A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions

A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods.     

An effective continuum approach for modeling non-equilibrium structural evolution of protein nanofiber networks

We quantify the formation and evolution of protein nanofibers using a new phase field modeling framework and compare the results to transmission electron microscopy measurements (TEM) and time-dependent growth measurements given in the literature. The modeling framework employs a set of effective continuum equations combined with underlying nanoscale forces and chemical potential relations governing protein nanofiber formation in solution. Calculations based on the theoretical framework are implemented numerically using a nonlinear finite element phase field modeling approach that couples homogenized protein molecular structure via a vector order parameter with chemical potential relations that describe interactions between the nanofibers and the surrounding solution. Homogenized, anisotropic molecular and chemical flux relations are found to be critical in obtaining nanofiber growth from seed particles or a random monomer bath. In addition, the model predicts both sigmoidal and first-order growth kinetics for protein nanofibers for unseeded and seeded models, respectively. These simulations include quantitative predictions on time scales of typical protein self-assembly behavior which qualitatively match TEM measurements of the RADA16-I protein and growth rate measurements for amyloid nanofibers from the literature. For comparisons with experiments, the numerical model performs multiple nanofiber protein evolution simulations with a characteristic length scale of ～2.4 nm and characteristic time scale of ～9.1 h. These results provide a new modeling tool that couples underlying monomer structure with self-assembling nanofiber behavior that is compatible with various external loadings and chemical environments.     

Interdiffusion of solvent into glassy polymer films: a molecular dynamics study

Large scale molecular dynamics and grand canonical Monte Carlo simulation techniques are used to study the behavior of the interdiffusion of a solvent into an entangled polymer matrix as the state of the polymer changes from a melt to a glass. The weight gain by the polymer increases with time t as t(1/2) in agreement with Fickian diffusion for all cases studied, although the diffusivity is found to be strongly concentration dependent especially as one approaches the glass transition temperature of the polymer. The diffusivity as a function of solvent concentration determined using the one-dimensional Fick's model of the diffusion equation is compared to the diffusivity calculated using the Darken equation from simulations of equilibrated solvent-polymer solutions. The diffusivity calculated using these two different approaches are in good agreement. The behavior of the diffusivity strongly depends on the state of the polymer and is related to the shape of the solvent concentration profile.     

气体在无定型聚异戊二烯中扩散的分子动力学模拟

采用分子动力学模拟方法研究了多个温度下氧气、氮气及甲烷在无定型顺式1,4-聚异戊二烯中的扩散系数。在模拟过程中,使用COMPASS力场作为分子力场。应用COMPASS力场的势能函数,聚合物的密度及玻璃化转变温度的计算结果与实验值有较好吻合。在278-378 K的温度范围内,通过3或1.5 ns时长的正则系综动力学模拟,计算了不同温度下氧气、氮气及甲烷的扩散系数。结果表明,根据爱因斯坦关系式计算得到的扩散系数与实验结果比较接近。对气体扩散系数与温度的关系进一步研究,发现在278-378 K温度范围内,甲烷的扩散系数随温度变化的半对数曲线图是非线性的,而氧气和氮气的扩散系数随温度变化的半对数曲线图是线性的。本文研究结果有助于理解温度对气体扩散的影响机制,并为高温下气体在天然橡胶中扩散系数的测定及天然橡胶热氧老化建模分析提供依据。     

Diffusion behavior of polyelectrolytes in dilute solution: coupling effects of hydrodynamic and Coulomb interactions

The diffusion behavior of polyelectrolytes in dilute salt-free solution is studied through a hybrid mesoscale simulation technique that combines the molecular dynamics method and the multiparticle collision dynamics approach. To elucidate the effects of hydrodynamic interactions (HI), we compare results for hydrodynamic and random solvents. When HI are taken into account, we find that the chain diffusivity decreases initially and then increases gradually with the increasing strength of the Coulomb interaction. By contrast, when HI are switched off, the electrostatic-dependent diffusivity shows three distinct regions, and a plateau of approximately constant diffusivity manifests between two decreasing regions. The findings reveal that the dynamics of polyelectrolytes in dilute solution depend on the coupling effects of hydrodynamic and Coulomb interactions, and that these dynamics can be understood by considering the conformational changes of chains, the counterion condensation, and the dynamics of counterions.     

Incorporation of a QM/MM buffer zone in the variational double self-consistent field method

The explicit polarization (X-Pol) potential is an electronic-structure-based polarization force field, designed for molecular dynamics simulations and modeling of biopolymers. In this approach, molecular polarization and charge transfer effects are explicitly treated by a combined quantum mechanical and molecular mechanical (QM/MM) scheme, and the wave function of the entire system is variationally optimized by a double self-consistent field (DSCF) method. In the present article, we introduce a QM buffer zone for a smooth transition from a QM region to an MM region. Instead of using the Mulliken charge approximation for all QM/MM interactions, the Coulombic interactions between the adjacent fragments are determined directly by electronic structure theory. The present method is designed to accelerate the speed of convergence of the total energy and charge density of the system.     

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein–water HBs, and less protein–PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein–solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.     

Structural properties of charge-stabilized ferrofluids under a magnetic field: a Brownian dynamics study

We present Brownian dynamics simulations of real charge-stabilized ferrofluids, which are stable colloidal dispersions of magnetic nanoparticles, with and without the presence of an external magnetic field. The colloidal suspensions are treated as collections of monodisperse spherical particles, bearing point dipoles at their centers and undergoing translational and rotational Brownian motions. The overall repulsive isotropic interactions between particles, governed by electrostatic repulsions, are taken into account by a one-component effective pair interaction potential. The potential parameters are fitted in order that computed structure factors are close to the experimental ones. Two samples of ferrofluid differing by the particle diameter and consequently by the intensity of the magnetic interaction are considered here. The magnetization and birefringence curves are computed: a deviation from the ideal Langevin behaviors is observed if the dipolar moment of particles is sufficiently large. Structure factors are also computed from simulations with and without an applied magnetic field H: the microstructure of the repulsive ferrofluid becomes anisotropic under H. Even our simple modeling of the suspension allows us to account for the main experimental features: an increase of the peak intensity is observed in the direction perpendicular to the field whereas the peak intensity decreases in the direction parallel to the field.     

Size and pH effect on electrical and conformational behavior of poly(acrylic acid): Simulation and experiment

Monte Carlo simulations, experimental titrations and fluorescence correlation spectroscopy experiments were used to investigate the conformational and electrical properties of polyacrylic acids (PAA). On the one hand, titration curves were calculated to get an insight into the role of pH on the degree of ionization and conformation of PAA chains. On the other hand, experimental potentiometric titrations of PAA were also achieved for different PAA molecular weights and compared to the calculated titration curves obtained by Monte Carlo coarse grained simulations. It was found that for a large range at intermediate PAA ionizations, a good correlation is obtained between experimental and simulations data thanks to the prominence of electrostatic interactions in this domain. The effect of ionic concentration and PAA molecular weight on the titration curves was also investigated. In order to get a better understanding of PAA conformational behavior, we also investigated PAA diffusion properties in aqueous solutions as a function of pH and ionic strength by fluorescence correlation spectroscopy (FCS), thanks to its high sensitivity to measure diffusion coefficients of tracer solutes. Good qualitative agreements were observed between experimental diffusivities and polymer properties calculated from MC simulations. It was shown that the high molecular weight PAA chains display more significant changes in diffusivity in agreement with the ionization degrees and conformational changes observed in the simulations.     

Mechanism of nitromethane liquid membrane oscillator containing sodium oleate

The oscillatory behavior of a liquid membrane oscillator with anionic surfactant was investigated in order to understand the oscillation mechanism at the molecular level. As a theoretical framework, an approach based on chemical kinetics laws has been used. The chosen system involved nitromethane with 2,2(')-bipyridine as liquid membrane. The aqueous donor phase contained sodium oleate and butanol, while sodium chloride was added to the aqueous acceptor phase. It was established that the oscillations take place exclusively at the aqueous acceptor phase/membrane interface. Therefore, liquid membrane oscillators with anionic surfactants behave the same way as oscillators with cationic surfactants as to the location of oscillations. An oscillation mechanism involving three stages is proposed and confirmed by numerical simulations. The oscillations of electrical potential differences between the two aqueous phases are produced by sudden adsorption and desorption of anionic surfactant in solvated form and butanol at the acceptor/membrane interface. The whole process is controlled by the slow diffusion of these species across the liquid membrane. The chaotic character of the oscillations was demonstrated by Lyapunov exponents obtained from the strange attractor of the system.     

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Theta temperature: a Brownian dynamics study

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Theta conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.     

良溶剂中接枝型聚两性电解质单链构象的布朗动力学模拟

采用布朗动力学研究了在良溶剂中荷电平衡的接枝聚两性电解质(GPA)的单链构象转变行为,讨论了主链链长、支链数及电荷密度对GPA分子链构象转变的影响.研究发现,随着静电相互作用的增强,GPA分子链构象转变过程由线团、主链与支链间的折叠、链段塌缩和电荷配对形成偶极子与四极子等4个阶段构成.与线型聚两性电解质不同,GPA存在的额外支链间空间排斥与静电排斥作用随着分子结构的变化而改变,并影响构象转变行为.在强静电相互作用下,良溶剂中的GPA链由于溶剂化作用会再伸展,以保证偶极子完全配对成四极子.减小主链长度或电荷密度或增加支链数目都会增大体系的排斥力和主链的刚性,阻滞分子链的塌缩,并使得分子链再伸展的幅度增大.     

Multicomponent diffusion in nanosystems

We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties varying on the atomic scale. The present treatment is based on different areas of liquid state theory, namely, kinetic and density functional theory and their implementation as an effective numerical method via the lattice Boltzmann approach. By combining the first two methods, it is possible to obtain a closed set of kinetic equations for the singlet phase space distribution functions of each species. The interactions among particles are considered within a self-consistent approximation and the resulting effective molecular fields are analyzed. We focus on multispecies diffusion in systems with short-range hard-core repulsion between particles of unequal sizes and weak attractive long-range interactions. As a result, the attractive part of the potential does not contribute explicitly to viscosity but to diffusivity and the thermodynamic properties. Finally, we obtain a practical scheme to solve the kinetic equations by employing a discretization procedure derived from the lattice Boltzmann approach. Within this framework, we present numerical data concerning the mutual diffusion properties both in the case of a quiescent bulk fluid and shear flow inducing Taylor dispersion.     

Insertion of dipolar molecules in channels of a centrosymmetric organic zeolite: molecular modeling and experimental investigations on diffusion and polarity formation

The mechanism of insertion of p-nitroaniline (PNA) and its diffusion behavior in channels of the hexagonal host structure of tris(o-phenylenedioxy)cyclotriphosphazene (TPP) was investigated by means of molecular modeling tools. Strong preferential sites in the bulk were found to be due to pi-pi and NH-pi interactions between PNA and channel walls of TPP. MD simulations showed that diffusion can be characterized by jumps from one site to the next, occurring mainly because of the dynamic flexibility of the host structure. Calculations of host-guest interactions between the TPP surface and PNA approaching the entrance of channels with its terminal H2N-first or O2N-first revealed that the H2N-first insertion is clearly preferred. Preferential insertion of PNA is found to be the reason for polar effects, observed experimentally. Because of a distinct guest-host recognition at the surface, guest-guest interactions were found to have a minor influence on polarity.     

Anomalous transport in molecularly confined spaces

We develop a novel theory to predict the density dependence of the diffusivity of simple fluids in a molecularly sized nanopore with diffusely reflecting walls, incorporating nearest neighbor intermolecular interactions within the framework of the recent oscillator model of low density transport arising from this laboratory. It is shown that when the pore width is about two molecular diameters, at sufficiently high densities these interactions lead to a repulsive inner core, as a result of which the diffusing molecules undergo more frequent reflections at the wall. This leads to a reduction in diffusivity with increase in density, which is consistent with molecular dynamics simulation results, and contrasts with the behavior in larger pores where the transport coefficient has previously been shown to increase with increase in density due to viscouslike intermolecular interactions. At low densities the behavior is opposite, with the inner core becoming more attractive with increase in density, which can lead to an increase in diffusivity. The theory consistently explains molecular dynamics simulation results when the inhomogeneous pair distribution function of moving particles in the pore is axially periodic, suggesting concerted motion of neighboring molecules. It is also shown that a potential of mean force concept is inadequate for describing the influence of intermolecular interactions on transport.     

Non-equilibrium molecular dynamics simulation study on permeation phenomena of LJ particles in slit-shaped membranes with periodic belt-like heterogeneous surfaces

In order to make clear the relationship between the pore structure and the diffusivity, we have carried out permeation simulations of pure gases through simple model membranes by using the external-field non-equilibrium molecular dynamics method. As the membrane, we model slit-shaped pores with periodic belt-like heterogeneous pore surfaces which are caused by the upheaval of surface atoms. Applying simulation results for membranes with several upheaval interval distances to Maxwell–Stefan (MS) theory, we calculate the effects of the molecular loading of permeating molecules in the pores on MS diffusivity (D_MS). In addition, the permeation potential barrier is estimated as the difference between the maximum and minimum permeation potential energies. The effect of the molecular loading on the permeation potential barrier and the D_MS are in inverse proportion. It is noted that, when the width of the adsorption area in the permeation direction is not common multiples of the molecular diameter, the permeation potential barrier decreases with the increase in the molecular loading. This is because the positive force against the permeation direction is caused to the permeating molecules by interactions with permeating molecules in the adsorpton area between adjacent upheavals. Therefore, we could suggest that the key factor for controlling diffusion property is the structural relationship between the adsorption area and the permeating molecules.     

Diffusion behavior in polymer–clay nanocomposites

This paper reviews our previous studies on the diffusion behavior in polymers clay nanocomposites. A geometric model for predicting the effective diffusivity through this type of systems as a function of clay sheets orientation, volume fraction, polymer clay interaction, and aspect ratio is proposed. Model predictions are compared to the effective diffusivity generated using random walk simulations as well as with predictions obtained from already existing theoretical models. Fair agreement is found between the model prediction and the results of numerical simulations. With respect to the already existing theoretical models, the present mathematical derivation seems more adequate to describe diffusion behavior in conventional nanocomposites systems (i.e. when fillers present very low values of volume to surface ratio). Experimental diffusion tests are discussed and interpreted with the aid of the proposed model. In addition to the aspect ratio and clay concentration, the polymer clay interactions as well as the sheets orientation are the factors controlling the barrier properties of polymer‐layered silicate nanocomposites. Good agreement was found in the case of samples containing exfoliated clay, whereas the model fails in the case of micro‐composites, in which the inorganic lamellae are agglomerated in clusters. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 265–274, 2006     

Molecular dynamics simulations of polymer transport in nanocomposites

Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration R(g) away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.     

Evolution of glassy gratings with variable aspect ratios under surface diffusion

The structural evolution of surface gratings on a glassy material is investigated by means of molecular simulations. The gratings provide a means to probe surface diffusion in the vicinity of the glass transition temperature. A theory by Mullins [J. Appl. Phys. 30, 77 (1959)] is used to extract qu-antitative measures of surface diffusivity that rely on calculation of grating amplitude as a function of time. The simulations are implemented in the context of a model binary glass mixture [S. S. Ashwin and S. Sastry, J. Phys.: Condens. Matter 15, S1253 (2003)]. We find that surface diffusion is faster than bulk diffusion by several orders of magnitude, consistent with recent experimental data for an organic glass former. The diffusivities extracted by the grating-decay approach are consistent with those estimated on the basis of mean-squared particle displacements. The grating-decay approach, however, is more efficient than traditional techniques based on Einstein's diffusion equation. Grating decay is also more versatile and is shown to be applicable in a variety of sample geometries.