A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model

An understanding of protein folding/unfolding processes has important implications for all biological processes, including protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics(MD) simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational capabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temperature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature(500 K)was performed to investigate the unfolding process of a small protein, chicken villin headpiece(HP-35). To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.     

Molecular dynamic studies on materials under laser shocks

Molecular dynamic (MD) simulations offer a powerful means of understanding the microscopic characteristics of shock-propagation through solids and fluids, especially for the short spatial and temporal scales relevant to laser-driven shocks. First-principles molecular dynamics can be directly compared with time-resolved experimental measurements, and methods based on empirical (embedded-atom) potentials fitted to first-principles quantum-mechanical calculations are effective for MD simulations of shock propagation through many millions of atoms. In comparison, thermodynamic approaches based on free-energy considerations do not provide detailed information about mechanical-relaxation or phase-transformation processes within the shock front. We illustrate these ideas by way of embedded-atom simulations of shock-wave propagation through copper crystals of different orientation.     

冲击压缩下铝、铜、钨的剪切模量和屈服强度与压力和温度的相关性

对铝、铜和钨在冲击压缩状态下的剪切模量和屈服强度的实验数据进行了综合分析，并与St einberg-Cochran-Guinan(SCG)模型的计算结果进行了比较，结果表明，铝在50 GPa、铜在1 00 GPa、钨在200 GPa冲击压力以内，三种材料的剪切模量和屈服强度随温度和压力的变化 趋势基本相似，即SCG模型的假设Y′_pY₀=G′_pG ₀,Y′_TY₀=G′_TG₀对这三种材料在上述冲击压力范围内近似成立，利用该模型可以较好地描述材料在冲击压缩 下的本构行为. 关键词： 剪切模量 屈服强度 压力 温度     

Properties of MgO at high pressures: Shell-model molecular dynamics simulation

Shell-model molecular dynamics (MD) simulation has been performed to investigate the melting of the major Earth-forming mineral: periclase (MgO), at elevated temperatures and high pressures, based on the thermal instability analysis. The interatomic potential is taken to be the sum of pair-wise additive Coulomb, van der Waals attraction, and repulsive interactions. The MD simulation with selected Lewis–Catlow (LC) potential parameters is found to be very successful in describing the melting behavior for MgO, by taking account of the overheating of a crystalline solid at ambient pressure. The thermodynamic melting curve is estimated on the basis of the thermal instability MD simulations and compared with the available experimental data and other theoretical results in the pressure ranges 0–150 GPa. Our simulated melting curve of MgO is consistent with results obtained from Lindemann melting equation and two-phase simulated data at constant pressure by Belonoshko and Dubrovinsky, in the pressure below 20 GPa. The extrapolated melting temperatures in the lower mantle are in good agreement with the results obtained from Wang's empirical model up to 100 GPa. Compared with experimental measurements, our results are substantially higher than that determined by Zerr and Boehler, and the discrepancy between DAC and MD melting temperatures may be well explained with different melting mechanisms. Meanwhile, the radial distribution functions (RDFs) of Mg–Mg, O–Mg, and O–O ion pairs near the melting temperature have been investigated.     

Shock waves in high-energy materials: the initial chemical events in nitramine RDX

We extend the reactive force field ReaxFF to describe the high energy nitramine RDX and use it with molecular dynamics (MD) to study its shock-induced chemistry. We studied shock propagation via nonequilibrium MD simulations at various collision velocities. We find that for high impact velocities (>6 km/s) the RDX molecules decompose and react to form a variety of small molecules in very short time scales (<3 ps). These products are consistent with those found experimentally at longer times. For lower velocities only NO2 is formed, also in agreement with experiments.     

Ultrastability and enhanced stiffness of approximately 6 nm TiO2 nanoanatase and eventual pressure-induced disorder on the nanometer scale

At 300 K ultrafine approximately 6 nm grain-size nanoanatase retains its structural integrity up to 18 GPa. There is progressive pressure-induced structural disorder to a highly disordered state at P>18 GPa. Signatures of short-range order persist to well beyond 18 GPa in both the synchrotron-x-ray diffraction and Raman data. Molecular dynamics simulations suggest disorder initiated in the surface shell of a nanograin with crystallinity being retained in the core. A bulk modulus B0=237+/-3 GPa for the nanoanatase (approximately 30% higher than the bulk value) is derived from the P-V data, concordant with the MD calculations.     

Displacement fields around Guinier–Preston 1 zones in Al–Cu alloys: investigations using MD and ADF-STEM image simulations

The displacements of atoms around Guinier–Preston 1 (GP1) zones in Al–Cu alloys at a temperature of 295?K have been investigated using molecular dynamics (MD) simulations. The magnitude of the displacements at the first Al layer adjacent to a GP1 zone reached 24% strain and this value decreased with distance from the zone to zero at about 40th Al layer. Strain fields near a GP1 zone were evaluated by calculating strain tensors around individual atoms. The obtained strain maps suggested that the equilibrium Cu content in a GP1 zone should be 100%. The atomic configurations determined by MD simulations were utilised for multislice image simulations of annular dark-field scanning transmission electron microscopy (ADF-STEM) to investigate the effect of foil thickness and the depth position of a GP1 zone in a foil on ADF-STEM images. The atomic displacements in ADF-STEM images were smaller than the MD result due to foil thickness and electron channelling.     

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.     

Uncovering a pressure-tuned electronic transition in Bi(1.98)Sr(2.06)Y(0.68)Cu(2)O(8+delta) using Raman scattering and x-ray diffraction

We report pressure-tuned Raman and x-ray diffraction data of Bi(1.98.)Sr(2.06)Y(0.68)Cu(2)O(8+delta) revealing a critical pressure at 21 GPa with anomalies in electronic Raman background, electron-phonon coupling lambda, spectral weight transfer, density dependent behavior of phonons and magnons, and a compressibility change in the c axis. For the first time in a cuprate, mobile charge carriers, lattice, and magnetism all show anomalies at a distinct critical pressure in the same experimental setting. Furthermore, the spectral changes suggest that the critical pressure at 21 GPa is related to the critical point at optimal doping.     

高压下液态硝基甲烷的分子动力学模拟

 对高压下液态硝基甲烷的性质进行经典和基于第一性原理计算的Car-Parrinello分子动力学（CPMD）模拟。利用经典势的分子动力学（MD）模拟研究了高压压缩状态下液态硝基甲烷的结构和热力学性质,得到了高达14.2 GPa压力下的理论Hugoniot数据。对于一些热力学函数,如总能和粒子速度,经典势模拟给出了很好的总趋势,基本特征和实验观测一致。但是在给定的密度下,经典模拟预言的Hugoniot压力偏高。在几个选定的密度下,进行了CPMD模拟,得到了二体相关函数、速度自相关函数、振动光谱和其它的热力学性质,并与经典模拟结果进行了比较。对二体相关函数的分析表明经典势的短程部分的刚性可能太强,从而导致了比实验值高的理论压力值。对于某些二体相关函数,CPMD模拟和经典模拟结果差别很大,可以归结为量子效应。当压力增高时,量子模拟得到的振动光谱向高频部分移动的现象与实验观测相符合。     

Atomistic investigation of phase transition in solid argon induced by shock wave transmission

A molecular dynamics (MD) simulation is employed to study the phase transition process in argon induced by shock wave transmission. Deriving the relation between the shock and piston velocities, the theoretical equation of state for argon is presented. Also, argon equation of state is obtained by measuring the quantities directly from simulations to be able to detect the phase transitions. The phase transition is also detected by using argon phase diagram and free energy calculations. A comparison shows good agreement between the theoretical and MD results for the phase transitions. Based on these simulations, it is concluded that under a shock wave transmission with suitable energy, the solid argon experiences a phase transition from solid to liquid and another from liquid to supercritical fluid. By reflecting the shock wave back at the end of its passage, the whole argon may reach the supercritical state.     

无氧铜动态卸载行为的数值模拟

 分别利用Johnson-Cook（JC）本构模型和Steinberg-Cochran-Guinan（SCG）本构模型对无氧铜在10~20 GPa冲击压力下的卸载过程进行了数值模拟,与冲击-卸载实验结果比较表明,在这样的冲击压力下无氧铜的应变率效应仍然明显,JC模型对无氧铜的动态卸载行为有较好的描述。     

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.     

Large-Nc confinement and turbulence

We suggest that the transition that occurs at large N_{c} in the eigenvalue distribution of a Wilson loop may have a turbulent origin. We arrived at this conclusion by studying the complex-valued inviscid Burgers-Hopf equation that corresponds to the Makeenko-Migdal loop equation, and we demonstrate the appearance of a shock in the spectral flow of the Wilson loop eigenvalues. This picture supplements that of the Durhuus-Olesen transition with a particular realization of disorder. The critical behavior at the formation of the shock allows us to infer exponents that have been measured recently in lattice simulations by Narayanan and Neuberger in d=2 and d=3. Our analysis leads us to speculate that the universal behavior observed in these lattice simulations might be a generic feature of confinement, also in d=4 Yang-Mills theory.     

In situ TEM study of mechanical behaviour of twinned nanoparticles

There is strong interest in studying changes in mechanical properties with reducing grain size. The rational is that consequent dislocation glide cannot be sustained, resulting in an increase in material strength. However, this comes with the cost of a reduction in ductility. It has been shown that coherent twin boundaries in nanostructured Cu improve the ductility to 14% [Lu et al., Science 324 (2009) p. 349]. In this paper, we report for the first time the compression of individual nanoparticles using an in situ force probing holder in the transmission electron microscope. Four types of nanoparticles were tested, three with twin boundaries (decahedra, icosahedra and a single twin) and one free of defects (octahedral). Our results indicate the yield strength of the twinned nanoparticles is between 0.5 and 2.0 GPa. The total malleability for the twinned particles range from 80 to 100%. In addition, experimental results were reproduced by MD simulations of the compression phenomena and suggest that the outstanding mechanical properties are related with partial dislocation multiplication at twin boundaries.     

静-动加载相结合的材料状态方程实验平台的研制

根据神光-Ⅱ第九路高功率激光加载的特点,对传统静高压金刚石压砧装置进行了改进和优化设计,研制出了适合高功率激光加载条件下材料宽域状态方程研究的新型静高压靶.在神光-Ⅱ高功率激光装置上建立了基于静高压金刚石压砧和动高压激光相结合的材料宽域状态方程研究平台.利用这一平台开展了超纯水的宽域状态方程实验探索,获得了较好的实验结果.     

Complex fields in heterogeneous materials under shock: modeling,simulation and analysis

In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the problem into different scales. Construct/Choose a model according to the scale and main mechanisms working at that scale. Perform numerical simulations using the relatively mature schemes. The physical information is transferred between neighboring scales in such a way: The statistical information of results in smaller scale contributes to establishing the constitutive equation in larger one. Except for the microscopic Molecular Dynamics(MD) model, both the mesoscopic and macroscopic models can be further classified into two categories,solidic and fluidic models, respectively. The basic ideas and key techniques of the MD, material point method and discrete Boltzmann method are briefly reviewed. Among various schemes used in analyzing the complex fields and structures, the morphological analysis and the home-built software, GISO, are briefly introduced. New observations are summarized for scales from the larger to the smaller.     

Shock compressing diamond to a conducting fluid

Laser generated shock reflectance data show that diamond undergoes a continuous transition from optically absorbing to reflecting between Hugoniot pressures 600相似文献   

Probing structural integrity of single walled carbon nanotubes by dynamic and static compression

We report on a first study of single walled carbon nanotubes (SWCNTs) after application of dynamic (shock) compression. The experiments were conducted at 19 GPa and 36 GPa in a recovery assembly. For comparison, an experiment at a static pressure of 36 GPa was performed on the material from the same batch in a diamond anvil cell (DAC). After the high pressure treatment the samples were characterized by Raman spectroscopy and transmission electron microscopy (TEM). After exposure to 19 GPa of shock compression the CNT material exhibited substantial structural damage such as CNT wall disruption, opening of the tube along its axis (“unzipping”) and tube shortening (“cutting”). Dynamic compression to 36 GPa resulted in essentially complete CNT destruction whereas at least a fraction of the nanotubes was recovered after 36 GPa of static compression though severely damaged. The results of these shock wave experiments underline the prospect of using SWCNTs as reinforcing units in material WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

溴仿在冲击压缩下的光辐射及化学反应

 利用多通道光学高温计测量了溴仿在37 GPa到85 GPa压力范围内的温度,并观察了溴仿/单晶氯化钠界面的热驰豫过程。结果发现,当冲击波压力升高到46 GPa时,溴仿的光辐射强度随时间的变化呈现出“双阶梯”或“双台阶”形状的剖面结构,且台阶之间的时间间隔随冲击压力的增高而减小。当压力达到85 GPa时,上述“双台阶”结构消失,呈现为普通的单台阶剖面结构。冲击波温度测量表明,当压力低于50 GPa时,实测温度与Gokulya报道的数据一致;当压力增至76 GPa以上时,冲击波温度出现突跃性增加。结合对溴仿/氯化钠界面上的热驰豫过程的分析,文中提出,溴仿在上述冲击压力区间内发生了一次带有时间驰豫（或化学诱导期）的化学放热反应。