Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer

We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups.     

Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis

The concepts of hydrophobicity and hydrophobic moments have been applied in attempts to predict membrane protein secondary and tertiary structure. The current paper uses molecular dynamics computer calculations of individual bacteriorhodopsin helices in explicit dimyristoylphosphatidylcholine bilayers to examine the atomic basis of these approaches. The results suggest that the types of interactions between a particular amino acid and the surrounding bilayer depend on the position and type of the amino acid. In particular, aromatic residues are seen to interact favorably at the interface region. Analysis of the trajectories in terms of hydrophobic moments suggests the presence of a particular face that prefers lipid. The results of these simulations may be used to improve secondary structure prediction methods and to provide further insights into the two-stage model of protein folding.     

Molecular dynamics simulation of martensitic transformations in NiAI

Both thermally induced and stress-induced coherent nucleation and growth of an L1₀ martensitic phase have been examined and analyzed at the atomic level in molecular dynamics (MD) computer simulations of an ordered B2 NiAl lattice array using embedded atom method (EAM) interatomic potentials. Both heterogeneous and homogeneous nucleation are observed, the latter requiring an applied stress. The heterogeneous process occurs at ledge corners on stepped free surfaces and can be analyzed in terms of localized soft modes. The homogeneous nucleation can be understood as resulting from a strain spinodal instability which produces a morphology reminiscent of chemical spinodal decomposition. Self-accommodating martensite variants appear very early in the growth process, and all interfaces remain coherent with no detectable presence of dislocations in these early stages. Formerly Graduate Student, Department of Metallurgy, Institute of Materials Science, University of Connecticut. This article is based on a presentation made during TMS/ASM Materials Week in the symposium entitled “Atomistic Mechanisms of Nucleation and Growth in Solids,” organized in honor of H.I. Aaronson’s 70th Anniversary and given October 3“5, 1994, in Rosemont, Illinois.     

Molecular dynamics simulation of hydrated phospholipid bilayers

Understanding of microscopic behaviour of biological membrane is crucial for designing of molecules to control transport properties of the membranes. Phospholipid-water forms a good model system to study ligand induced structural and dynamical changes in membrane. The review has its main focus on molecular dynamics (MD) simulation of phospholipid bilayers. A brief summary of the current status of structure of phospholipid membranes based on different physico-chemical measurements is given. We discuss here mainly results of MD simulations in the recent years on hydrated phospholipid bilayers and their interaction with ligands. Simulation parameters as: choice of initial system, force fields, protocols for simulation are compared. Main results on: order parameter, head group and chain conformation, water penetration profile, chain tilts, pair-correlation function between atoms of lipid and water, diffusion of ions and ligands are discussed. The review gives application and limitation of MD method for studying lipid water system.     

纳米尺度孔隙内气体导热系数的分子动力学模拟

应用Lennard-Jone作用势,在300K和0.1MPa条件下,对边长20nm的立方体孔隙内氮气的导热系数进行了平衡分子动力学模拟.结果得出分子分速度和速率的分布与统计力学得到的Maxwell速度和速率分布曲线基本一致,并且分子的平均自由程受到孔隙壁的严格限制.通过Green-Kubo关系式计算得出了孔隙内氮气的导热系数,并与文献中的结果进行了比较,模拟结果接近于实验值,仅为同样条件下自由空间氮气的导热系数的1/3左右.     

Molecular dynamics simulation of a 13-mer duplex DNA: a PvuII substrate

Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water are carried out under following conditions: (i) unconstrained at 300 K (230 ps); (ii) unconstrained at 283 K (500 ps); (iii) Watson-Crick basepair constrained at 283 K (1 ns); and (iv) Watson-Crick basepair constrained with ions at 283 K (1.2 ns). In all these simulation studies, the molecule was observed to be bending and maximum distortions in the double helix around was seen around the G7:C7' basepair, which is the phosphodiester bond that is cleaved by PvuII. Analysis of MD simulation with ions carried out for 1.2 ns also pointed out that the conformation of double helix alternates between a conformation close to B-form and close to A-form. It is argued that a bent non-standard conformation is recognised by the PvuII enzyme. The maximum bend occurs at the G7:C7' region, weakening the phosphodiester bond and allows His48 to get placed in such a fashion to permit the scission through a general base mechanism. The bending and distortion observed is a property of the sequence which acts as a substrate for PvuII enzyme. This is confirmed by carrying out MD studies on the Dickerson's sequence d(CGCGAATTCGCG)2 as a reference molecule, which practically does not bend or get deformed.     

液态Cu等温凝固的分子动力学模拟

使用Tight-binding势函数,对液态Cu在等温凝固过程中的结构变化进行了分子动力学模拟(MD模拟)计算,得到体系在不同温度下的双体分布函数和配位数分布等静态结构信息,对等温凝固过程中FCC短程有序结构可能发生的变化以及由此导致的H-A键型变化进行了分析,并结合键对分析方法计算了不同弛豫时间下典型短程有序结构的分布.计算表明,在Cu凝固结晶相变过程中1551键应是先向1541键转化,初始三维结构的形成可能主要依赖于Cu原子在两个方向上的扩散和弛豫.     

Oligomeric assemblies of transport adenosine triphosphatases in a membrane bilayer

The comparative analysis of the own and literature data concerning the oligomeric organization of membrane-bound transport ATPases is presented. The results show that functional activity of protomeres is distinct from that of oligomeric assembly. It was demonstrated that ATP regulated interprotomer interaction in the oligomers including their dissociation into individual protomers. Evidence for changeable amount of protomers interacting with each other at different stages of the hydrolytic cycle is presented. The hypothesis that membrane lipids regulate the activity of membrane-bound oligomeric proteins affecting the efficiency of interprotomer interactions within the oligomeric complexes is justified.     

分子动力学模拟及其在冶金炉渣中的应用研究

细阐述分子动力学模拟的发展历程,分子动力学模拟的基本原理、运动方程的数值积分、边界条件的选取、原子间相互作用势函数、常用的系综以及热力学性质的计算. 介绍国内外学者对高温冶金炉渣结构以及炉渣的聚合度、黏滞度、致密度、离子结合强度、扩散系数等热力学性质的分子动力学模拟研究,结合实际存在的势函数发展缓慢及冶金炉渣结构的复杂性等问题,提出今后分子动力学模拟在冶金炉渣研究应用的发展方向.      

受限Lennard-Jones流体自扩散系数的分子动力学模拟

基于平衡态分子动力学(EMD)方法,建立了受限空间中的Lennard-Jones(LJ)流体自扩散模型.采用径向分布函数对LJ流体微观结构进行了表征,模拟了LJ流体在纳米尺度受限空间中的自扩散系数,并将其与相应的自由空间内LJ流体自扩散系数进行了比较,同时从分子水平分析了温度、密度和受限尺度对自扩散系数的影响.研究结果表明:受限空间内LJ流体自扩散系数随受限尺度的增大而逐渐增大;与自由空间一样,受限LJ流体自扩散系数也随温度的升高而近似线性增加,随密度的增加而逐渐减小,但始终小于相同温度、密度条件下自由空间所对应值.并且根据文献中的实验数据验证了该模型的准确性.     

Molecular dynamics simulation of the melting of uranium dioxide nanocrystals

The melting of vacuum-isolated uranium dioxide (UO₂) nanocrystals is studied by molecular dynamics simulation using the approximation of pair potentials and point ions. The size dependences of the melting temperature, the heat of melting, and the density jump of cubic crystals up to 1000 nm³ in size are measured for the ten most relevant sets of pair potentials. The linear and parabolic extrapolations of these dependences to macroscopic sizes are considered, and the parabolic extrapolation is found to be better for analyzing data on the melting temperature and heat.     

Molecular dynamics simulation of protein folding with supersecondary structure constraints

We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 A.     

金纳米颗粒烧结的分子动力学模拟

采用分子动力学模拟方法研究了不同尺寸Au纳米颗粒在烧结过程中晶型转变及烧结颈长大机制.研究发现纳米颗粒的烧结颈生长主要分为两个阶段：初始烧结颈的快速形成阶段和烧结颈的稳定长大阶段.不同尺寸纳米颗粒烧结过程中烧结颈长大的主要机制不同：当颗粒尺寸为4 nm时,原子迁移主要受晶界（或位错）滑移、表面扩散和黏性流动控制;当尺寸在6nm左右时,原子迁移主要受晶界扩散、表面扩散和黏性流动控制;当颗粒尺寸为9 nm时,原子迁移主要受晶界扩散和表面扩散控制.烧结过程中Au颗粒的fcc结构会向无定形结构转变.此外,小尺寸的纳米颗粒在烧结过程中由于位错或晶界滑移、原子的黏性流动等因素会形成hcp结构.     

Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature

Molecular dynamics simulations of 500 ps were performed on a system consisting of a bilayer of 64 molecules of the lipid dipalmitoylphosphatidylcholine and 23 water molecules per lipid at an isotropic pressure of 1 atm and 50 degrees C. Special attention was devoted to reproduce the correct density of the lipid, because this quantity is known experimentally with a precision better than 1%. For this purpose, the Lennard-Jones parameters of the hydrocarbon chains were adjusted by simulating a system consisting of 128 pentadecane molecules and varying the Lennard-Jones parameters until the experimental density and heat of vaporization were obtained. With these parameters the lipid density resulted in perfect agreement with the experimental density. The orientational order parameter of the hydrocarbon chains agreed perfectly well with the experimental values, which, because of its correlation with the area per lipid, makes it possible to give a proper estimate of the area per lipid of 0.61 +/- 0.01 nm2.     

Molecular dynamics simulation of glycoprotein-glycans of immunoglobulin G and immunoglobulin M

In this paper, the authors introduce a workflow model. The development of computer network technology enables us to share the distributed data in real time. It is a considerable significance in the practical application of network capabilities not only to office work but also to the medical environment. In order to construct a well-connected, managed post (environment, scene), a model is needed to design the workflow. Here we propose a workflow model to cope with the scene of unforeseen events that we usually encounter in daily clinical activities. We give careful consideration to the ability of this model to manage dynamic changes within the workflow and describe its application to a medical scene (triage) and then carry out simulations based on this model. The authors are able to demonstrate the validity of this model through this simulation.     

Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes

The class I major histocompatibility complex-encoded HLA-B*2705 protein was simulated in complex with six different peptides exhibiting unexpected structure-activity relationships. Various structural and dynamical properties of the solvated protein-peptide complexes (atomic fluctuations, solvent-accessible surface areas, hydrogen bonding pattern) were found to be in qualitative agreement with the available binding data. Peptides that have been experimentally shown to bind to the protein remained tightly anchored to the MHC molecule, whereas nonbinders were significantly more weakly complexes to the protein and progressively dissociate from it at their N- and C-terminal ends. The molecular dynamics simulations emphasize the unexpectedly important role of secondary anchors (positions 1 and 3) in influencing the MHC-bound conformation of antigenic nonapeptides. Furthermore, it confirms that dominant anchor residues cannot solely account for peptide binding to a class I MHC molecule. The molecular dynamics method could be used as a complementary tool to T cell epitope predictions from the primary sequences of proteins of immunological interest. It is better suited to MHC proteins for which a crystal structure already exists. Furthermore, it may facilitate the engineering of T cell epitopes as well as the rational design of new MHC inhibitors designed to fit optimally the peptide binding cleft.