NVT Molecular Dynamics Simulations Research Articles

Domain formation in model lipid–cholesterol liquid-crystalline aggregation

ABSTRACT To understand the mechanism of cell-membrane compartmentalisation, we studied coarse-grained model systems consisting of lipid and cholesterol molecules. Cholesterol plays crucial role in lateral phase segregation in the bilayered lipid membrane to form cholesterol-rich liquid-ordered domains. In this NVT Molecular Dynamics simulation study, we have investigated the role of cholesterol in lipid bilayer destabilisation and domain formation. This study also reveals that the strength of cholesterol interaction is an important factor behind the phase segregation to form cholesterol-rich domains, whereas the relative dipolar strength of lipid and cholesterol molecules along with the concentration of cholesterol controls the formation of multi-bilayered stack.

Carbon ene-yne working in oxygenator: A theoretical study

Traditional hollow-fiber membranes (HFM) in the oxygenator are in short supply due to their complicated manufacturing process, high price, and tight production capacity. To address these challenges, herein we designed a simplified molecular dynamics (MD) model that mimics the working procedure of HFM to explore whether carbon ene-yne (CEY) and other two carbon-based 2-dimensional (2D) materials: γ-graphyne and graphdiyne (GDY) could be used in an oxygenator. With the aid of the Density Functional based Tight Binding (DFTB) method, Density Functional Theory (DFT), Adaptive Steered Molecular Dynamics (ASMD), and NVT molecular dynamics (MD) simulations, the penetration barriers of the O2, CO2, and H2O molecules through these three 2D membranes are estimated. Furthermore, their permeance under various differential pressures are also discussed. According to our simulations, the CEY membrane can provide a much better performance for O2 and CO2 exchange than the most commonly used HFM material. CEY should be a promising candidate as O2 and CO2 exchange membrane working in the oxygenator.

Molecular dynamics and DFT study of 38-atom coinage metal clusters

The thermal behavior of 38-atom mono-, bi-, and trimetallic clusters consisting of Cu, Ag, and Au atoms, is analyzed employing molecular dynamics simulations and DFT calculations for selected cluster compositions. Low-energy structures were singled out to perform NVT molecular dynamics simulations at several temperatures, using the Andersen thermostat for temperature control. The caloric curve is used to estimate the melting temperature and the specific heat. The pair distribution function g(r) of the solid and liquid-phase clusters is examined at different temperatures. When comparing the estimated melting points (Tm) among the monatomic clusters, the order becomes TmCu38>TmAg38>TmAu38. For bimetallic clusters, an increase of Tm is observed for Cu-Au compared to their monatomic counterparts, while the opposite occurs for Cu-Ag clusters. For trimetallic clusters, two low-energy isomers of the Cu36Ag1Au1 cluster are investigated. In this case, Tm is estimated to be 475 K, for the two isomers with the lowest-energy and second-to-lowest energy, respectively. For all the clusters studied, the pair distribution function g(r) shows that the first peak position is not shifted as an effect of temperature and its maximum value varies with composition, while the second peak essentially vanishes upon melting. The common-neighbor analysis (CNA) technique is used to analyze the local structural changes for the trimetallic clusters, again demonstrating a clear structural change upon melting. The HOMO-LUMO energy gap indicates that the trimetallic isomers' behavior is metallic, while the average binding energy show these clusters' energetic stability to be similar.

Origin and structure of liquid crystalline Blue Phase III

We report here an off-lattice NVT molecular dynamics simulation study of a system of polar chiral ellipsoidal molecules, which spontaneously exhibits Blue Phase III (BPIII), considering coarse-grained attractive-repulsive pair interaction appropriate for anisotropic liquid crystal mesogens. We have observed that suitable selection of chiral and dipolar strengths not only gives rise to thermodynamically stable BPIII but novel Smectic and Bilayered BPIII as well. Further, we have demonstrated that the occurrence of BPIII and its layered counterparts depend crucially on molecular elongation.

Molecular dynamics simulations to study the interaction between carbon nanotube and calmodulin protein

Carbon nanotubes are important from the point of view of their vast applications in fields such as electronics, sensors, drug delivery, air & water filtration and catalyst supports. In this work we study the interaction between a single walled carbon nanotube and calmodulin protein from the point of view of their application in drug delivery. The interaction between the two entities viz., carbon nanotube & calmodulin protein is studied at different temperatures to monitor the dynamics in detail. We performed NVT molecular dynamics (MD) simulation for 100 ns at different temperatures such as 300 K, 400 K, 500 K & constant pressure 1 atm. The open source codes NAMD and VMD are used throughout this study. The CNT and the protein are not observed to show any significant interaction at 300 K and 400 K, except minor modification in the protein structure is observed at 400 K as the two lobes are observed to come close to each other. On the other hand, at 500 K some very interesting dynamics is observed at the end of the simulation. The protein is observed to wrap around the carbon nanotube at this temperature. These interesting dynamics at different temperatures can be due to the inherent property of calmodulin protein and increase in Van Der Waals forces in protein and CNT at higher temperature.

Classical and path-integral molecular-dynamics study on liquid water and ice melting using non-empirical TTM2.1-F model

The TTMF2.1-F model is a non-empirical intermolecular water potential parametrised from ab-initio calculations of the water dimer with a complete basis set limit including dispersion correction from second-order Moller-Plesset perturbation theory. In this work, using two-phase ice-water NVT molecular-dynamics (MD) simulations, we found the ice melting temperature using the TTM2.1-F potential is close to 273 K when the nuclear quantum effects (NQEs) were included using path-integral centroid MD. Detailed analysis of the radial distribution functions, angle distribution functions, and associated joint probability for both liquid water and the two-phase cases showed that the melting-point-temperature drop when using path-integral simulation is due to the weakening of hydrogen bonds vis-à-vis classically-propagated MD.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics.

Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.

Orbital-free density functional theory study of amorphous Li–Si alloys and introduction of a simple density decomposition formalism

We propose a simple density decomposition formalism within orbital-free (OF) density functional theory (DFT) based on the Wang-Govind-Carter-decomposition (WGCD) kinetic energy density functional (KEDF). The resulting simple-WGCD (sWGCD) KEDF provides efficient density optimization, full cell relaxation, reasonable bulk properties for various materials compared to both the original OFDFT-WGCD and the Kohn-Sham (KS) DFT values, and has various numerical benefits including more stable convergence and lower computational cost (twice as fast as the WGCD KEDF). We also study amorphous (a-) Li–Si alloys with KSDFT and OFDFT using the Huang-Carter (HC), WGCD, and sWGCD KEDFs. The a-Li–Si alloy samples are prepared with the anneal-and-quench method using NVT molecular dynamics simulations. We report structural properties, equilibrium volumes, bulk moduli, and alloy formation energies for each a-alloy. The HC, WGCD, and sWGCD KEDFs within OFDFT all predict accurate equilibrium volumes compared against KSDFT benchmarks. The HC KEDF bulk moduli agree with KSDFT benchmarks whereas the WGCD/sWGCD KEDFs generally overestimate the bulk moduli, especially for alloys with low Li concentrations. All three KEDFs show limited ability to predict alloy formation energies, which indicates the lack of transferability of these KEDFs among such systems and motivates future developments in OFDFT and KEDF formalisms.

NVT 分子動力学シミュレーションを用いたメタンハイドレート/水/メタン系における三相平衡点の解析

NVT 分子動力学シミュレーションを用いたメタンハイドレート/水/メタン系における三相平衡点の解析

Critical Analysis of the Accuracy of Models Predicting or Extracting Liquid Structure Information

This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.

Study on adsorption and desorption of urea in lignosulfonate with molecular simulations

The adsorption and desorption behavior of urea molecules in lignosulfonate has been studied through molecular simulation methods in this work. Firstly, the conformations of urea clusters around two small molecular models: methanesulfonic acid anion and methanol were optimized by ab initio calculations. Calculation results showed that through H-bonds, the number of urea molecules adsorbed around the sulfonic group was more than that of urea molecules adsorbed around the hydroxyl group. Secondly, a series of binary systems which were composed of the urea molecules and the lignosulfonate with the different contents of sulfonic groups were built. We calculated the diffusion constants of urea molecules from NVT molecular dynamics (MD) simulations for the built lignosulfonate–urea systems at 298K. Calculation results suggested that the interaction between the sulfonic groups and the urea molecules was stronger than that between the hydroxyl groups and the urea molecules in the binary composite systems. Moreover, a series of NVT MD simulations were also performed for the ternary systems composed of the lignosulfonate, the urea and the water molecules, which was to learn how the water affect the diffusivity of urea in the ternary systems. Simulation results obtained can match well with the results of ab initio calculations and experimental observations.

Reinterpretation of the bond-valence model with bond-order formalism: An improved bond-valence-based interatomic potential for PbTiO3

We present a modified bond-valence model of PbTiO${}_{3}$ based on the principles of bond-valence and bond-valence vector conservation. The relationship between the bond-valence model and the bond-order potential is derived analytically in the framework of a tight-binding model. An energy term, bond-valence vector energy, is introduced into the atomistic model and the potential parameters are reoptimized. This model potential can be applied both to canonical-ensemble (NVT) and isobaric-isothermal ensemble (NPT) molecular dynamics (MD) simulations. This model reproduces the experimental phase transition in NVT MD simulations and also exhibits the experimental sequence of temperature-driven and pressure-driven phase transitions in NPT simulations. We expect that this improved bond-valence model can be applied to a broad range of inorganic materials.

Aromatic Polyamides Density from Molecular Dynamics Simulation

AbstractMolecular dynamics simulations have been performed on seven aromatic polyamides to understand the structure‐property relationships on their densities. The aromatic polyamides studied in this work are based on poly(hexafluoroisopropylidene) isophthalamide, HFAISO. The aim of this research is to investigate the effect of the side groups attached to the diacid monomer on the density of the aromatic polyamides. Densities were obtained via NVT and NPT molecular dynamics simulation using the COMPASS forcefield. Reliability and accuracy of the simulations were compared with the experimental density data from HFAISO and HFATERT aromatic polyamides, which are in good agreement.

Molecular statics and molecular dynamics simulations of the critical stress for motion of a/3 [formula omitted] screw dislocations in α-Ti at low temperatures using a modified embedded atom method potential

Molecular statics and molecular dynamics, and constant temperature, constant volume (NVT) simulations, were performed to determine the core structure and critical stress for motion of a/3〈112¯0〉 screw dislocations in α-Ti at temperatures ranging from 0 to 50K using a modified embedded atom method (MEAM) potential. Five different core structures were obtained for the a/3〈112¯0〉 screw dislocations in α-Ti, one completely spread on the prism plane, three others partially spread on the prism plane and partially spread on the pyramidal and basal planes, and one with predominantly Shockley partial splitting on the basal plane. The core completely spread on the prism plane is found to be the lowest energy structure. The Peierls stress for the minimum energy structure completely spread on the prism plane at 0K is found to be a high value of 6.875×10−3μ, where μ is the shear modulus and is independent of the orientation of the applied stress. It is shown that this high Peierls stress at 0K is a consequence of the angular interactions in the MEAM potential. The kink-pair formation energy at zero applied stress is found to be low and equal to 0.16eV. NVT molecular dynamics simulations show that the minimum stress required to move the screw dislocations by kink-pair formation at temperatures ranging from 5 to 50K is significantly lower than the 0K Peierls stress value. A classical phenomenological kink-pair model is fitted to the molecular dynamics data and used to correct for the significantly lower strain rate of deformation present in experiments as compared to molecular dynamics simulations. The corrected simulation data are in reasonable agreement with low-temperature experimental observations of yield stress in single-crystal α-Ti oriented for a/3〈112¯0〉 prism slip. The developed kink-pair model for prism slip in α-Ti will be useful in higher length scale crystal plasticity models for the deformation behavior of α-Ti.

Solvation free energies and hydration structure of N-methyl-p-nitroaniline

Solvation Gibbs energies of N-methyl-p-nitroaniline (MNA) in water and 1-octanol are calculated using the expanded ensemble molecular dynamics method with a force field taken from the literature. The accuracy of the free energy calculations is verified with the experimental Gibbs free energy data and found to reproduce the experimental 1-octanol∕water partition coefficient to within ±0.1 in log unit. To investigate the hydration structure around N-methyl-p-nitroaniline, an independent NVT molecular dynamics simulation was performed at ambient conditions. The local organization of water molecules around the solute MNA molecule was investigated using the radial distribution function (RDF), the coordination number, and the extent of hydrogen bonding. The spatial distribution functions (SDFs) show that the water molecules are distributed above and below the nitrogen atoms parallel to the plane of aromatic ring for both the methylamino and nitro functional groups. It is found that these groups have a significant effect on the hydration of MNA with water molecules forming two weak hydrogen bonds with both the methylamino and nitro groups. The hydration structures around the functional groups in MNA in water are different from those that have been found for methylamine, nitrobenzene, and benzene in aqueous solutions, and these differences together with weak hydrogen bonds explain the lower solubility of MNA in water. The RDFs together with SDFs provide a tool for the understanding the hydration of MNA (and other molecules) and therefore their solubility.

Theoretical Study of the Competition between Intramolecular Hydrogen Bonds and Solvation in the Cys-Asn-Ser Tripeptide

A study of the competition between intra- and intermolecular hydrogen bonds and its influence on the stability of the Cys-Asn-Ser tripeptide in aqueous solution was performed by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a DFT-B3LYP/6-311+G(d) quantum treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In gas phase, the most stable structure adopts a C5 conformation. Somewhat higher in energy are found the PP(II) and C7eq structures. In solution, the stability order of the different conformers is reversed: the PP(II) structure becomes the most stable, and the C5 structure is strongly destabilized. The conformational equilibrium is shifted toward conformations in which the intramolecular hydrogen bonds (IHB) have been substituted with intermolecular hydrogen bonds with the water molecules. The solvent stabilizes extended structures without IHBs that are not stable in vacuum. The effect of the protonation state on the conformational equilibrium was also analyzed.

Computer Simulation Study of Model Nafion Membrane in Water/Methanol Solvent

Using NPT and NVT molecular dynamics simulation techniques, we have simulated an atomistic model of solvated Nafion in the lithium salt form, with the following three main objectives: (i) to obtain details on the local environment of the lithium cations and to assess the solvent effect on their binding, (ii) to investigate the translational and rotational motion of solvent molecules (water and methanol) absorbed in the polymer matrix, and (iii) to elucidate details of the ionic transport though the hydrophilic regions of the membrane and to study the ionic conductivity as a function of solvent (water/methanol) composition. A property which is of central importance for understanding the functional features of Nafion materials, including direct methanol fuel cells, is the ionic conductivity and methanol crossover. We have found that conductivity parameter is strongly dependent on the solvent composition and determined by the solvation effects and the spatial distribution of polar sulfonate groups in ion-conductive channels.

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

Molecular dynamics simulations of organolithium aggregates in solution are reported for the first time. We use a combined quantum/classical force field (the so-called QM/MM approach) and study ethyl-lithium aggregates in dimethyl ether (DME) solvent. The solutes are described at the Density Functional Theory level while solvent molecules are described using molecular mechanics. NVT Molecular Dynamics simulations at 200 K are carried out in the Born–Oppenheimer approximation. After equilibration, the production phase was run for 80 ps (monomer), 40 ps (dimer) and 26 ps (tetramer). The analysis of the results focuses on Li coordination as a function of aggregate size and we show that the total Li coordination number is always 4. No decoordination has been observed along the simulations. Fluctuations of the structures are predicted to be large in some cases and possible implications on reactivity are discussed.

A CASPT2//CASSCF Study of Vertical and Adiabatic Electron Transitions of Acrolein in Water Solution

The 1(n --> pi*) excited-state of acrolein in liquid water was studied theoretically by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a multireference perturbational CASPT2//CASSCF treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In this paper, we present two alternative methods for calculating solvent shift on adiabatic transitions and their performance is analyzed. In the first method, the free energy change during an adiabatic transition is calculated classically by using the free energy perturbation method. In the second method, it is calculated from the quantum values of the vertical absorption and emission electron transition energies. The 1(n --> pi*) excitation is accompanied by a charge flux from the oxygen to the carbon skeleton, this charge flux decreases the dipole moment of the excited-state with respect to the ground state value and, consequently, the solute-solvent interaction energy. This effect destabilizes the excited-state with respect to the ground state and produces a blue shift in the absorption and emission bands. For the emission process, there also exists an additional destabilization due to a partial desolvation of the excited state. The effect of the solvent electron polarization, the inclusion of the solute electron correlation, and the use of relaxed geometries in solution on the calculated solvent shift of the absorption and emission spectra are also analyzed.