QSAR modeling with the electrotopological state indices: Corticosteroids

A structure-activity analysis of a series of steroids binding to corticosteroid-binding globulin was made using the electrotopological state index for each atom in the molecule. Two indices were found to correlate well with the binding affinity. The indices encode structural characteristics in the A and the D rings of the steroids in the study. One of the indices was formulated as the difference between two indices in the A ring. The two were not intercorrelated, suggesting that the composite index signals the influence of structure changes in or near the A ring that can be monitored by the composite index. This is a new observation using this structure-activity method. It is suggested that this model makes some contributions towards detection of the pharmacophore.     

Metastability and exponential approach to equilibrium for low-temperature stochastic Ising models

We present a proof of the exponential convergence to equilibrium of single-spin-flip stochastic dynamics for the two-dimensional Ising ferromagnet in the low-temperature case with not too small external magnetic fieldh uniformly in the volume and in the boundary conditions.     

Stochastic flows on a countable set: Convergence in distribution

Consider a sequenceF ₁,F ₂,... of i.i.d. random transformations from a countable setV toV. Such a sequence describes a discrete-time stochastic flow onV, in which the position at timen of a particle that started at sitex isM _n(x), whereM _n =F _n F _n–1 F ₁. We give conditions on the law ofF ₁ for the sequence (M _n) to be tight, and describe the possible limiting law. an example called the block charge model is introduced. The results can be formulated as a statement about the convergence in distribution of products of infinite-dimensional random stochastic matrices. In practical terms, they describe the possible equilibria for random motions of systems of particles on a countable set, without births or deaths, where each site may be occupied by any number of particles, and all particles at a particular site move together.     

Stochastic modeling of a billiard in a gravitational field: Power law behavior of Lyapunov exponents

We consider the motion of a point particle (billiard) in a uniform gravitational field constrained to move in a symmetric wedge-shaped region. The billiard is reflected at the wedge boundary. The phase space of the system naturally divides itself into two regions in which the tangent maps are respectively parabolic and hyperbolic. It is known that the system is integrable for two values of the wedge half-angle ₁ and ₂ and chaotic for ₁<< ₂. We study the system at three levels of approximation: first, where the deterministic dynamics is replaced by a random evolution; second, where, in addition, the tangent map in each region is, replaced by its average; and third, where the tangent map is replaced by a single global average. We show that at all three levels the Lyapunov exponent exhibits power law behavior near ₁ and ₂ with exponents 1/2 and 1, respectively. We indicate the origin of the exponent 1, which has not been observed in unaccelerated billiards.     

Dynamics of the current-driven Josephson junction

The irreversible macroscopic dynamics of the Josephson junction coupled to external wires acting as a current source is derived rigorously from the underlying microscopic Hamiltonian quantum mechanics. The external systems are treated in the singular coupling limit. The use of this limit is explicitly justified via an interpretation of the singular coupling limit in terms of the relative magnitudes of system, reservoir, and coupling energies. The qualitative behavior of the macroscopic dynamical equations is shown to depend sensitively and crucially on the interaction between the wires and the superconductors and on the size of the wires: the dc Josephson effect only happens when one lets Cooper pairs be driven into the junction by collective (i.e., small) reservoirs.     

Ar—Kr溶液扩散系数的分子动力学模拟及其与温度的关系

用分子动力学模拟方法研究确定Ａｒ－Ｋｒ溶液的自扩散系数Ｄ１、Ｄ２和互扩散系数Ｄ１２以及它们随温度变化的规律。结果表明，分别用Ｇｒｅｅｎ－Ｋｕｂｏ法和Ｅｉｎｓｔｅｉｎ法得到的扩散系数在数值上一致；该溶液的３种扩散系数均满足Ｄ＝Ｄ０ｅ＾Ｅ／ＲＴ关系。     

液体和非晶态Ni64B36合金结构的从头算分子动力学模拟

运用从头算分子动力学模拟了液体以及猝冷后形成的非晶态Ni₆₄B₃₆合金体系, 得到了它们的对相关函数、结构因子、键对分析方面的结构信息, 与实验结果相当一致; 结果表明, 猝冷得到的合金性质与液体合金性质相似, 为非晶态结构. B原子多数以B—B双原子成键形式分散于Ni原子构成的骨架中. 电子态密度分析表明, Ni 3d电子最活泼, 因此在合金中Ni为活性位. 轨道电荷分析从电子结构角度揭示了在NiB 催化剂中B作为修饰剂的机理.     

取代脂环烃物理化学性质的拓扑化学研究

为了探讨有机化合物的分子结构与理化性质的关系,作者在以前的工作基础上,基于一阶分子连通性拓扑指数构建了一个信息拓扑指数.将拓扑指数与取代脂环烃系列分子的气态标准生成热、气态标准熵、气态标准生成自由能、沸点、临界温度、临界压力、临界体积、汽化热、密度、热容及表面张力等十一种热力学性质及物理化学性质相关联,用一个通用公式对各类性质进行概括,然后用已有的实验数据与拓扑指数进行回归分析,得到一系列计算各性质的经验公式.回归结果发现,分子的理化性质与拓扑指数有较好的相关性,有5类性质的复相关系数大于0.99.用经验公式对各类性质进行重新计算,其结果与实验值比较符合,用实验值对计算值作图,发现各数据点紧靠对角线,说明误差较小.残差分布呈正态分布.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

Summary Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.