A physical organic mechanistic approach to understanding the complex reaction network of hemostasis (blood clotting)

This review focuses on how the mechanistic approach of physical organic chemistry can be used to elucidate the mechanisms behind complex biochemical networks. The dynamics of biochemical reaction networks is difficult to describe by considering their individual reactions, just as the dynamics of organic reactions is difficult to describe by considering individual electrons and atomic nuclei. Physical organic chemists have developed a useful set of tools to predict the outcome of organic reactions by separating the interacting molecules into modules (functional groups), and defining general rules for how these modules interact (mechanisms). This review shows how these tools of physical organic chemistry may be used to describe reaction networks. In addition, it describes the application of these tools to develop a mechanistic understanding of the dynamics of the complex network of hemostasis, which regulates blood clotting. Copyright © 2007 John Wiley & Sons, Ltd.     

岩盐结构氧化锌物态方程的分子动力学模拟

利用分子动力学方法和有效经验对势模型对ZnO岩盐结构高温高压下的物态方程进行了研究， 发现分子动力学方法得到的ZnO岩盐结构的摩尔体积(300?1273 K，3.2?10.4 GPa)和实验结果吻合；另外，基于经验势模型的可靠性预测了1373?2273 K和0? 50 GPa的ZnO岩盐结构的P-V -T关系，并利用相应的热力学公式拟合得到了ZnO岩盐结构常态下的线性热膨胀系数、等温体模量及其对压力的一阶导数等重要的热力学参量．     

Investigation of the behavior of an Ising metamagnet under the influence of a field using Glauber dynamics

In this study, the kinetics of the Ising metamagnet where the interlayer interactions are ferromagnetic has been investigated under the mean field approximation. In describing the kinetics of the system, Glauber stochastic dynamics in the presence of an external field which performs time-dependent oscillations, has been utilized. Obtained results could be identified by two distinct types: the asymmetric solutions oscillating in the vicinity of finite values where the lattice magnetization has different values and the symmetric solutions being zero where the sublattice magnetizations are equal to each other. On the other hand, it has been observed that in the case where the system's initial state has a homogenous magnetization it exhibits two different periodical behaviors in the course of time.     

A continuous model of human dynamics

Ideas and tools from statistical physics have recently been applied to the investigation of human dynamics. The timing of human activities, in particular, has been studied both experimentally and analytically. Empirical data show that, in many different situations, the time interval separating two consecutive tasks executed by an individual follows a heavy-tailed probability distribution rather than Poisson statistics. To account for this data, human behaviour has been viewed as a decision-based queuing system where individuals select and execute tasks belonging to a finite list of items as an increasing function of a task priority parameter. It is then possible to obtain analytically the empirical result P(τ)∼1/τ, where P(τ) is the waiting time probability distribution.Here a continuous model of human dynamics is introduced using instead an infinite queuing list. In contrast with the results obtained by other models in the finite case we find a waiting time distribution explicitly depending on the priority distribution density function ρ. The power-law scaling P(τ)∼1/τ is then recovered when ρ is exponentially distributed.     

Effects of thermal energy deposition on material ejection in poly(methyl methacrylate)

The effects of absorption of 7.9 and 5.0 eV photons by the polymer poly(methyl methacrylate) are studied using molecular dynamics simulations. By rapidly depositing a critical amount of thermal energy in the surface region (greater than 0.03 eV Å⁻³), a pressure wave is formed which causes spallation of the substrate. If there is only one photon absorbed per monomer unit of the polymer, the 7.9 eV photons can supply sufficient energy density to initiate ejection.     

Transient soot dynamics in turbulent nonpremixed ethylene-air counterflow flames

The dynamics of soot formation in turbulent ethylene-air nonpremixed counterflow flames is studied using direct numerical simulation (DNS) with a semi-empirical soot model and the discrete ordinate method (DOM) as a radiation solver. Transient characteristics of soot behavior are studies by a model problem of flame interaction with turbulence inflow at various intensities. The interaction between soot and turbulence reveals that the soot volume fraction depends on the combined effects of the local conditions of flow, temperature, and fuel concentration, while the soot number density depends predominantly on the high temperature regions. Depending on the relative strength between mixing and reaction, the effects of turbulence on the soot formation lead to three distinct paths in deviating the data points away from the laminar flame conditions. It is found that turbulence has twofold effects of increasing the overall soot yield by generating additional flame volume and of reducing soot by dissipating soot pockets out of high-temperature regions. The relative importance between the two effects depends on the relative length scales of turbulence and flame, suggesting that a nonmonotonic response of soot yield to turbulence level may be expected in turbulent combustion.     

Traffic dispersion induced by noise in off-lattice model

We study the dispersion of vehicles induced by speed fluctuation on a single-lane highway under open boundary. We extend the cellular automaton model on one-dimensional lattice to the real-variable model on off-lattice (continuous-in space model) in order to take into account the fluctuation of vehicular speed. Vehicles extend over the highway when moving forward. The characteristics of traffic dispersion are derived. It is shown that vehicular traffic exhibits scaling property. When a vehicle accelerates for following the vehicle ahead, vehicles move forming a cluster without dispersion. The relationship between the width of vehicular cluster and acceleration rate is clarified.     

束团磁压缩的高阶限制

研究了束团压缩中的高阶效应, 结果表明存在高阶项的压缩限制, 压缩后束团的长度比线性理论值长, 初始为均匀分布的束团较高斯分布更易压缩, 在相同的加速段与磁压缩器条件下, 其所获得的束团长度较短, 最后作了数值计算, 结果与理论相符.     

基于PIC方法的二维束流动力学模拟程序及其初步应用

为了深入研究强流负氢束在强流质子回旋加速器CYCIAE-100轴向注入线中的传输, 利用split-operator方法分解外场和束流自身的空间电荷场的作用. 对外 场利用单粒子跟踪技术, 采用一阶线性近似; 对空间电荷场采用PIC方法, 利用 快速傅里叶变换求解Poisson方程. 用FORTRAN95语言开发了一个基于面向对象技术的二维宏粒子传输计算程序CYCPIC2D, 本程序可以计算任意分布的强流束在输运线上的传输.最后给出了对CYCIAE-100注入线的模拟计算结果, 并和程序ORBIT, TRACE 3-D的结果进行比对验证, 结果表明: 空间电荷效应在此注入线上有较大的影响, 而且3个程序计算的不同中性化的结果基本上一致; 束流强度达到几十毫安时, 基于PIC方法的两个程序CYCPIC2D和ORBIT的计算结果完全吻合, 而线性近似程序TRACE 3-D有明显差异.     

Adsorbate motions induced by vibrational mode coupling

Adsorbate motions are discussed with a primary attention focused on the coupling between a vibrational mode excited by ultrafast laser heated hot-electrons or by inelastic tunneling electrons with scanning tunneling microscope and the reaction coordinate (RC) mode. Recent experimental results have demonstrated an efficient reaction pathways involving an indirect excitation of a frustrated translational mode, rather than its direct excitation for adsorbate hopping on surfaces. Elementary processes are briefly described for hopping of CO molecules on a laser heated stepped Pt surface, where excitation of the frustrated rotation mode has been found to plays an indispensable. Calculation of the inelastic tunneling current (ITC) for excitation of the C-O stretch mode of a CO molecule is combined with a theory of anharmonic mode coupling to activate the frustrated translation mode above the barrier. The hopping rate as a function of the bias voltage agrees with the experimental result. An unified theory of single-, and two-electron processes for ITC-induced motions induced by an indirect excitation of the RC-mode via mode coupling is also applied to reproduce a crossover from hopping to desorption of a single NH₃ molecule on Cu(1 0 0) with an increase in the tunneling current.