遗传算法在构象搜寻中的应用

遗传算法是一种模仿自然进化进程的新颖的启发式优化方法。通过它，人们可以在计算机上对所需的各种问题实施进化操作，最终产生理想的结果。遗传算法现已被广泛于计算机辅助设计、工程设计、系统模拟等领域并取得了极大的成功。本文拟对遗传算法在对大、中、小分子的构象搜寻中的应用作一较全面的综述。     

Industrial multi-stage continuous filtration process: influence of operating parameters

This paper presents a theoretical study of the effects of operating parameters on the behaviour of an industrial crossflow filtration unit. A continuous three stage unit and its application to yeast cell harvesting are considered. A model of standard industrial processing is developed, and the influence of dead volumes, start-up procedure, crossflow and permeation velocities and maximum transmembrane pressure are investigated. Concentration factors are discussed with respect to the effects due to dead volumes.     

几种改进的CoMFA方法比较研究血小板活化因子拮抗剂

由于传统的比较分子场分析(CoMFA)方法本身存在一些缺陷，使得分子的叠合 规则以及叠合分子的空间取向和空间位置等因素对q~2的影响很大，因此相继提出 了几种改进的CoMFA方法。为了优化CoMFA结果，应用传统的CoMFA方法和交叉验证 的R~2引导的区域选择法(q~2-GRS)、全取向搜索法（AOS）、全空间搜索法（APS） 以及比较分子相似性指数(CoMSIA)等四种改进的CoMFA方法，对18个pinusolide类 衍生物这类新发现的血小板活化因子（PAF）拮抗剂进行了比较研究。结果表明四 种改进的CoMFA方法得到的q~2值均比传统CoMFA的高。q~2-GRS方法得到的q~2值有 所提高，但综合结果并不理想，AOS与APS得到的q~2较为理想，而在CoMSIA中， q~2几乎不受空间取向或空间位置的影响。同时我们引人基于样本的偏最小二乘法 （SAMPLS）取代原AOS／APS程序中的传统PLS进行统计分析，明显提高了其运行速 度。最后，根据q~2最高的CoMFA模型和CoMSIA模型设计了几个预测活性更高的 pinusolide类似物。     

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.     

Indirect automatic atomic absorption determination of sulphate based on its precipitation with barium

A continuous precipitation flame atomization atomic absorption spectrometric method for the indirect determination of sulphate is proposed. By using a reversed flow-injection configuration for precipitation as barium sulphate, this anion was determined in the range 10–150 g/ml, with a relative standard deviation of 2.6%. The sensitivity was increased by a factor of seven by using a nitrous oxide-acetylene flame to measure barium.     

Study on pyrolysis kinetics of walnut shell

Slow pyrolysis of walnut shell which is a cheap and abundantly available solid waste was carried out using thermogravimetric analysis. The effects of raw material heating rate on the pyrolysis properties and kinetic parameters were investigated. A two-step consecutive reaction model were used to simulate the pyrolysis process. The kinetic parameters were established by using the pattern search method. Comparison between experimental data and the model prediction indicated that the two-step consecutive reaction model can better describe the slow pyrolysis of walnut shell as the formation of an intermediate during the pyrolysis process was taken into account.     

Reaction Engineering Aspects of α-l,4-D-Glucan Phosphorylase Catalysis

Some important process properties of α-l,4-D-ghican phosphorylases isolated from the bacteriumCorynebacterium callunae and potato tubers (Solatium tuberosum) were compared. Apart from minor differences in their stability and specificity (represented by the maximum degree of maltodextrin conversion) and a 10-fold higher affinity of the plant phosphorylase for maltodextrin (K _M of 1.3 g/L at 300 mM of orthophosphate), the performances of both enzymes in a continuous ultrafiltration membrane reactor were almost identical. Product synthesis was carried out over a time course of 300–400 h in the presence or absence of auxiliary pullulanase (increasing the accessibility of the glucan substrate for phosphorolytic attack up to 15–20%). The effect of varied dilution rate and reaction temperature on the resulting productivities was quantitated, and a maximum operational temperature of 40°C was identified.     

Existence of finitely optimal solutions for infinite-horizon optimal control problems

In this paper, we investigate the existence of finitely optimal solutions for the Lagrange problem of optimal control defined on [0, ) under weaker convexity and seminormality hypotheses than those of previous authors. The notion of finite optimality has been introduced into the literature as the weakest of a hierarchy of types of optimality that have been defined to permit the study of Lagrange problems, arising in mathematical economics, whose cost functions either diverge or are not bounded below. Our method of proof requires us to analyze the continuous dependence of finite-interval Lagrange problems with respect to a prescribed terminal condition. Once this is done, we show that a finitely optimal solution can be obtained as the limit of a sequence of solutions to a sequence of corresponding finite-horizon optimal control problems. Our results utilize the convexity and seminormality hypotheses which are now classical in the existence theory of optimal control.This research forms part of the author's doctoral dissertation written at the University of Delaware, Newark, Delaware under the supervision of Professor Thomas S. Angell.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Hybrid genetic algorithm–tabu search approach for optimising multilayer optical coatings

Constructing multilayer optical coatings (MOCs) is a difficult large-scale optimisation problem due to the enormous size of the search space. In the present paper, a new approach for designing MOCs is presented using genetic algorithms (GAs) and tabu search (TS). In this approach, it is not necessary to specify how many layers will be present in a design, only a maximum needs to be defined. As it is generally recognised that the existence of specific repeating blocks is beneficial for a design, a specific GA representation of a design is used which promotes the occurrence of repeating blocks. Solutions found by GAs are improved by a new refinement method, based on TS, a global optimisation method which is loosely based on artificial intelligence. The improvements are demonstrated by creating a visible transmitting/infrared reflecting filter with a wide variety of materials.