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.     

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.     

Comments on the primary and scatter dose-spread kernels used for convolution methods

The basic primary and scatter dose-spread kernels used for convolution methods are usually produced by Monte Carlo simulations with the interaction point forced to the center of a large water phantom. However, it is still not clear whether such Monte Carlo based kernels allow accurate dose calculations with a wide range of field sizes and depths, especially in thorax phantoms. Using the differential primary and scatter concept, this paper proposes another type of basic kernel, with which perfectly accurate primary and scatter absorbed dose calculations can be performed under conditions that the beam is parallel, the incident beam intensity is uniform within and zero outside the field, and the primary beam attenuation coefficient along raylines is not a function of depth and off-axis distance.     

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.     

Cavity search: An algorithm for the isolation and display of cavity-like binding regions

Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.     

修正PRP共轭梯度方法求解无约束最优化问题

基于著名的PRP共轭梯度方法,利用CG_DESCENT共轭梯度方法的结构,本文提出了一种求解大规模无约束最优化问题的修正PRP共轭梯度方法。该方法在每一步迭代中均能够产生一个充分下降的搜索方向,且独立于任何线搜索条件。在标准Wolfe线搜索条件下,证明了修正PRP共轭梯度方法的全局收敛性和线性收敛速度。数值结果展示了修正PRP方法对给定的测试问题是非常有效的。     

供应商不确定情景下药品物流多中心选址优化研究

根据国家4+7药品带量集中采购评审标准,基于药品生产企业生产质量、供应能力、相关资质和同类药品参标结果等数据进行梳理和分析,针对药品供应商不确定情景下药品物流多中心选址问题,构建药品物流整体费用最优的多中心选址模型,设计多阶段改进禁忌搜索算法,最后通过4+7带量集中采购具体算例对模型和算法进行验证,结果显示该模型和算法是可行和有效的。