Electrostatic screening in molecular dynamics simulations

The screened Coulombic potential has been shown to describesatisfactorily equilibrium properties like pK shifts, the effectsof charged groups on redox potentials and binding constantsof metal ions. To test how well the screening of the electrostaticpotential describes the dynamical trajectory of a macromolecularsystem, a series of comparative simulations have been carriedout on a protein system which explicitly included water moleculesand a system in vacuo. For the system without solvent the resultsof using (i) the standard potential form were compared withresults of (ii) the potential where the Coulomb term was modifiedby the inclusion of a distance dependent dielectric, (r), tomodel the screening effect of bulk water, and (iii) standardpotential modified by reducing the charge on ionized residueside chains. All molecular dynamics simulations have been carriedout on bovine pancreatic trypsin inhibitor. Comparisons betweenthe resulting trajectories, averaged structures, hydrogen bondingpatterns and properties such as solvent accessible surface areaand radius of gyration are described. The results show thatthe dynamical behaviour of the protein calculated with a screenedelectrostatic term compares more favourably with the time-dependentstructural changes of the full system with explicitly includedwater than the standard vacuum simulation.     

分子动力学模拟中氦分子势函数的应用

为了能够在关于氦的分子动力学的模拟中准确地使用其势函数,并确定其量纲1分子间相互作用力,通过对比分析可用于氦的势函数的数学形式和使用条件,指出虽然标准Lennard-Jones（LJ-12-6）势函数的物理意义清晰、形式简化、应用广泛,但对于氦而言,分子间的排斥力不再适宜采用原子中心间距r的-12次方的形式,而更适合采用指数形式的排斥项。在具有指数形式排斥项的势函数中,EXP-6势函数较好地反映了液氦原子间的多体相互作用,其吸引项是van der Waals吸引力的主要组成部分;Bruch-McGee组合半经验势函数多具有分段函数的形式,在模拟过程中转变为分子间作用力的过程和最终的形式较复杂;而Tang-Toennies势函数更适合于描述低密度氦气的性质。通过将势函数的物理参数量纲1化,确定量纲1分子间相互作用力,目的是可以在随后的分子动力学模拟中依使用条件采用。     

Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.     

Motional coherency in chain dynamics of polybutadiene studied by molecular dynamics simulations

Molecular dynamics simulations of 1,4-polybutadiene in bulk amorphous state were performed. Results were compared with the recent neutron spin-echo measurements. To investigate motional coherency the relaxation rates for the collective and self-motions, the collective and self-relaxation rates, were evaluated for the short and long time regimes of the normalized intermediate scattering functions. The scattering vector dependence of the collective relaxation rates estimated for both fast and slow processes indicated a minimum at scattering vector q = 1.5 Å⁻¹, corresponding to the position of a peak in the static structure factor. The self-relaxation rates increased monotonously with q. A phenomenon known as de Gennes narrowing was reproduced well in the simulation and found to be originated from the inter-molecular correlation. The collective relaxation rate evaluated for fast process appeared to modulate around a peak of q = 2.9 Å⁻¹, corresponding to the intra-molecular correlation.     

Nanoscale molecular cavity in crystalline polymer membranes studied by molecular dynamics simulation

The size, shape, and connectivity of cavities in the crystals of syndiotactic polystyrene were investigated by molecular dynamics simulation. Cluster analysis of the free volume in the crystals clearly reveals the cavity structures: large individual holes are in an orderly manner connected by narrow channels. We call such a cavity structure a ‘molecular cavity’. The diffusion behavior and solubility of gases in the molecular cavity were also simulated. The extremely high solubility of a larger gas and the controllable diffusion path in the narrow channels proved the applicability of the concept of the molecular cavity to high performance separation membranes.     

Inelastic relaxation in silica via reactive molecular dynamics

Silica glass exhibits rate-dependent and irreversible processes during deformation and failure, resulting in inelastic effects. To explore this phenomena, molecular dynamics simulations of structural relaxation surrounding a crack tip in silica glass were performed at four different temperatures (100, 300, 600, 900 K) using a reactive force field. Per-atom stresses were found to relax during the simulation, with the highest stress relaxation occurring at 900 K. Stress relaxation was radially dependent relative to the crack tip, with stress dissipation occurring primarily within a 25–30 Å inelastic region. Within 10 Å of the crack tip, the defect concentration decreased from 0.18 to 0.09 #/nm² during inelastic relaxation at 900 K. Conversely, the defect concentration 20 Å from the crack tip increased from 0.105 to 0.118 #/nm² at 300 K, and from 0.113 to 0.126 #/nm² at 600 K, which formed a defect-enriched region ahead of the crack tip. The difference in defect concentrations suggests the possibility of a stress mediated defect migration mechanism, where defects move away from the crack tip during inelastic relaxation. Additionally, defect speciation indicated that undercoordinated silica defects, such as non-bridging oxygen, were removed through the formation of higher coordination defects during relaxation. Overall, stress relaxation causes changes in the defect concentration profile near the crack tip, which has the potential to alter the properties of silica glass in the inelastic region during relaxation.     

Spin dynamics of an ultra-small nanoscale molecular magnet

We present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high) Heisenberg spins. We derive exact analytic expressions (in integral form) for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail. The author wants to thank Dr. Gary Erickson for proof-reading the final draft of the paper.     

基于分子动力学的橡胶聚合物计算机辅助设计方法

聚合物分子设计的关键步骤是得到能够满足多种性质要求的重复单元结构。作为化学产品工程中的新型发展手段，计算机辅助分子设计(CAMD)技术可以通过基团贡献法生成满足约束条件的聚合物重复单元结构，分子动力学(MD)技术则可以在微观层面上进行计算机实验模拟系统性质。建立了聚合物的CAMD-MD通用设计方法，并进行轮胎橡胶聚合物的分子设计，首先基于基团贡献法进行重复单元的设计；其次，利用层次分析法确定多性质权重排名，并基于分子动力学方法探究候选结构的性质；最后将方法应用于实际橡胶结构中，模拟得到聚能密度、密度、玻璃化转换温度和热导率性质，验证了方法的可行性。     

Tracking dynamics of glass formers and modifiers via correlation maps of molecular dynamics simulation

In this study, we describe a method to construct a correlation map that captures the evolution of species-specific dynamic information through the spatial correlation of high-dimensional time-series molecular dynamics (MD) simulation dataset for a series of borosilicate glasses. The correlation is based on ‘displacement’ between a pair of atomic configurations determined by the root mean square distance (RMSD) metric. We implement the correlation map as a quantitative visualization tool that provides a compressed representation of a high-dimensional molecular dynamics dataset to inspect various physical aspects and capture distinct atomic dynamics—from large fluctuations to small local oscillations—for high-temperature melt, linear cooling, and low-temperature equilibration processes during molecular dynamics simulation of glasses. We capture species-specific dynamics using this method that show different cooling dynamics for different glass formers and modifiers, especially the onset of slow dynamics and the variation of atomic dynamics at high temperatures. Furthermore, we show that the species-specific atomic dynamics have structural origins that depend on the composition of the simulated borosilicate glasses. The correlation map serves as a visualization tool to rapidly survey changes in atomic configurations during different simulation conditions.     

Determination of molecular orientation using molecular dynamics for polymer melt flows in circular ducts

Molecular dynamic simulations have been used to develop a mathematical model to investigate the extension of the polymer chains and the polymer chain orientations in the circular duct flows. The effects of pressure loss and molecular weight are also investigated on the polymer chain orientation. The model's outputs indicate that with increasing pressure loss and subsequently the shear stress at wall, the trace of the conformation tensor increases. This is interpreted as an increase in the extension of polymer chains and the polymer chain orientation in the flow direction. The model also predicts that the increase of the molecular weight of polymer results in decrease of the trace of the conformation tensor and the extension of the polymer chains. POLYM. ENG. SCI., 55:1196–1202, 2015. © 2014 Society of Plastics Engineers     

纳米流体中纳米颗粒微运动的分子动力学模拟

建立了以水分子为基础液、以铜纳米颗粒为悬浮粒子的纳米流体模型,利用分子动力学模拟方法对纳米颗粒的微运动行为进行分析。研究发现纳米颗粒在基础液中具有高速的随机旋转与平移运动,旋转运动的角速度为1×10⁹~1×10¹⁰ rad·s^-1,平移运动的速度为1~10 m·s^-1。纳米流体速度分布与温度分布主要区别于单相基础液的位置在近壁面附近,纳米流体无论是速度梯度还是温度梯度均比单相流体的情况大,其主要原因是纳米颗粒在基础液中的随机运动,而改变的流体速度特性又会进一步影响传热过程。     

分子蒸馏过程的计算流体力学模拟

采用计算流体力学(CFD)方法,分析了蒸发器上液体负荷、刮膜器旋转速度对蒸发器上液膜厚度变化及液膜中速度矢量的影响。将CFD模拟结果与文献报道的计算值和实验值进行比较,发现具有较好的吻合性,同时可以用模拟计算结果解释一些实验现象。采用脉冲注射示踪剂法测定了蒸发器上流体的平均停留时间分布,与CFD模拟的在刮膜器作用下蒸发器上流体平均停留时间分布数据进行比较,二者的偏差在±8%以内,验证了CFD模拟的准确性。     

Droplets sliding over shearing surfaces studied by molecular dynamics

Through molecular dynamics, the sliding motion of a liquid drop embedded in another liquid over a substrate as a result of a shear flow is studied. The two immiscible Lennard‐Jones liquids have the same density and viscosity. The system is isothermal. Viscosity, surface tension, and static contact angles follow from calibration simulations. Sliding speeds and drop deformations (in terms of dynamic contact angles) are determined as a function of the shear rate. The latter is nondimensionalized as a capillary number (Ca) that has been varied in the range 0.02–0.64. For Ca up to 0.32, sliding speeds are approximately linear in Ca. For larger Ca, very strong droplet deformations are observed. © 2015 American Institute of Chemical Engineers AIChE J, 61: 4020–4027, 2015     

High-harmonic spectroscopy: from femtosecond to attosecond molecular dynamics

The principles of high-harmonic spectroscopy (HHS) are illustrated using two recent examples from the literature. The method can be applied as a probe to measure the evolution of the electronic structure of a molecule during a chemical reaction on the femtosecond time scale. Alternatively, it can be used as a comprehensive method unifying pump and probe steps into a single laser cycle to measure electronic dynamics on the attosecond time scale.     

Tensile deformation of semi-crystalline polymers by molecular dynamics simulation

In this work, the microstructure evolution of semi-crystalline polymers during tensile deformation is analyzed by molecular dynamics simulation. A perfect semi-crystalline lamellar structure with crystalline/amorphous interface perpendicular to tensile direction is created with the help of coarse-grained (CG) model of poly(vinyl alcohol) (PVA). During the tensile test, two kinds of strain rates are applied to the lamellar stack to determine the stress–strain curves, yield stresses, and crystallinities. Consistent with experimental findings, two yield points were observed in the semi-crystalline sample which was corresponded to the fine and coarse crystallographic slips in the lamellar structure, where the crystal stems gradually rotated into the direction of applied stress during chain slips. After the second yielding point when the crystal stems had been rotated fully into the direction of applied stress, the lamellar structure was destroyed and it resulted in a decrease of crystallinity. In addition, the increase of the strain rate led to the acceleration of destruction of crystal structures. It is worth noting that the stress induced crystallization was observed in the interfacial region, and newly crystallized beads were belonged to the same microcrystalline domain as crystalline region due to memory effects. This work provides direct comparison of structure evolution between crystalline and amorphous region in semi-crystalline polymers during tensile deformation, and it is helpful for the design and mechanical property analysis of semi-crystalline polymers.     

First-principles molecular dynamics study of small molecules in zeolites

We present first-principles (based on electronic structure calculations) molecular dynamics simulations of the adsorption of methanol and water in zeolites. In contrast to most previous calculations we take the infinite zeolite structure fully into account. Our calculations reproduce the measured IR spectra, and thus allow for the first time a direct assignment of the measured bands. Methanol and water appear not to be protonated at low (one molecule per acid site) coverages. At higher coverages, however, the proton detaches from the framework and is available for acid catalyzed reactions in the zeolite. We precede our discussion with a critical evaluation of available theoretical approaches.     

Force field generation and molecular dynamics simulations of Li-Nafion

A new molecular dynamics force field for Nafion^® containing Li⁺ ions has been generated using Density Functional Theory calculations (B3LYP) on a Nafion side-chain, a Li⁺ ion and a H₂O molecule. The depth of the potential energy well between Li⁺ and the sulphonate group was decreased with ∼10 kcal/mol and the optimal Li-S distance 0.5 Å shorter, as compared to force fields generated without water present. Molecular dynamics simulations based on the new force field result in a self-diffusion coefficient for Li⁺ of 8.0 × 10⁻⁸ cm²/s at 353 K, which is closer to experimental result than previous simulations using force fields based on pure Nafion-cation interactions.     

Structure and molecular dynamics of highly mobile polymer membranes

The function of lipid bilayer membranes crucially depends on their mobility and their ability to incorporate components that, e.g., can change molecular order and dynamics or form channels. Since polymerization increases the stability of model membranes at the expense of their mobility a compromise must be sought. Therefore, the effect of different polymerization schemes on the structure and dynamics of polymer membranes has to be checked. To this end X-ray scattering, DSC-thermal analysis and a variety of spectroscopic techniques probing the dynamics on largely different time--- and length scales were employed, i.e. ²H-NMR, ESR, fluorescense anisotropy and FRAP. These studies showed that in model membranes polymerized in the hydrophylic region the head group mobility can be controlled by the length and the nature of the spacer connecting it to the polymer backbone. The head group region is much less affected, if the polymerization is achieved in the hydrophobic region. By use of a lipid analogue carrying a polymerizable group on only one of its two alkyl chains, membranes retaining high mobility in the hydrophobic region can be generated. Typical membrane constituents, i.e. cholesterol, gramicidin and ubiquinone can be incorporated and the mixtures show a behaviour similar to natural model membranes, although lateral diffusion of the lipids is frozen as a consequence of the polymerization.