Classical Molecular Simulations Research Articles

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage.

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomic instability. In this article we show, by using classical molecular simulation techniques, that compared to canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show remarkable structural stability, even in the presence of two strand breaks. Since G4-DNA is recognized for its regulatory roles in cell senescence and gene expression, including oncogenes, this stability may be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.

Effects of structure relaxation and surface oxidation on nanoscopic wear behaviors of metallic glass

Both structure relaxation and oxidation of surface layer induced by thermal treatment or friction heat play significant roles in reducing wear of metallic glasses (MGs). To distinguish the effects of structure relaxation and surface oxidation, we prepared Zr-based MGs at different states, i.e., as-cast MG; the annealed MGs under argon atmosphere (referred to as structure-relaxed MG) and oxygen atmosphere (referred to as oxidized MG). Nano-wear tests were carried out by atomic force microscope (AFM) to quantitatively clarify these two effects on the wear performance. Compared with the as-cast MG, the structure-relaxed MG shows an increased adhesive but slightly decreased ploughing friction. While, the oxidized MG shows the best anti-wear performance with dramatic reductions in both adhesive and ploughing friction. Classic molecular dynamics (MD) and ab initio MD simulations revealed that the introduction of O hinders the MG atoms from forming interfacial bonds with diamond, and reduces significantly the adhesion between the diamond tip and passivated MG. In addition, the synergistic effect of high hardness and elastic recovery associated with oxidization reduces ploughing friction and enhances wear resistance. This finding clarifies the importance of surface chemistry over structure modification during wear, and offers a generic pathway for tailoring ultra-wear resistant MGs.

Influence of partial fluorination on growth modes of organic molecules on amorphous silicon dioxide

We study the influence of fluorination on nucleation and growth of the organic parasexiphenyl molecule ($p$-6P) on amorphous silicon dioxide ($a\text{\ensuremath{-}}\mathrm{Si}{\mathrm{O}}_{2}$) by means of atomistically resolved classical molecular dynamics computer simulations. We use a simulation model that mimics the experimental deposition from the vapor and subsequent self-assembly onto the underlying surface. Our model reproduces the experimentally observed orientational changes from lying to upright standing configurations of the grown layers. We demonstrate that the increase in the number of fluorinated groups inside the $p$-6P leads to a smoother, layer-by-layer growth on the $a\text{\ensuremath{-}}\mathrm{Si}{\mathrm{O}}_{2}$ surface: We observe that in the first layers, due to strong molecule-substrate interactions the molecules first grow in chiral (fan-like) structures, where each consecutive molecule has a higher angle, supported by molecules lying underneath. Subsequently deposited molecules bind to the already standing molecules of the chiral structures until all molecules are standing. The growth of chiral islands is the main mechanism for growth of the fluorinated $p$-6P derivative, while the $p$-6P, due to the lower interaction with the underlying substrate, forms less chiral structures. The higher degree of chirality leads to a lower-energy barrier for step-edge crossing for the fluorinated molecules. We find that partial fluorination of the $p$-6P molecule can, in this way, significantly alter its growth behavior by modifying rough, three-dimensional growth into smooth, layer-by-layer growth. This has implications for the rational design of molecules and their functionalized forms, which could be tailored for a desired growth behavior and structure formation.

Simulation Models for Prediction of Bioavailability of Medicinal Drugs-the Interface Between Experiment and Computation.

The oral drug bioavailability (BA) problems have remained inevitable over the years, impairing drug efficacy and indirectly leading to eventual human morbidity and mortality. However, some conventional lab-based methods improve drug absorption leading to enhanced BA, and the recent experimental techniques are up-and-coming. Nevertheless, some have inherent drawbacks in improving the efficacy of poorly insoluble and low impermeable drugs. Drug BA and strategies to overcome these challenges were briefly highlighted. This review has significantly unravelled the different computational models for studying and predicting drug bioavailability. Several computational approaches provide mechanistic insights into the oral drug delivery system simulation of descriptors like solubility, permeability, transport protein-ligand interactions, and molecular structures. The in silico techniques have long been known still are just being applied to unravel drug bioavailability issues. Many publications have reported novel applications of the computational models towards achieving improved drug BA, including predicting gastrointestinal tract (GIT) drug absorption properties and passive intestinal membrane permeability, thus maximizing time and resources. Also, the classical molecular simulation models for free solvation energies of soluble-related processes such as solubilization, dissolutions, supersaturation, and precipitation have been used in virtual screening studies. A few of the tools are GastroPlusTM that supports biowaiver for drugs, mainly BCS class III and predicts drug compounds' absorption and pharmacokinetic process; SimCyp® simulator for mechanistic modelling and simulation of drug formulation processes; pharmacodynamics analysis on non-linear mixed-effects modelling; and mathematical models, predicting absorption potential/maximum absorption dose. This review provides in silico-experiment annexation in the drug bioavailability enhancement, possible insights that lead to critical opinion on the applications and reliability of the various in silico models as a growing tool for drug development and discovery, thus accelerating drug development processes.

Wigner energy in irradiated graphite: A first-principles study

First-principles calculations were performed to examine the defect-induced energy storage in graphite. The accumulation of energy resulting from inducing defects in graphite is a well-known phenomenon. Given the recent interest in exploiting this process for energy-storing purposes, more careful investigation is necessary. Some of the earliest studies of damaged graphite, and the stored energy associated with that, were motivated by the associated technological issues in nuclear reactor operation. A large number of excited state defects, for example Frenkel pairs, can be generated in graphite through bombardment of high-energy neutrons. The sudden release of this energy (also called Wigner energy) poses a serious concern to the safe operation of nuclear reactors. At the same time, controlled defect generation in graphite using neutron/ion irradiation might represent a potential energy storage mechanism. In recently published papers, the design of an integrated energy system that couples a nuclear reactor with a Wigner effect-based energy storing system was proposed. To accurately estimate the performance that can be achieved in terms of stored energy density through defect generation, density functional theory (DFT) based first-principles calculations were performed. In this work, stored energy accumulation was modeled in two ways - by Frenkel pair accumulation and overlapping collision cascade methods. The former was done with ab initio molecular dynamics (AIMD) simulations, and the latter was done with combined classical molecular dynamics (MD) and AIMD simulations. The agreement between the calculated and experimental results for how stored energy changes with dosage suggests that this model could be useful for the on-going research into damaged graphite as an energy storage medium.

Thermodynamic integration combined with molecular dynamic simulations to explore the cross-resistance mechanism of isoniazid and ethionamide.

Tuberculosis is an ancient disease of mankind, and its causative bacterium is Mycobacterium tuberculosis. Isoniazid is one of the most effective first-line antituberculosis drugs. As prodrugs, it and its derivative ethionamide act on enoyl-acyl carrier protein reductase (InhA) after being oxidized in bacteria, and kill the bacteria by inhibiting the formation of M. tuberculosis cell walls. However, the S94A mutation of InhA causes M. tuberculosis to develop cross-resistance to isoniazid and ethionamide. This work is dedicated to studying the cross-resistance mechanism of isoniazid and ethionamide through theoretical calculations. First, thermodynamic integral simulations are used to accurately calculate the relative binding energy of two drugs in the mutant and wild-type system. Furthermore, through classic molecular dynamic simulations and molecular mechanics generalized-Born surface area calculation, some key residues are identified and the binding affinity of isoniazid and ethionamide reduced by 9-13 kcal/mol due to S94A mutation. The hydrogen bond between Ala94 and isoniazid (ethionamide) disappeared and the energy contribution of Ala94 decreased after the mutation. In addition, the dynamic network analysis indicated that the mutation of Ser94 also indirectly affected the conformation of key residues such as Met147, Thr196, and Leu97, resulting in a reduction in the energy contribution of these residues. Finally, the binding conformation of isoniazid and ethionamide has also undergone major changes. The obtained results could provide valuable information for the future molecular design to overcome the drug resistance.

Large-scale dynamics of event-chain Monte Carlo.

Event-chain Monte Carlo (ECMC) accelerates the sampling of hard-sphere systems, and has been generalized to the potentials used in classical molecular simulations. Rather than imposing detailed balance on the transition probabilities, the method enforces a weaker global-balance condition in order to guarantee convergence to equilibrium. In this paper, we generalize the factor-field variant of ECMC to higher space dimensions. In the two-dimensional fluid phase, factor-field ECMC saturates the lower bound z=0 for the dynamical scaling exponent for local dynamics, whereas molecular dynamics is characterized by z=1 and local Metropolis Monte Carlo by z=2. In the presence of hexatic order, factor fields are not found to speed up the convergence. We note that generalizations of factor fields could couple to orientational order.

Temperature-dependent structure of 3.5 wt.% NaCl aqueous solution: Theoretical and Raman investigation

In the laboratory, the 3.5 wt.% NaCl aqueous solution is commonly used to simulate the seawater environment. The thermodynamic and kinetic research on the aqueous solution structure is intriguing, and it would aid in explaining the initial mechanism of the seawater-related physical and chemical phenomena. In this paper, the solution structure and evolution of the hydrogen bond network at the temperature range of the marine environment were obtained using classical molecular simulation and in-situ Raman spectroscopy. Specifically, the tetrahedral hydrogen bond structure was decomposed into two types: DDAAa affected by ions and DDAAn unaffected by ions. Furthermore, the enthalpy and entropy change of hydrogen bond evolution in the temperature range were calculated to be 14.05 ± 0.75 J·mol−1 and 53.38 ± 2.49 J·mol−1·K−1. This work lays the groundwork for preliminary mechanism research of life phenomena, physical properties, and chemical reactions in the marine environment.

Computational Design of MOF-Based Electronic Noses for Dilute Gas Species Detection: Application to Kidney Disease Detection.

The diverse chemical composition of exhaled human breath contains a vast amount of information about the health of the body, and yet this is seldom taken advantage of for diagnostic purposes due to the lack of appropriate gas-sensing technologies. In this work, we apply computational methods to design mass-based gas sensor arrays, often called electronic noses, that are optimized for detecting kidney disease from breath, for which ammonia is a known biomarker. We define combined linear adsorption coefficients (CLACs), which are closely related to Henry's law coefficients, for calculating gas adsorption in metal-organic frameworks (MOFs) of gases commonly found in breath (i.e., carbon dioxide, argon, and ammonia). These CLACs were determined computationally using classical atomistic molecular simulation techniques and subsequently used to design and evaluate gas sensor arrays. We also describe a novel numerical algorithm for determining the composition of a breath sample given a set of sensor outputs and a library of CLACs. After identifying an optimal array of five MOFs, we screened a set of 100 simplified computer-generated, water-free breath samples for kidney disease and were able to successfully quantify the amount of ammonia in all samples within the tolerances needed to classify them as either healthy or diseased, demonstrating the promise of such devices for disease detection applications.

Uranium (VI) Adsorbate Structures on Portlandite [Ca(OH)2] Type Surfaces Determined by Computational Modelling and X-ray Absorption Spectroscopy

Portlandite [Ca(OH)2] is a potentially dominant solid phase in the high pH fluids expected within the cementitious engineered barriers of Geological Disposal Facilities (GDF). This study combined X-ray Absorption Spectroscopy with computational modelling in order to provide atomic-scale data which improves our understanding of how a critically important radionuclide (U) will be adsorbed onto this phase under conditions relevant to a GDF environment. Such data are fundamental for predicting radionuclide mass transfer. Surface coordination chemistry and speciation of uranium with portlandite [Ca(OH)2] under alkaline groundwater conditions (ca. pH 12) were determined by both in situ and ex situ grazing incidence extended X-ray absorption fine structure analysis (EXAFS) and by computational modelling at the atomic level. Free energies of sorption of aqueous uranyl hydroxides, [UO2(OH)n]2–n (n = 0–5) with the (001), (100) and (203) or (101) surfaces of portlandite are predicted from the potential of mean force using classical molecular umbrella sampling simulation methods and the structural interactions are further explored using fully periodic density functional theory computations. Although uranyl is predicted to only weakly adsorb to the (001) and (100) clean surfaces, there should be significantly stronger interactions with the (203/101) surface or at hydroxyl vacancies, both prevalent under groundwater conditions. The uranyl surface complex is typically found to include four equatorially coordinated hydroxyl ligands, forming an inner-sphere sorbate by direct interaction of a uranyl oxygen with surface calcium ions in both the (001) and (203/101) cases. In contrast, on the (100) surface, uranyl is sorbed with its axis more parallel to the surface plane. The EXAFS data are largely consistent with a surface structural layer or film similar to calcium uranate, but also show distinct uranyl characteristics, with the uranyl ion exhibiting the classic dioxygenyl oxygens at 1.8 Å and between four and five equatorial oxygen atoms at distances between 2.28 and 2.35 Å from the central U absorber. These experimental data are wholly consistent with the adsorbate configuration predicted by the computational models. These findings suggest that, under the strongly alkaline conditions of a cementitious backfill engineered barrier, there would be significant uptake of uranyl by portlandite to inhibit the mobility of U(VI) from the near field of a geological disposal facility.

Deep learning potential for superionic phase of Ag2S

Artificial neural networks are used for describing potential energy surface of β-Ag2S silver sulfide. It has allowed performing accurate and fast atomistic simulations for describing behavior of investigated system. We develop neural network potential for high temperature ionic conductor β-Ag2S using DeePMD approach. Reference ab initio dataset was generated using active learning technique implemented in DP-GEN package. Classical molecular simulations with developed neural network potential were performed. Partial radial distribution function for S-S pair and bond-angle distribution function for S-S-S triplet demonstrate crystalline behavior, while the same functions for Ag-Ag pair and Ag-Ag-Ag triplet demonstrate liquid-like behavior. Mean squared displacement of S atoms indicates absence of diffusion for sulfur atoms, while the same function for Ag atoms has linear form at large times that indicates presence of diffusion for this sort of atoms. Velocity autocorrelation functions for S atoms have oscillatory behavior, while for Ag atoms no oscillations are observed. Comparison of mean squared displacement for S atoms and diffusivity for Ag atoms is performed to other ab initio and classical simulations as well as experimental data and demonstrates good agreement in all the cases. Obtained by active learning technique dataset could be expanded to other Ag2S phases for describing Ag2S in wider range of temperatures. Thus accurate, productive, almost free of parameters and promising for future use model for β-Ag2S was created.

Equilibrium properties of warm dense deuterium calculated by the wave packet molecular dynamics and density functional theory method.

A joint simulation method based on the wave packet molecular dynamics and density functional theory (WPMD-DFT) is applied to study warm dense deuterium (nonideal deuterium plasmas). This method was developed recently as an extension of the wave packet molecular dynamics (WPMD) in which the equations of motion are solved simultaneously for classical ions and semiclassical electrons represented as Gaussian wave packets. Compared to the classical molecular dynamics and WPMD simulations, the method of WPMD-DFT provides a more accurate representation of quantum effects such as electron-ion coupling and electron degeneracy. It allows studying nonadiabatic dynamics of electrons and ions in equilibrium and nonequilibrium states while being more accurate and efficient at high densities than WPMD and classical molecular dynamics. In the paper, we discuss particular features of the method such as special boundary conditions and the procedure of isentrope calculation as well as the results obtained by WPMD-DFT for the shock-compressed deuterium. The compression isentrope and principal Hugoniot curves obtained by WPMD-DFT are compared with available experimental data and other simulation approaches to validate the method. It opens up a possibility of further application of the method to study nonequilibrium states and relaxation processes.

Local structure elucidation and properties prediction on KCl–CaCl2 molten salt: A deep potential molecular dynamics study

KCl–CaCl 2 molten salt has emerged as a potential candidate which can be used for heat transfer and thermal energy storage in the next concentrating solar power generation. In this work, deep potential molecular dynamics (DPMD) simulations, based on a many-body potential and interatomic forces generated by a deep neural network trained with the first-principles simulation results, were carried out to predict the local structure and thermophysical properties of KCl–CaCl 2 molten salt at 1100 K. It was found that the steric hindrance effect became more and more intense as the network structure forming and growing with the addition of CaCl 2 , but the increase of CaCl 2 made the coordination shell of Ca 2+ more dynamic and active, and the two reactions constantly compete. Afterwards, thermophysical properties like shear viscosity, heat capacity and thermal conductivity were calculated from DPMD simulations. DPMD simulations could balance the proper description of complex atomic interactions to overcome the challenge of missing potential parameters in classical molecular simulations and become more efficient than first-principles molecular dynamics simulations. Our work based on deep potentials development will provide a promising alternative way to explore more molten eutectic salts for the next concentrating solar power generation. • Deep potential molecular dynamics simulations were carried out to explore the KCl–CaCl 2 molten salt. • Cl − ions more likely to be associated with Ca 2+ ions than K + ions in the KCl–CaCl 2 molten salt. • For KCl–CaCl 2 molten salt, heat capacity decreases with the addition of the CaCl 2 , shear viscosity and thermal conductivity increase slightly with the addition of the CaCl 2 .

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.

Effect of interfacial structures on phonon transport across atomically precise Si/Al heterojunctions

Phonons are important carriers of energy and information in many cryogenic devices used for quantum information science and in fundamental physics experiments such as dark matter detectors. In these systems phonon behaviors can be dominated by interfaces and their atomic structures; hence, there is increasing demand for a more detailed understanding of interfacial phonon transport in relevant material systems. Previous studies have focused on understanding thermal transport over the entire phonon spectrum at and above room temperature. At ultralow temperatures, however, knowledge is missing regarding athermal phonon behavior due to the challenge in modeling the extreme conditions in microscale, heterogeneous cryogenic systems, as well as extracting single-phonon information from a large ensemble. In this paper, we delineate the effects of interfacial atomic structures on phonon transport using a combination of classical molecular dynamics (MD) and phonon wave-packet simulations, to illustrate the consistency and differences between the ensemble- and single-phonon dynamics. We consider three single-crystal Si surface reconstructions---$(1\ifmmode\times\else\texttimes\fi{}1), (\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ and $(7\ifmmode\times\else\texttimes\fi{}7)$---and model both experimentally observed $\mathrm{Si}(1\ifmmode\times\else\texttimes\fi{}1)/\mathrm{Al}$ interfaces and hypothesized $\mathrm{Si}(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$/Al and $\mathrm{Si}(7\ifmmode\times\else\texttimes\fi{}7)/\mathrm{Al}$ interfaces. The overall interfacial thermal conductance calculated from non-equilibrium MD shows that for the $\mathrm{Si}(1\ifmmode\times\else\texttimes\fi{}1)/\mathrm{Al}$ system, the presence of Al twin boundaries can hinder phonon transport and reduce thermal conductance by 2--12% relative to single-crystal Al; whereas the Si $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ and $(7\ifmmode\times\else\texttimes\fi{}7)$ reconstructions can enhance it by 6--19%. Normal mode decomposition reveals that both the increase and decrease in conductance are related to inelastic phonon scattering. Single-phonon wave-packet simulations predict phonon transport properties consistent with non-equilibrium MD, while further suggesting that phonon polarization conversion is significant even when elastic transmission dominates, and that the interfacial structures have anisotropic impacts on atomic vibrations along different lattice directions. Our findings suggest avenues for achieving selective phonon transport via controlling interfacial structures of materials using atomically precise fabrication techniques, and that the phonon wave-packet formalism is a potentially powerful method for developing a detailed understanding of non-equilibrium phenomena in the low-temperature limit.

Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses.

X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.

Multiscale study of thermal conductivity of boron nitride nanosheets/paraffin thermal energy storage materials

Dispersion of nanofillers into phase change materials is found to be useful for improving the thermal conductivity (TC) of materials. To achieve a high TC of composites, the geometry factors of nanofillers should be considered. In this paper, classic molecular dynamic simulations and theoretical analysis model based on the effective medium theory were adopted to investigate the effect mechanism of layer number and size of hexagonal boron nitride nanosheets (h-BN) on TC of h-BN/paraffin composites. Research results showed that TC of the encased h-BN is lower than that of the suspended one due to the suppression ofparaffin. Along with the rise of layer number, the phonon vibrational power of h-BN is partially recovered, which results in the increase of TC of h-BN and the decrease of interfacial thermal resistance of h-BN/paraffin. With the size of 5μm, the volume fraction of 5% andlayer number of 15, TC of h-BN/paraffin composites increases to 1.5 W/m·K by nearly 6 times compared with paraffin. To obtain a high TC of composites, layer number and lateral size of h-BN must be simultaneously increased. This finding is a guide for using multi-layer nanosheets as thermal conductive fillers in the field of enhanced heat transfer.

Shear deformations in crystalline alkali-silica reaction products at the molecular scale: anisotropy and role of specific ion effects

Alkali-silica reaction (ASR) products exhibit viscoelastic behavior. Creep of nanolayered adsorbing materials is associated with shear deformations at the molecular scale. Crystalline ASR products are layered silicates with potassium and/or sodium as a charge balance ion in the interlayer space. These products are formed only in small quantities, exhibit long-range disorder, and are often mixed with other phases present in hydrated cement systems. In this context, experimental assessment of these products is a challenge and atomistic simulations arise as a valuable alternative. In this work, the shear response of crystalline ASR products is studied using classical molecular simulations. Understanding shear deformations are important to fully characterize the behavior of ASR products and may constitute a first step towards the comprehension of the viscoelastic behavior of these products. Further, the charge balance cation affects the shear modulus, von Mises yield stress, and residual strain, showing that the chemistry plays a crucial role in the mechanical response of these layered materials.

High performance wave packet molecular dynamics with density functional exchange-correlation term for non-ideal plasma simulations

We report on development of the wave packet molecular dynamics (WPMD) with density functional theory (DFT) simulation technique that we proposed earlier for nonideal plasma and warm dense matter simulations. The method is based on the WPMD where the electron exchange-correlation effects are taken into account using the DFT approach. It is aimed at studying simultaneous dynamics of electrons and ions in equilibrium and non-equilibrium conditions for a wide range of temperatures and densities. Compared to classical molecular dynamics and WPMD simulations the method of WPMD-DFT provides more accurate representation of quantum effects such as electron–ion coupling and electron degeneracy. At this stage of the method development we pay a special attention to the performance issues such as acceleration with graphical processing units, the choice of an optimal simulation box size with respect to the boundary conditions, the use of an adaptive mesh for calculation of the exchange-correlation energy, and implementation of our algorithm in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The results for internal energy of equilibrium dense hydrogen plasma are presented for evaluation of the method.

Molecular Simulation of Electrode-Solution Interfaces.

Many key industrial processes, from electricity production, conversion, and storage to electrocatalysis or electrochemistry in general, rely on physical mechanisms occurring at the interface between a metallic electrode and an electrolyte solution, summarized by the concept of an electric double layer, with the accumulation/depletion of electrons on the metal side and of ions on the liquid side. While electrostatic interactions play an essential role in the structure, thermodynamics, dynamics, and reactivity of electrode-electrolyte interfaces, these properties also crucially depend on the nature of the ions and solvent, as well as that of the metal itself. Such interfaces pose many challenges for modeling because they are a place where quantum chemistry meets statistical physics. In the present review, we explore the recent advances in the description and understanding of electrode-electrolyte interfaces with classical molecular simulations, with a focus on planar interfaces and solvent-based liquids, from pure solvent to water-in-salt electrolytes.