lignin in native biomass is dependent on the bioresources used and the isolation and purifi cation procedures employed. The three most commonly employed isolation methods are milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL). Common characterization techniques for determining the molecular weight of lignin will be addressed, with an emphasis on gel permeation chromatography (GPC). This review also examines the mechanisms behind several biological, physical, andmore » chemical pre-treatments and their impact on the molecular weight of lignin. The number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (D) all vary in magnitude depending on the biomass source, pre-treatment conditions, and isolation method. Additionally, there is a growing body of literature that supports changes in the molecular weight of lignin in response to genetic modifi cations in the lignin biosynthetic pathways. This review summarizes different procedures for obtaining the molecular weight of lignin that have been used in recent years and highlight future opportunities for applications of lignin.« less

Numerical investigation of the relationship between magnetic stiffness and minor loop size in the HTS levitation system

NASA Astrophysics Data System (ADS)

Yang, Yong; Li, Chengshan

2017-10-01

The effect of minor loop size on the magnetic stiffness has not been paid attention to by most researchers in experimental and theoretical studies about the high temperature superconductor (HTS) magnetic levitation system. In this work, we numerically investigate the average magnetic stiffness obtained by the minor loop traverses Δz (or Δx) varying from 0.1 mm to 2 mm in zero field cooling and field cooling regimes, respectively. The approximate values of the magnetic stiffness with zero traverse are obtained using the method of linear extrapolation. Compared with the average magnetic stiffness gained by any minor loop traverse, these approximate values are Not always close to the average magnetic stiffness produced by the smallest size of minor loops. The relative deviation ranges of average magnetic stiffness gained by the usually minor loop traverse (1 or 2 mm) are presented by the ratios of approximate values to average stiffness for different moving processes and two typical cooling conditions. The results show that most of average magnetic stiffness are remarkably influenced by the sizes of minor loop, which indicates that the magnetic stiffness obtained by a single minor loop traverse Δ z or Δ x, for example, 1 or 2 mm, can be generally caused a large deviation.

Automatic vision-based grain optimization and analysis of multi-crystalline solar wafers using hierarchical region growing

NASA Astrophysics Data System (ADS)

Fan, Shu-Kai S.; Tsai, Du-Ming; Chuang, Wei-Che

2017-04-01

Solar power has become an attractive alternative source of energy. The multi-crystalline solar cell has been widely accepted in the market because it has a relatively low manufacturing cost. Multi-crystalline solar wafers with larger grain sizes and fewer grain boundaries are higher quality and convert energy more efficiently than mono-crystalline solar cells. In this article, a new image processing method is proposed for assessing the wafer quality. An adaptive segmentation algorithm based on region growing is developed to separate the closed regions of individual grains. Using the proposed method, the shape and size of each grain in the wafer image can be precisely evaluated. Two measures of average grain size are taken from the literature and modified to estimate the average grain size. The resulting average grain size estimate dictates the quality of the crystalline solar wafers and can be considered a viable quantitative indicator of conversion efficiency.

Improving consensus structure by eliminating averaging artifacts

PubMed Central

KC, Dukka B

2009-01-01

Background Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA [1], our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction [2], which could also benefit from our approach. PMID:19267905

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

Wu, Fuke, E-mail: wufuke@mail.hust.edu.cn; Tian, Tianhai, E-mail: tianhai.tian@sci.monash.edu.au; Rawlings, James B., E-mail: james.rawlings@wisc.edu

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in themore » work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.« less

Parental investment in the chicken turtle (Deirochelys reticularia)

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

Congdon, J.D.; Gibbons, J.W.; Greene, J.L.

1983-01-01

Eggs of the chicken turtle (Deirochelys reticularia) were collected in South Carolina from clutches laid in the spring and fall. Clutch size averaged 8.0 eggs (2 SE = 1.6; n = 15) and was weakly correlated with body size of the female. Wet mass of the clutch averaged 72.4 g (2 SE = 11.6, n = 15). There were no significant differences in clutch size or wet mass between spring and fall nesting seasons. Individual eggs laid in the fall (anti x = 10.7 g) were significantly larger than those laid in the spring (anti x = 8.5 g). Fifteenmore » eggs laid in the spring and incubated at 29/sup 0/ +- 2/sup 0/C averaged 152 d to hatching. Hatchling plastron length averaged 24.3 mm, and body wet mass was 6.7 g. Hatchlings (dry mass) contained 27.4% lipid, and the lipids remaining in the neonate at hatching represented 61% of the lipids originally present in the egg. The wet mass of a hatchling is highly correlated with wet mass of the egg. In contrast to clutch size, egg size had a strong positive relationship to body size. A morphological constraint, the width of the pelvic canal, is proposed as having an influence on this relationship. The negative relationship between an optimized egg size and clutch size was not evident, so current optimality models do not appear to be applicable to Deirochelys.« less

The Whole Warps the Sum of Its Parts.

PubMed

Corbett, Jennifer E

2017-01-01

The efficiency of averaging properties of sets without encoding redundant details is analogous to gestalt proposals that perception is parsimoniously organized as a function of recurrent order in the world. This similarity suggests that grouping and averaging are part of a broader set of strategies allowing the visual system to circumvent capacity limitations. To examine how gestalt grouping affects the manner in which information is averaged and remembered, I compared the error in observers' adjustments of remembered sizes of individual circles in two different mean-size sets defined by similarity, proximity, connectedness, or a common region. Overall, errors were more similar within the same gestalt-defined groups than between different gestalt-defined groups, such that the remembered sizes of individual circles were biased toward the mean size of their respective gestalt-defined groups. These results imply that gestalt grouping facilitates perceptual averaging to minimize the error with which individual items are encoded, thereby optimizing the efficiency of visual short-term memory.

Generation of Comprehensive Surrogate Kinetic Models and Validation Databases for Simulating Large Molecular Weight Hydrocarbon Fuels

DTIC Science & Technology

2012-10-25

of hydrogen/ carbon molar ratio (H/C), derived cetane number (DCN), threshold sooting index (TSI), and average mean molecular weight (MWave) of...diffusive soot extinction configurations. Matching the “real fuel combustion property targets” of hydrogen/ carbon molar ratio (H/C), derived cetane number...combustion property targets - hydrogen/ carbon molar ratio (H/C), derived cetane number (DCN), threshold sooting index (TSI), and average mean

Effect of molecular anisotropy on beam scattering measurements

NASA Technical Reports Server (NTRS)

Goldflam, R.; Green, S.; Kouri, D. J.; Monchick, L.

1978-01-01

Within the energy sudden approximation, the total integral and total differential scattering cross sections are given by the angle average of scattering cross sections computed at fixed rotor orientations. Using this formalism the effect of molecular anisotropy on scattering of He by HCl and by CO is examined. Comparisons with accurate close coupling calculations indicate that this approximation is quite reliable, even at very low collision energies, for both of these systems. Comparisons are also made with predictions based on the spherical average of the interaction. For HCl the anisotropy is rather weak and its main effect is a slight quenching of the oscillations in the differential cross sections relative to predictions of the spherical averaged potential. For CO the anisotropy is much stronger, so that the oscillatory pattern is strongly quenched and somewhat shifted. It appears that the sudden approximation provides a simple yet accurate method for describing the effect of molecular anisotropy on scattering measurements.

Theoretical and Experimental Triple Differential Cross Sections for Electron Impact Ionization of SF6

NASA Astrophysics Data System (ADS)

Chaluvadi, Hari; Nixon, Kate; Murray, Andrew; Ning, Chuangang; Colgan, James; Madison, Don

2014-10-01

Experimental and theoretical Triply Differential Cross Sections (TDCS) will be presented for electron-impact ionization of sulfur hexafluoride (SF6) for the molecular orbital 1t1g. M3DW (molecular 3-body distorted wave) results will be compared with experiment for coplanar geometry and for perpendicular plane geometry (a plane which is perpendicular to the incident beam direction). In both cases, the final state electron energies and observation angles are symmetric and the final state electron energies range from 5 eV to 40 eV. It will be shown that there is a large difference between using the OAMO (orientation averaged molecular orbital) approximation and the proper average over all orientations and also that the proper averaged results are in much better agreement with experiment. Work supported by NSF under Grant Number PHY-1068237. Computational work was performed with Institutional resources made available through Los Alamos National Laboratory.

Correlation of the protein structure and gelling properties in dried egg white products.

PubMed

Handa, A; Hayashi, K; Shidara, H; Kuroda, N

2001-08-01

The relationship between protein structure and aggregation, as well as heat-induced gelling properties, of seven dried egg white (DEW) products was investigated. Strong correlations were found between average molecular weight and hydrophobicity plus surface SH groups of DEW-soluble protein aggregate (SPA). This suggests that hydrophobic interactions and disulfide bond formation between protein molecules were involved in the aggregation. The average molecular weight of DEW products with alkaline pHs was relatively higher than those with neutral pHs and the same degree of protein unfolding, probably because of more disulfide bond formation between protein molecules. In addition, strong correlations were found between hydrophobicity, surface SH groups plus average molecular weight of DEW-SPA, and physical properties of the gels from DEW products. These data indicated that controlling the aggregation of DEW proteins in the dry state is crucial to controlling the gelling properties of DEW.

High-yield fabrication and properties of 1.4 nm nanodiamonds with narrow size distribution

NASA Astrophysics Data System (ADS)

Stehlik, Stepan; Varga, Marian; Ledinsky, Martin; Miliaieva, Daria; Kozak, Halyna; Skakalova, Viera; Mangler, Clemens; Pennycook, Timothy J.; Meyer, Jannik C.; Kromka, Alexander; Rezek, Bohuslav

2016-12-01

Detonation nanodiamonds (DNDs) with a typical size of 5 nm have attracted broad interest in science and technology. Further size reduction of DNDs would bring these nanoparticles to the molecular-size level and open new prospects for research and applications in various fields, ranging from quantum physics to biomedicine. Here we show a controllable size reduction of the DND mean size down to 1.4 nm without significant particle loss and with additional disintegration of DND core agglutinates by air annealing, leading to a significantly narrowed size distribution (±0.7 nm). This process is scalable to large quantities. Such molecular-sized DNDs keep their diamond structure and characteristic DND features as shown by Raman spectroscopy, infrared spectroscopy, STEM and EELS. The size of 1 nm is identified as a limit, below which the DNDs become amorphous.

High-yield fabrication and properties of 1.4 nm nanodiamonds with narrow size distribution

PubMed Central

Stehlik, Stepan; Varga, Marian; Ledinsky, Martin; Miliaieva, Daria; Kozak, Halyna; Skakalova, Viera; Mangler, Clemens; Pennycook, Timothy J.; Meyer, Jannik C.; Kromka, Alexander; Rezek, Bohuslav

2016-01-01

Detonation nanodiamonds (DNDs) with a typical size of 5 nm have attracted broad interest in science and technology. Further size reduction of DNDs would bring these nanoparticles to the molecular-size level and open new prospects for research and applications in various fields, ranging from quantum physics to biomedicine. Here we show a controllable size reduction of the DND mean size down to 1.4 nm without significant particle loss and with additional disintegration of DND core agglutinates by air annealing, leading to a significantly narrowed size distribution (±0.7 nm). This process is scalable to large quantities. Such molecular-sized DNDs keep their diamond structure and characteristic DND features as shown by Raman spectroscopy, infrared spectroscopy, STEM and EELS. The size of 1 nm is identified as a limit, below which the DNDs become amorphous. PMID:27910924

High-yield fabrication and properties of 1.4 nm nanodiamonds with narrow size distribution.

PubMed

Stehlik, Stepan; Varga, Marian; Ledinsky, Martin; Miliaieva, Daria; Kozak, Halyna; Skakalova, Viera; Mangler, Clemens; Pennycook, Timothy J; Meyer, Jannik C; Kromka, Alexander; Rezek, Bohuslav

2016-12-02

Detonation nanodiamonds (DNDs) with a typical size of 5 nm have attracted broad interest in science and technology. Further size reduction of DNDs would bring these nanoparticles to the molecular-size level and open new prospects for research and applications in various fields, ranging from quantum physics to biomedicine. Here we show a controllable size reduction of the DND mean size down to 1.4 nm without significant particle loss and with additional disintegration of DND core agglutinates by air annealing, leading to a significantly narrowed size distribution (±0.7 nm). This process is scalable to large quantities. Such molecular-sized DNDs keep their diamond structure and characteristic DND features as shown by Raman spectroscopy, infrared spectroscopy, STEM and EELS. The size of 1 nm is identified as a limit, below which the DNDs become amorphous.

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

NASA Astrophysics Data System (ADS)

Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

1992-04-01

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Determination of Molecular Size and Avogadro's Number: A Student Experiment

ERIC Educational Resources Information Center

Alexandrakis, George C.

1978-01-01

Describes an experiment for estimating molecular size and Avogadro's number. Uses the diffusion length of iodine in air at 100 degrees Celsius as a function of time, and the change in volume of a small quantity of carbon dioxide as it goes from the solid to the gaseous state. (GA)

Next Generation Spectrometers for Rapid Analysis of Complex Mixtures

DTIC Science & Technology

2014-05-29

digitizer by collecting 1 and 100 million averages of a molecular sample ( nitromethane ) and verifying the expected factor of 10 improvement in signal-to...spectra of nitromethane . The positive-going spectrum represents 100 million averages while the negative-going spectrum represents 1 million averages

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly

NASA Astrophysics Data System (ADS)

Buono, Ronald A.; Kucharczyk, Nathalie; Neuenschwander, Magrit; Kemmink, Johan; Hwang, Lih-Yueh; Fauchère, Jean-Luc; Venanzi, Carol A.

1996-06-01

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L-and d-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Time and size resolved Measurement of Mass Concentration at an Urban Site

NASA Astrophysics Data System (ADS)

Karg, E.; Ferron, G. A.; Heyder, J.

2003-04-01

Time- and size-resolved measurements of ambient particles are necessary for modelling of atmospheric particle transport, the interpretation of particulate pollution events and the estimation of particle deposition in the human lungs. In the size range 0.01 - 2 µm time- and size-resolved data are obtained from differential mobility and optical particle counter measurements and from gravimetric filter analyses on a daily basis (PM2.5). By comparison of the time averaged and size integrated particle volume concentration with PM2.5 data, an average density of ambient particles can be estimated. Using this density, the number concentration data can be converted in time- and size-resolved mass concentration. Such measurements were carried out at a Munich downtown crossroads. The spectra were integrated in the size ranges 10 - 100 nm, 100 - 500 nm and 500 - 2000 nm. Particles in these ranges are named ultrafine, fine and coarse particles. These ranges roughly represent freshly emitted particles, aged/accumulated particles and particles entrained by erosive processes. An average number concentration of 80000 1/cm3 (s.d. 67%), a particle volume concentration of 53 µm3/cm3 (s.d. 76%) and a PM2.5 mass concentration of 27 µg/m3 was found. These particle volume- and PM2.5 data imply an average density of 0.51 g/cm3. Average number concentration showed 95.3%, 4.7% and 0.006% of the total particle concentration in the size ranges mentioned above. Mass concentration was 14.7%, 80.2% and 5.1% of the total, assuming the average density to be valid for all particles. The variability in mass concentration was 94%, 75% and 33% for the three size ranges. Nearly all ambient particles were in the ultrafine size range, whereas most of the mass concentration was in the fine size range. However, a considerable mass fraction of nearly 15% was found in the ultrafine size range. As the sampling site was close to the road and traffic emissions were the major source of the particles, 1) the density was very low due to agglomerated and porous structures of freshly emitted combustion particles and 2) the variability was highest in the ultrafine range, obviously correlated to traffic activity and lowest in the micron size range. In conclusion, almost all ambient particles were ultrafine particles, whereas most of the particle mass was associated with fine particles. Nevertheless, a considerable mass fraction was found in the ultrafine size range. These particles had a very low density so that they can be considered as agglomerated and porous particles emitted from vehicles passing the crossroads. Therefore they showed a much higher variation in mass concentration than the fine and coarse particles.

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

PubMed

Koes, David R; Vries, John K

2017-01-01

Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1 H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13 C a and 15 N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.

PubMed

Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

2011-11-01

Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.

A log-normal distribution model for the molecular weight of aquatic fulvic acids

USGS Publications Warehouse

Cabaniss, S.E.; Zhou, Q.; Maurice, P.A.; Chin, Y.-P.; Aiken, G.R.

2000-01-01

The molecular weight of humic substances influences their proton and metal binding, organic pollutant partitioning, adsorption onto minerals and activated carbon, and behavior during water treatment. We propose a lognormal model for the molecular weight distribution in aquatic fulvic acids to provide a conceptual framework for studying these size effects. The normal curve mean and standard deviation are readily calculated from measured M(n) and M(w) and vary from 2.7 to 3 for the means and from 0.28 to 0.37 for the standard deviations for typical aquatic fulvic acids. The model is consistent with several types of molecular weight data, including the shapes of high- pressure size-exclusion chromatography (HP-SEC) peaks. Applications of the model to electrostatic interactions, pollutant solubilization, and adsorption are explored in illustrative calculations.The molecular weight of humic substances influences their proton and metal binding, organic pollutant partitioning, adsorption onto minerals and activated carbon, and behavior during water treatment. We propose a log-normal model for the molecular weight distribution in aquatic fulvic acids to provide a conceptual framework for studying these size effects. The normal curve mean and standard deviation are readily calculated from measured Mn and Mw and vary from 2.7 to 3 for the means and from 0.28 to 0.37 for the standard deviations for typical aquatic fulvic acids. The model is consistent with several type's of molecular weight data, including the shapes of high-pressure size-exclusion chromatography (HP-SEC) peaks. Applications of the model to electrostatic interactions, pollutant solubilization, and adsorption are explored in illustrative calculations.

Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics

PubMed Central

2018-01-01

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

Size-dependent chemical ageing of oleic acid aerosol under dry and humidified conditions

NASA Astrophysics Data System (ADS)

Al-Kindi, Suad S.; Pope, Francis D.; Beddows, David C.; Bloss, William J.; Harrison, Roy M.

2016-12-01

A chemical reaction chamber system has been developed for the processing of oleic acid aerosol particles with ozone under two relative humidity conditions: dry and humidified to 65 %. The apparatus consists of an aerosol flow tube, in which the ozonolysis occurs, coupled to a scanning mobility particle sizer (SMPS) and an aerosol time-of-flight mass spectrometer (ATOFMS) which measure the evolving particle size and composition. Under both relative humidity conditions, ozonolysis results in a significant decrease in particle size and mass which is consistent with the formation of volatile products that partition from the particle to the gas phase. Mass spectra derived from the ATOFMS reveal the presence of the typically observed reaction products: azelaic acid, nonanal, oxononanoic acid and nonanoic acid, as well as a range of higher molecular weight products deriving from the reactions of reaction intermediates with oleic acid and its oxidation products. These include octanoic acid and 9- and 10-oxooctadecanoic acid, as well as products of considerably higher molecular weight. Quantitative evaluation of product yields with the ATOFMS shows a marked dependence upon both particle size association (from 0.3 to 2.1 µm diameter) and relative humidity. Under both relative humidity conditions, the percentage residual of oleic acid increases with increasing particle size and the main lower molecular weight products are nonanal and oxononanoic acid. Under dry conditions, the percentage of higher molecular weight products increases with increasing particle size due to the poorer internal mixing of the larger particles. Under humidified conditions, the percentage of unreacted oleic acid is greater, except in the smallest particle fraction, with little formation of high molecular weight products relative to the dry particles. It is postulated that water reacts with reactive intermediates, competing with the processes which produce high molecular weight products. Whilst the oleic acid model aerosol system is of limited relevance to complex internally mixed atmospheric aerosol, the generic findings presented in this paper give useful insights into the nature of heterogeneous chemical processes.

Lignin nanoparticle synthesis

DOEpatents

Dirk, Shawn M.; Cicotte, Kirsten Nicole; Wheeler, David R.; Benko, David A.

2015-08-11

A method including reducing a particle size of lignin particles to an average particle size less than 40 nanometers; after reducing the particle size, combining the lignin particles with a polymeric material; and forming a structure of the combination. A method including exposing lignin to a diazonium precursor including a functional group; modifying the lignin by introducing the functional group to the lignin; and combining the modified lignin with a polymeric material to form a composite. An apparatus including a composite of a polymer and lignin wherein the lignin has an average particle size less than 100 micrometers.

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

NASA Astrophysics Data System (ADS)

Yu, Dindi; Ruangchaithaweesuk, Songtham; Yao, Li; Xu, Shoujun

2012-09-01

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/√Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 μm with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 μm, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules

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

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

2014-01-21

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

Effects of gene carrier polyethyleneimines on the structure and binding capability of bovine serum albumin

NASA Astrophysics Data System (ADS)

Guo, Zhiyong; Kong, Zhijie; Wei, Yanshan; Li, Hua; Wang, Yajing; Huang, Aimin; Ma, Lin

2017-02-01

Polyethyleneimine (PEI), one of the most effective non-viral gene carriers, is also cytotoxic, however the molecular basis is poorly understood. Little is known about the effects of PEI on the structure and functions of the biomacromolecules. In this work, fluorescence, UV-vis absorption, circular dichroism (CD) spectroscopy and zeta-potential measurement were conducted to reveal the interaction between PEIs (average molecular weight 25, 10 and 1.8 kDa) and bovine serum albumin (BSA), and to evaluate the effects on the conformation of BSA as long as its binding capability to the model compounds, 8-anilino-1-naphthalenesulfonic acid (ANS) and quercetin. PEIs were found to complex with BSA and induced a conformational change of the protein by a major reduction of α-helix at PEI concentration < 0.2 mg·mL- 1 and an increase at higher PEI concentration. The binding efficacy of ANS and quercetin to BSA was greatly reduced by the competitive binding by PEI and influenced by the conformational change of BSA, which was found to display a similar trend to the change of the α-helix content of the protein. The polymer size played an important role in PEI-BSA interaction. PEI of higher molecular weight was more favorable to interact with BSA and more efficient to perturb the conformation and binding capability of the protein.

Transcriptome assembly and expression profiling of molecular responses to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense

NASA Astrophysics Data System (ADS)

Sun, Min; Ting Li, Yi; Liu, Yang; Chin Lee, Shao; Wang, Lan

2016-01-01

Cadmium (Cd) pollution is a serious global problem, which causes irreversible toxic effects on animals. Freshwater crab, Sinopotamon henanense, is a useful environmental indicator since it is widely distributed in benthic habitats whereby it tends to accumulate Cd and other toxicants. However, its molecular responses to Cd toxicity remain unclear. In this study, we performed transcriptome sequencing and gene expression analyses of its hepatopancreas with and without Cd treatments. A total of 7.78 G clean reads were obtained from the pooled samples, and 68,648 unigenes with an average size of 622 bp were assembled, in which 5,436 were metabolism-associated and 2,728 were stimulus response-associated that include 380 immunity-related unigenes. Expression profile analysis demonstrated that most genes involved in macromolecular metabolism, oxidative phosphorylation, detoxification and anti-oxidant defense were up-regulated by Cd exposure, whereas immunity-related genes were down-regulated, except the genes involved in phagocytosis were up-regulated. The current data indicate that Cd exposure alters gene expressions in a concentration-dependent manner. Therefore, our results provide the first comprehensive S.henanense transcriptome dataset, which is useful for biological and ecotoxicological studies on this crab and its related species at molecular level, and some key Cd-responsive genes may provide candidate biomarkers for monitoring aquatic pollution by heavy metals.

Electronic shift register memory based on molecular electron-transfer reactions

NASA Technical Reports Server (NTRS)

Hopfield, J. J.; Onuchic, Jose Nelson; Beratan, David N.

1989-01-01

The design of a shift register memory at the molecular level is described in detail. The memory elements are based on a chain of electron-transfer molecules incorporated on a very large scale integrated (VLSI) substrate, and the information is shifted by photoinduced electron-transfer reactions. The design requirements for such a system are discussed, and several realistic strategies for synthesizing these systems are presented. The immediate advantage of such a hybrid molecular/VLSI device would arise from the possible information storage density. The prospect of considerable savings of energy per bit processed also exists. This molecular shift register memory element design solves the conceptual problems associated with integrating molecular size components with larger (micron) size features on a chip.

Particle size distribution and respiratory deposition estimates of airborne perfluoroalkyl acids during the haze period in the megacity of Shanghai.

PubMed

Guo, Mengjie; Lyu, Yan; Xu, Tingting; Yao, Bo; Song, Weihua; Li, Mei; Yang, Xin; Cheng, Tiantao; Li, Xiang

2018-03-01

This study presents the particle size distribution and respiratory deposition estimates of airborne perfluoroalkyl acids (PFAAs) during the haze period. Size-segregated haze aerosols were collected from an urban location in Shanghai using an eight-stage air sampler. The samples were analyzed for eight PFAAs using ultra-high-performance liquid chromatography tandem triple quadrupole mass spectrometry. The quantification results showed that the concentrations of particle-bound Σ 8PFAAs ranged from 0.26 to 1.90 ng m -3 (mean: 1.44 ng m -3 ). All of the measured PFAAs particle size distributions had a bimodal mode that peaked respectively in accumulation size range (0.4 < Dp < 2.1 μm) and coarse size ranges (Dp > 2.1 μm), but the width of each distribution somewhat varied by compound. The emission source, molecular weight, and volatility of the PFAAs were important factors influencing the size distribution of particle-bound PFAAs. Of these compounds, PFUnDA presented a strong accumulation in the fine size range (average 75% associated with particles <2.1 μm), followed by PFOA (69%) and PFDA (64%). The human risk assessment of PFOS via inhalation was addressed and followed the same pattern as the size distribution, with a 2-fold higher risk for the fine particle fraction compared to the coarse particle fraction at urban sites. Approximately 30.3-82.0% of PFAA deposition (∑PFAA: 72.5%) in the alveolar region was associated with particles <2.1 μm, although the contribution of fine particles to the total PFAAs concentration in urban air was only 28-57% (∑8PFAAs: 48%). These results suggested that fine particles are significant contributors to the deposition of PFAAs in the alveolar region of the lung. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ensemble coding remains accurate under object and spatial visual working memory load.

PubMed

Epstein, Michael L; Emmanouil, Tatiana A

2017-10-01

A number of studies have provided evidence that the visual system statistically summarizes large amounts of information that would exceed the limitations of attention and working memory (ensemble coding). However the necessity of working memory resources for ensemble coding has not yet been tested directly. In the current study, we used a dual task design to test the effect of object and spatial visual working memory load on size averaging accuracy. In Experiment 1, we tested participants' accuracy in comparing the mean size of two sets under various levels of object visual working memory load. Although the accuracy of average size judgments depended on the difference in mean size between the two sets, we found no effect of working memory load. In Experiment 2, we tested the same average size judgment while participants were under spatial visual working memory load, again finding no effect of load on averaging accuracy. Overall our results reveal that ensemble coding can proceed unimpeded and highly accurately under both object and spatial visual working memory load, providing further evidence that ensemble coding reflects a basic perceptual process distinct from that of individual object processing.

Isolation of a thermophilic bacterium capable of low-molecular-weight polyethylene degradation.

PubMed

Jeon, Hyun Jeong; Kim, Mal Nam

2013-02-01

A thermophilic bacterium capable of low-molecular-weight polyethylene (LMWPE) degradation was isolated from a compost sample, and was identified as Chelatococcus sp. E1, through sequencing of the 16S rRNA gene. LMWPE was prepared by thermal degradation of commercial PE in a strict nitrogen atmosphere. LMWPE with a weight-average-molecular-weight (Mw) in the range of 1,700-23,700 was noticeably mineralized into CO(2) by the bacterium. The biodegradability of LMWPE decreased as the Mw increased. The low molecular weight fraction of LMWPE decreased significantly as a result of the degradation process, and thereby both the number-average-molecular-weight and Mw increased after biodegradation. The polydispersity of LMWPE was either narrowed or widened, depending on the initial Mw of LMWPE, due to the preferential elimination of the low molecular weight fraction, in comparison to the high molecular weight portion. LMWPE free from an extremely low molecular weight fraction was also mineralized by the strain at a remarkable rate, and FTIR peaks assignable to C-O stretching appeared as a result of microbial action. The FTIR peaks corresponding to alkenes also became more intense, indicating that dehydrogenations occurred concomitantly with microbial induced oxidation.

Comparison of wing-span averaging effects on lift, rolling moment, and bending moment for two span load distributions and for two turbulence representations

NASA Technical Reports Server (NTRS)

Lichtenstein, J. H.

1978-01-01

An analytical method of computing the averaging effect of wing-span size on the loading of a wing induced by random turbulence was adapted for use on a digital electronic computer. The turbulence input was assumed to have a Dryden power spectral density. The computations were made for lift, rolling moment, and bending moment for two span load distributions, rectangular and elliptic. Data are presented to show the wing-span averaging effect for wing-span ratios encompassing current airplane sizes. The rectangular wing-span loading showed a slightly greater averaging effect than did the elliptic loading. In the frequency range most bothersome to airplane passengers, the wing-span averaging effect can reduce the normal lift load, and thus the acceleration, by about 7 percent for a typical medium-sized transport. Some calculations were made to evaluate the effect of using a Von Karman turbulence representation. These results showed that using the Von Karman representation generally resulted in a span averaging effect about 3 percent larger.

Time-dependent Gas-liquid Interaction in Molecular-sized Nanopores

PubMed Central

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

2014-01-01

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

Facile high-yield synthesis of polyaniline nanosticks with intrinsic stability and electrical conductivity.

PubMed

Li, Xin-Gui; Li, Ang; Huang, Mei-Rong

2008-01-01

Chemical oxidative polymerization at 15 degrees C was used for the simple and productive synthesis of polyaniline (PAN) nanosticks. The effect of polymerization media on the yield, size, stability, and electrical conductivity of the PAN nanosticks was studied by changing the concentration and nature of the acid medium and oxidant and by introducing organic solvent. Molecular and supramolecular structure, size, and size distribution of the PAN nanosticks were characterized by UV/Vis and IR spectroscopy, X-ray diffraction, laser particle-size analysis, and transmission electron microscopy. Introduction of organic solvent is advantageous for enhancing the yield of PAN nanosticks but disadvantageous for formation of PAN nanosticks with small size and high conductivity. The concentration and nature of the acid medium have a major influence on the polymerization yield and conductivity of the nanosized PAN. The average diameter and length of PAN nanosticks produced with 2 M HNO(3) and 0.5 M H(2)SO(4) as acid media are about 40 and 300 nm, respectively. The PAN nanosticks obtained in an optimal medium (i.e., 2 M HNO(3)) exhibit the highest conductivity of 2.23 S cm(-1) and the highest yield of 80.7 %. A mechanism of formation of nanosticks instead of nanoparticles is proposed. Nanocomposite films of the PAN nanosticks with poly(vinyl alcohol) show a low percolation threshold of 0.2 wt %, at which the film retains almost the same transparency and strength as pure poly(vinyl alcohol) but 262 000 times the conductivity of pure poly(vinyl alcohol) film. The present synthesis of PAN nanosticks requires no external stabilizer and provides a facile and direct route for fabrication of PAN nanosticks with high yield, controllable size, intrinsic self-stability, strong redispersibility, high purity, and optimizable conductivity.

Molecular Weight of Deoxyribonucleic Acid Synthesized During Initiation of Chromosome Replication in Escherichia coli

PubMed Central

Kuempel, Peter L.

1972-01-01

Alkaline sucrose gradients were used to study the molecular weight of deoxyribonucleic acid (DNA) synthesized during the initiation of chromosome replication in Escherichia coli 15 TAU-bar. The experiments were conducted to determine whether newly synthesized, replication origin DNA is attached to higher-molecular-weight parental DNA. Little of the DNA synthesized after readdition of required amino acids to cells previously deprived of the amino acids was present in DNA with a molecular weight comparable to that of the parental DNA. The newly synthesized, low-molecular-weight DNA rapidly appeared in higher-molecular-weight material, but there was an upper limit to the size of this intermediate-molecular-weight DNA. This limit was not observed when exponentially growing cells converted newly synthesized DNA to higher-molecular-weight material. The size of the intermediate-molecular-weight DNA was related to the age of the replication forks, and the size increased as the replication forks moved further from the replication origin. The results indicate that the newly synthesized replication origin DNA is not attached to parental DNA, but it is rapidly attached to the growing strands that extend from the replication fork to the replication origin, or to the other replication fork if replication is bidirectional. Experiments are reported which demonstrate that the DNA investigated was from the vicinity of the replication origin and was not plasmid DNA or DNA from random positions on the chromosome. PMID:4562387

Method of generating hydrocarbon reagents from diesel, natural gas and other logistical fuels

DOEpatents

Herling, Darrell R [Richland, WA; Aardahl, Chris L [Richland, WA; Rozmiarek, Robert T [Middleton, WI; Rappe, Kenneth G [Richland, WA; Wang, Yong [Richland, WA; Holladay, Jamelyn D [Kennewick, WA

2010-06-29

The present invention provides a process for producing reagents for a chemical reaction by introducing a fuel containing hydrocarbons into a flash distillation process wherein the fuel is separated into a first component having a lower average molecular weight and a second component having a higher average molecular weight. The first component is then reformed to produce synthesis gas wherein the synthesis gas is reacted catalytically to produce the desire reagent.

Method of Generating Hydrocarbon Reagents from Diesel, Natural Gas and Other Logistical Fuels

DOEpatents

Herling, Darrell R [Richland, WA; Aardahl, Chris L [Richland, WA; Rozmiarek, Robert T [Middleton, WI; Rappe, Kenneth G [Richland, WA; Wang, Yong [Richland, WA; Holladay, Jamelyn D [Kennewick, WA

2008-10-14

The present invention provides a process for producing reagents for a chemical reaction by introducing a fuel containing hydrocarbons into a flash distillation process wherein the fuel is separated into a first component having a lower average molecular weight and a second component having a higher average molecular weight. The first component is then reformed to produce synthesis gas wherein the synthesis gas is reacted catalytically to produce the desire reagent.

Effect of the granule size in porous silicon on the photosensitization efficiency of molecular oxygen on the surface of silicon nanocrystals

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

Demin, V. A.; Konstantinova, E. A., E-mail: liza35@mail.ru; Gongal'skii, M. B.

2009-03-15

Photoluminescence is used to study the effect of the granule size in porous silicon on the generation efficiency of the excited state of molecular oxygen ({sup 1}O{sub 2}) on the surface of silicon nanocrystals. The generation efficiency is found to increase as the granule size becomes smaller than 100 nm, which can be explained by a change in the conditions of exciton diffusion along a network of silicon nanocrystals.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging.

PubMed

Kennard, Raymond; DeSisto, William J; Giririjan, Thanu Praba; Mason, Michael D

2008-04-07

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5 nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50 degrees C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging

NASA Astrophysics Data System (ADS)

Kennard, Raymond; DeSisto, William J.; Giririjan, Thanu Praba; Mason, Michael D.

2008-04-01

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50°C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution.

PubMed

Jas, Gouri S; Middaugh, C Russell; Kuczera, Krzysztof

2016-07-21

Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment. A small change in pH significantly slows orientation time in water and GdmCl and less markedly in urea. Computationally, we use molecular dynamics with dihedral restraints to separately analyze the motions and interactions of the representative NATA conformers in the four different solvent environments. This novel analysis provides a dissection of the observed overall diffusion rates into contributions from individual dipeptide conformations. The variation of rotational diffusion rates with conformation are quite large. Population-weighted averaging or using properties of the major cluster reproduces the dynamical features of the full unrestrained dynamics. Additionally, we correlate the observable diffusion rates with microscopic features of conformer size, shape, and solvation. This analysis uncovered underlying differences in detailed atomistic behavior of the three cosolvents-urea, GdmCl, and proline. For both urea and the pure water system we find good agreement with hydrodynamic theory, with diffusion rates primarily correlated with conformer size and shape. In contrast, for GdmCl and proline solutions, the variation in conformer diffusion rates was mostly determined by specific interactions with the cosolvents. We also find preferences for different molecular shapes by the three cosolvents, with increased preferential solvation of smaller and more spherical conformers by urea and larger and more elongated conformers by GdmCl and proline. Additionally, our results provide a basis for a simple approximate model of the effects of pH lowering on dipeptide conformational equilibria. The translational diffusion rates of NATA are less sensitive to conformations, but variation with solvation strength is similar to rotational diffusion. Our results, combining experiment and simulation, show that we can identify the individual peptide conformers with definite microscopic properties of shape, size, and solvation, that are responsible for producing physical observables, such as translational and orientational diffusion in the complex solvent environments of denaturants and osmolytes.

Electron-intramolecular-vibration interactions in positively charged phenanthrene-edge-type hydrocarbons

NASA Astrophysics Data System (ADS)

Kato, Takashi; Yamabe, Tokio

2004-02-01

Electron-phonon interactions in positively charged phenanthrene-edge-type hydrocarbons such as phenanthrene, chrysene, and picene are studied. The C-C stretching modes around 1500 cm-1 and the low-frequency modes around 500 cm-1 strongly couple to the highest occupied molecular orbitals (HOMO) in phenanthrene-edge-type hydrocarbons. The total electron-phonon coupling constants for the monocations (lHOMO) of 0.251, 0.135, and 0.149 eV for phenanthrene, chrysene, and picene, respectively, are estimated to be larger than those of 0.130, 0.107, and 0.094 eV for anthracene, tetracene, and pentacene, respectively. The phase patterns difference between the HOMO localized on carbon atoms which are located at the molecular edge in acene-edge-type hydrocarbons and the delocalized HOMO in phenanthrene-edge-type hydrocarbons is the main reason for the result. Strengths of orbital interactions between two neighboring carbon atoms in the HOMO become weaker with an increase in molecular size because the electron density on each carbon atom in the HOMO becomes smaller with an increase in molecular size in phenanthrene-edge-type hydrocarbons. On the other hand, the frontier orbitals of acene-edge-type hydrocarbons have somewhat nonbonding characters and thus cannot strongly couple to the totally symmetric vibrational modes compared with the frontier orbitals of phenanthrene-edge-type hydrocarbons. This is the reason why the lHOMO value for phenanthrene-edge-type hydrocarbons decreases with an increase in molecular size more significantly than that for acene-edge-type hydrocarbons, and the reason why the lHOMO value for polyphenanthrene with C2v geometry (0.033 eV) is estimated to be similar to that for polyacene (0.036 eV). The reorganization energies between the neutral molecules and the corresponding monocations for phenanthrene-edge-type hydrocarbons with large molecular size are estimated to be larger than those for acene-edge-type hydrocarbons with large molecular size.

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

Orientational dynamics in a room temperature ionic liquid: Are angular jumps predominant?

NASA Astrophysics Data System (ADS)

Das, Suman; Mukherjee, Biswaroop; Biswas, Ranjit

2018-05-01

Reorientational dynamics of the constituent ions in a room temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), are explored via molecular dynamics simulations, and several features of orientation dynamics are summarized. The anion, [PF6]-, not only exhibits a higher propensity to orientation jumps than the cation, [BMIM]+ but also accesses a wider jump angle distribution and larger peak-angle. Jump and waiting time distributions for both the ions depict power-law dependences, suggesting temporally heterogeneous dynamics for the medium. This heterogeneity feature is further highlighted by the finding that the simulated first rank (ℓ = 1) and second rank (ℓ = 2) average reorientational correlation times reflect a severe break-down of Debye's ℓ(ℓ + 1) law for orientational diffusion in an isotropic homogeneous medium. Simulated average H-bond lifetime resides between the mean orientation jump and waiting times, while the structural H-bond relaxation suggests, as in normal liquids, a pronounced presence of translational motion of the partnering ions. Average simulated jump trajectories reveal a strong rotation-translation coupling and indicate relatively larger changes in spatial and angular arrangements for the anion during an orientation jump. In fact, a closer inspection of all these results points toward more heterogeneous dynamics for [PF6]- than [BMIM]+. This is a new observation and may simply be linked to the ion-size. However, such a generalization warrants further study.

Membrane protein extraction and purification using styrene-maleic acid (SMA) copolymer: effect of variations in polymer structure.

PubMed

Morrison, Kerrie A; Akram, Aneel; Mathews, Ashlyn; Khan, Zoeya A; Patel, Jaimin H; Zhou, Chumin; Hardy, David J; Moore-Kelly, Charles; Patel, Roshani; Odiba, Victor; Knowles, Tim J; Javed, Masood-Ul-Hassan; Chmel, Nikola P; Dafforn, Timothy R; Rothnie, Alice J

2016-12-01

The use of styrene-maleic acid (SMA) copolymers to extract and purify transmembrane proteins, while retaining their native bilayer environment, overcomes many of the disadvantages associated with conventional detergent-based procedures. This approach has huge potential for the future of membrane protein structural and functional studies. In this investigation, we have systematically tested a range of commercially available SMA polymers, varying in both the ratio of styrene and maleic acid and in total size, for the ability to extract, purify and stabilise transmembrane proteins. Three different membrane proteins (BmrA, LeuT and ZipA), which vary in size and shape, were used. Our results show that several polymers, can be used to extract membrane proteins, comparably to conventional detergents. A styrene:maleic acid ratio of either 2:1 or 3:1, combined with a relatively small average molecular mass (7.5-10 kDa), is optimal for membrane extraction, and this appears to be independent of the protein size, shape or expression system. A subset of polymers were taken forward for purification, functional and stability tests. Following a one-step affinity purification, SMA 2000 was found to be the best choice for yield, purity and function. However, the other polymers offer subtle differences in size and sensitivity to divalent cations that may be useful for a variety of downstream applications. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Aerosol Fragmentation Driven by Coupling of Acid-Base and Free-Radical Chemistry in the Heterogeneous Oxidation of Aqueous Citric Acid by OH Radicals.

PubMed

Liu, Matthew J; Wiegel, Aaron A; Wilson, Kevin R; Houle, Frances A

2017-08-10

A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity. The reaction scheme, containing both free-radical and acid-base elementary reaction steps with physically validated rate coefficients, accurately predicts the experimentally observed molecular composition, particle size, and average elemental composition of the aerosol upon oxidation. The difference between the two reaction channels centers on the reactivity of carboxylic acid groups. Free-radical reactions mainly add functional groups to the carbon skeleton of neutral citric acid, because carboxylic acid moieties deactivate the unimolecular fragmentation of alkoxy radicals. In contrast, the conjugate carboxylate groups originating from acid-base equilibria activate both acyloxy radical formation and carbon-carbon bond scission of alkoxy radicals, leading to the formation of low molecular weight, highly oxidized products such as oxalic and mesoxalic acid. Subsequent hydration of carbonyl groups in the oxidized products increases the aerosol hygroscopicity and accelerates the substantial water uptake and volume growth that accompany oxidation. These results frame the oxidative lifecycle of atmospheric aerosol: it is governed by feedbacks between reactions that first increase the particle oxidation state, then eventually promote water uptake and acid-base chemistry. When coupled to free-radical reactions, acid-base channels lead to formation of low molecular weight gas-phase reaction products and decreasing particle size.

Aerosol Fragmentation Driven by Coupling of Acid–Base and Free-Radical Chemistry in the Heterogeneous Oxidation of Aqueous Citric Acid by OH Radicals

DOE PAGES

Liu, Matthew J.; Wiegel, Aaron A.; Wilson, Kevin R.; ...

2017-07-14

A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity. The reaction scheme, containing both free-radical and acid-base elementary reaction steps withmore » physically validated rate coefficients, accurately predicts the experimentally observed molecular composition, particle size, and average elemental composition of the aerosol upon oxidation. The difference between the two reaction channels centers on the reactivity of carboxylic acid groups. Free-radical reactions mainly add functional groups to the carbon skeleton of neutral citric acid, because carboxylic acid moieties deactivate the unimolecular fragmentation of alkoxy radicals. In contrast, the conjugate carboxylate groups originating from acid-base equilibria activate both acyloxy radical formation and carbon-carbon bond scission of alkoxy radicals, leading to the formation of low molecular weight, highly oxidized products such as oxalic and mesoxalic acid. Subsequent hydration of carbonyl groups in the oxidized products increases the aerosol hygroscopicity and accelerates the substantial water uptake and volume growth that accompany oxidation. These results frame the oxidative lifecycle of atmospheric aerosol: it is governed by feedbacks between reactions that first increase the particle oxidation state, then eventually promote water uptake and acid-base chemistry. When coupled to free-radical reactions, acid-base channels lead to formation of low molecular weight gas-phase reaction products and decreasing particle size.« less

Agrobacterium-assisted selenium nanoparticles: molecular aspect of antifungal activity

NASA Astrophysics Data System (ADS)

Kumar, Anil; Bera, Smritilekha; Singh, Man; Mondal, Dhananjoy

2018-03-01

Selenium nanoparticles (SeNPs) were synthesized through the bioreduction of sodium selenite (Na2SeO3) using gram-negative agrobacterium (AGBT) species. Subsequently, their physicochemical properties (pH, viscosity and surface tension) and medicinal activities as anti-dermatophyte against soil keratinophilic fungi at the molecular level were assessed. UV-visible and FTIR spectroscopic data of the biologically synthesized SeNPs were then recorded for confirming the presence of native biological materials adhered to nanoparticles, which are inherently required to enhance the stability and solubility through inhibition of the nanoparticle’s natural aggregation and agglomeration. The λ max value between 290-300 nm in the absorption spectra of the biogenic materials in different concentrations of the Na2SeO3 corroborated the presence of SeNPs in the solution. The interaction of SeNPs in solution state was further studied through the determination of pH, viscosity and surface tension values of agrobacterium-derived SeNPs in different solvents. The pH value of SeNPs dispersed in water is reported as above 7.0 and the average viscosity, and surface tensions of the SeNPs are appeared as near to the water. The particle size distribution was further determined by DLS and the highest % of particle size of the synthesized SeNPs is found in between 200-300 nm. The anti-dermatophyte activity and molecular interaction with fungi DNA molecules were assessed providing the highest anti-dermatophyte activity at 0.1 M concentration and it is observed that the quantities and qualities of fungi DNA were affected by SeNPs. Considering all the outcomes of the studies together, our findings suggest that agrobacterium-mediated synthesis of SeNPs is dependent on bacterial metabolisms but not on the concentration of Na2SeO3 and are promising selenium-derived species with potential application in the prevention of fungal infection through denaturation of fungi DNA.

Aerosol Fragmentation Driven by Coupling of Acid–Base and Free-Radical Chemistry in the Heterogeneous Oxidation of Aqueous Citric Acid by OH Radicals

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

Liu, Matthew J.; Wiegel, Aaron A.; Wilson, Kevin R.

A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity. The reaction scheme, containing both free-radical and acid-base elementary reaction steps withmore » physically validated rate coefficients, accurately predicts the experimentally observed molecular composition, particle size, and average elemental composition of the aerosol upon oxidation. The difference between the two reaction channels centers on the reactivity of carboxylic acid groups. Free-radical reactions mainly add functional groups to the carbon skeleton of neutral citric acid, because carboxylic acid moieties deactivate the unimolecular fragmentation of alkoxy radicals. In contrast, the conjugate carboxylate groups originating from acid-base equilibria activate both acyloxy radical formation and carbon-carbon bond scission of alkoxy radicals, leading to the formation of low molecular weight, highly oxidized products such as oxalic and mesoxalic acid. Subsequent hydration of carbonyl groups in the oxidized products increases the aerosol hygroscopicity and accelerates the substantial water uptake and volume growth that accompany oxidation. These results frame the oxidative lifecycle of atmospheric aerosol: it is governed by feedbacks between reactions that first increase the particle oxidation state, then eventually promote water uptake and acid-base chemistry. When coupled to free-radical reactions, acid-base channels lead to formation of low molecular weight gas-phase reaction products and decreasing particle size.« less

Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

PubMed

O'Hagan, Steve; Kell, Douglas B

2018-01-01

Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Conformation and activity alteration of horseradish peroxidase induced by the interaction with gene carrier polyethyleneimines

NASA Astrophysics Data System (ADS)

Huang, Aimin; Wei, Bangzhi; Mo, Junyong; Wang, Yajing; Ma, Lin

2018-01-01

Polyethyleneimine (PEI) has long been considered as "golden standard" for polymeric gene delivery carriers. However the molecular basis of the cytotoxicity of PEI is poorly understood. Little is known about the effects of PEI on the structure and functions of biomacromolecules. In this work, fluorescence, UV-vis absorption, circular dichroism spectroscopy were conducted to investigate the influence of PEI of average molecular weight 25, 10 and 1.8 kDa (denoted as PEI25k, PEI10k and PEI1.8k) on the conformation of horseradish peroxidase (HRP) and its catalytic efficiency. Zeta-potential measurement and isothermal titration calorimetry were used to reveal the mechanism of the interaction between PEIs and HRP. PEIs were found to bind onto the surface of HRP predominantly via hydrophobic interaction and hydrogen bond or van der Waals interaction. The complex formation between HRP and PEI induced a more compact conformation of the enzyme and an increased hydrophobicity of the microenvironment surrounding heme pocket. The conformational change of HRP had little impact on the affinity towards H2O2 and phenol. However, the increase in the non-planarity of porphyrin ring in the heme group led to an increase in the exposure degree of the active center and thus an enhancement of catalytic efficiency of HRP in the presence of high molecular weight PEIs (PEI25k and PEI10k). The polymer size played an important role in PEI-HRP interaction. PEI of low molecular weight (PEI1.8k) was less efficient to alter the conformation and catalytic activity of HRP in aqueous solutions.

Ultraviolet-B radiation mobilizes uranium from uranium-dissolved organic carbon complexes in aquatic systems, demonstrated by asymmetrical flow field-flow fractionation.

PubMed

Nehete, Sachin Vilas; Christensen, Terje; Salbu, Brit; Teien, Hans-Christian

2017-05-05

Humic substances have a tendency to form complexes with metal ions in aquatic medium, impacting the metal mobility, decreasing bioavailability and toxicity. Ultraviolet-B (UV-B) radiation exposure degrades the humic substance, changes their molecular weight distribution and their metal binding capacity in aquatic medium. In this study, we experimented the effect of UV-B radiation on the uranium complexed with fulvic acids and humic acids in a soft water system at different pH, uranium concentrations and radiant exposure. The concentration and distribution of uranium in a complexed form were investigated by asymmetrical flow field-flow fractionation coupled to multi detection technique (AsFlFFF-UV-ICP-MS). The major concentration of uranium present in complexes was primarily associated with average and higher molecular weight fulvic and humic acids components. The concentration of uranium in a complexed form increased with increasing fulvic and humic acid concentrations as well as pH of the solution. The higher molecular weight fraction of uranium was degraded due to the UV-B exposure, transforming about 50% of the uranium-dissolved organic carbon complexes into low molecular weight uranium species in complex form with organic ligands and/or free form. The result also suggests AsFlFFF-UV-ICP-MS to be an important separation and detection technique for understanding the interaction of radionuclides with dissolved organic matter, tracking size distribution changes during degradation of organic complexes for understanding mobility, bioavailability and ecosystem transfer of radionuclides as well as metals. Copyright © 2017 Elsevier B.V. All rights reserved.

Method of assembly of molecular-sized nets and scaffolding

DOEpatents

Michl, Josef; Magnera, Thomas F.; David, Donald E.; Harrison, Robin M.

1999-01-01

The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures.

Size-dependent single electron transfer and semi-metal-to-insulator transitions in molecular metal oxide electronics

NASA Astrophysics Data System (ADS)

Balliou, Angelika; Bouroushian, Mirtat; Douvas, Antonios M.; Skoulatakis, George; Kennou, Stella; Glezos, Nikos

2018-07-01

All-inorganic self-arranged molecular transition metal oxide hyperstructures based on polyoxometalate molecules (POMs) are fabricated and tested as electronically tunable components in emerging electronic devices. POM hyperstructures reveal great potential as charging nodes of tunable charging level for molecular memories and as enhancers of interfacial electron/hole injection for photovoltaic stacks. STM, UPS, UV–vis spectroscopy and AFM measurements show that this functionality stems from the films’ ability to structurally tune their HOMO–LUMO levels and electron localization length at room temperature. By adapting POM nanocluster size in solution, self-doping and current modulation of four orders of magnitude is monitored on a single nanocluster on SiO2 at voltages as low as 3 Volt. Structurally driven insulator-to-semi-metal transitions and size-dependent current regulation through single electron tunneling are demonstrated and examined with respect to the stereochemical and electronic structure of the molecular entities. This extends the value of self-assembly as a tool for correlation length and electronic properties tuning and demonstrate POM hyperstructures’ plausibility for on-chip molecular electronics operative at room temperature.

Size-dependent single electron transfer and semi-metal-to-insulator transitions in molecular metal oxide electronics.

PubMed

Balliou, Angelika; Bouroushian, Mirtat; Douvas, Antonios M; Skoulatakis, George; Kennou, Stella; Glezos, Nikos

2018-07-06

All-inorganic self-arranged molecular transition metal oxide hyperstructures based on polyoxometalate molecules (POMs) are fabricated and tested as electronically tunable components in emerging electronic devices. POM hyperstructures reveal great potential as charging nodes of tunable charging level for molecular memories and as enhancers of interfacial electron/hole injection for photovoltaic stacks. STM, UPS, UV-vis spectroscopy and AFM measurements show that this functionality stems from the films' ability to structurally tune their HOMO-LUMO levels and electron localization length at room temperature. By adapting POM nanocluster size in solution, self-doping and current modulation of four orders of magnitude is monitored on a single nanocluster on SiO 2 at voltages as low as 3 Volt. Structurally driven insulator-to-semi-metal transitions and size-dependent current regulation through single electron tunneling are demonstrated and examined with respect to the stereochemical and electronic structure of the molecular entities. This extends the value of self-assembly as a tool for correlation length and electronic properties tuning and demonstrate POM hyperstructures' plausibility for on-chip molecular electronics operative at room temperature.

Mixed matrix formulations with MOF molecular sieving for key energy-intensive separations

NASA Astrophysics Data System (ADS)

Liu, Gongping; Chernikova, Valeriya; Liu, Yang; Zhang, Kuang; Belmabkhout, Youssef; Shekhah, Osama; Zhang, Chen; Yi, Shouliang; Eddaoudi, Mohamed; Koros, William J.

2018-03-01

Membrane-based separations can improve energy efficiency and reduce the environmental impacts associated with traditional approaches. Nevertheless, many challenges must be overcome to design membranes that can replace conventional gas separation processes. Here, we report on the incorporation of engineered submicrometre-sized metal-organic framework (MOF) crystals into polymers to form hybrid materials that successfully translate the excellent molecular sieving properties of face-centred cubic (fcu)-MOFs into the resultant membranes. We demonstrate, simultaneously, exceptionally enhanced separation performance in hybrid membranes for two challenging and economically important applications: the removal of CO2 and H2S from natural gas and the separation of butane isomers. Notably, the membrane molecular sieving properties demonstrate that the deliberately regulated and contracted MOF pore-aperture size can discriminate between molecular pairs. The improved performance results from precise control of the linkers delimiting the triangular window, which is the sole entrance to the fcu-MOF pore. This rational-design hybrid approach provides a general toolbox for enhancing the transport properties of advanced membranes bearing molecular sieve fillers with sub-nanometre-sized pore-apertures.

Turbulence and star formation in molecular clouds

NASA Astrophysics Data System (ADS)

Larson, R. B.

1981-03-01

Consideration is given to the turbulence properties of molecular clouds and their implications for star formation. Data for 54 molecular clouds and condensations is presented which reveals cloud velocity dispersion and region size to follow a power-law relation, similar to the Kolmogoroff law for subsonic turbulence. Examination of the dynamics of the molecular clouds for which mass determinations are available reveals essentially all of them to be gravitationally bound, and to approximately satisfy the virial theorem. The observation of moderate scatter in the dispersion-size relation is noted to imply that most regions have not collapsed much since formation, suggesting that processes of turbulent hydrodynamics have played an important role in producing the observed substructures. A lower limit to the size of subcondensations at which their internal motions are no longer supersonic is shown to predict a minimum protostellar mass on the order of a few tenths of a solar mass, while massive protostellar clumps are found to develop complex internal structures, probably leading to the formation of prestellar condensation nuclei. The observed turbulence of molecular clouds is noted to imply lifetimes of less than 10 million years.

Method of assembly of molecular-sized nets and scaffolding

DOEpatents

Michl, J.; Magnera, T.F.; David, D.E.; Harrison, R.M.

1999-03-02

The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures. 9 figs.

Processing vertical size disparities in distinct depth planes.

PubMed

Duke, Philip A; Howard, Ian P

2012-08-17

A textured surface appears slanted about a vertical axis when the image in one eye is horizontally enlarged relative to the image in the other eye. The surface appears slanted in the opposite direction when the same image is vertically enlarged. Two superimposed textured surfaces with different horizontal size disparities appear as two surfaces that differ in slant. Superimposed textured surfaces with equal and opposite vertical size disparities appear as a single frontal surface. The vertical disparities are averaged. We investigated whether vertical size disparities are averaged across two superimposed textured surfaces in different depth planes or whether they induce distinct slants in the two depth planes. In Experiment 1, two superimposed textured surfaces with different vertical size disparities were presented in two depth planes defined by horizontal disparity. The surfaces induced distinct slants when the horizontal disparity was more than ±5 arcmin. Thus, vertical size disparities are not averaged over surfaces with different horizontal disparities. In Experiment 2 we confirmed that vertical size disparities are processed in surfaces away from the horopter, so the results of Experiment 1 cannot be explained by the processing of vertical size disparities in a fixated surface only. Together, these results show that vertical size disparities are processed separately in distinct depth planes. The results also suggest that vertical size disparities are not used to register slant globally by their effect on the registration of binocular direction of gaze.

Effects of the nanoplasma on the energetics of Coulomb explosion of molecular clusters in ultraintense laser fields

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

Last, Isidore; Jortner, Joshua

We report on theoretical and computational studies of electron and nuclear energies in the Coulomb explosion of (D{sub 2}){sub n/2} clusters (n=250-33 000, cluster radius R{sub 0}=11 A-55 A) coupled to ultraintense Gaussian laser fields (laser peak intensities I{sub M}=10{sup 15}-10{sup 18} W cm{sup -2}, pulse widths {tau}=25-50 fs, and frequency {nu}=0.35 fs{sup -1}). Molecular dynamics simulations were fit by semiempirical relations for the average E{sub av} and maximal E{sub M} ion energies and for their dependence on the cluster radius (R{sub 0}) and on the laser parameters. This revealed two kinds of Coulomb explosion domains separated by the bordermore » radius R{sub 0}{sup (I)}, which marks complete cluster outer ionization and which depends on I{sub M} and {tau}, (i) the cluster vertical ionization (CVI) domain (R{sub 0}R{sub 0}{sup (I)}), which prevails at lower laser intensities over a broad region of cluster sizes (i.e., at I{sub M}=10{sup 15} W cm{sup -2}, R{sub 0}>R{sub 0}{sup (I)}=6.2 A for {tau}=25 fs, and R{sub 0}>R{sub 0}{sup (I)}=9.5 A for {tau}=50 fs). The effects of the persistent nanoplasma on Coulomb explosion in the non-CVI domain are manifested by a distinct cluster size dependence, i.e., E{sub av}{proportional_to}R{sub 0}{sup {eta}} ({eta}=0) and E{sub M}{proportional_to}R{sub 0}{sup {eta}} ({eta}=1) for R{sub 0}>(2.0-2.5)R{sub 0}{sup (I)}, and by a bimodal distribution of the ion kinetic energies. The energetics of Coulomb explosion in the non-CVI domain and its dependence (or independence) on the cluster size and laser parameters was semiquantitatively described by a cold nanoplasma model, which is based on a lychee configuration of the cluster charge, and which induces Coulomb explosion in the presence of the persistent nanoplasma. The results of our analyses are general for the cluster size dependence of the energetics of Coulomb explosion of multicharged elemental and molecular Xe{sub n}, (CH{sub 4}){sub n}, and (DI){sub n} clusters in the non-CVI domain.« less

Effect of heating rate and plant species on the size and uniformity of silver nanoparticles synthesized using aromatic plant extracts

NASA Astrophysics Data System (ADS)

Hernández-Pinero, Jorge Luis; Terrón-Rebolledo, Manuel; Foroughbakhch, Rahim; Moreno-Limón, Sergio; Melendrez, M. F.; Solís-Pomar, Francisco; Pérez-Tijerina, Eduardo

2016-11-01

Mixing aqueous silver solutions with aqueous leaf aromatic plant extracts from basil, mint, marjoram and peppermint resulted in the synthesis of quasi-spherical silver nanoparticles in a range of size between 2 and 80 nm in diameter as analyzed by analytical high-resolution electron microscopy. The average size could be controlled by applying heat to the initial reaction system at different rates of heating, and by the specific botanical species employed for the reaction. Increasing the rate of heating resulted in a statistically significant decrease in the size of the nanoparticles produced, regardless of the species employed. This fact was more evident in the case of marjoram, which decreased the average diameter from 27 nm at a slow rate of heating to 8 nm at a high rate of heating. With regard to the species, minimum sizes of <10 nm were obtained with basil and peppermint, while marjoram and mint yielded an average size between 10 and 25 nm. The results indicate that aromatic plant extracts can be used to achieve the controlled synthesis of metal nanoparticles.

Polydiacetylene chromism towards toxic chemical detection via molecular size-dependent selectivity

NASA Astrophysics Data System (ADS)

Seo, Donghwan

Polydiacetylene (PDA) is a pi-conjugated polymer that has unique optical properties. PDA changes color from blue to red when subjected to various stimuli such as mechanical stress, heat, photoirradiation, pH change, and binding of specific ligands. The steric effect induced by those stimuli on PDA headgroup has been investigated to understand the mechanism of PDA chromism and to apply those optical properties to the development of various sensors. In this work, pH chromism of PDA was examined in terms of the effects of the molecular size and acidity of acid analytes with the consideration of the molecular design aspect of diacetylene lipids. The pH level is an important parameter, since a low pH will produce a charge on the amine headgroup of PDA, but this does not necessarily result in PDA chromatic transition from 'blue phase' to 'red phase.' The molecular size of the counter anion was identified as another determinant condition to ensure the perturbation of the ene-yne conjugated backbone of PDA, which produces the chromatic transition. In the molecular design of the sensory diacetylene lipids, the alkyl spacer length between the amine as a receptor and the amide linker was found to strongly affect the degree of PDA chromatic transition. The longer alkyl spacer showed the less chromatic transition. The length of alkyl spacer seems to promote the flexibility of the molecule diminishing the extent of the transfer of the steric effect at PDA headgroup to the conjugated backbone. Finally, PDA chromism dependent on the molecular size of acid analytes was applied to develop the colorimetric detection of diethyl phosphate (DEP), a degraded nerve agent simulant. PDA liposome sensors successfully showed selective chromatic transition with fluorescent emission upon binding of DEP compared to other acid analytes. The molecular size and acidity of acid analytes, and alkyl spacer length have proven to be correlated with PDA chromism. These new findings provide further understanding of the mechanism of PDA chromism and the molecular design principle of diacetylene in fundamental studies and in the development of various applications.

Linkage map of the fragments of herpesvirus papio DNA.

PubMed Central

Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H

1981-01-01

Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015

The molecular content of the Rosette's teardrops

NASA Astrophysics Data System (ADS)

Gonzalez-Alfonso, E.; Cernicharo, J.

1994-08-01

We report the detection of the J = 1 to 0 and J = 2 to 1 lines of (12)CO and (13)CO, and of the J = 2 to 1 and J = 3 to 2 lines of CS, in the direction of the small teardrops of the Rosette nebula. These objects appear in the optical as dark patches of 3 arcseconds - 30 arcseconds diameter against the bright H II region of the Rosette nebula. The CO lines were detected in all the observed globules. One of the observed teardrops is still connected to a large elephant trunk by a tenuous filament, which has also been detected in (12)CO. The sizes of the (12)CO J = 2 to 1 emitting regions are found to be similar to the optical sizes. The kinetic temperature of the globules is 15-20 K, and the beam-averaged molecular hydrogen densities inferred fron the (13)CO lines range from 2 x 103 to 7 x 103 per cu cm. CS J = 2 to 1 emission was detected toward two small teardrops and marginally toward another one. The CS J = 3 to 2 line was detected in one of the above globules. Analysis of these lines yields to an upper limit of the density of (1-3) x 104 per cu cm for this teardrop. The masses range from approximately 0.02 solar mass for a well-isolated and defined teardrop to approximately 0.5 solar mass for one which is still connected to a larger globule. Visual extinctions are also very low with typical values of approximately 1-3 mag.

Mapping PAH sizes in NGC 7023 with SOFIA

NASA Astrophysics Data System (ADS)

Croiset, B. A.; Candian, A.; Berné, O.; Tielens, A. G. G. M.

2016-05-01

Context. NGC 7023 is a well-studied reflection nebula, which shows strong emission from polycyclic aromatic hydrocarbon (PAH) molecules in the form of aromatic infrared bands (AIBs). The spectral variations of the AIBs in this region are connected to the chemical evolution of the PAH molecules which, in turn, depends on the local physical conditions. Aims: Our goal is to map PAH sizes in NGC 7023 with respect to the location of the star. We focus on the north west (NW) photo-dissociation region (PDR) and the south PDR of NGC 7023 to understand the photochemical evolution of PAHs, using size as a proxy. Methods: We use the unique capabilities of the Stratospheric Observatory for Infrared Astronomy (SOFIA) to observe a 3.2' × 3.4' region of NGC 7023 at wavelengths that we observe with high spatial resolution (2.7'') at 3.3 and 11.2 μm. We compare the SOFIA images with existing images of the PAH emission at 8.0 μm (Spitzer), emission from evaporating very small grains (eVSG) extracted from Spitzer-IRS spectral cubes, the extended red emission (Hubble Space Telescope and Canadian French Hawaiian Telescope), and H2 (2.12 μm). We create maps of the 11.2/3.3 μm ratio to probe the morphology of the PAH size distribution and the 8.0/11.2 μm ratio to probe the PAH ionization. We make use of an emission model and of vibrational spectra from the NASA Ames PAH database to translate the 11.2/3.3 μm ratio to PAH sizes. Results: The 11.2/3.3 μm ratio map shows the smallest PAH concentrate on the PDR surface (H2 and extended red emission) in the NW and south PDR. We estimated that PAHs in the NW PDR bear, on average, a number of carbon atoms (Nc) of ~70 in the PDR cavity and ~50 at the PDR surface. In the entire nebula, the results reveal a factor of 2 variation in the size of the PAH. We relate these size variations to several models for the evolution of the PAH families when they traverse from the molecular cloud to the PDR. Conclusions: The high-resolution PAH size map enables us to follow the photochemical evolution of PAHs in NGC 7023. Small PAHs result from the photo-evaporation of VSGs as they reach the PDR surface. Inside the PDR cavity, the PAH abundance drops as the smallest PAH are broken down. The average PAH size increases in the cavity where only the largest species survive or are converted into C60 by photochemical processing.

Influences of Co doping on the structural and optical properties of ZnO nanostructured

NASA Astrophysics Data System (ADS)

Majeed Khan, M. A.; Wasi Khan, M.; Alhoshan, Mansour; Alsalhi, M. S.; Aldwayyan, A. S.

2010-07-01

Pure and Co-doped ZnO nanostructured samples have been synthesized by a chemical route. We have studied the structural and optical properties of the samples by using X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), field-emission transmission electron microscope (FETEM), energy-dispersive X-ray (EDX) analysis and UV-VIS spectroscopy. The XRD patterns show that all the samples are hexagonal wurtzite structures. Changes in crystallite size due to mechanical activation were also determined from X-ray measurements. These results were correlated with changes in particle size followed by SEM and TEM. The average crystallite sizes obtained from XRD were between 20 to 25 nm. The TEM images showed the average particle size of undoped ZnO nanostructure was about 20 nm whereas the smallest average grain size at 3% Co was about 15 nm. Optical parameters such as absorption coefficient ( α), energy band gap ( E g ), the refractive index ( n), and dielectric constants ( σ) have been determined using different methods.

Perylenetetracarboxylic anhydride as a precursor of fluorescent carbon nanoonion rings.

PubMed

Baldoví, Herme G; Herance, José Raul; Manuel Víctor, Víctor; Alvaro, Mercedes; Garcia, Hermenegildo

2015-08-07

Thermal annealing at 400 °C of perylenetetracarboxylic anhydride in low molecular mass PEG gives rise to the formation of well defined nanoobjects of 2.5 nm height and size distribution from 10 to 65 nm (average 40 nm) after purification of the raw mixture with silicagel chromatography. TEM reveals that the flat nanoobjects are constituted of concentric graphenic rings (0.34 nm interlayer distance). The morphology of the nanoparticles resembles onion rings of nanometric dimensions (nanoonion rings C-NOR). C-NOR particles have an excitation dependent emission with λem from 430 to 570 nm and a maximum emission quantum yield of 0.49. C-NOR particles can be internalized into Hep3B human hepatoma cells as determined by confocal fluorescence microscopy and are remarkably biocompatible affecting slightly cell viability according to the MTT test.

A simple tagging system for protein encapsulation.

PubMed

Seebeck, Florian P; Woycechowsky, Kenneth J; Zhuang, Wei; Rabe, Jürgen P; Hilvert, Donald

2006-04-12

Molecular containers that encapsulate specific cargo can be useful for many natural and non-natural processes. We report a simple system, based on charge complementarity, for the encapsulation of appropriately tagged proteins within an engineered, proteinaceous capsid. Four negative charges per monomer were added to the lumazine synthase from Aquifex aeolicus (AaLS). The capsids formed by the engineered AaLS associate with green fluorescent protein bearing a positively charged deca-arginine tag upon coproduction in Escherichia coli. Analytical ultracentrifugation and scanning force microscopy studies indicated that the engineered AaLS retains the ability to form capsids, but that their average size was substantially increased. The success of this strategy demonstrates that both the container and guest components of protein-based encapsulation systems can be convergently designed in a straightforward manner, which may help to extend their versatility.

High-velocity projectile impact induced 9R phase in ultrafine-grained aluminium.

PubMed

Xue, Sichuang; Fan, Zhe; Lawal, Olawale B; Thevamaran, Ramathasan; Li, Qiang; Liu, Yue; Yu, K Y; Wang, Jian; Thomas, Edwin L; Wang, Haiyan; Zhang, Xinghang

2017-11-21

Aluminium typically deforms via full dislocations due to its high stacking fault energy. Twinning in aluminium, although difficult, may occur at low temperature and high strain rate. However, the 9R phase rarely occurs in aluminium simply because of its giant stacking fault energy. Here, by using a laser-induced projectile impact testing technique, we discover a deformation-induced 9R phase with tens of nm in width in ultrafine-grained aluminium with an average grain size of 140 nm, as confirmed by extensive post-impact microscopy analyses. The stability of the 9R phase is related to the existence of sessile Frank loops. Molecular dynamics simulations reveal the formation mechanisms of the 9R phase in aluminium. This study sheds lights on a deformation mechanism in metals with high stacking fault energies.

Transport coefficients for dense hard-disk systems.

PubMed

García-Rojo, Ramón; Luding, Stefan; Brey, J Javier

2006-12-01

A study of the transport coefficients of a system of elastic hard disks based on the use of Helfand-Einstein expressions is reported. The self-diffusion, the viscosity, and the heat conductivity are examined with averaging techniques especially appropriate for event-driven molecular dynamics algorithms with periodic boundary conditions. The density and size dependence of the results are analyzed, and comparison with the predictions from Enskog's theory is carried out. In particular, the behavior of the transport coefficients in the vicinity of the fluid-solid transition is investigated and a striking power law divergence of the viscosity with density is obtained in this region, while all other examined transport coefficients show a drop in that density range in relation to the Enskog's prediction. Finally, the deviations are related to shear band instabilities and the concept of dilatancy.

Supported inorganic membranes

DOEpatents

Sehgal, Rakesh; Brinker, Charles Jeffrey

1998-01-01

Supported inorganic membranes capable of molecular sieving, and methods for their production, are provided. The subject membranes exhibit high flux and high selectivity. The subject membranes are substantially defect free and less than about 100 nm thick. The pores of the subject membranes have an average critical pore radius of less than about 5 .ANG., and have a narrow pore size distribution. The subject membranes are prepared by coating a porous substrate with a polymeric sol, preferably under conditions of low relative pressure of the liquid constituents of the sol. The coated substrate is dried and calcined to produce the subject supported membrane. Also provided are methods of derivatizing the surface of supported inorganic membranes with metal alkoxides. The subject membranes find use in a variety of applications, such as the separation of constituents of gaseous streams, as catalysts and catalyst supports, and the like.

Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker)

PubMed Central

Duan, Yun; Gong, ZhongJun; Wu, RenHai; Miao, Jin; Jiang, YueLi; Li, Tong; Wu, XiaoBo; Wu, YuQing

2017-01-01

Light is an important environmental signal for most insects. The Oriental Armyworm, Mythimna separata, is a serious pest of cereal crops worldwide, and is highly sensitive to light signals during its developmental and reproductive stages. However, molecular biological studies of its response to light stress are scarce, and related genomic information is not available. In this study, we sequenced and de novo assembled the transcriptomes of M. separata exposed to four different light conditions: dark, white light (WL), UV light (UVL) and yellow light (YL). A total of 46,327 unigenes with an average size of 571 base pairs (bp) were obtained, among which 24,344 (52.55%) matched to public databases. The numbers of genes differentially expressed between dark vs WL, dark vs UVL, dark vs YL, and UVL vs YL were 12,012, 12,950, 14,855, and 13,504, respectively. These results suggest that light exposure altered gene expression patterns in M. separata. Putative genes involved in phototransduction-fly, phototransduction, circadian rhythm-fly, olfactory transduction, and taste transduction were identified. This study thus identified a series of candidate genes and pathways potentially related to light stress in M. separata. PMID:28345615

Detecting vapour bubbles in simulations of metastable water

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

González, Miguel A.; Abascal, Jose L. F.; Valeriani, Chantal, E-mail: christoph.dellago@univie.ac.at, E-mail: cvaleriani@quim.ucm.es

2014-11-14

The investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguishmore » between liquid- and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure.« less

Structural analysis of a sulfated galactan from the tunic of the ascidian Microcosmus exasperatus and its inhibitory effect of the intrinsic coagulation pathway.

PubMed

Restrepo-Espinosa, Diana C; Román, Yony; Colorado-Ríos, Jhonny; de Santana-Filho, Arquimedes Paixão; Sassaki, Guilherme Lanzi; Cipriani, Thales R; Martínez, Alejandro; Iacomini, Marcello; Pavão, Mauro S G

2017-12-01

Several bioactive sulfated galactans have been isolated from the tunic of different species of ascidians. The biological activity of this kind of polysaccharides has been related with the presence and position of sulfate groups, and by the chemical composition of this kind of polysaccharides. A sulfated galactan (1000RS) was isolated from the tunic of the Brazilian ascidia Microcosmus exasperatus through proteolytic digestion, ethanol precipitation, dialysis and freeze-thaw cycles. Homogeneity and molecular weight were estimated by using size exclusion chromatography. Monosaccharide composition and type of linkage were assessed by Gas chromatography coupled to mass spectrometry and the sulfate content was quantified through gelatin/BaCl 2 method. These experiments along with NMR and FTIR analysis allowed to claim that the galactan backbone is mainly composed of 4-linked α-l-Galp units. In addition, they permitted to establish that some of the galactose residues are sulfated at the 3-position. This sulfated polysaccharide, which has an average molecular mass of 439.5kDa, presents anticoagulant effect in a dose-dependent manner through the inhibition of the intrinsic coagulation pathway. Copyright © 2017 Elsevier B.V. All rights reserved.

Spontaneously formed high-performance charge-transport layers of organic single-crystal semiconductors on precisely synthesized insulating polymers

NASA Astrophysics Data System (ADS)

Makita, Tatsuyuki; Sasaki, Masayuki; Annaka, Tatsuro; Sasaki, Mari; Matsui, Hiroyuki; Mitsui, Chikahiko; Kumagai, Shohei; Watanabe, Shun; Hayakawa, Teruaki; Okamoto, Toshihiro; Takeya, Jun

2017-04-01

Charge-transporting semiconductor layers with high carrier mobility and low trap-density, desired for high-performance organic transistors, are spontaneously formed as a result of thermodynamic phase separation from a blend of π-conjugated small molecules and precisely synthesized insulating polymers dissolved in an aromatic solvent. A crystal film grows continuously to the size of centimeters, with the critical conditions of temperature, concentrations, and atmosphere. It turns out that the molecular weight of the insulating polymers plays an essential role in stable film growth and interfacial homogeneity at the phase separation boundary. Fabricating the transistor devices directly at the semiconductor-insulator boundaries, we demonstrate that the mixture of 3,11-didecyldinaphtho[2,3-d:2',3'-d']benzo[1,2-b:4,5-b']dithiophene and poly(methyl methacrylate) with the optimized weight-average molecular weight shows excellent device performances. The spontaneous phase separation with a one-step fabrication process leads to a high mobility up to 10 cm2 V-1 s-1 and a low subthreshold swing of 0.25 V dec-1 even without any surface treatment such as self-assembled monolayer modifications on oxide gate insulators.

Fractionation and Characterization of Biologically-active Polysaccharides from Artemisia tripartita

PubMed Central

Xie, Gang; Schepetkin, Igor A.; Siemsen, Daniel W.; Kirpotina, Liliya N.; Wiley, James A.; Quinn, Mark T.

2008-01-01

The leaves of Artemisia species have been traditionally used for prevention and treatment of a number of diseases. In this study, five polysaccharide fractions (designated A-I to A-V) were isolated from the leaves of Artemisia tripartita Rydb. by the sequential use of hot-water extraction, ethanol precipitation, ultra-filtration, and chromatography. The homogeneity and average molecular weight of each fraction were determined by high performance size-exclusion chromatography. Sugar composition analysis revealed that Artemisia polysaccharides consisted primarily of xylose, glucose, arabinose, galactose, and galactosamine. Moreover, all fractions contained at least 3.4% sulfate, and fractions A-II through A-V contained an arabinogalactan type II structure. All fractions exhibited macrophage-activating activity, enhancing production of intracellular reactive oxygen species and release of nitric oxide, interleukin 6, interleukin 10, tumor necrosis factor α, and monocyte chemotactic protein-1. In addition, all fractions exhibited scavenging activity for reactive oxygen species generated enzymatically or produced extracellularly by human neutrophils. Finally, fractions A-I and A-V exhibited complement-fixing activity. Taken together, our results provide a molecular basis to explain at least part of the beneficial therapeutic effects of Artemisia extracts, and suggest the possibility of using Artemisia polysaccharides as an immunotherapeutic adjuvant. PMID:18325553

Hybridization in the section Mentha (Lamiaceae) inferred from AFLP markers.

PubMed

Gobert, V; Moja, S; Colson, M; Taberlet, P

2002-12-01

The amplified fragment length polymorphism (AFLP) method was used to evaluate genetic diversity and to assess genetic relationships within the section Mentha in order to clarify the taxonomy of several interspecific mint hybrids with molecular markers. To this end, genetic diversity of 62 Mentha accessions from different geographic origins, representing five species and three hybrids, was assessed. Three EcoRI/MseI AFLP primer combinations generated an average of 40 AFLP markers per primer combination, ranging in size from 50 to 500 base pairs (bp). The percentage of markers polymorphic ranged from 50% to 60% across all accessions studied. According to phenetic and cladistic analysis, the 62 mint accessions were grouped into two major clusters. Principal coordinates analysis separated species into well-defined groups, and clear relationships between species and hybrids could be described. Our AFLP analysis supports taxonomic classification established among Mentha species by conventional (morphological, cytological, and chemical) methods. It allows the assessment of phenetic relationships between species and the hybrids M. spicata and M. × piperita, largely cultivated all over the world for their menthol source, and provides new insights into the subdivision of M. spicata, based for the first time on molecular markers.

Continuous-Time Random Walk Models of DNA Electrophoresis in a Post Array: II. Mobility and Sources of Band Broadening

PubMed Central

Olson, Daniel W.; Dutta, Sarit; Laachi, Nabil; Tian, Mingwei; Dorfman, Kevin D.

2011-01-01

Using the two-state, continuous-time random walk model, we develop expressions for the mobility and the plate height during DNA electrophoresis in an ordered post array that delineate the contributions due to (i) the random distance between collisions and (ii) the random duration of a collision. These contributions are expressed in terms of the means and variances of the underlying stochastic processes, which we evaluate from a large ensemble of Brownian dynamics simulations performed using different electric fields and molecular weights in a hexagonal array of 1 μm posts with a 3 μm center-to-center distance. If we fix the molecular weight, we find that the collision frequency governs the mobility. In contrast, the average collision duration is the most important factor for predicting the mobility as a function of DNA size at constant Péclet number. The plate height is reasonably well-described by a single post rope-over-pulley model, provided that the extension of the molecule is small. Our results only account for dispersion inside the post array and thus represent a theoretical lower bound on the plate height in an actual device. PMID:21290387

Electron- and photon-impact ionization of furfural

NASA Astrophysics Data System (ADS)

Jones, D. B.; Ali, E.; Nixon, K. L.; Limão-Vieira, P.; Hubin-Franskin, M.-J.; Delwiche, J.; Ning, C. G.; Colgan, J.; Murray, A. J.; Madison, D. H.; Brunger, M. J.

2015-11-01

The He(i) photoelectron spectrum of furfural has been investigated, with its vibrational structure assigned for the first time. The ground and excited ionized states are assigned through ab initio calculations performed at the outer-valence Green's function level. Triple differential cross sections (TDCSs) for electron-impact ionization of the unresolved combination of the 4a″ + 21a' highest and next-highest occupied molecular orbitals have also been obtained. Experimental TDCSs are recorded in a combination of asymmetric coplanar and doubly symmetric coplanar kinematics. The experimental TDCSs are compared to theoretical calculations, obtained within a molecular 3-body distorted wave framework that employed either an orientation average or proper TDCS average. The proper average calculations suggest that they may resolve some of the discrepancies regarding the angular distributions of the TDCS, when compared to calculations employing the orbital average.

Metal Sorbing Vesicles: Light Scattering Characterization and Metal Sorbtion Behavior.

NASA Astrophysics Data System (ADS)

van Zanten, John Hollis

1992-01-01

The research described herein consisted of two parts: light scattering characterization of vesicles and kinetic investigations of metal sorbing vesicles. Static light scattering techniques can be used to determine the geometric size, shape and apparent molecular weight of phosphatidylcholine vesicles in aqueous suspension. A Rayleigh-Gans-Debye (RGD) approximation analysis of multiangle scattered light intensity data yields the size and degree of polydispersity of the vesicles in solution, while the Zimm plot technique provides the radius of gyration and apparent weight-average molecular weight. Together the RGD approximation and Zimm plots can be used to confirm the geometric shape of vesicles and can give a good estimate of the vesicle wall thickness in some cases. Vesicles varying from 40 to 115 nm in diameter have been characterized effectively. The static light scattering measurements indicate that, as expected, phosphatidylcholine vesicles in this size range scatter light as isotropic hollow spheres. Additionally, static and dynamic light scattering measurements have been made and compared with one another. The values for geometric radii determined by static light scattering typically agree with those estimated by dynamic light scattering to within a few percent. Interestingly however, dynamic measurements suggest that there is a significant degree of polydispersity present in the vesicle dispersions, while static measurements indicate near size monodisperse dispersions. Metal sorbing vesicles which harbor ionophores, such as antibiotic A23187 and synthetic carriers, in their bilayer membranes have been produced. These vesicles also encapsulate the chelating compound, nitrilotriacetate, to provide the driving force for metal ion uptake. Very dilute dispersions (on the order of 0.03% w/v) of these metal sorbing vesicles were capable of removing Cd ^{2+} and Pb^{2+ } from dilute aqueous solution (5 ppm and less) and concentrating these metal ions several hundred to more than a thousand fold in the vesicle interior in a few minutes time. Synthetic ionophores were found to preferentially transport Pb^{2+} over Cd^{2+}, thus suggesting that engineered vesicle dispersions can be used as selective separations media. The effect of ionophore concentration, solution pH, solution ionic strength, initial metal ion concentration and vesicle concentration have been investigated.

Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-06-07

We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction k B T/6 ηV with k B Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.