Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum

采用分子动力学模拟方法结合核磁共振化学位移和粘度对尿素水溶液在稀浓度范围内的结构和弱相互作用进行研究. 从径向分布函数(RDF)分析看出,尿素水溶液中存在着几种不同类型、不同氢键形成能力的传统氢键. 氢键网络分析发现尿素水溶液体系在水富集区域,水分子倾向于自身缔合形成稳定的分子簇结构,而随着尿素浓度的逐渐增加,水的有序结构受到破坏,水分子和尿素分子发生了交叉缔合作用形成氢键,尿素分子有形成自身缔合的趋势. 分子动力学统计的平均氢键数与核磁共振化学位移和粘度数据结果进行比较,发现它们的变化趋势一致,证明了实验和理论结果有很强的可靠性.     

Test of the Gouy-Chapman theory for a charged lipid membrane against explicit-solvent molecular dynamics simulations

A wealth of experimental data has verified the applicability of the Gouy-Chapman (GC) theory to charged lipid membranes. Surprisingly, a validation of GC by molecular dynamics (MD) simulations has been elusive. Here, we report a test of GC against extensive MD simulations of an anionic lipid bilayer solvated by water at different concentrations of NaCl or KCl. We demonstrate that the ion distributions from the simulations agree remarkably well with GC predictions when information on the adsorption of counterions to the bilayer is incorporated.     

Speed dependence of atomic stick-slip friction in optimally matched experiments and molecular dynamics simulations

The atomic stick-slip behavior of a Pt tip sliding on a Au(111) surface is studied with atomic force microscopy (AFM) experiments and accelerated (i.e., reduced sliding speed) molecular dynamics (MD) simulations. The MD and AFM conditions are controlled to match, as closely as possible, the geometry and orientation, load, temperature, and compliance. We observe clear stick-slip without any damage. Comparison of both MD and AFM results with the thermally activated Prandtl-Tomlinson model shows that MD results at the highest speeds are not in the thermally activated regime. At lower speeds, within the thermally activated regime, AFM and MD provide consistent energetics, but attempt frequencies differ by orders of magnitude. Because this discrepancy lies in attempt frequencies and not energetics, atomistic details in MD simulations can be reliably used in interpreting AFM data if the MD speeds are slow enough.     

Assessment of Timoshenko Beam Models for Vibrational Behavior of Single-Walled Carbon Nanotubes Using Molecular Dynamics

In this paper, we study the flexural vibration behavior of single-walled carbon nanotubes (SWCNTs) for the assessment of Timoshenko beam models. Extensive molecular dynamics (MD) simulations based on second-generation reactive empirical bond-order (REBO) potential and Timoshenko beam modeling are performed to determine the vibration frequencies for SWCNTs with various length-to-diameter ratios, boundary conditions, chiral angles and initial strain. The effectiveness of the local and nonlocal Timoshenko beam models in the vibration analysis is assessed using the vibration frequencies of MD simulations as the benchmark. It is shown herein that the Timoshenko beam models with properly chosen parameters are applicable for the vibration analysis of SWCNTs. The simulation results show that the fundamental frequencies are independent of the chiral angles, but the chirality has an appreciable effect on higher vibration frequencies. The SWCNTs is very sensitive to the initial strain even if the strain is extremely small.     

Melting and Grüneisen parameters of NaCl at high pressure

The Buckingham potential has been employed to simulate the melting and thermodynamic parameters of sodium chloride (NaCl) using the molecular dynamics (MD) method. The constant-volume heat capacity and Grüneisen parameters have been obtained in a wide range of temperatures. The calculated thermodynamic parameters are found to be in good agreement with the available experimental data. The NaCl melting simulations appear to validate the interpretation of superheating of the solid in the one-phase MD simulations. The melting curve of NaCl is compared with the experiments and other calculations at pressure 0－30GPa range.     

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer–solvent and polymer–wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.     

In situ observation of antisite defect formation during crystal growth

In?situ x-ray diffraction (XRD) coupled with molecular dynamics (MD) simulations have been used to quantify antisite defect trapping during crystallization. Rietveld refinement of the XRD data revealed a marked lattice distortion which involves an a axis expansion and a c axis contraction of the stable C11b phase. The observed lattice response is proportional in magnitude to the growth rate, suggesting that the behavior is associated with the kinetic trapping of lattice defects. MD simulations demonstrate that this lattice response is due to incorporation of 1% to 2% antisite defects during growth.     

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.     

Molecular dynamics of NaCl melting under pressure

We have performed one-phase molecular dynamics (MD) simulations to investigate the melting curve of NaCl over a wide range of pressures. To ensure faithful MD simulations, two types of potentials, the shell-model (SM) and the two-body rigid-ion Born-Mayer-Huggins-Fumi-Tosi (BMHFT) potentials, are fully tested. Compared with SM potential, the MD simulation with BMHFT potential is very successful in reproducing accurately the measured volumes of NaCl. The BMHFT potential can also produce a satisfactory melting curve, consistent with both experiments and two-phase simulations. Hence we recommend that the BMHFT should be the reliable potential for simulating high-pressure properties of NaCl.     

Quasi-coarse-grained dynamics: modelling of metallic materials at mesoscales

A computationally efficient modelling method called quasi-coarse-grained dynamics (QCGD) is developed to expand the capabilities of molecular dynamics (MD) simulations to model behaviour of metallic materials at the mesoscales. This mesoscale method is based on solving the equations of motion for a chosen set of representative atoms from an atomistic microstructure and using scaling relationships for the atomic-scale interatomic potentials in MD simulations to define the interactions between representative atoms. The scaling relationships retain the atomic-scale degrees of freedom and therefore energetics of the representative atoms as would be predicted in MD simulations. The total energetics of the system is retained by scaling the energetics and the atomic-scale degrees of freedom of these representative atoms to account for the missing atoms in the microstructure. This scaling of the energetics renders improved time steps for the QCGD simulations. The success of the QCGD method is demonstrated by the prediction of the structural energetics, high-temperature thermodynamics, deformation behaviour of interfaces, phase transformation behaviour, plastic deformation behaviour, heat generation during plastic deformation, as well as the wave propagation behaviour, as would be predicted using MD simulations for a reduced number of representative atoms. The reduced number of atoms and the improved time steps enables the modelling of metallic materials at the mesoscale in extreme environments.     

Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise

Residual dipolar couplings (RDCs) provide excellent probes for the exploration of dynamics in biomolecules on biologically relevant time-scales. Applying geometric motional models in combination with high-resolution structures to fit experimental RDCs allows the extraction of local dynamic amplitudes of peptide planes in proteins using only a limited number of data points. Here we compare the behaviour of three simple and intuitive dynamic modes: the Gaussian axial fluctuation model (1D-GAF), the two-site jump model, and a model supposing axially symmetric motion about a mean orientation. The requirement of a structural model makes this kind of methodology potentially very sensitive to structural imprecision. Numerical simulations of RDC dynamic averaging under different regimes show that the anisotropic motional models are more geometrically stringent than the axially symmetric model making it more difficult to alias structural noise as artificial dynamic amplitudes. Indeed, it appears that the model extracts accurate motional amplitudes even in the presence of significant structural error. We also show that a two-site jump model, also assuming the (alpha)C(i-1)-(alpha)C(i) as rotation axis, can only be distinguished from the previously developed GAF model beyond amplitude/jumps of around 40 degrees. The importance of appropriate estimation of the molecular alignment tensor for determination of local motional amplitudes is also illustrated here. We demonstrate a systematic scaling of extracted dynamic amplitudes if a static structure is assumed when determining the alignment tensor from dynamically averaged RDCs. As an example an artificial increase of 0.14 (0.85 compared to the expected 0.71) is observed in the extracted S2 if a pervasive 20 degrees GAF motion is present that is ignored in the tensor determination. Finally we apply a combined approach using the most appropriate motional model, to complete the analysis of dynamic motions from protein G.     

Simulation of screw dislocation motion in iron by molecular dynamics simulations

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.     

导热系数的分子动力学模拟研究及相关问题的探讨

对于采用分子动力学方法研究导热系数的背景、研究现状及存在的问题进行了综述和分析。总结了通过分子动力学模拟方法求得导热系数的物理模型和基本算法。讨论了目前在微尺度导热问题的研究中引入分子动力学模拟方法需要考察的影响因素和几个重要问题。     

全原子分子动力学模拟结合核磁共振波谱研究N-甘氨酰甘氨酸水溶液的结构和弱相互作用

采用分子动力学模拟方法结合核磁共振化学位移系统研究了甘氨酰甘氨酸水溶液体系饱和溶解度范围的弱相互作用. 径向分布函数表明体系中不同类型的原子显示出形成氢键的不同能力. 氢键网络分析发现了不同氢键所能形成的分子簇结构. 随温度变化核磁共振化学位移值用于研究形成氢键的变化情况,并和模拟得到的结果进行比较,模拟和实验结果得到了较好的吻合.     

Ultrafast core-hole-induced dynamics in water probed by x-ray emission spectroscopy

The isotope effect and excitation-energy dependence have been measured in the oxygen K-edge x-ray emission spectrum (XES). The use of XES to monitor core decay processes provides information about molecular dynamics (MD) on an ultrafast time scale through the O1s lifetime of a few femtoseconds. Different nuclear masses give rise to differences in the dynamics and the observed isotope effect in XES is direct evidence of the importance of such processes. MD simulations show that even the excitation-energy dependence in the XES is mainly related to differences in core-excited-state dynamics.     

Lattice boltzmann versus molecular dynamics simulation of nanoscale hydrodynamic flows

A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by molecular dynamics (MD) computer simulation and compared to results of lattice Boltzmann (LB) simulations. By the appropriate mapping of length and time units from LB to MD, the velocity field as obtained from MD is quantitatively reproduced by LB. The implications of this finding for prospective LB-MD multiscale applications are discussed.     

Thickness and in-plane elasticity of graphane

The thickness and in-plane mechanical properties (Young?s, shear modulus, Poisson?s ratios) of fully hydrogenated graphene (graphane) sheets are predicted using a molecular mechanics approach. The equilibrium lengths and bond angles distortions used for the graphane models are obtained from Density Functional Theory (DFT) simulations. Our models compare well with existing data on the uniaxial properties of graphane and graphene sheets from first principle and Molecular Dynamics (MD) simulations, highlight a special orthotropic mechanical behaviour for graphane, and identify thickness and shear stiffness values which are peculiar of hydrogenated graphene.     

Periodicity, planarity, residual dipolar coupling, and structures

The periodic behavior of residual dipolar couplings (RDCs) arising from nucleic acid and protein secondary structures is shown to be more complex and information-rich than previously believed. We have developed a theoretical framework which allows the bond vector orientation of nucleic acids and the peptide plane orientations of protein secondary structures to be extracted from their Dipolar waves. In this article, we focus on utilizing "Dipolar waves" of peptides to extract structure information, and describe in more detail the fundamental principles of the relationship between the periodicities in structure and RDCs, the practical procedure to extract peptide plane orientation information from RDC data, and assessment of errors using Monte-Carlo simulations. We demonstrate the utility of our method for two model alpha-helices, one kinked and one curved, and as well as an irregular beta-strand.     

Energy control of a molecular dynamics cell for the promotion of crystal phase transitions

A method for promoting crystal phase transitions in molecular dynamics (MD) simulations is proposed in which the temperature of a variable MD cell is controlled within the framework of the ParrinelleRahman constant-pressure method. This control is independent of the terqperature control of the molecules. The implementation makes it possible to perform MD simulations in which the temperature of the cell is high enough to enhance the deformation of the cell, while that of molecules is kept low so as not to lose the order of the crystal. The method successfully induced the phase transition of benzene crystals, which has not been obtained in MD simulations under usual conditions. Compared with the previously proposed method, i.e., momentum control of the cell, the present method is more favourable for reproducing experimentally observed structures.