Non-linear dynamic phenomena in the behaviour of a railway wheelset model

A dicone moving on a pair of cylindrical rails can be considered as a simplified model of a railway wheelset. Taking into account the non-linear friction laws of rolling contact, the equations of motion for this non-linear mechanical system result in a set of differential-algebraic equations. Previous simulations performed with the differential-algebraic solver DASSL, [2], and experiments, [7], indicated non-linear phenomena such as limit-cycles, bifurcations as well as chaotic behaviour. In this paper the non-linear phenomena are investigated in more detail with the aid of special in-house software and the path-following algorithm PATH [10]. We apply Poincaré sections and Poincaré maps to describe the structure of periodic, quasiperiodic and chaotic motions. The analyses show that part of the chaotic behaviour of the non-linear system can be fully understood as a non-linear iterative process. The resulting stretching and folding processes are illustrated by series of Poincaré sections.     

受控多体复摆的定性分析

本文讨论多体复摆的运动规律,作为具有单个支点的人体运动模型。系统中各邻接刚体之间作受控的相对运动。利用通路矢量和增广体概念导出系统的动力学普遍方程。对于平面运动的特殊情形,可在相平面内进行定性分析。以人体的站立稳定性和自激摆动为例。     

Molecular Dynamics Simulation of HIV-1 Integrase Dimer Complexed with Viral DNA

The biological function of HIV‐1 integrase (IN) is to integrate viral DNA into the host cell chromosome, and the specific binding of IN with viral DNA is a precondition for IN to function correctly. Beforehand, the binding mode of IN dimer (IN₂) with the 27 bp segment of viral DNA before 3′ processing (3′‐P) was obtained via a molecular docking method. Based on the binding mode, the aim of this article was to explore the changes of motive mode and correlative motion for the IN₂ and DNA systems after their binding through dynamical cross‐correlation map (DCCM) and principal component analysis (PCA). Finally, solvent effect during the association was analyzed briefly. The results show that there is a significantly increased positive correlation in the interface region between IN₂ and viral DNA, and some obvious motive mode changes of the two systems (IN₂ and DNA) were also observed after their binding. It was found that water molecules played an important role in the recognition between IN₂ and viral DNA through analyzing the water‐mediated hydrogen bonds.     

Molecular dynamics simulation of the equilibrium liquid–vapor interphase with solidification

The equilibrium structure of the finite, interphase interfacial region that exists between a liquid film and a bulk vapor is resolved by molecular dynamics simulation. Argon systems are considered for a temperature range that extends below the melting point. Physically consistent procedures are developed to define the boundaries between the interphase and the liquid and vapor phases. The procedures involve counting of neighboring molecules and comparing the results with boundary criteria that permit the boundaries to be precisely established. Two-dimensional radial distribution functions at the liquid and vapor boundaries and within the interphase region demonstrate the physical consistency of the boundary criteria and the state of transition within the region. The method developed for interphase boundary definitions can be extended to nonequilibrium systems. Spatial profiles of macroscopic properties across the interphase region are presented. A number of interfacial thermodynamic properties and profile curve-fit parameters are tabulated, including evaporation/condensation coefficients determined from molecular flux statistics. The evaporation/condensation coefficients away from the melting point compare more favorably with transition state theory than those of previous simulations. Near the melting point, transition theory approximations are less valid and the present results differ from the theory. The effects of film substrate wetting on evaporation/condensation coefficients are also presented.     

分子动力学研究V82A和L90M变异对HIV PR-IDV复合物的影响

为了说明V82A和L90M变异对蛋白酶(PR)和茚地那韦(IDV)复合物的影响,进行了5.5ns的MD模拟.用MM-PBSA方法计算了体系的结合自由能,计算和实验结果一致.分解自由能为不同能量项说明,这两个变异引起熵的贡献变化大于焓的贡献变化.分解自由能到每个残基说明Wild,V82A和L90M具有相似的结合模式,结合能的贡献主要来源于A28/A28',I50/I50'和I84/I84'这六个残基组,详细分析了Wild和IDV的结合模式,对比分析了V82A和L90M变异引起结合模式的细小变化.V82A变异引起结合模式的变化是由于变异后位阻减小导致的.L90M变异引起D25和L90间的作用增强并引起结合模式的细小变化.研究结果有助于更好地理解变异对抑制剂和HIV-1PR结合模式的影响,并可以用来帮助设计更高效的PR抑制剂.     

分子动力学方法研究纳米摩擦问题

分子动力学方法中忽略了电子相互作用,因而具有高效率,可以从原子水平研究大体系的动态过程。随着计算技术的进步,分子动力学逐渐在纳米工程领域显现了巨大的应用前景。本文综述了利用分子动力学方法从微观角度研究摩擦行为的进展,同时也就其进一步的应用做了展望。     

Exploring Group 14 Structures: 1D to 2D to 3D

Various one‐, two‐ and three‐dimensional Group 14 (C, Si, Ge, Sn, and Pb) element structures at P=1 atm are studied in this work. As expected, coordination number (CN)—not an unambiguous concept for extended structures—plays an important part in the stability of structures. Carbon not only favors four‐coordination, but also is quite happy with π‐bonding, allowing three‐ and even two‐coordination to compete. Highly coordinated (CN>4) discrete carbon molecules are rare; that “saturation of valence” is reflected in the instability of C extended structures with CN>4. Si and Ge are quite similar to each other in their preferences. They are less biased in their coordination than C, allowing (as their molecular structures do) CN=5 and 6, but tending towards four‐coordination. Sn and Pb 3D structures are very flexible in their bonding, so that in these elements four‐ to twelve‐coordinate structures are close in energy. This lack of discrimination among ordered structures also points to an approach to the liquid state, consistent with the low melting point of Sn and Pb. The Group 14 liquid structures we simulate in molecular dynamics calculations show the expected, effective, first coordination number increase from 5.1 for Si to 10.4 for Pb. A special point of interest emerging from our study is the instability of potential multilayer graphene structures down Group 14. Only for C will these be stable; for all the other Group 14 elements pristine, unprotected, bi‐ and multilayer graphenes should collapse, forming “vertical” bonds as short as the in‐plane ones.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Non-adiabatic dynamics of pyrrole: Dependence of deactivation mechanisms on the excitation energy

Non-adiabatic dynamics simulations were performed for pyrrole at time-dependent density functional theory level using the trajectory surface hopping approach. Initial conditions were prepared based on the UV-absorption spectrum so as to simulate monochromatic absorption in three distinct spectral regions. The results showed predominance of the NH-stretch mechanism for excited-state relaxation. With increasing initial energy, however, other mechanisms are activated as well, even though they still occurred for a minor fraction of the trajectories. Dynamics starting at the origin of the absorption spectrum exhibited internal conversion to the ground state with a time constant of 20 fs. In contrast, dynamics starting at higher energies gave rise to much longer time constants for internal conversion near 200 fs.