A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603

Different simple solvent models have been implemented in anextended simulated annealing process (ESAP), developed by Higoet al. [(1992) Biopolymers, 32, 33–43] and proven to beable to predict ab initio the conformation of the antigen-combiningloop H2 from FAB McPC603. Hie rationale used here provides auseful new method for testing solvent models in general. Thedifferent solvent models comprise a high dielectric constant,a screened coulomb potential, a dummy water model and a statisticalcontinuum treatment of the solvent effect in which the reactionfield and the solvent accessible area is accounted for. To assessthe effect of the solvent, we tested the ability of simulationsto retain the experimental conformation of loop H2. We comparedthe different structures obtained at the end of the annealingprocess in terms of root mean square deviation (r.m.s.d.), forboth the backbone and for all atoms, root mean square (r.m.s.)fluctuation, solvent accessible surface area (ASA), hydrogenbonding network and - plot distribution. The relationship betweenthe r.m.s.d. and the internal energy of a structure is alsoevaluated in terms of precision and another possible methodfor obtaining the best conformation is discussed. The accuracyof modelling the coarse effect of the solvent and the similaritiesof the resulting structures with respect to the X-ray referencestructure are examined. The possible choice of one of thesesolvent models in the structure determination of an unknownloop structure is discussed     

A Constraint-Based Approach for Deriving 3-D Structures of Cyclic Polypeptides

This paper presents an hybrid algorithm for deriving 3-D structures of cyclic polypeptides. The algorithm combines constraint-based techniques with the most widely used methods for non-cyclic polypeptides. The empirical results demonstrate that the proposed hybrid algorithm outperforms traditional methods especially with respect to running times.     

A new neural network algorithm for planarization problems

To deal with the planarization problem widely used in many applications including routing very-large-scale integration （VLSI） circuits, this paper points out that only when its vertices are arranged in some specific order in a line can a planar graph be embedded on a line without any cross connections or cross edges. Energy function is proposed to meet the need of embedding a graph on a single line and route it correctly. A Hopfield network is designed according to the proposed energy function for such embedding and routing. The advantage of the proposed method is that it not only can detect if a graph is a planar one or not, but also can embed a planar graph or the maximal planar subgraph of a non-planar graph on a single line. In addition, simulated annealing is employed for helping the network to escape from local minima during the running of the Hopfield network. Experiments of the proposed method and its comparison with some existent conventional methods were performed and the results indicate that the proposed method is of great feasibility and effectiveness especially for the planarization problem of large graphs.     

A Review of the Application of Meta-Heuristic Algorithms to 2D Strip Packing Problems

This paper is a review of the approachesdeveloped to solve 2D packing problems withmeta-heuristic algorithms. As packing tasks arecombinatorial problems with very large searchspaces, the recent literature encourages theuse of meta-heuristic search methods, inparticular genetic algorithms. The objective ofthis paper is to present and categorise thesolution approaches in the literature for 2Dregular and irregular strip packing problems.The focus is hereby on the analysis of themethods involving genetic algorithms. Anoverview of the methods applying othermeta-heuristic algorithms including simulatedannealing, tabu search, and artificial neuralnetworks is also given.     

供应链集成化模型与优化

本文建立了一个包括供应商、制造商、销售商 在内的集成化模型,这一模型含有线性状态方程和神经网络非线性模型,提出了库存成本、 供应成本、生产水平等在内的供应链目标函数和约束条件．对于供应链集成化模型采用模拟 退火方法进行优化,并以辽化公司为背景进行了初步条件的仿真工作．     

森林林冠对降雨量截留的实验分析

以实测资料为基础，分析了林冠对降雨量的截留量。     

A simulated annealing algorithm for multi-agent systems: a job-shop scheduling application

In this paper, a parallel implementation of the modular simulated annealing algorithm for classical job-shop scheduling is presented. The implementation is for a multi agent system running on the distributed resource machine, which is a novel, scalable, distributed virtual machine based on Java technology. The problems tackled are well known, difficult benchmarks, widely used to measure the efficiency of metaheuristics with respect to both the quality of the solutions and the central processing unit time. The empirical results obtained show that the method proposed is successful in comparison with a sequential version of modular simulated annealing algorithm and other methods described in the literature.     

Diagnosis of a Moist Thermodynamic Advection Parameter in Heavy-Rainfall Events

A moist thermodynamic advection parameter,defined as an absolute value of the dot product of horizontal gradients of three-dimensional potential temperature advection and general potential temperature,is introduced to diagnose frontal heavy rainfall events in the north of China.It is shown that the parameter is closely related to observed 6-h accumulative surface rainfall and simulated cloud hydrometeors.Since the parameter is capable of describing the typical vertical structural characteristics of dynamic,thermodynamic and water vapor fields above a strong precipitation region near the front surface,it may serve as a physical tracker to detect precipitable weather systems near to a front.A tendency equation of the parameter was derived in Cartesian coordinates and calculated with the simulation output data of a heavy rainfall event.Results revealed that the advection of the parameter by the three-dimensional velocity vector,the covariance of potential temperature advection by local change of the velocity vector and general potential temperature,and the interaction between potential temperature advection and the source or sink of general potential temperature,accounted for local change in the parameter.This indicated that the parameter was determined by a combination of dynamic processes and cloud microphysical processes.     

模拟退火法在耦合电容器优化设计中的应用

耦合电容器作为线路载波装置及电容式电压互感器的主要组成部分,已在电力系统中被广泛应用。研究如何合理的进行耦合电容器设计,对缩小产品体积、降低成本、提高产品性能是十分必要的。笔者将耦合电容器的设计问题与现代优化方法相结合,应用模拟退火优化策略进行优化设计,改进了产品的设计技术。     

降雨衰减对移动卫星系统通信的影响及补偿

针对移动卫星系统的特点，分析了降雨引起的信号衰减的原因，给出了雨衰的计算方法。Ka波段一般用于移动通信业务，从分析结果上看该波段信号受降雨影响较大。提出几种补偿雨衰的方法，给出了上行功率控制法的系统原理图。