颅内压动力学仿真

颅内压(Intracranial Pressure,ICP)研究在临床上有十分重要的意义。生理上由于内外多种原因会引起颅内压变化,而同时心搏、呼吸、以及神经调节等的影响也会使颅内压出现波动。本研究在动物(犬)实验结果的基础上,建立了反映颅内压变化的集中参数数学模型。模型中包括了脑血管床、脑脊液的生成和吸收、颅脑顺应性等模块以及这些模块之间的相互作用。脑血管顺应性是表征脑血管弹性程度的重要参量,仿真采用指数拟合的脑血管容积压力实验关系来表示脑血管顺应性。模型较好地模拟了颅内压动力学以及颅内压的波动,模型参数的变化和动物实验状况的变化相吻合,可以为临床颅内压监护及诊疗提供一定的参考。     

运动生物力学的计算机仿真研究

本文叙述运动生物力学计算仿真研究的原理和方法。介绍已经专家鉴定的人体腾空运动仿真软件系统的总体设计，对该系统已实现数学模型。三维影片解析技术，人体三维消隐藏线的动静态显示以及运动动作的定量分析和设计技术作了较详细的说明，文章最后给出了利用该仿真软件系统研究背跃式跳高过杆动作的实例，具体说明仿真研究的过程和对运动科学训练的意义。     

一个人体运动的数学模型

本文采用L-E法和铰分解法研究了人体运动的数学模型问题,给出了一种人体运动的规范建模方法。该方法适用于多种拓扑结构形式的人体运动（如空翻、步行、滑行等）,所得方程具有适合于计算机程式求解的特点。     

人眼房水动力学系统的建模与仿真方法研究

为从宏观上应用工程方法进一步研究房水运行机理,提出了人眼前节房水流动系统的动力学仿真模型。依据目前眼科界较为公认的房水运行和眼压反馈机制建立系统构架,基于对眼科解剖学与生理学相关理论的分析、流体力学基本原理和临床参数进行系统辨识与参数确定。运用数字仿真的方法分剐在正常生理平稳状况和激发试验状况下对模型进行了仿真运行,获得了和临床结论较为一致的结果。能较好地模拟房水运行机制,在与临床可测量参数一致的同时能获得一些不易测量的参数,为研究房水动力学提供依据。     

家蝇幼虫开发生态工程系统动力学仿真的研究

家蝇（Ｍｕｓｃａｄｏｍｅｓｔｉｃａ）幼虫以营养成分全、蛋白质含量高而逐渐引起人们重视,具有很高的开发利用价值和广阔的前景。系统动力学的发展为研究复杂系统提供了有效途径［１,２］。本文试用系统动力学方法建立家蝇幼虫开发生态工程仿真模型,以期解决这一研究...     

基于AnyBodyTM技术的人体运动建模方法

人体运动的建模与仿真是当今运动生物力学研究的一个热点.利用数值模型研究人体的运动规律,是人体运动研究的一个重要手段和有效工具.其关键技术在于应用逆向运动学方法求解人体运动,并获取人体运动中各个肌肉力学上技术参数.文中主要探讨基于AnyBodyTM System软件人体运动仿真的建模方法来研究人体运动力学规律,结合The AnyBodyTM system对人体运动具体应用,说明The AnyBodyTM system技术在人体运动仿真领域的优势.     

锦界生态工业园水资源系统动力学仿真与调控

如何合理开发利用水资源,保护区域生态环境,实现人与自然的和谐发展,是当今世界所面临的共同问题.以陕北锦界生态工业园水资源系统为例,在分析系统结构的基础上,构建了水资源系统动力学模型,确定水技术进步因子、水资源循环利用率、污水处理投资率、万元产值年耗水量、日人均用水量为调控参数,进行仿真模拟.结果表明,当水技术进步因子由1提高到1.6,水资源循环利用率由0.45提高到0.85,污水处理投资率由0.18提高到0.25,万元产值年耗水量由236.8 t·a-1降为175.4 t·a-1,日人均用水量由0.18 t·d-1降为0.12 t·d-1时,园区工业总产值增长率5年可达到44.4%,水资源存量年均增幅为0.03%,水资源供需比为2.25,系统达到相对最优状态.     

人体无支撑运动的数学模型

基于Hanavan[1]人体模型,本文建立了人体空中运动的一般数学模型,并利用微分方程数值解法对某些实际运动进行了模拟．结果表明该模型能用于反映人体空中无支撑运动的运动过程,并可应用于宇航、体操、技巧、跳水、舞蹈等等运动的研究．     

人体中的水

水是人体不可缺少的组成成分,是维持人体正常生理活动的重要营养物质。文中介绍了人体中水的含量,分布及生理功能,阐述了人体对水的需求与平衡以及人体内水平衡紊乱时所出现的脱水或水中毒的原因和特征。     

能源重化工工业园环境系统动力学仿真与调控

以锦界工业园环境系统为对象,在系统结构分析基础上,构建其系统动力学模型,并确定生产性投资比例、科技投资比例、环保投资比例、污水处理投资率、废气处理投资率、固废处理投资率为调控参数进行仿真。结果表明,当生产性投资比例由0.14提高到0.16,科技投资比例由0.02提高到0.04,环保投资比例由0.04提高到0.08,污水处理投资率由0.4下调为0.36,废气处理投资率由0.2提高到0.34,固废处理投资率由0.4下调为0.3时,园区年均工业总产值增长率达到21%,环境相对污染度年均降幅为8.1%,人口年增长率为4.7%,系统达到相对最优状态。因此,锦界工业园在环境管理中应采取以下措施:一是合理的调整生产、科技和环保的投资比例,适当降低生产性投资比例,增加科技投资和环保投资比例;二是合理的调整污水、废气和固废处理的投资比例,加强三废处理的基础设施建设,为构建完整的三废回收和处理系统奠定基础。     

Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules

We report a multiple time step algorithm applied to an atomistic Brownian dynamics simulation for simulating the long time scale dynamics of biomolecules. The algorithm was based on the original multiple time step method; a short time step was used to keep faster motions in local equilibrium. When applied to a 28-mer # # ! folded peptide, the simulation gave stable trajectories and the computation time was reduced by a factor of 160 compared to a conventional molecular dynamics simulation using explicit water molecules. We applied it for the folding simulation of a 13-mer ! -helical peptide, giving a successful folding simulation. These results indicate that the Brownian dynamics with the multiple time step algorithm is useful for studies of biomolecular motions by long time simulation.     

Molecular Dynamics Simulation of Hexamine and Suberic Acid

In order to perform a molecular dynamics (MD) simulation of the incommensurate crystalline structure hexamethylenetetramine suberate (C 6 H 12 N 4 )(HOOC-(CH 2 ) 6 -COOH), we present in a first step the separate simulations of the crystalline structure of each of the two pure components, hexamethylenetetramine (HMT) and suberic acid. The domain decomposition parallel MD program ddgmq is used for this purpose. A second-generation consistent force field (CFF91) is employed to describe the interactions between atoms. Starting from experimental crystal structures, both pure components were heated from low to high temperatures. Our MD results show that the HMT system can be well represented by CFF91. In the case of suberic acid the layered structure of the crystal is largely preserved although deviations in the unit cell lengths from the experimental values are ～10%. Rather than attempt a complex re-parametrisation of CFF91 we chose to impose a fixed compensating external pressure tensor to correct for the deficiencies of the chosen force field. After optimising this compensating external pressure tensor at one temperature we find that experimental lattice constants and angles can be well reproduced over a range of temperatures.     

Molecular Dynamics Simulation of Collective Motions in Binary Liquids

Collective dynamic properties of different kind of binary liquid mixtures have been investigated by molecular dynamics simulation. The study includes both the longitudinal and the transverse current spectra in simple liquid alloys, 1:1 molten salts and liquid binary mixtures of neutral particles with an ionic-like structure. These systems were chosen as representative of binary liquids with different static structures in order to analyse the effects of structural ordering on the mechanisms of dynamic collective properties. The effect of the mass asymmetry between the two species in the mixture has been also discussed from the results for two different mass ratios for each kind of structure. Two length scales have been considered. On the one hand, the hydrodynamic scale (low wave numbers), where the modes for the partial currents of the two species are characterised by very close frequencies. On the other hand, the molecular scale (higher wave numbers), where the characteristic frequencies for the two species show noticeable differences. Vibrational concentration current modes (optic modes) have been found in neutral mixtures though their influence is rather weak, being the collective dynamic properties of this kind of systems dominated by the mass current modes (acoustic modes). On the contrary, in mixtures of charged particles such as molten salts the contribution of the concentration (charge) currents to the collective dynamics is important and optic modes can be characterised by a well-defined frequency for a wide range of wave numbers. It has been observed that heavy particles have a more relevant role on the mass current correlations whereas light particles play a dominant role on the concentration current correlations. The overall results for the three kinds of liquid mixtures analysed in this paper show that both the longitudinal and transverse current spectra are little dependent on the static structure of the system whereas marked differences are revealed when the particles in the system are either neutral or carry an electric charge.     

Molecular Dynamics Simulation of Model Lipid Membranes: Structural Effects of Impurities

Abstract

The gel to fluid phase transition or ordered to disordered phase transition observed in biological membranes are simulated by using constant energy Molecular Dynamics. The surface part of the membrane is modelled as a two-dimensional matrix formed by the head groups of the phospholipid molecules. Head molecules which are modelled as three spheres fused with three force centers, interact with each other via van der Waals and Coulomb type interactions. The -so called- impurity or foreign molecule embedded in the surface represents the protein type molecule which is present in biological membranes and control its activity. It is modelled as a pentagon having one force centers in each corner. It also interacts with the surface molecules again via van der Waals and Coulomb type interactions. The surface density is kept constant in the simulations of the systems with or without impurity. Structural and orientational changes due to impurity were observed and proved by monitoring two-dimensional order parameter. It has been shown that melting of the surface or breakage of the ordering of the surface molecules becomes easier and ordered to disordered phase transition temperature was lowered by 100 K if the impurity is present.     

嗜温冷休克蛋白力致去折叠研究

嗜温冷休克蛋白拥有一个由五个β股形成的反平行β桶结构,目前已被用于蛋白质去折叠的研究。当使用机械力对嗜温冷休克蛋白进行拉伸研究时,发现嗜温冷休克蛋白的去折叠过程具有明显的中间态。在常速和常力两种情况下对嗜温冷休克蛋白进行拉伸分子动力学模拟,发现其在两种情况下具有相同的去折叠次序,即C端β片层首先去折叠,随后N端β片层去折叠;同时这两种模拟都表现出明确的中间态。研究结果表明,嗜温冷休克蛋白抵抗外力作用除了依赖链间氢键外,分子内的静电相互作用也发挥着重要的作用。     

Molecular Dynamics Simulation of Limiting Conductance for Li + Ion in Supercritical Water using Polarizable Models

We report results of molecular dynamics simulations of the limiting conductance of Li + ion in ambient water and in supercritical water using polarizable models for water and Li + . The limiting conductances of Li + in ambient water calculated from mean square displacement (MSD) using four points transferable intermolecular potential model (TIP4P), extended simple point charge model (SPC/E), and revised polarizable model 1 (RPOL1) are larger than the experimental value. The behavior of the limiting conductance of Li + in supercritical water using the RPOL models results in good agreement with experimental results for the limiting conductance of LiCl. The agreement of the RPOL1 model with the experimental results is much better than the RPOL2 model in the higher-density regime, whereas that of the RPOL2 model is much better than the RPOL1 model in the lower-density regime. Using the RPOL models (in contrast to the SPC/E model), the number of hydration water molecules around Li + is the dominating contributor to the limiting conductance in the higher-density regime. In agreement with the SPC/E model, the interaction strength between Li + and the hydration water molecules is a non-factor in the lower-density region since the potential energy per hydration water molecule decreases with decreasing water density at the lowest water densities.     

Simulation of Suspensions in Constricted Geometries by Dissipative Particle Dynamics

We investigate the flow of a suspension through a constriction by means of the mesoscopic technique known as dissipative particle dynamics (DPD). The dispersed phase was modeled as a set of soft spheres interacting through a conservative force while suspended and continuum phases interact via DPD forces. It is shown that a Poiseuille steady state is achieved in the presence of bounding walls and under a pressure gradient in a cylindrical pipe. Flow geometry in the laminar regime is explored and discussed for periodic conditions in the presence of a cylindrical narrowing or constriction.     

Classical Molecular Dynamics Simulation of Kappa Squared Factor in Resonance Energy Transfer for Linear Dipole Models

Molecular dynamics simulations of linear models interacting through a dipolar Kihara intermolecular potential are presented. Molecular orientation correlations are used to calculate the orientational factor kappa squared in the resonance energy transfer (RET) as a function of the intermolecular separation. The distance, R 0 (2/3), at which the simulated systems show an isotropic behavior is calculated and an analysis of the dependence of R 0 (2/3) on microscopic properties (molecular aspect ratio and dipole moment) as well on thermodynamics (temperature and density) is presented. An explanation of the use of metallic cations as probes in RET is given and some relations of our models with biological molecules are pointed out.     

Molecular Dynamics Simulation Study of the Interaction of Piscidin 1 with DPPC Bilayers: Structure-Activity Relationship

Abstract

To study structure-activity relationship of antimicrobial peptides and to design novel antimicrobial peptides with selectivity for bacterial cells, we have performed molecular dynamics simulations of the interaction of Piscidin (Pis1) and its two analogues (Pis1-AA and Pis1-PG) with dipalmitoylphosphatidylcholine (DPPC) bilayer through 45 ns. Our results inform us of the detailed location and orientation of the peptide with respect to the bilayer as well as provide about hydrogen-bond-formation patterns and electrostatics interactions. Simulations show that Pis1 and Pis-AA form the most hydrogen bonds and Pis-PG forms the fewest hydrogen bonds with lipid. Thus, Pis1 and Pis-AA should have stronger interactions with the lipid head group when compared to Pis-PG. Experimental studies have shown that Pis1 and Pis1-AA have a high antimicrobial and hemolytic activities, and Pis1-PG has low hemolytic activity while keeps potent antimicrobial activity. Our results complement the previous experimental studies. According to our MD results and previous experimental studies, Pis1 and Pis1-AA are more effective at the zwitterionic bilayer comparing Pis1-PG. These properties of Pis1-PG could be accordance with its low hemolytic activities.