生物柴油分子系统凝固过程的分子动力学模拟

具有良好的低温流动性是生物柴油的重要特性之一,而这一性质与系统的凝点相关联.本文以硬脂酸甲酯、油酸甲酯等7种常见生物柴油组成分子为研究对象,通过建模构建了7种单组份生物柴油分子的模拟液态模型.利用分子动力学方法对7种液态模型系统的凝固过程进行了研究.采用PCFF力场,在一定的模拟条件下,对系统进行逐次降温分子动力学模拟.根据分子动力学轨迹,计算了不同温度下系统的热容、碳原子自扩散系数以及分子链的头尾距.模拟计算得到的液态热容合理.利用“热容法”和“扩散系数法”对不同系统的凝点进行判断,发现凝点区间基本一致,且与实际凝点基本相吻合.而采用2种区间交集的方法得到的凝点区间则与实际凝点十分相近.以油酸甲酯为例,模拟观察到,随着温度降低,分子链总体呈伸展趋势,符合热力学基本原理.在油酸甲酯的凝点前后,链长及链的微观结构存在明显差异.模拟结果表明,本实验方法对研究生物柴油分子系统确实有效.     

分子动力学模拟的柔性对接

分子自动对接技术在过去二十年里取得很大发展和成功,但是仍然面对如何处理分子柔性这样一个难题。这篇综述概要介绍分子柔性对接技术的进展并重点介绍分子动力学模拟技术。     

Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy

The state transitions of solvated H-Ras protein with GTP were theoretically analyzed through molecular dynamics (MD) simulations. To accelerate the structural changes associated with the locations of two switch regions (I and II), the Parallel Cascade Selection MD (PaCS-MD) method was employed in this study. The interconversions between the State 1 and State 2 were thus studied in atomic details, leading to a reasonable agreement with experimental observations and consequent scenarios concerning the transition mechanism that would be essential for the development of Ras inhibitors as anti-cancer agents. Furthermore, the state-transition-based local network entropy (SNE) was calculated for the transition process from State 1 to State 2, by which the temporal evolution of information entropy associated with the dynamical behavior of hydrogen bond network composed of hydration water molecules was described. The calculated results of SNE thus proved to provide a good indicator to detect the dynamical state transition of solvated Ras protein system (and probably more general systems) from a viewpoint of nonequilibrium statistical thermodynamics.     

Molecular docking and molecular dynamics simulation studies of Trypanosoma cruzi triosephosphate isomerase inhibitors. Insights into the inhibition mechanism and selectivity

Trypanosoma cruzi (T. cruzi) triosephosphate isomerase (TcTIM) is a glycolytic enzyme essential for parasite survival and has been considered an interesting target for the development of new antichagasic compounds. The homodimeric enzyme is catalytically active only as a dimer. Interestingly, significant differences exist between the human and parasite TIMs interfaces with a sequence identity of 52%. Therefore, compounds able to specifically disrupt TcTIM but not Homo sapiens TIM (hTIM) dimer interface could become selective antichagasic drugs. In the present work, the binding modes of 1,2,4-thiadiazol, phenazine and 1,2,6-thiadiazine derivatives to TcTIM were investigated using molecular docking combined with molecular dynamics (MD) simulations. The results show that phenazine and 1,2,6-thiadiazine derivatives, 2 and 3, act as dimer-disrupting inhibitors of TcTIM having also allosteric effects in the conformation of the active site. On the other hand, the 1,2,4-thiadiazol derivative 1 binds into the active site causing a significant decrease in enzyme mobility in both monomers. The loss of conformational flexibility upon compound 1 binding suggests that this inhibitor could be preventing essential motions of the enzyme required for optimal activity. The lack of inhibitory activity of 1 against hTIM was also investigated and seems to be related with the high mobility of hTIM which would hinder the formation of a stable ligand–enzyme complex. This work has contributed to understand the mechanism of action of this kind of inhibitors and could result of great help for future rational novel drug design.     

Molecular dynamics method for simulation of thermodynamic equilibrium

Simulation of a system of particles consisting of argon atoms using the molecular dynamics method is considered. An original molecular dynamics program was developed to calculate the parameters of gases on the basis of the Lennard-Jones potential. the conservativeness of the system in the process of calculation is provided by optimization of the time-step value. The process of establishing a uniform distribution of atoms in velocity is investigated.     

Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters

Many computer vision applications, such as object recognition and content-based image retrieval could function more reliably and effectively if regions of interest were isolated from their background. A new method for regions of interest extraction from color image based on visual saliency in HSV color space is proposed in this paper. Color saliency is calculated by a two-dimensional sigmoid function using the saturation component and brightness component, and we can identify regions with vivid color. Discrete Moment Transform (DMT)-based saliency can determine large areas of interest. A visual saliency map is obtained by combining color saliency and DMT-based saliency, which is denoted the S image. A criterion for the local homogeneity called the E image is calculated in the image. Based on S image and E image, the high visual saliency object seed points set and low visual saliency object seed points set are determined. The seeded regions growing and merging are used to extract regions of interest. Experimental results demonstrate the effectiveness and efficiency of the method for the natural color images.     

氯化钾溶液中离子水化的分子动力学模拟

使用Material Studio软件包中的COMPASS力场,采用分子动力学模拟的方法研究了温度为298.15 K时,浓度分别为1.065 mol/L、2.140 mol/L、3.129 mol/L的氯化钾溶液中离子水化的微观结构和动力学性质.发现浓度对离子近程水化的结构有一定的影响,随着溶液浓度的增加O-O径向分布...     

Molecular dynamics simulation of ribosome jam

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models.     

Molecular dynamics simulation for phase behavior of amphiphilic solution

The phase behavior of amphiphilic solution is investigated by molecular dynamics simulation of amphiphilic rigid dimers with explicit solvent molecules. Our simulations show that three kinds of phases (isotropic micellar, hexagonal and lamellar phases) are formed at a lower temperature by quenching from a random configuration of amphiphilic molecules in solution at a higher temperature. It is ascertained that an isotropic micellar phase changes into a hexagonal phase, and then into a lamellar phase as the amphiphilic concentration increases. It is also found that the global orientational order parameter can be used to distinguish these three kinds of phases. From the detailed analyses of the phase behavior, it is concluded that the hydrophilic repulsion plays an important role in the formation of the hexagonal phase while the hydrophobic attraction plays a crucial role in the formation of the lamellar phase.     

Parallel implementation of molecular dynamics simulation for short-ranged interaction

A parallel molecular dynamics simulation method, designed for large-scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. Parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (∼60%), while it is comparably lower for the vaporized state (∼40%).     

The effects of wall roughness on the methane flow in nano-channels using non-equilibrium multiscale molecular dynamics simulation

This paper presents a non-equilibrium multiscale molecular dynamics simulation method to investigate the effects of periodic wall surface roughness on the structure and mass transfer of methane fluid through the silicon nano-channels. In order to accurately capture the trajectories and microstructure of methane nano-fluidics, the present modification of OPLS fully atomic model is employed. Meanwhile, we introduce the corresponding coarse-grained model to solve the problem of wall–fluid interaction for methane Poiseuille flow within silicon atomic walls using the classical Lorentz–Berthelot mixing rules. The geometries of the upper wall roughness are modeled by rectangular waves with different amplitudes and wavelengths. The three-dimensional number densities of C (H) atom and kinetic energy distribution plots give a clear observation of the impacts of surface roughness on the localization micro-information of methane fluid. Moreover, the slip length of fluid over rough surface decreases with the increase in amplitude. The diffusion coefficients appear anisotropic, and the radial distribution functions decrease with the increase in the amplitude. These properties should be taken into account in the design of energy-saving emission reduction nano-fluidic devices. All numerical results also indicate that the presented method not only can well solve the issue of wall–fluid interactions, but also could accurately predict the micro-information and dynamic properties of methane Poiseuille flow.     

氮化铝陶瓷薄膜热导率的分子动力学模拟

采用平衡分子动力学方法(EMD)研究了平衡温度为300K的氮化铝薄膜的法向热导率.利用Stillinger-Weber势函数以及Green-Kubo线性响应理论计算热导率.计算结果表明,氮化铝薄膜的热导率值显著小于对应大体积材料的实验值,具有明显的尺寸效应.在氮化铝薄膜为1.47～5.39 nm的范围内,氮化铝薄膜的热导率随着薄膜厚度的增加而近似的线性增加.     

环糊精-卟啉与二苯乙烯衍生物包结作用的分子动力学模拟研究

为了考察环糊精-卟啉与二苯乙烯所形成包结物的稳定性对环糊精-卟啉催化二苯乙烯环氧化选择性的影响,本文采用分子动力学方法研究了环糊精-卟啉与一系列二苯乙烯衍牛物所形成的包结物,并从主客体之间的相互作用能、相对距离的变化及包结结构3个方面考察了包结物的稳定性.计算结果表明,不同的二苯乙烯衍生物与环糊精-卟啉所形成包结物的稳定性不同,二苯乙烯两端的取代基与卟啉两端环糊精空腔的几何尺寸越匹配,环糊精-卟啉与二苯乙烯衍生物所形成包结物的结合稳定性越强,越有利于环糊精-卟啉对二苯乙烯进行选择性催化环氧化.     

I型甲烷水合物晶体稳定性的分子动力学模拟

采用分子动力学方法，模拟了晶穴占有率和温度变化对I型甲烷水合物晶体稳定性的影响。通过考察晶体破坏过程中最终构象、均方位移、扩散系数、径向分布函数等分子的动力学和结构性质的变化，分析了分子动力学模拟中晶体结构失稳的微观特征，并提出了判断甲烷水合物晶体结构失稳的依据，这对水合物形成和分解过程的研究具有重要的参考价值。     

丁二酰亚胺类分散剂在伪烟炱表面吸附行为的分子动力学模拟

丁二酰亚胺类分散剂是一种典型的用于各种润滑油中的无灰分散剂。由于烟炱颗粒结构的复杂性,从实验研究的角度对分散剂的作用机理尚未给出满意的解释。本文应用分子动力学模拟方法,研究了丁二酰亚胺类分散剂模型分子在伪烟炱表面的吸附行为。模拟结果可以为分散剂的分子设计提供参考。     

Huge-scale molecular dynamics simulation of multibubble nuclei

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers.     

Ⅰ型甲烷水合物晶体稳定性的分子动力学模拟

采用分子动力学方法,模拟了晶穴占有率和温度变化对I型甲烷水合物晶体稳定性的影响。通过考察晶体破坏过程中最终构象、均方位移、扩散系数、径向分布函数等分子的动力学和结构性质的变化,分析了分子动力学模拟中晶体结构失稳的微观特征,并提出了判断甲烷水合物晶体结构失稳的依据,这对水合物形成和分解过程的研究具有重要的参考价值。     

Molecular dynamics simulation of nanoscale liquid flows

Molecular dynamics (MD) simulation is a powerful tool to investigate the nanoscale fluid flow. In this article, we review the methods and the applications of MD simulation in liquid flows in nanochannels. For pressure-driven flows, we focus on the fundamental research and the rationality of the model hypotheses. For electrokinetic-driven flows and the thermal-driven flows, we concentrate on the principle of generating liquid motion. The slip boundary condition is one of the marked differences between the macro- and micro-scale flows and the nanoscale flows. In this article, we review the parameters controlling the degree of boundary slip and the new findings. MD simulation is based on the Newton's second law to simulate the particles' interactions and consists of several important processing methods, such as the thermal wall model, the cut-off radius, and the initial condition. Therefore, we also reviewed the recent improvement in these key methods to make the MD simulation more rational and efficient. Finally, we summarized the important discoveries in this research field and proposed some worthwhile future research directions.     

A parallel algorithm for molecular dynamics simulation of branched molecules

To get an insight into the effects of molecular architecture in the behaviour of thin lubricant films we have devised an algorithm for simulation of branched molecules. We have used this algorithm successfully to simulate branched isomers of C₃₀. However the algorithm is flexible enough to be used for the simulation of more complex branched molecules. The resulting algorithm can be used in molecular dynamics simulation of branched molecules and could be helpful in designing new materials at the molecular level.