Properties of a genetic algorithm extended by a random self-learning operator and asymmetric mutations: A convergence study for a task of powder-pattern indexing

Genetic algorithms represent a powerful global-optimisation tool applicable in solving tasks of high complexity in science, technology, medicine, communication, etc. The usual genetic-algorithm calculation scheme is extended here by introduction of a quadratic self-learning operator, which performs a partial local search for randomly selected representatives of the population. This operator is aimed as a minor deterministic contribution to the (stochastic) genetic search. The population representing the trial solutions is split into two equal subpopulations allowed to exhibit different mutation rates (so called asymmetric mutation). The convergence is studied in detail exploiting a crystallographic-test example of indexing of powder diffraction data of orthorhombic lithium copper oxide, varying such parameters as mutation rates and the learning rate. It is shown through the averaged (over the subpopulation) fitness behaviour, how the genetic diversity in the population depends on the mutation rate of the given subpopulation. Conditions and algorithm parameter values favourable for convergence in the framework of proposed approach are discussed using the results for the mentioned example. Further data are studied with a somewhat modified algorithm using periodically varying mutation rates and a problem-specific operator. The chance of finding the global optimum and the convergence speed are observed to be strongly influenced by the effective mutation level and on the self-learning level. The optimal values of these two parameters are about 6 and 5%, respectively. The periodic changes of mutation rate are found to improve the explorative abilities of the algorithm. The results of the study confirm that the applied methodology leads to improvement of the classical genetic algorithm and, therefore, it is expected to be helpful in constructing of algorithms permitting to solve similar tasks of higher complexity.     

用数值遗传算法改进非线性PLS法进行构效关系研究

将数值遗传算法同非线性ＰＬＳ结合，改进和完善了非线性ＰＬＳ，推导了指数，对数，倒数和Ｓｉｇｍｏｉｄ函数的公式，构造了可以处理多种非线性函数关系的算法，可用于解决复杂的结构与性能相互关系。     

A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

南京椴群体遗传多样性和遗传结构分析

【目的】 南京椴(Tilia miqueliana)为江苏省重要的乡土树种,野外资源稀缺。南京椴野外群体遗传多样性和遗传结构的探索,可为资源保护、品种选育及遗传改良提供依据。【方法】 以南京椴5个天然群体[江苏宝华山(P1)、牛首山(P2)、安徽皇藏峪(P3)、安徽蜀山(P4)和浙江天台山(P5)]93个体为实验材料,选用15对多态性EST-SSR引物,进行遗传多样性及群体遗传结构分析。【结果】 ①用15对引物共检测等位基因数(A)总和为96,平均值为6.4,四倍体基因型(G)和四倍体特异基因型(G_i)总和分别为441和251,特异基因型比率(R₁)和种质鉴别率(R₂)均值分别为45.73%和17.99%。②在5个群体中,每个位点等位基因数(A_loc)和四倍体基因型丰富度均值(G_loc)分别为5.50±2.43和9.41±4.29;平均观测杂合度(H_o)和平均期望杂合度(H_e)为0.61±1.43和0.62±0.14。参考各群体G_loc和H_e值,确定遗传多样性较高的群体为P1和P3。③群体间遗传分化较小,遗传分化系数(G_st)仅为0.030;AMOVA分子变异分析显示,群体多样性水平变异来自于群体内(96%)。④聚类和遗传结构Structure分析显示,5个群体可划分为2组(组1包括P1、P2和P5;组2包括P3和P4)。Mental检验结果表明遗传距离与地理距离之间无显著相关。【结论】 南京椴群体均具有丰富的遗传多样性,其中宝华山群体和皇藏峪群体多样性较高,群体扩张可能是以这两个种群为中心,经人类活动迁移至其他区域。但南京椴群体间未形成明显分化,主要是由于植株寿命长,群体缺乏自然更新,加之群体间存在人为种子传播。因此,本研究提出通过建立隔离区,明确优先保护群体、加大植株异交,并采用人工繁育及种质回迁的方式保护南京椴野外群体。     

两地点8年生柏木生长性状家系变异及选择

【目的】揭示柏木生长性状的遗传变异规律,为高阶遗传改良筛选优良种质,选择优良家系,及其区域推广奠定基础。【方法】以营建在浙江省开化县林场(KH)和湖北省太子山林场(TZS)两个试验点的8年生柏木优树子代家系为材料,分析其生长性状的遗传变异,估算其育种值、遗传力等参数。【结果】柏木生长性状(树高、胸径和材积)的遗传变异系数为3.08%～13.93%,其中材积的变异最大。子代家系的树高、胸径和材积在地点间差异显著,TZS点的单株材积高于KH点315.79%,且家系与地点间的交互效应显著。胸径、树高和材积具有显著的家系效应,KH和TZS试验点的家系遗传力变幅分别为0.42～0.61和0.58～0.74。KH和TZS试验点分别以单株材积育种值大于CK的10%和45%为标准,各选出6个优良家系,现实增益分别为33.51%和67.95%。利用独立淘汰法,在KH点和TZS点各筛选优良单株17和12株,材积的遗传增益分别为41.38%和40.92%。【结论】8年生柏木优树子代家系生长性状具有较大的遗传改良潜力,但家系与环境的互作效应显著;通过子代家系的遗传评价有助于种子园建园亲本的再选择和现有种子园的...     

基于荧光SSR标记的紫薇遗传多样性分析

【目的】以收集的239份紫薇属(Lagerstroemia)种质和1份黄薇属(Heimia)种质为材料,开展种质种间特征分析和紫薇种内资源的遗传多样性分析,为进一步优化紫薇种质资源收集保存及合理利用提供科学依据。【方法】基于16对荧光引物鉴定样品基因型,利用GeneMarker软件进行基因型数据的读取;对239份紫薇属种质和1份黄薇属种质进行特征位点分析;并利用Popgene、Cervus、NTSYS和GenAlEx软件对227份紫薇种质进行遗传多样性参数估算、聚类分析和主成分分析。【结果】紫薇(L.indica)种内的特征位点信息最为丰富,其中15个引物所体现出的特征位点信息中,紫薇都有其独特的位点区别于其他6个种,而在福建紫薇(L.limii)、川黔紫薇(L.excelsa)和尾叶紫薇(L.caudata)中也有部分特异的特征位点是紫薇中没有的;16对紫薇SSR荧光引物共检测出143个等位基因,平均每个位点有8.938个等位基因,平均有效等位基因数(N_e)为3.600,Shannon’s信息指数(I)均值为1.459,观测杂合度(H_o)均...     

一种磁流变弹性体执行器的联合优化方法研究

磁流变弹性体（magnetorheological elastomer, MRE）执行器作为智能减振应用系统的核心元件,其结构的优化是决定执行器性能上限及系统控制成效的关键。针对目前MRE执行器优化方法及理论研究欠缺的问题,文中面向一款横向隔振的MRE执行器,基于其机械结构和有效磁路,以优越磁控性能、低功耗和快速响应时间为优化目标,提出了一种新的MRE执行器联合参数优化方法。首先,基于MATLAB和COMSOL的联合仿真,将遗传优化算法和电磁有限元分析方法进行有效结合,实现对MRE执行器的优化编程;其次,完成对器件的全局尺寸结构优化设计,使得器件具备优越磁控性能（526.21 mT）、低功耗（44.05 W）及快速响应（5.43 ms）;最后,通过搭建测试系统对优化后装配的MRE执行器进行测试和评估,验证了文中优化方法的可行性和有效性。提出的联合优化方法不仅适用于MRE执行器结构,还可为多领域减/隔振应用的共性MRE器件优化设计提供理论参考。     

Lamination Design Optimization for Continuous Fiber Reinforced Composites of Variable Thicknesses北大核心CSCD

由于具备高的比强度、比刚度,利用连续纤维增强复合材料代替传统金属材料以实现结构轻量化正受到设计者们的广泛关注。然而,结构的复杂性给复合材料的铺层设计与优化带来了很大的挑战。针对航空用复合材料铺层设计约束多的问题,通过逐步构建设计变量准确表达结构的铺层信息。基于经典遗传算法框架,结合各设计变量特点,定义了铺层优化算法中的遗传算子,通过引入“修复”策略保证了每一代解都能满足设计约束,分布在可行域区间内。最后利用精英保留策略提高了算法的局部寻优能力,可以降低复杂复合材料结构铺层设计的计算成本。通过解决经典benchmark问题并与已有优化结果的比较,验证了前述铺层优化算法的全局、局部寻优能力,为工程实际中的复合材料铺层设计优化提供了理论支撑。