Semi-classical generalized Langevin equation for equilibrium and nonequilibrium molecular dynamics simulation

Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matter in different phases. Normally, the atomic dynamics are described by classical equations of motion and the effect of the environment is taken into account through the fluctuating and frictional forces. Generally, the nuclear quantum effects and their coupling to other degrees of freedom are difficult to include in an efficient way. This could be a serious limitation on its application to the study of dynamical properties of materials made from light elements, in the presence of external driving electrical or thermal fields. One example of such system is single molecule dynamics on metal surface, an important system that has received intense study in surface science. In this review, we summarize recent effort in extending the Langevin MD to include nuclear quantum effect and their coupling to flowing electrical current. We discuss its applications in the study of adsorbate dynamics on metal surface, current-induced dynamics in molecular junctions, and quantum thermal transport between different reservoirs.     

Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms

The fifth-order two-dimensional (2D) Raman signals have been calculated from the equilibrium and nonequilibrium (finite field) molecular dynamics simulations. The equilibrium method evaluates response functions with equilibrium trajectories, while the nonequilibrium method calculates a molecular polarizability from nonequilibrium trajectories for different pulse configurations and sequences. In this paper, we introduce an efficient algorithm which hybridizes the existing two methods to avoid the time-consuming calculations of the stability matrices which are inherent in the equilibrium method. Using nonequilibrium trajectories for a single laser excitation, we are able to dramatically simplify the sampling process. With this approach, the 2D Raman signals for liquid xenon, carbon disulfide, water, acetonitrile, and formamide are calculated and discussed. Intensities of 2D Raman signals are also estimated and the peak strength of formamide is found to be only five times smaller than that of carbon disulfide.     

First-principles simulation of molecular dissociation-recombination equilibrium

For the first time, the equilibrium composition of chemical dissociation-recombination reaction is simulated from first-principles, only. Furthermore, beyond the conventional ab initio Born-Oppenheimer quantum chemistry the effects from the thermal and quantum equilibrium dynamics of nuclei are consistently included, as well as, the nonadiabatic coupling between the electrons and the nuclei. This has been accomplished by the path integral Monte Carlo simulations for full NVT quantum statistics of the H(3)(+) ion. The molecular total energy, partition function, free energy, entropy, and heat capacity are evaluated in a large temperature range: from below room temperature to temperatures relevant for planetary atmospheric physics. Temperature and density dependent reaction balance of the molecular ion and its fragments above 4000 K is presented, and also the density dependence of thermal ionization above 10,000 K is demonstrated.     

Vapor-liquid equilibrium of aqueous crown ether solutions

The activity of water in crown ether solutions has been obtained at 298,313 and 333 K over a wide range of concentrations. A minimum in the activity coefficient of water is observed. The minimum becomes more pronounced with decreasing temperature.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Hydration of superoxide studied by molecular dynamics simulation

Molecular dynamics was used to study the hydration of superoxide (O). The Helmholtz free energy of hydration of O was estimated by the thermodynamic integration method. The diffusion of O and the water structure around O were also studied. Two water models were used in the calculations and the results were compared to experiments.     

Definition and computation of intermolecular contact in liquids using additively weighted Voronoi tessellation

We present a definition of intermolecular surface contact by applying weighted Voronoi tessellations to configurations of various organic liquids and water obtained from molecular dynamics simulations. This definition of surface contact is used to link the COSMO-RS model and molecular dynamics simulations. We demonstrate that additively weighted tessellation is the superior tessellation type to define intermolecular surface contact. Furthermore, we fit a set of weights for the elements C, H, O, N, F, and S for this tessellation type to obtain optimal agreement between the models. We use these radii to successfully predict contact statistics for compounds that were excluded from the fit and mixtures. The observed agreement between contact statistics from COSMO-RS and molecular dynamics simulations confirms the capability of the presented method to describe intermolecular contact. Furthermore, we observe that increasing polarity of the surfaces of the examined molecules leads to weaker agreement in the contact statistics. This is especially pronounced for pure water.     

Vapor-liquid equilibria of polymer solutions determined by molecular mechanics

A method of calculating interaction parameters used in phase equilibrium calculations was extended for predicting solvent activities of polymer solutions. A pair of interaction parameters are determined by calculating interaction energies between all pairs of molecules in the solution of interest with a molecular mechanics method called the consistent force field (CFF). The conformational space of a pair of molecules is sampled with a Monte Carlo algorithm followed by energy minimizations. The method is used to calculate solvent activities for the diethylketone/polypropylene system, giving results in good agreement with experimental values. In addition, solvent activities are predicted for the diethylketone/polyethylenesystem for which no experimental data are available. The method is fully predictive, as no fitting to experimental phase-equilibrium data is carried out.     

Rapid solidification of cobalt melt by molecular dynamics simulation

Molecular dynamics simulation was applied to investigating the evolvement rule of cobalt melt microstructure during solidification at different cooling rates. The cooling rate for the formation of amorphous phase is determined by analyzing the radial distribution function, the H–A bond-type index and the mean square displacement. The simulation results showed that the nucleation undercooling increases with the initial temperature, and in the undercooling versus temperature curve, there are two inflection points. Besides, when the initial temperature reaches 2450 K, the undercooling will be stabilized at 1061 K. As the cooling rate is less than 1.0?×?10^11.0 K s^?1, the FCC and HCP crystal structures will be obtained. Amorphous structure will be obtained if the cooling rate is more than 1.0?×?10^13.0 K s^?1. If the cooling rate of the Co melt is between 1.0?×?10^11.0 and 1.0?×?10^13.0 K s^?1, the crystal and amorphous structures will be coexistent, which indicates that the critical cooling rate of crystal–amorphous transition is 1.0?×?10^11.0 K s^?1.

     

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h=0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h=0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at approximately 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than that in other regions in the full hydration state, but the mobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interaction and solvent mobility are important to understand the glass-like transition in proteins.     

Detailed insight into the hydrogen bonding interactions in acetone-methanol mixtures. A molecular dynamics simulation and Voronoi polyhedra analysis study

Voronoi polyhedra (VP) analysis of mixtures of acetone and methanol is reported on the basis of molecular dynamics computer simulations, performed at 300 K and 1 bar. The composition of the systems investigated covers the entire range from neat acetone to neat methanol. Distribution of the volume, reciprocal volume and asphericity parameter of the VP as well as that of the area of the individual VP faces and of the radius of the empty voids located between the molecules are calculated. To investigate the tendency of the like molecules to self-associate the analyses are repeated by disregarding one of the two components. The self-aggregates of the disregarded component thus turn into large empty voids, which are easily detectable in VP analysis. The obtained results reveal that both molecules show self-association, but this behavior is considerably stronger among the acetone than among the methanol molecules. The strongest self-association of the acetone and methanol molecules is found in their mole fraction ranges of 02-0.5 and 0.5-0.6, respectively. The caging effect around the methanol molecules is found to be stronger than around acetones. Finally, the local environment of the acetone molecules turns out to be more spherical than that of the methanols, not only in the respective neat liquids, but also in their mixtures.     

Single- and two-phase flow in microfluidic porous media analogs based on Voronoi tessellation

The objective of this study was to create a microfluidic model of complex porous media for studying single and multiphase flows. Most experimental porous media models consist of periodic geometries that lend themselves to comparison with well-developed theoretical predictions. However, many real porous media such as geological formations and biological tissues contain a degree of randomness and complexity at certain length scales that is not adequately represented in periodic geometries. To design an experimental tool to study these complex geometries, we created microfluidic models of random homogeneous and heterogeneous networks based on Voronoi tessellations. These networks consisted of approximately 600 grains separated by a highly connected network of channels with an overall porosity of 0.11-0.20. We found that introducing heterogeneities in the form of large cavities within the network changed the permeability in a way that cannot be predicted by the classical porosity-permeability relationship known as the Kozeny equation. The values of permeability found in experiments were in excellent agreement with those calculated from three-dimensional lattice Boltzmann simulations. In two-phase flow experiments of oil displacement with water we found that the wettability of channel walls determined the pattern of water invasion, while the network topology determined the residual oil saturation. The presence of cavities increased the microscopic sweeping efficiency in water-oil displacement. These results suggest that complex network topologies lead to fluid flow behavior that is difficult to predict based solely on porosity. The novelty of this approach is a unique geometry generation algorithm coupled with microfabrication techniques to produce pore scale models of stochastic homogeneous and heterogeneous porous media. The ability to perform and visualize multiphase flow experiments within these geometries will be useful in measuring the mechanism(s) of displacement within micro- and nanoscale pores.     

Capturing coacervate formation and protein partition by molecular dynamics simulation

Biomolecules localize and function in microenvironments where their local concentration, spatial organization, and biochemical reactivity are regulated. To compartmentalize and control the local properties of the native microenvironment, cellular mimics and artificial bioreactors have been developed to study the properties of membraneless organelles or mimic the bio-environment for life origin. Here, we carried out molecular dynamics simulation with the Martini 3.0 model to reproduce the experimental salt concentration and pH dependency of different complex coacervates. We showed that coacervates inside vesicles are able to change their shape. In addition, we used these coacervate systems to explore the partitioning of the ubiquitous cytoskeletal protein actin and found that actin spontaneously partitions to all the coacervate peripheries. Therefore, we believe that our study can provide a better understanding of the versatile coacervate platform, where biomolecules partition and gather to fulfill their biological duties.

We carried out molecular dynamics simulation with the Martini 3.0 model to reproduce the experimental salt concentration and pH dependency of different complex coacervates. We showed that coacervates inside vesicles are able to change their shape.     

Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation

Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities beta(T,int). To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of beta(T,int) varies with protein species considerably: beta-lactoglobulin (14.15 x 10(-2) GPa(-1)) is more than twice as compressible as ribonuclease A (6.77 x 10(-2) GPa(-1)). Beta-lactoglobulin and myoglobin (13.95 x 10(-2) GPa(-1)) have similar values of beta(T,int), but the mechanisms responsible for them are significantly different. The volume fluctuations of internal cavities and the magnitudes of the crosscorrelation between them are the key factors determining beta(T,int) of proteins. Though the volume fractions of internal cavity for the five studied proteins are nearly equal to one another, the mean cavity compressibilities beta(T,cav) vary considerably with protein species and range from 0.35 to 0.69 GPa(-1), which are much smaller than those of normal organic liquids such as methanol, ethanol, and benzene and close to that of glycerol (0.55 GPa(-1)), a strongly associated liquid.     

Vapor-liquid equilibrium for phenanthrene-toluene mixtures at elevated temperatures and pressures

Vapor and liquid equilibrium compositions are reported for the phenanthrene-toluene system at 593, 633, and 675 K and at pressures ranging from 7.3 bar to the binary mixture critical pressure at each temperature. Mixture critical pressures were obtained by visual observation of critical opalescence within a view cell. A flow apparatus for measuring VLE and LLE that is capable of operation at pressures up to 350 bar and temperatures to 675 K is also described. The apparatus can be used with materials such as phenanthrene and petroleum pitches which are solids at room temperature.     

Thermal analysis via molecular dynamics simulation

Thermal analysis by classical molecular dynamics simulations is discussed on hand of heat capacity of crystals of 9600 atoms. The differences between quantum mechanical and classical mechanical calculations are shown. Anharmonicity is proven to be an important factor. Finally, it is found that defects contribute to an increase in heat capacity before melting. The energy of conformational gauche defects within the crystal is only about 10% due to internal rotation. The other energy must be generated by cooperative strain. The conclusion is that the next generation of faster computers may permit wider use of molecular dynamics simulations in support of the interpretation of thermal analysis.Dedicated to Professor Bernhard Wunderlich on the occasion of his 65th birthday     

Investigation of vapor-deposited amorphous ice and irradiated ice by molecular dynamics simulation

With the purpose of clarifying a number of points raised in the experimental literature, we investigate by molecular dynamics simulation the thermodynamics, the structure and the vibrational properties of vapor-deposited amorphous ice (ASW) as well as the phase transformations experienced by crystalline and vitreous ice under ion bombardment. Concerning ASW, we have shown that by changing the conditions of the deposition process, it is possible to form either a nonmicroporous amorphous deposit whose density (approximately 1.0 g/cm3) is essentially invariant with the temperature of deposition, or a microporous sample whose density varies drastically upon temperature annealing. We find that ASW is energetically different from glassy water except at the glass transition temperature and above. Moreover, the molecular dynamics simulation shows no evidence for the formation of a high-density phase when depositing water molecules at very low temperature. In order to model the processing of interstellar ices by cosmic ray protons and heavy ions coming from the magnetospheric radiation environment around the giant planets, we bombarded samples of vitreous ice and cubic ice with 35 eV water molecules. After irradiation the recovered samples were found to be densified, the lower the temperature, the higher the density of the recovered sample. The analysis of the structure and vibrational properties of this new high-density phase of amorphous ice shows a close relationship with those of high-density amorphous ice obtained by pressure-induced amorphization.     

A mimetic porous carbon model by quench molecular dynamics simulation

A mimetic porous carbon model is generated using quench molecular dynamics simulations that reproduces experimental radial distribution functions of activated carbon. The resulting structure is composed of curved and defected graphene sheets. The curvature is induced by nonhexagonal rings. The quench conditions are systematically varied and the final porous structure is scrutinized in terms of its pore size distribution, pore connectivity, and fractal dimension. It is found that the initial carbon density affects the fractal dimension but only causes a minor shift in the pore size distribution. On the other hand, the quench rate affects the pore size distribution but only causes a minor shift in the fractal dimension.     

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation

The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is alpha-helical; there is no discernible 3(10)- or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.     

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation

Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.