Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

Flexible representations of dynamics are used in object manipulation.

To manipulate an object skillfully, the brain must learn its dynamics, specifying the mapping between applied force and motion. A fundamental issue in sensorimotor control is whether such dynamics are represented in an extrinsic frame of reference tied to the object or an intrinsic frame of reference linked to the arm. Although previous studies have suggested that objects are represented in arm-centered coordinates [1-6], all of these studies have used objects with unusual and complex dynamics. Thus, it is not known how objects with natural dynamics are represented. Here we show that objects with simple (or familiar) dynamics and those with complex (or unfamiliar) dynamics are represented in object- and arm-centered coordinates, respectively. We also show that objects with simple dynamics are represented with an intermediate coordinate frame when vision of the object is removed. These results indicate that object dynamics can be flexibly represented in different coordinate frames by the brain. We suggest that with experience, the representation of the dynamics of a manipulated object may shift from a coordinate frame tied to the arm toward one that is linked to the object. The additional complexity required to represent dynamics in object-centered coordinates would be economical for familiar objects because such a representation allows object use regardless of the orientation of the object in hand.

Molecular dynamics simulation of hydrogen enhancing dislocation emission

The interactive pair potential between Al and H is obtained based on the ab initio calculation and the Chen-Mobius 3D lattice inversion formula. By utilizing the pair potentials calculated, the effects of hydrogen on the dislocation emission from crack tip have been studied. The simulated result shows that hydrogen can reduce the cohesive strength for Al single crystal, and then the critical stress intensity factor for partial dislocation emission decreases from 0.11 MPa root m (C-H = 0) to 0.075 MPa root m (C-H=0.72%) and 0.06 MPa root m (C-H = 1.44%). This indicates thar hydrogen can enhance the dislocation emission. The simulation also shows that atoms of hydrogen can gather and turn into small bubbles, resulting in enhancement of the equilibrium vacancy concentration.

Intracellular demography and the dynamics of Salmonella enterica infections.

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.

Modelling within-host spatiotemporal dynamics of invasive bacterial disease

Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS]) in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host-pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host-pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics. © 2008 Grant et al.

Get Acquaited with Rarefied Gas Dynamics

以通俗易懂的方式介绍了空气动力学当气体间断分子效应显著时发展起来的特殊分支--稀薄气体动力学。讨论了非平衡现象与稀薄气体动力学的关系。通过与8速度气体模型的间断Boltzmann方程的对比,解释了Boltzmann方程碰撞项的物理意义和数学困难,简要综述了其一般解法。讨论了分子在物体表面的反射和问题的边界条件,着重介绍了直接模拟Monte Carlo(DSMC)方法和为克服低速稀薄流动(如MEMS中流动)中模拟困难的信息保存(IP)方法。

Molecular Dynamics Modeling of Diffusion Bonding

Molecular dynamics simulations on diffusion bonding of Cu-Ag showed that the thickness of the interfacial region depended on the stress. The interfacial region became amorphous during diffusion bonding, and it would normally transform from amorphous into crystalline structure when the structure was cooled to the room temperature.

Molecular Dynamics Simulation of the Uniaxial Tensile Deformation of Nanocrystalline Copper

纳米材料是由尺度在1～100 nm的微小颗粒组成的体系,由于它具有独特的性能而备受关注.本文简要地回顾了分子动力学在纳米材料研究中的应用,并运用它模拟了平均晶粒尺寸从1.79～5.38nm的纳米晶体的力学性质.模拟结果显示:随着晶粒尺寸的减小,系统与晶粒内部的原子平均能量升高,而晶界上则有所下降;纳米晶体的弹性模量要小于普通多晶体,并随着晶粒尺寸的减小而减小;纳米晶铜的强度随着晶粒的减小而减小,显示了反常的Hall-Petch效应;纳米晶体的塑性变形主要是通过晶界滑移与运动,以及晶粒的转动来实现的;位错运动起着次要的、有限的作用;在较大的应变下(约大于5%),位错运动开始起作用;这种作用随着晶粒尺寸的增加而愈加明显.

The Influence of Grain Size and Temperature on the mechanical Deformation of Nanocrystalline Materials: Molecular Dynamics Simulation

Nanocrystalline (nc) materials are characterized by a typical grain size of 1-100nm. The uniaxial tensile deformation of computer-generated nc samples, with several average grain sizes ranging from 5.38 to 1.79nm, is simulated by using molecular dynamics with the Finnis-Sinclair potential. The influence of grain size and temperature on the mechanical deformation is studied in this paper. The simulated nc samples show a reverse Hall-Petch effect. Grain boundary sliding and motion, as well as grain rotation are mainly responsible for the plastic deformation. At low temperatures, partial dislocation activities play a minor role during the deformation. This role begins to occur at the strain of 5%, and is progressively remarkable with increasing average grain size. However, at elevated temperatures no dislocation activity is detected, and the diffusion of grain boundaries may come into play.