Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase‐AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional‐ and QM/MM‐FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase‐AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution

The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET.     

纳米结构泡沫金冲击响应的分子动力学模拟

采用分子动力学计算程序对纳米结构泡沫金(Au)的冲击响应进行了模拟,得到了不同疏松度条件下泡沫Au的冲击压缩特性。通过获取不同势函数条件下实密Au的冲击Hugoniot关系以及泡沫结构稳定性测试选取适合描述Au泡沫冲击过程中原子的相互作用势。采用密堆积球壳的方式建立泡沫Au的初始构型。通过改变空心球壳的尺寸得到不同疏松度的稳定的泡沫Au结构。对泡沫Au的冲击过程进行分子动力学模拟,获得了不同疏松度泡沫Au在不同冲击压缩强度下的热力学状态参数。将模拟结果与已有的状态方程数据库以及疏松物质冲击压缩模型进行比较,结果表明,计算和理论模型给出的结果仍然存在明显的差异性,亟需通过进一步实验研究来验证模拟计算和理论模型结果的可靠性。     

Feedback controlled periodic states for different kinds of photorefractive nonlinear response

We investigate analytically and numerically the influence of the type of the photorefractive nonlinear response on the periodic states (attractors) which occur during feedback controlled 2W-coupling and correspond to almost 100% diffraction efficiency of the dynamic index grating. In addition to the case of the local response typical, for example, for LiNbO₃ crystals we consider the cases of nonlocal (diffusive) response (BaTiO₃, SBN) and resonant response (DC-biased BSO, BTO, and BGO crystals). It is shown that the conditions for the transition to the periodic states and their apparent characteristics are strongly different for the two limiting cases above. Received 16 July 2002 / Received in final form 29 October 2002 Published online 4 March 2003     

Dynamics of water in real space and time

Owing to marked advances in instrumentation in X-ray and neutron scattering the time-dependent pair correlation function, the Van Hove function, can now be determined by inelastic X-ray and neutron scattering measurements. The local dynamics of water in real space and time is visualised by this approach. We discuss how the dynamic properties, such as viscosity and diffusion, can be elucidated through the Van Hove function of water.     

赤潮藻类非线性动力学模型的分岔及稳定性研究

选取两种常见赤潮藻类和一种浮游动物,考虑生态环境的富营养化及赤潮藻类与浮游动物的相互作用,建立了多种群赤潮藻类的非线性动力学模型．首次运用现代非线性动力学理论,对模型的稳定性及分岔行为进行了研究．得到了发生Hopf分岔时的分岔参数值,判断了极限环的稳定性,并发现了该模型通过准周期分岔产生混沌．     

Ward's identity in critical dynamics

We consider the relaxation of an order-parameter fluctuation of wave numberk in a system undergoing a second-order phase transition. In general, close to the critical point, wherek ^{–1 –1} (the correlation length) the relaxation rate has a linear dependence on/k of the form (k, ) = (k, 0)x(1–a/k). In analogy with the use of Ward's identity in elementary particle physics, we show that the numerical coefficienta is readily calculated by means of a mass insertion. We demonstrate, furthermore, that this initial linear drop is the main feature of the full/k dependence of the scaling functionR ^–x (k,), wherex is the dynamic critical exponent andR=(k²+ ²)^1/2 is the distance variable.     

Molecular dynamics simulation for surface melting and self-preservation effect of methane hydrate

The surface melting process of structure sI methane hydrate is simulated at T = 240, 260, 280, and 300 K using NVT molecular dynamics method. The simulation results show that a quasi-liquid layer will be formed during the melting process. The density distribution, translation, orientation, and dynamic properties of water molecules in the quasi-liquid layer are calculated as a function of the distance normal to the interface, which indicates the performance of quasi-liquid layer exhibits a continuous change from crystal-like to liquid-like. The quasi-liquid layer plays as a resistance of mass transfer restraining the diffusion of water and methane molecules during the melting process. The resistance of quasi-liquid layer will restrain methane molecules diffuse from hydrate phase to gas phase and slow the melting process, which can be considered as a possible mechanism of self-preservation effect. The performance of quasi-liquid layer is more crystal-like when the temperature is lower than the melt- ing-point of water, which will exhibit an obvious self-preservation. The self-preservation will weaken while the temperature is higher than the melting-point of water because of the liquid-like performance of the quasi-liquid layer.     

分子动力学模拟研究[Bmim][PF_6]+水+醇三元体系的微观结构和分子间相互作用(英文)

研究离子液体体系的微观结构和分子间相互作用具有重要意义.本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF6])+水+乙醇和[Bmim][PF6]+水+异丙醇三元体系进行了分子模拟研究,计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能,并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能.在此基础上,研究了溶液体系的微观结构、分子间相互作用和相行为.结果表明,水倾向于与离子液体阴离子和阳离子极性部分作用,醇倾向于与阴离子和阳离子非极性部分作用;库仑力主导阴离子-溶剂相互作用,色散力主导阳离子-溶剂相互作用,阴阳离子的缔合状态对色散力影响较小,对库仑力的影响非常显著.