蛋白质折叠的非格子模型

用粒子群算法对蛋白质的简化模型进行研究,体系中各原子间的相互作用由一物理势表示.通过全局优化体系的势函数得到蛋白质的结构数据,与实验测得的结构数据之间的均方根偏差RMSD为6.12(A).记录了能量最小值及回转半径随程序运行步骤的变化以及RMSD值与最低能量值的分布关系,这些结果反映了蛋白质折叠的一些基本特征.     

Energy Profile Fluctuations in Dissipative Nonequilibrium Stationary States

The exact large deviation function (ldf) for the fluctuations of the energy density field is computed for a chain of Ising (or more generally Potts) spins driven by a zero-temperature (dissipative) Glauber dynamics and sustained in a nontrivial stationary regime by an arbitrary energy injection mechanism at the boundary of the system. It is found that this ldf is independent of the dynamical details of the energy injection, and that the energy fluctuations, unlike conservative systems in a nonequilibrium state, are not spatially correlated in the stationary regime.This revised version was published online in March 2005 with corrections to the page numbers.     

Quasi-physical Algorithm for Protein Folding in an Off-Lattice Model

We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard-Jones potentials. By incorporating an extra energy contribution into the original potential function, we replace the original constrained problem with an unconstrained minimization of a mixed potential function. As such an efficient quasi-physical algorithm for solving the protein folding problem is presented. We apply the proposed algorithm to sequences with up to 55 residues and compare the computational results with the putative lowest energy found by several of the most famous algorithms, showing the advantages of our method. The dynamic behavior of the quasi-physlcal algorithm is also discussed.     

耗散粒子动力学模拟方法在软物质体系研究中的一些进展与应用

软物质是指处于固体和理想流体之间的复杂态物质,主要包括聚合物、表面活性剂、液晶、胶体悬浮液、以及生物大分子等。软物质能够对外界微小的作用产生强烈的非线性响应,并展现出丰富的有序自组装相态。作为一种新颖的模拟技术,耗散粒子动力学方法非常适合在介观尺度上对软物质体系的复杂行为进行合理的描述。本文对耗散粒子动力学模拟方法的发展及一些应用进行了系统评述。耗散粒子动力学模拟方法体现了分子动力学与格子Boltzmann模型的优点,通过与其它理论模型（如Flory-Huggins理论、Smoothed particle hydrodynamics模型等）相结合,该方法能够在介观尺度上有效地研究聚合物熔体和溶液体系、生物膜及囊泡体系以及胶体悬浮液等体系的行为。这些研究结果,对新材料的研发、特殊材料的制备、以及材料加工条件的选择具有十分重要的科学意义和实际应用价值。     

Self-Assembly Behavior of Amphiphilic Copolymer Characterized by Dissipative Particle Dynamics Simulation

Amphiphilic polyacrylamide copolymer aqueous solutions have a special behavior of self-assembly, which is attributed to their composition and molecular structure. In this work, methoxy polyethylene glycol acrylate (PEGA) and/or dodecafluoroheptyl methacrylate (DF) were introduced into the partially hydrolyzed polyacrylamide (HDPAM) molecular chains to enhance their hydrophilicity and hydrophobicity, respectively. The self-assembly behaviors of these copolymers in water solution and salt solution were studied by dissipative particle dynamics (DPD). Results showed that the amphiphilic copolymer (HDPAM-PEGA-DF) had a stronger self-assembly behavior than the hydrophobic modified polyacrylamide copolymer (HDPAM-DF).     

Nonextensive Statistical Mechanics Application to Vibrational Dynamics of Protein Folding

The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. We employ exact expressions for classical harmonic oscillators by considering the unnormalized constraints. As q→1, we show that these approximations agree with the result of Gaussian network model.     

Dynamics of Entanglement for a Two-Parameter Class of States in a Qubit-Qutrit System

We investigate the dynamics of entanglement for a two-parameter class of states in a hybrid qubit-qutrit system under the influence of various dissipative channels. Our results show that entanglement sudden death (ESD) is a general phenomenon and it usually takes place in a qubit-qutrit system interacting with various noisy channels, not only the case with dephasing and depolarizing channels observed by others. ESD can only be avoided for some initially entangled states under some particular noisy channels. Moreover, the environment affects the entanglement and the coherence of the system in very different ways.     

Effects of f(R) Model on Dynamics of Axial Shear-Free Dissipative Fluids

We present a general analysis on non-static axial system with dissipative shear-free anisotropic fluid using polynomial inflationary f(R) model.We study the effects of dissipation on the dynamics of geodesic matter distribution.This leads the system either to rotation-free or expansion-free but not both simultaneously under geodesic condition.It is found that the system preserves its symmetry in both cases.For the rotation-free case,when there is no dissipation and Ricci scalar is constant,the axial system reduces to FRW universe model.This is exactly the same result obtained in general relativity.     

介观尺度通道内多相流动的耗散粒子动力学模拟

采用四次方光滑函数构造了包含远程吸引近距排斥的保守力势函数, 应用该势函数, 采用耗散粒子动力学方法, 对十字型微通道内的多相流动进行了计算. 计算结果表明, 该势函数能有效模拟十字型微通道内的流动过程及模式. 关键词： 多相流 耗散粒子动力学 保守力势函数     

介观尺度流体绕流球体的耗散粒子动力学模拟

采用耗散粒子动力学(dissipative particle dynamics, DPD)方法, 对两平行平板间流体绕流三维球体进行了计算. 球体和平行平板由达到平衡状态的冻结DPD粒子组成, 流体在不同无量纲外力驱动下流动, 球体受力由组成球体的所有冻结DPD粒子求和得到. 流动达到充分发展后, 输出球体在流动方向的受力, 并计算球体的阻力系数, 与文献中的关联式进行了对比. 结果表明, 在Re≤qslant 100的范围内, DPD方法能较准确地计算出阻力系数, 在较大雷诺数时, 由于流     

介观尺度流体绕流球体的耗散粒子动力学模拟

采用耗散粒子动力学(dissipative particle dynamics, DPD)方法, 对两平行平板间流体绕流三维球体进行了计算. 球体和平行平板由达到平衡状态的冻结DPD粒子组成, 流体在不同无量纲外力驱动下流动, 球体受力由组成球体的所有冻结DPD粒子求和得到. 流动达到充分发展后, 输出球体在流动方向的受力, 并计算球体的阻力系数, 与文献中的关联式进行了对比. 结果表明, 在Re≤qslant 100的范围内, DPD方法能较准确地计算出阻力系数, 在较大雷诺数时, 由于流体的压缩性导致计算结果出现差异.     

高压NMR在蛋白质结构和动力学研究中的应用

与温度一样,压力是基本的热力学变量.蛋白质在溶液中是多种构象的热力学平衡体.在不同的温度和压力等条件下,蛋白质包括折叠构象、变性构象以及各种中间体在内的不同构象的存在频率各不相同.当用压力作为扰动时,由于这些构象的偏摩尔体积不同,它们的存在频率便会因而发生变化,加压可将平衡向具有较小偏摩尔体积的方向移动.因此,利用高压核磁共振(NMR)技术,不仅可以研究高压对蛋白质结构和动力学的影响,还可以通过改变压力,在更为广泛的构象空间研究蛋白质结构和动力学.例如,利用平衡体系在加压时向体积小的构象方向移动这一特性,能够对在常压下因其存在频率低而难于检测、但在高压下因其体积小而存在频率增加了的构象进行深入研究,而这些构象往往与蛋白质的功能密切相关.该篇综述首先介绍了高压在蛋白质科学研究中的历史、有关概念和高压NMR技术;其次,结合实例,阐述高压NMR技术在蛋白质结构、折叠以及动力学研究中的应用;最后,对高压NMR技术在蛋白质研究中的应用前景进行展望.     

Dissipative particle dynamics simulation for the effect of interaction on the self-assembly behaviours of heterogemini surfactant in aqueous solution

Self-assembly behaviours of heterogemini surfactant in aqueous solution have been explored by means of dissipative particle dynamics simulation. Five kinds of heterogemini molecules are involved and a variety of novel morphologies have been obtained. Results based on detailed analyses show that head–tail and tail–water interactions play different roles in the formation of six kinds of self-assembly morphologies. The key factors are tail–water and head–tail repulsions separately for morphology with small (sphere) and relatively large scales (rod, planar grid, lamella and tunnels). Besides, the appearance of network in only one system can be regarded as a particular type of intermediate state. Coexistence of several sphere micelles in an amplified dissipative particle dynamics system gives us a better understanding of interactions inside the soft matter. Our simulation results can provide a theoretical guide to further research towards self-assembly behaviours of heterogemini surfactants and practical applications of these matters.     

用于真实蛋白质结构预测的一种新的优化方法

用“相对熵”作为优化函数 ,提出了一个有效快速的折叠预测优化算法 .使用了非格点模型 ,预测只关心蛋白质主链的走向 .其中只用到了蛋白质主链上的两两连续的Cα 原子间的距离信息以及 2 0种氨基酸的接触势的一个扩展形式 .对几个真实蛋白质做了算法测试 ,预测的初始结构都为比较大的去折叠态 ,预测构象相对于它们天然结构的均方根偏差 (RMSD)为 5～ 7 .从原理上讲 ,该方法是对能量优化的改进 .     

Kerr介质中J-C模型的色散近似耗散动力学

应用全量子论研究了含Kerr介质的Jaynes-Cummings模型在色散近似下系统和子系统的相干性丢失及纠缠特性,在输入场为相干场假设下计算了线性熵.结果表明,原子相干性丢失与Kerr效应无关,场和原子-场系统的相干性丢失因Kerr介质的存在而增强,原子与场之间的纠缠因Kerr效应而受到压制,场的相干性时间演化规律在定性和定量两方面都受到腔耗的影响.Kerr介质对场线性熵的作用要通过腔耗才能展现出来.     

抗冻蛋白与细胞色素蛋白P450水合层重定向动力学的比较分析

抗冻蛋白抑制冰结晶的机制仍不清晰. 例如,抗冻蛋白的水合水动力学及其与抗冻活性之间的关系尚无定论. 本文通过理论模拟,比较研究了来自云杉蚜虫的抗冻蛋白和细胞色素蛋白P450第一水合层中的水分子重定向动力学. 氢键供体水分子周围潜在受体水分子数量的增加导致水分子之间氢键交换的加速. 因此,抗冻蛋白抗冻活性区周围水分子的跳跃重定向动力学加速. 由于氢键交换的相互耦合和激发,随着氢键交换的加速,整个氢键网络的重排和水分子的框架重定向也被加速. 因此,抗冻蛋白的水分子重定向动力学比细胞色素蛋白P450更快. 本研究为理解抗冻蛋白提供了新的物理图像,并对抗冻蛋白的抗冻机理有了新的认识.     

基于NMR自旋弛豫技术的蛋白质动力学研究

蛋白质的三维结构在很多情况下不能很好地解释其在生理过程中的作用机制. 动力学研究能够获悉蛋白质在不同时间尺度下的内运动信息,建立起动态结构和生物功能的联系. 该文综述了通过NMR自旋弛豫技术研究蛋白质动力学的原理和方法：ps~ns的快运动分析主要采用约化谱密度函数映射和Modelfree方法;μs~ms的慢运动涉及化学/构象交换过程,常借助CPMG和R_1ρ弛豫色散手段. 基于NMR的蛋白质动力学研究,将蛋白质科学从三维空间结构推进到四维时空结构的新层面.     

Study on the Amyloid A $beta$42 with Accelerated Molecular Dynamics Simulations *

One major cause of Alzheimer's disease (AD) is evidently due to the aggregation and deposition of amyloid $beta$ peptides (A$beta$) in the brain tissue of the patient. Preventing misfolding and self-aggregation of A$beta$ protein can reduce the formation of highly toxic polymer, which is important for the treatment of AD. Among them, the $alpha$-helix consisting of 42 residues (A$beta$42) is the main component of senile plaques in AD. In this paper, 500 ns accelerated molecular dynamics are performed at different temperatures (300 K, 350 K, 400 K, 450 K) to study of the effect of temperature-induced conformation changes of A$beta$42 protein during the unfolding process respectively.     

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics(MD) simulation in aqueous solution four fragments cut out of a protein G, including oneα-helix(seq B: KVFKQYAN), two β-turns(seq A: LNGKTLKG and seq C: YDDATKTF), and one β-strand(seq D:DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seq A and seq B have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seq D alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seq C is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seq C in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.