Towards larger spatiotemporal scales in polymer simulations

Molecular dynamics simulations are useful tools to unveil molecular mechanisms of polymer phase separation,self-assembly,adsorption,and so on.Due to large molecular size and slow relaxation of the polymer chains,a great amount of issues related to large-distance chain displacement cannot be tackled easily with conventional molecular dynamic simulations.Systematic coarse-graining and enhanced sampling methods are two types of improvements that can boost spatiotemporal scales in polymer simulations.We present two typical ways to obtain the coarse-graining potential either by fitting to correct liquid structures or by fitting to available thermodynamic properties of polymer systems.The newly proposed anisotropic coarse-grained particle model can be used to describe aggregation and assembly of polymeric building blocks from disk-like micelles to Janus particles.We also present a stochastic polymerization model combined with coarse-grained simulations to investigate the problems strongly influenced by the coupling of polymerization and excluded volume effects.Finally,a facile implementation of integrated tempering sampling method is illustrated to be very efficient on bypassing local energy minima and having access to true equilibrium polymer structures.     

小蛋白天然结构与折叠速度关系的分子动力学模拟研究

用分子动力学模拟方法研究了小蛋白天然结构集合与其折叠速度的关系．根据蛋白质内存在接触的不同定义方式．利用分子动力学模拟方法得到了10个小蛋白的一系列构象集合,分析了其拓扑参数与折叠速度的关系,并与PDB单构象的情况进行了比较．用含主链重原子的方式定义接触,所计算的结果较好,天然结构集合所计算的拓扑参数与蛋白质折叠速度的关系可以更真实地反映实际情况．     

吹填中疏浚泥颗粒运移及分选若干关键问题的探讨

为了确定处理面积和选择合理的处理方法,以节约工程成本和达到良好的处理效果,需要对吹填时疏浚泥颗粒在堆场内运移及分选的规律进行研究。以泥沙运动力学为理论基础,结合南水北调东线江苏段淮安金宝航道N1疏浚泥堆场的现场调查和试验结果,对吹填时疏浚泥颗粒运移及分选若干关键问题(如堆场分区、疏浚泥分层特性、疏浚泥沉降行为、疏浚泥流体类型等)进行了深入的探讨,得出如下结论:①美国的疏浚工程手册EM1110-2-5027以粒径0.075 mm将堆场分为粗颗粒区和细颗粒区是合理、可应用于国内疏浚工程实践的,颗粒分选发生于细颗粒区;②吹填过程中堆场内上层泥浆一般为牛顿体和过渡区流体,淡水环境下颗粒的沉降行为主要为絮凝沉降,颗粒运移及分选主要发生于上层泥浆中,参与分选的颗粒主要为悬移质;③疏浚泥颗粒分选是在一定的水动力条件和堆场边界条件下,细颗粒在液相泥浆中运移时,由于粒度的差异而产生的分区域沉降行为。     

Simultaneous determination of protein structure and dynamics

We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy--for obtaining experimental information at the atomic level about the structural and dynamical features of proteins--with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.     

具有周期间断振荡系数抛物型方程的多尺度有限元法

针对一类具有周期间断振荡系数抛物型方程的初边值问题,提出了多尺度渐进展开式,在此基础上,发展了多尺度有限元方法,并给出相关的收敛性分析.数值计算结果表明该算法是有效的.     

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

Protein folding is inherently a heterogeneous process because of the very large number of microscopic pathways that connect the myriad unfolded conformations to the unique conformation of the native structure. In a first step towards the long-range goal of describing the distribution of pathways experimentally, F?rster resonance energy transfer (FRET) has been measured on single, freely diffusing molecules. Here we use this method to determine properties of the free-energy surface for folding that have not been obtained from ensemble experiments. We show that single-molecule FRET measurements of a small cold-shock protein expose equilibrium collapse of the unfolded polypeptide and allow us to calculate limits on the polypeptide reconfiguration time. From these results, limits on the height of the free-energy barrier to folding are obtained that are consistent with a simple statistical mechanical model, but not with the barriers derived from simulations using molecular dynamics. Unlike the activation energy, the free-energy barrier includes the activation entropy and thus has been elusive to experimental determination for any kinetic process in solution.     

Hybrid Decomposition Method in Parallel Molecular Dynamics Simulation Based on SMP Cluster Architecture

A hybrid decomposition method for molecular dynamics simulations was presented, using simultaneously spatial decomposition and force decomposition to fit the architecture of a cluster of symmetric multi-processor (SMP) nodes. The method distributes particles between nodes based on the spatial decom-position strategy to reduce inter-node communication costs. The method also partitions particle pairs within each node using the force decomposition strategy to improve the load balance for each node. Simulation results for a nucleation process with 4 000 000 particles show that the hybrid method achieves better parallel performance than either spatial or force decomposition alone, especially when applied to a large scale particle system with non-uniform spatial density.     

Vibrational properties of uracil

1 Introduction Spectroscopic behavior of biological macromole- cules, such as the nucleic acid (NA) bases, contained in non-interacting environments or their solvation, may help us clarify the role of these molecules in biological systems. There are many …     

Fractional stochastic description of hinge motions in single protein molecules

In this study, it is demonstrated that the motion of hinges in single protein molecules can be modeled as general fractional Langevin dynamics of harmonically bound particles driven by non-local Gaussian noise with a power-law correlation. This conclusion was justified by comparing the theoretical predictions of the proposed model to the existing molecular dynamics simulations performed on the M6I mutant of phage T4 lysozyme and E. coli ribonuclease H1.     

一种减小TOA测量距离中NLOS影响的DMS模型和估计算法

有效的滤波方法和多尺度估计是无线定位技术的重要研究方向。为了减小在蜂窝网无线定位中非视距传 播(NLOS)对波达时间(TOA)测量距离的误差影响,先结合NLOS误差特性对标准Kalman滤波进行修正,然后提 出将不同采样率的修正Kalman滤波方程与多个尺度联系起来,建立了一种动态多尺度系统(DMS)模型,并给出基 于Haar小波的实现方法。仿真结果表明,基于上述方法优于直接进行Kalman滤波的效果,能较大幅度地提高 TOA测量距离的精度。     

基于稳定流形的方法实现混沌系统的同步

在非保守自治系统中,许多混沌系统都可作为耗散系统,因此,在这样的混沌系统中存在至少一维的稳定流形,利用这些流形可以设计恰当的控制策略.基于稳定流形的方法实现混沌系统的同步是当混沌轨道进入到稳定流形的小邻域内的时候,开始施加控制信号.一旦两个非直接耦合的混沌系统的轨迹到达这些稳定流形,其误差系统渐进趋于原点,从而实现两系统的同步.并通过Chen系统和Rossler系统的分析和数值模拟研究验证了这种方法的可行性与有效性.     

含非线性摩擦的伺服系统连续模型直接辨识

为准确描述伺服系统的动态特性与摩擦非线性,提出了一种非线性连续模型直接辨识方法. 该方法以离散输入输出数据与速度方向的逻辑值作为辨识输入,通过等价变换将未知参数都转移到模型的线性部分中,再运用基于状态变量滤波器的直接辨识法求得未知参数,从而获得伺服系统的非线性连续模型. 通过仿真及在双向转台伺服系统的实验表明,该方法在有噪声的情况下仍能准确辨识出非线性连续模型,能准确描述伺服系统的动态特性.     

Transforming binding affinities from three dimensions to two with application to cadherin clustering

Membrane-bound receptors often form large assemblies resulting from binding to soluble ligands, cell-surface molecules on other cells and extracellular matrix proteins. For example, the association of membrane proteins with proteins on different cells (trans-interactions) can drive the oligomerization of proteins on the same cell (cis-interactions). A central problem in understanding the molecular basis of such phenomena is that equilibrium constants are generally measured in three-dimensional solution and are thus difficult to relate to the two-dimensional environment of a membrane surface. Here we present a theoretical treatment that converts three-dimensional affinities to two dimensions, accounting directly for the structure and dynamics of the membrane-bound molecules. Using a multiscale simulation approach, we apply the theory to explain the formation of ordered, junction-like clusters by classical cadherin adhesion proteins. The approach features atomic-scale molecular dynamics simulations to determine interdomain flexibility, Monte Carlo simulations of multidomain motion and lattice simulations of junction formation. A finding of general relevance is that changes in interdomain motion on trans-binding have a crucial role in driving the lateral, cis-, clustering of adhesion receptors.     

蛋白质折叠的计算机模拟

介绍了计算机模拟蛋白质折叠问题的背景、模型和意义。在对模型问题采用Ｍｏｎｔｅ－Ｃａｒｌｏ方法和单纯遗传算法得到能量最小构象的基础上,提出了适用的混合遗传算法,并通过计算机模拟试验对三种方法作了比较。     

基于非解析计算流体力学和离散单元法的大颗粒在流场中的高效率运动模拟

为实现占据多个流体网格的大颗粒在流场中运动的仿真,基于计算流体力学和离散单元法耦合(computational fluid dy namics-discrete element mothod,CFD-DEM),提出了一种新的数值方法.使用黏结颗粒模型将大颗粒近似表示为多个小球形颗粒黏结而成,基于非解析CFD-DEM方法计算流体对每个小球颗粒的作用力,将所有小球颗粒运动参数的平均值用于描述整个黏结颗粒的运动状态.通过黏性流体中球形大颗粒的沉降运动模拟,比较仿真结果与相关实验数据,结果表明:该方法不仅能准确模拟球形大颗粒的沉降运动,而且与浸没边界法相比计算效率更高.与传统的解析CFD-DEM方法相比,此方法还可以方便且准确地模拟三维情况下非球形大颗粒在流场中的运动.     

Structural mechanism of plant aquaporin gating

Plants counteract fluctuations in water supply by regulating all aquaporins in the cell plasma membrane. Channel closure results either from the dephosphorylation of two conserved serine residues under conditions of drought stress, or from the protonation of a conserved histidine residue following a drop in cytoplasmic pH due to anoxia during flooding. Here we report the X-ray structure of the spinach plasma membrane aquaporin SoPIP2;1 in its closed conformation at 2.1 A resolution and in its open conformation at 3.9 A resolution, and molecular dynamics simulations of the initial events governing gating. In the closed conformation loop D caps the channel from the cytoplasm and thereby occludes the pore. In the open conformation loop D is displaced up to 16 A and this movement opens a hydrophobic gate blocking the channel entrance from the cytoplasm. These results reveal a molecular gating mechanism which appears conserved throughout all plant plasma membrane aquaporins.     

基于改进遗传算法的最快爬升航迹的优化分析

主要介绍一种基于改进遗传算法的优化技术,利用遗传算法优越的全局搜索的能力,研究了飞行性能中的最快爬升性能.使用改进遗传算法对快升航迹和最佳爬升速度进行了寻优优化,对遗传算法优化快升的航迹和接近最快爬升方式的航迹进行了对比,表明,以遗传算法优化的快升航迹进行爬升,飞机可以最快的爬升到巡航高度.而且本算法以及程序具有一定的通用性适用于其它求最佳轨迹爬升的航迹优化.     

Structure and function of an irreversible agonist-β(2) adrenoceptor complex

G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, the molecular basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystallization of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human β(2) adrenergic receptor (β(2)AR) as a guide, we designed a β(2)AR agonist that can be covalently tethered to a specific site on the receptor through a disulphide bond. The covalent β(2)AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystallized a covalent agonist-bound β(2)AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and determined its structure at 3.5?? resolution. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30?μs) molecular dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.     

基于多尺度跃层卷积神经网络的精细车型识别

为解决精细车型识别中特征不具有代表性,且识别准确率低的问题,提出了基于多尺度跃层卷积神经网络(CNN)的车型识别方法。通过多个不同尺度的跃层卷积神经网络,提取适用于精细车型识别的低层局部特征和高层全局特征,并分别训练Softmax分类器。利用自适应方式融合方法,将多个单一尺度跃层卷积神经网络的识别结果进行融合,调整不同网络对识别结果的贡献。实验中车型识别准确率达到97.59%。实验结果表明多尺度跃层卷积神经网络适用于精细的车型识别,并能提高识别的准确率。     

反馈线性化方法在锅炉-汽轮机系统控制中的应用

为提高锅炉 -汽轮机系统的信号跟踪和抗干扰能力 ,利用输入 -状态反馈线性化和输入 -输出反馈线性化方法分别设计了锅炉 -汽轮机系统的控制律。对于输入 -状态线性化方法由于输入状态为线性关系 ,因此系统可以在较大的范围内正常的工作。对于输入 -输出线性化方法可以验证系统在平衡点邻域零动态稳定 ,然而计算机仿真表明利用输入 -输出反馈线性化设计的控制器由于零动态的稳定范围较小 ,系统只能工作在工作点的邻域。基于以上结果对输入 -状态和输入 -输出反馈线性化方法进行了比较分析。计算机仿真表明利用输入 -状态线性化方法所设计的控制器具有良好的信号跟踪和抗干扰能力