Showing papers on "Molecular dynamics published in 2016"

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Abstract: Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of s...

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

Abstract: The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.

Simulations of inorganic–bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

Abstract: Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

Abstract: Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized ...

Neural network molecular dynamics simulations of solid–liquid interfaces: water at low-index copper surfaces

Abstract: Solid–liquid interfaces have received considerable attention in recent years due to their central role in many technologically relevant fields like electrochemistry, heterogeneous catalysis and corrosion. As the chemical processes in these examples take place primarily at the interface, understanding the structural and dynamical properties of the interfacial water molecules is of vital importance. Here, we use a first-principles quality high-dimensional neural network potential built from dispersion-corrected density functional theory data in molecular dynamics simulations to investigate water–copper interfaces as a prototypical case. After performing convergence tests concerning the required supercell size and water film diameter, we investigate numerous properties of the interfacial water molecules at the low-index copper (111), (100) and (110) surfaces. These include density profiles, hydrogen bond properties, lateral mean squared displacements and residence times of the water molecules at the surface. We find that in general the copper–water interaction is rather weak with the strongest interactions observed at the Cu(110) surface, followed by the Cu(100) and Cu(111) surfaces. The distribution of the water molecules in the first hydration layer exhibits a double peak structure. In all cases, the molecules closest to the surface are predominantly allocated on top of the metal sites and are aligned nearly parallel with the oxygen pointing slightly to the surface. The more distant molecules in the first hydration layer at the Cu(111) and Cu(100) surfaces are mainly found in between the top sites, whereas at the Cu(110) surface most of these water molecules are found above the trenches of the close packed atom rows at the surface.

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

Abstract: We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agree...

Structural Transformation of MXene (V2C, Cr2C, and Ta2C) with O Groups during Lithiation: A First-Principles Investigation.

Abstract: For high capacities and extremely fast charging rates, two-dimensional (2D) crystals exhibit a significant promising application on lithium-ion batteries. With density functional calculations, this paper systematically investigated the Li storage properties of eight 2D M2CO2 (M = V, Cr, Ta, Sc, Ti, Zr, Nb, and Hf), which are the recently synthesized transition-metal carbides (called MXenes) with O groups. According to whether the structural transformation occurs or not during the adsorption of the first Li layer, the adsorption of Li can be grouped into two types: V-type (V2CO2, Cr2CO2, and Ta2CO2) and Sc-type (Sc2CO2, Ti2CO2, Zr2CO2, Nb2CO2, and Hf2CO2). The structural transformation behaviors of V-type are reversible during lithiation/delithiation and are confirmed by ab initio molecular dynamic simulations. Except for Nb-MXene, the V-type prefers the sandwich H2H1T-M2CO2Li4 structure and the Sc-type prefers the TH1H2-M2CO2Li4 structure during the adsorption of the second Li layer. The H2H1T-M2CO2Li4 st...

Quantum and classical dynamics of reactive scattering of H2 from metal surfaces.

Abstract: We review the state-of-the art in dynamics calculations on the reactive scattering of H2 from metal surfaces, which is an important model system of an elementary reaction that is relevant to heterogeneous catalysis. In many applications, quantum dynamics and classical trajectory calculations are performed within the Born–Oppenheimer static surface model. However, ab initio molecular dynamics (AIMD) is finding increased use in applications aimed at modeling the effect of surface phonons on the dynamics. Molecular dynamics with electronic friction has been used to model the effect of electron–hole pair excitation. Most applications are still based on potential energy surfaces (PESs) or forces computed with density functional theory (DFT), using a density functional within the generalized gradient approximation to the exchange–correlation energy. A new development is the use of a semi-empirical version of DFT (the specific reaction parameter (SRP) approach to DFT). We also discuss the accurate methods that have become available to represent electronic structure data for the molecule–surface interaction in global PESs. It has now become possible to describe highly activated H2 + metal surface reactions with chemical accuracy using the SRP-DFT approach, as has been shown for H2 + Cu(111) and Cu(100). However, chemical accuracy with SRP-DFT has yet to be demonstrated for weakly activated systems like H2 + Ru(0001) and non-activated systems like H2 + Pd(111), for which SRP DFs are not yet available. There is now considerable evidence that electron–hole pair (ehp) excitation does not need to be modeled to achieve the (chemically) accurate calculation of dissociative chemisorption and scattering probabilities. Dynamics calculations show that phonons can be safely neglected in the chemically accurate calculation of sticking probabilities on cold metal surfaces for activated systems, and in the calculation of a number of other observables. However, there is now sufficient evidence to suggest that the decision on whether or not to neglect phonons should be taken with care, with appropriate consideration of the observable to be computed and of the relevant surface temperature. AIMD calculations have provided valuable insights into the mechanisms that are operative in the dissociative adsorption and absorption of hydrogen on/in precovered metal surfaces. Classical and quantum dynamics calculations have shown that the reaction probability of H2 on Pt surfaces consisting of (100) steps and (111) terraces can to a very good approximation be computed as a weighted average of the reactivities on the steps and terraces. Progress obtained with dynamics calculations on the scattering of H2 from alloys and from simple low index metal surfaces is also reported. Insights that may be obtained on the reactivity of a metal surface from the prominent presence of out-of-plane diffraction or, conversely, the complete absence of diffraction, are discussed. A new field has been opened up by experiments on H2 scattering from surfaces at fast grazing incidence, and we discuss new predictions regarding diffraction and dissociative scattering of H2 under such conditions.

Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

Abstract: Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields, which have been developed and validated using relatively short simulations of small molecules, become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge–charge interactions. Here, we report a systematic atom pair-specific refinement of Lennard-Jones parameters (NBFIX) describing amine–carboxylate and amine–phosphate interactions, which bring MD simulations of basic peptide-mediated nucleic acid assemblies and lipid bilayer membranes into better agreement with experimental data. As our refinement does not affect the existing parametrization of bonded interactions or alter the solvation free energies, it improves the realism of an MD simulation without introducing additional artifacts.

5-Arylpyrimido-[4,5-b]quinoline-diones as new and sustainable corrosion inhibitors for mild steel in 1 M HCl: a combined experimental and theoretical approach

Abstract: The inhibition of mild steel corrosion in 1 M HCl by four 5-arylpyrimido-[4,5-b]quinoline-diones (APQDs), namely 5-(4-nitrophenyl)-5,10-dihydropyrimido [4,5-b]quinoline-2,4(1H,3H)-dione (APQD-1), 5-phenyl-5,10-dihydropyrimido[4,5-b]quinoline-2,4(1H,3H)-dione (APQD-2), 5-(4-hydroxyphenyl)-5,10-dihydropyrimido[4,5-b]quinoline-2,4(1H,3H)-dione (APQD-3) and 5-(2,4-dihydroxyphenyl)-5,10-dihydropyrimido[4,5-b]quinoline-2,4(1H,3H)-dione (APQD-4) has been investigated using weight loss, electrochemical, surface, and quantum chemical calculations and molecular dynamics simulation methods. The results showed that the inhibition efficiency (η%) increased with increasing concentration of the inhibitors. Among the studied compounds, APQD-4 exhibited the highest inhibition efficiency of 98.30% at 20 mg l−1 concentration. The studied compounds effectively retarded the corrosion of mild steel in 1 M HCl by adsorbing onto the steel surface, and the adsorption data conformed to the Langmuir adsorption isotherm. The results of potentiodynamic polarization measurements revealed that the studied compounds are cathodic-type inhibitors. Scanning electron microscopy (SEM) study confirmed the formation of adsorbed films of the inhibitor molecules on the steel surface. Quantum chemical calculations and molecular dynamics simulations were undertaken to corroborate experimental findings and provide adequate insight into the corrosion inhibition mechanisms and adsorption characteristics of the studied compounds.

A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers

Abstract: Atomistic molecular dynamics simulations have become an important source of information for the structure and dynamics of biomembranes at molecular detail difficult to access in experiments. A number of force fields for lipid membrane simulations have been derived in the past; the choice of the most suitable force field is, however, frequently hampered by the availability of parameters for specific lipids. Additionally, the comparison of different quantities among force fields is often aggravated by varying simulation parameters. Here, we compare four atomistic lipid force fields, namely, the united-atom GROMOS54a7 and the all-atom force fields CHARMM36, Slipids, and Lipid14, for a broad range of structural and dynamical properties of saturated and monounsaturated phosphatidylcholine bilayers (DMPC and POPC) as well as for monounsaturated phosphatidylethanolamine bilayers (POPE). Additionally, the ability of the different force fields to describe the gel–liquid crystalline phase transition is compared and...

ZIF-67 Framework: A Promising New Candidate for Propylene/Propane Separation. Experimental Data and Molecular Simulations

Abstract: ZIF-67, a Co-substituted ZIF-8 structure, is investigated as a candidate for the industrially highly demanding propylene/propane separation, with the use of computational techniques for the first time. A new force field for the ZIF-67 framework based on density functional theory calculations is reported along with a recently developed force field for ZIF-8. The new force field is validated through comparison with structural data for ZIF-67 from the literature. Molecular dynamics simulations are reported for ZIF-67, showing a dramatic increase of propylene/propane corrected diffusivities ratio when compared to ZIF-8, implying a huge improvement in the separation of the mixture. The sieving mechanism of ZIF frameworks is investigated, and the results yield a dependency of the swelling motion of the gates from the bonding of the metal atom with its surrounding atoms. The presence of Co in the modified framework results in a tighter structure with a smaller oscillation of the gate opening, which leads to a na...

CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State.

Abstract: The accuracy of molecular dynamics simulations depends on the underlying force field, defined by the form and parametrization of the interparticle potential functions and the water model. The treatment of the solvent is crucial in molecular dynamics force fields, as hydrophobic interactions and hydrogen bonding are important molecular forces. The widely used CHARMM force field was originally parametrized using a modified version of the TIP3P water model (mTIP3P), including Lennard-Jones interactions between hydrogens and oxygens. The latest version, CHARMM36, was optimized using the standard TIP3P water model (sTIP3P) for proteins, while mTIP3P is still being used for lipids. Our replica exchange molecular dynamics simulations on dynamic peptides show that the CHARMM36 force field with mTIP3P water yields less realistic folding than with sTIP3P water. Analysis of the dimensions and hydrogen bonding of the unfolded state reveals that the peptides are more solvated and extended in mTIP3P, due to a higher solvation energy of the peptide in this water model. We recommend using CHARMM36 with sTIP3P when simulating peptides, folded proteins, and natively unfolded proteins, but combinations of proteins with lipids would require a reparametrization to make their water models compatible.

Molecular dynamic simulation of Copper and Platinum nanoparticles Poiseuille flow in a nanochannels

Abstract: In this paper, simulation of Poiseuille flow within nanochannel containing Copper and Platinum particles has been performed using molecular dynamic (MD). In this simulation LAMMPS code is used to simulate three-dimensional Poiseuille flow. The atomic interaction is governed by the modified Lennard–Jones potential. To study the wall effects on the surface tension and density profile, we placed two solid walls, one at the bottom boundary and the other at the top boundary. For solid–liquid interactions, the modified Lennard–Jones potential function was used. Velocity profiles and distribution of temperature and density have been obtained, and agglutination of nanoparticles has been discussed. It has also shown that with more particles, less time is required for the particles to fuse or agglutinate. Also, we can conclude that the agglutination time in nanochannel with Copper particles is faster that in Platinum nanoparticles. Finally, it is demonstrated that using nanoparticles raises thermal conduction in the channel.

Development of an interatomic potential for the simulation of defects, plasticity, and phase transformations in titanium

Abstract: New interatomic potentials describing defects, plasticity, and high temperature phase transitions for Ti are presented. Fitting the martensitic hcp-bcc phase transformation temperature requires an efficient and accurate method to determine it. We apply a molecular dynamics method based on determination of the melting temperature of competing solid phases, and Gibbs-Helmholtz integration, and a lattice-switch Monte Carlo method: these agree on the hcp-bcc transformation temperatures to within 2 K. We were able to develop embedded atom potentials which give a good fit to either low or high temperature data, but not both. The first developed potential (Ti1) reproduces the hcp-bcc transformation and melting temperatures and is suitable for the simulation of phase transitions and bcc Ti. Two other potentials (Ti2 and Ti3) correctly describe defect properties and can be used to simulate plasticity or radiation damage in hcp Ti. The fact that a single embedded atom method potential cannot describe both low and high temperature phases may be attributed to neglect of electronic degrees of freedom, notably bcc has a much higher electronic entropy. A temperature-dependent potential obtained from the combination of potentials Ti1 and Ti2 may be used to simulate Ti properties at any temperature.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

Abstract: Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by comp...

Dynamical Disorder in the DNA Hydration Shell.

Abstract: The reorientation and hydrogen-bond dynamics of water molecules within the hydration shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are investigated via molecular dynamics simulations and an analytic jump model, which provide valuable new molecular level insights into these dynamics. Different sources of heterogeneity in the hydration shell dynamics are determined. First, a pronounced spatial heterogeneity is found at the DNA interface and explained via the jump model by the diversity in local DNA interfacial topographies and DNA–water H-bond interactions. While most of the hydration shell is moderately retarded with respect to the bulk, some water molecules confined in the narrow minor groove exhibit very slow dynamics. An additional source of heterogeneity is found to be caused by the DNA conformational fluctuations, which modulate the water dynamics. The groove widening aids the approach of, and the jump to, a new water H-bond partner. This temporal heterogenei...

Atomistic-Scale Analysis of Carbon Coating and Its Effect on the Oxidation of Aluminum Nanoparticles by ReaxFF-Molecular Dynamics Simulations

Abstract: We developed a ReaxFF reactive force field for Al/C interactions to investigate carbon coating and its effect on the oxidation of aluminum nanoparticles (ANPs). The ReaxFF parameters were optimized against quantum mechanics-based (QM-based) training sets and validated with additional QM data and data from experimental literature. ReaxFF-molecular dynamics (MD) simulations were performed to determine whether this force field description was suitable to model the surface deposition and oxidation on complex materials (i.e., carbon-coated ANPs). Our results show that the ReaxFF description correctly reproduced the Al/C interaction energies obtained from the QM calculations and qualitatively captured the processes of the hydrocarbons’ binding and their subsequent reactions on the bare ANPs. The results of the MD simulations indicate that a carbon coating layer was formed on the surface of the bare ANPs, while H atoms were transferred from the hydrocarbons to the available Al binding sites typically without bre...

Thermal transport properties of MoS2 and MoSe2 monolayers

Abstract: The isolation of single- to few-layer transition metal dichalcogenides opens new directions in the application of two-dimensional materials to nanoelectronics. The characterization of thermal transport in these new low-dimensional materials is needed for their efficient implementation, either for general overheating issues or specific applications in thermoelectric devices. In this study, the lattice thermal conductivities of single-layer MoS2 and MoSe2 are evaluated using classical molecular dynamics methods. The interactions between atoms are defined by Stillinger-Weber-type empirical potentials that are developed to represent the structural, mechanical, and vibrational properties of the given materials. In the parameterization of the potentials, a stochastic optimization algorithm, namely particle swarm optimization, is utilized. The final parameter sets produce quite consistent results with density functional theory in terms of lattice parameters, bond distances, elastic constants, and vibrational properties of both single-layer MoS2 and MoSe2. The predicted thermal properties of both materials are in very good agreement with earlier first-principles calculations. The discrepancies between the calculations and experimental measurements are most probably caused by the pristine nature of the structures in our simulations.

Development of an Interatomic Potential for the Simulation of Defects, Plasticity and Phase Transformations in Titanium

Abstract: New interatomic potentials describing defects, plasticity and high temperature phase transitions for Ti are presented. Fitting the martensitic hcp-bcc phase transformation temperature requires an efficient and accurate method to determine it. We apply a molecular dynamics (MD) method based on determination of the melting temperature of competing solid phases, and Gibbs-Helmholtz integration, and a lattice-switch Monte Carlo method (LSMC): these agree on the hcp-bcc transformation temperatures to within 2 K. We were able to develop embedded atom potentials which give a good fit to either low or high temperature data, but not both. The first developed potential (Ti1) reproduces the hcp-bcc transformation and melting temperatures and is suitable for the simulation of phase transitions and bcc Ti. Two other potentials (Ti2 and Ti3) correctly describe defect properties, and can be used to simulate plasticity or radiation damage in hcp Ti. The fact that a single EAM potential cannot describe both low and high temperature phases may be attributed to neglect of electronic degrees of freedom, notably bcc has a much higher electronic entropy. A temperature-dependent potential obtained from the combination of potentials Ti1 and Ti2 may be used to simulate Ti properties at any temperature.

Revisiting silica with ReaxFF: Towards improved predictions of glass structure and properties via reactive molecular dynamics

Abstract: Reactive potentials, like ReaxFF, are becoming increasingly popular and are expected to bridge the gap between ab initio and classical molecular dynamics simulations. Yet, their applicability to glassy materials remains poorly understood. Here, by simulating a silica glass with both ReaxFF and a conventional classical potential, we critically assess the ability of reactive potentials to offer an accuracy equivalent or superior to that of classical potentials in describing the structure and properties of glassy silicates. We show that ReaxFF produces a realistic disordered structure, both at the short- and medium-range order. Interestingly, ReaxFF offers significant improvements with respect to classical potentials in describing the elastic properties of the glass and the dynamics of the supercooled liquid. Overall, while retaining a reasonable computational cost, ReaxFF appears as a promising potential to model the structure and properties silicate glasses and, in contrast to classical potential, could be used to assess their surface reactivity.

Wettability and friction of water on a MoS2 nanosheet

Abstract: The molybdenum disulfide (MoS2) nanosheet is a promising two-dimensional (2D) material and has recently been used in biological sensing. While the electronic structure of 2D MoS2 sheet has been actively studied, the role of its atomic structure and thus the interfacial interactions with bio-fluids are still elusive. Using Molecular dynamics simulations, we developed MoS2 force field parameters to reproduce the experimentally determined water contact angle of the MoS2 nanosheet and then predicted the slip-length of water that has not been measured in experiment yet. Simulation results suggest that the MoS2 nanosheet is a hydrophobic and low-friction surface, despite its seemingly significant charges of surface atoms and relatively strong strength of van der Waals potentials. We expect that the developed force fields for depicting surface atoms of MoS2 will facilitate future research in understanding biomolecule-MoS2 interactions in MoS2-based biosensors.

Microscopic theory and quantum simulation of atomic heat transport

Abstract: Quantum simulation methods based on electronic-structure theory are deemed unfit to cope with atomic heat transport within the Green–Kubo formalism, because quantum-mechanical energy densities and currents are inherently ill-defined at the atomic scale. We show that, although this difficulty would also affect classical simulations, thermal conductivity is indeed insensitive to such ill-definedness by virtue of a kind of gauge invariance resulting from energy extensivity and conservation. On the basis of these findings, we derive an expression for the adiabatic energy flux from density-functional theory, which allows heat transport to be simulated using ab initio equilibrium molecular dynamics. Our methodology is demonstrated by comparing its predictions to those of classical equilibrium and ab initio non-equilibrium (Muller–Plathe) simulations for a liquid-argon model, and by applying it to heavy water at ambient conditions. Heat transport is well described by the Green–Kubo formalism. Now, the formalism is combined with density-functional theory, enabling simulations of thermal conduction in systems that cannot be adequately modelled by classical interatomic potentials.

Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering.

Abstract: Modeled ions, described by nonpolarizable force fields, can suffer from unphysical ion pairing and clustering in aqueous solutions well below their solubility limit. The electronic continuum correction takes electronic polarization effects of the solvent into account in an effective way by scaling the charges on the ions, resulting in a much better description of the ionic behavior. Here, we present parameters for the sodium ion consistent with this effective polarizability approach and in agreement with experimental data from neutron scattering, which could be used for simulations of complex aqueous systems where polarization effects are important.