Molecular Dynamics Study of Phonon Screening in Graphene

Phonon interaction with electrons or phonons or with structural defects result in a phonon mode conversion. The mode conversion is governed by the frequency wave-vector dispersion relation. The control over phonon mode or the screening of phonon in graphene is studied using the propagation of amplitude modulated phonon wave-packet. Control over phonon properties like frequency and velocity opens up several wave guiding, energy transport and thermo-electric applications of graphene. One way to achieve this control is with the introduction of nano-structured scattering in the phonon path. Atomistic model of thermal energy transport is developed which is applicable to devices consisting of source, channel and drain parts. Longitudinal acoustic phonon mode is excited from one end of the device. Molecular dynamics based time integration is adopted for the propagation of excited phonon to the other end of the device. The amount of energy transfer is estimated from the relative change of kinetic energy. Increase in the phonon frequency decreases the kinetic energy transmission linearly in the frequency band of interest. Further reduction in transmission is observed with the tuning of channel height of the device by increasing the boundary scattering. Phonon mode selective transmission control have potential application in thermal insulation or thermo-electric application or photo-thermal amplification.

A molecular dynamics study of ambient and high pressure phases of silica: Structure and enthalpy variation with molar volume

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, alpha-PbO2-type, and pyrite-type for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase. (C) 2014 AIP Publishing LLC.

Kinetics of phase separation in polymer mixtures: A molecular dynamics study

We present detailed results from a molecular dynamics (MD) simulation of phase-separation kinetics in polymer mixtures. Our MD simulations naturally incorporate hydrodynamic effects. We find that polymeric phase separation (with dynamically symmetric components) is in the same universality class as segregation of simple fluids: the degree of polymerization only slows down the segregation kinetics. For d = 2 polymeric fluids, the domain growth law is L(t) similar to t(phi) with phi showing a crossover from 1/3 -> 1/2 -> 2/3. For d = 3 polymeric fluids, we see the crossover phi = 1/3 -> 1. Our MD simulations do not yet access the inertial hydrodynamic regime (with L similar to t(2/3)) of phase separation in 3-d fluids. (C) 2014 AIP Publishing LLC.

Orientation, Size, and Temperature Dependent Ductile Brittle Transition in NiAl Nanowire under Tensile Loading - A Molecular Dynamics Study

In the present paper, thermo-mechanical response of B2-NiAl nanowire along the < 100 >, < 110 >, and < 111 > orientations has been studied using molecular dynamics simulations. Nanowire with cross-sectional dimensions of similar to 20x20 angstrom(2), similar to 25x25 angstrom(2), and similar to 30x30 angstrom(2) and temperature range of 10 K-900 K has been considered. A Combined effect of size, orientation, and temperature on the stress-strain behavior under uniaxial tensile loading has been presented. It has been observed that < 111 > oriented NiAl nanowire that is energetically most stable gives highest yield stress which further reduces with < 110 > and < 100 > orientations. A remarkable ductile brittle transition (DBT) with an increase in temperature has also been reported for all the orientations considered in the present study. The DBT observed for the nanowire has also been compared with the reported DBT of bulk B2-NiAl obtained from experiments. Alternate technique has also been proposed to increase the toughness of a given material especially at lower temperature regions, i.e. below DBT.

Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Estimating successive pK(a) values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pK(a), of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pK(a) values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pK(a), the acid dissociation constant. We show that the method predicts the pK(a) value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pK(a) values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient. (c) 2015 AIP Publishing LLC.

Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant-pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study

The de novo purine biosynthesis is one of the highly conserved pathways among all organisms and is essential for the cell viability. A clear understanding of the enzymes in this pathway would pave way for the development of antimicrobial and anticancer drugs. Phosphoribosylaminoimidazole-succinocar boxamide (SAICAR) synthetase is one of the enzymes in this pathway that catalyzes ATP dependent ligation of carboxyaminoimidazole ribotide (CAIR) with L-aspartate (ASP). Here, we describe eight crystal structures of this enzyme, in C222(1) and H3 space groups, bound to various substrates and substrate mimics from a hyperthermophilic archaea Pyrococcus horikoshii along with molecular dynamics simulations of the structures with substrates. Complexes exhibit minimal deviation from its apo structure. The CAIR binding site displays a preference for pyrimidine nucleotides. In the ADP.TMP-ASP complex, the ASP binds at a position equivalent to that found in Saccharomyces cerevisiae structure (PDB: 2CNU) and thus, clears the ambiguity regarding ASP's position. A possible mode for the inhibition of the enzyme by CTP and UTP, observed earlier in the yeast enzyme, is clearly illustrated in the structures bound to CMP and UMP. The ADP.Mg2+.PO4.CD/MP complex having a phosphate ion between the ATP and CAIR sites strengthens one of the two probable pathways (proposed in Escherichia coli study) of catalytic mechanism and suggests the possibility of a phosphorylation taking place before the ASP's attack on CAIR. Molecular dynamic simulations of this enzyme along with its substrates at 90 degrees C reveal the relative strengths of substrate binding, possible antagonism and the role of Mg2+ ions. (C) 2015 Elsevier Inc. All rights reserved.

Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man(9)GlcNAc(2)). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct beta sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Influence of a Counterion on the Ion Atmosphere of an Anion: A Molecular Dynamics Study of LiX and CsX (X = F-, Cl-, I-) in Methanol

We report molecular dynamics (MD) simulations to explore the influence of a counterion on the structure and dynamics of cationic and anionic solvation shells for various ions in methanol at 298 K. We show that the variation in ionic size of either the cation or the anion in an ion pair influences the solvation structure of the other ion as well as the diffusivity in an electrolyte solution of methanol. The extent of ionic association between the cation and its counteranion of different ionic sizes has been investigated by analyzing the radial distribution functions (RDFs) and the orientation of methanol molecules in the first solvation shell (FSS) of ions. It is shown that the methanol in the FSS of the anion as well the cation exhibit quite different radial and orientational structures as compared to methanol which lie in the FSS of either the anion or the cation but not both. We find that the coordination number (CN) of F-, Cr-, and I- ions decreases with increasing size of the anion which is contrary to the trend reported for the anions in H2O. The mean residence time (MRT) of methanol molecules in the FSS of ions has been calculated using the stable states picture (SSP) approach. It is seen that the ion-counterion interaction has a considerable influence on the MRT of methanol molecules in the FSS of ions. We also discuss the stability order of the ion-counterion using the potentials of mean force (PMFs) for ion pairs with ions of different sizes. The PMF plots reveal that the Li+-F- pair (small-small) is highly stable and the Li+-I- pair is least stable (small-large) in electrolyte solutions.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Rational molecular dynamics scheme for predicting optimum concentration loading of nano-additive in phase change materials

The present study deals with the diffusion and phase transition behaviour of paraffin reinforced with carbon nano-additives namely graphene oxide (GO) and surface functionalized single walled carbon nanotubes (SWCNT). Bulk disordered systems of paraffin hydrocarbons impregnated with carbon nano-additives have been generated in realistic equilibrium conformations for potential application as latent heat storage systems. Ab initio molecular dynamics(MD) in conjugation with COMPASS forcefield has been implemented using periodic boundary conditions. The proposed scheme allows determination of optimum nano-additive loading for improving thermo-physical properties through analysis of mass, thermal and transport properties; and assists in determination of composite behaviour and related performance from microscopic point of view. It was observed that nanocomposites containing 7.8% surface functionalised SWCNT and 55% GO loading corresponds to best latent heat storage system. The propounded methodology could serve as a by-pass route for economically taxing and iterative experimental procedures required to attain the optimum composition for best performance. The results also hint at the large unexplored potential of ab-initio classical MD techniques for predicting performance of new nanocomposites for potential phase change material applications. (C) 2015 Author(s).

Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations

Molecular dynamics simulations of electroporation in POPC and DPPC lipid bilayers have been carried out at different temperatures ranging from 230 K to 350 K for varying electric fields. The dynamics of pore formation, including threshold field, pore initiation time, pore growth rate, and pore closure rate after the field is switched off, was studied in both the gel and liquid crystalline (L-alpha) phases of the bilayers. Using an Arrhenius model of pore initiation kinetics, the activation energy for pore opening was estimated to be 25.6 kJ mol(-1) and 32.6 kJ mol(-1) in the L-alpha phase of POPC and DPPC lipids respectively at a field strength of 0.32 V nm(-1). The activation energy decreases to 24.2 kJ mol(-1) and 23.7 kJ mol(-1) respectively at a higher field strength of 1.1 V nm(-1). At temperatures below the melting point, the activation energy in the gel phase of POPC and DPPC increases to 28.8 kJ mol(-1) and 34.4 kJ mol(-1) respectively at the same field of 1.1 V nm(-1). The pore closing time was found to be higher in the gel than in the L-alpha phase. The pore growth rate increases linearly with temperature and quadratically with field, consistent with viscosity limited growth models.