On the average length of lexicographic paths

A bound is given for the average length of a lexicographic path, a definition that is motivated by degeneracies encountered when using the randomized simplex method.     

Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

杂合型全局优化法优化水分子团簇结构

基于遗传算法、快速模拟退火及共轭梯度方法提出了一种快速的杂合型全局优化方法(fast hybrid global optimization algorithm, FHGOA),并将这一方法应用于TIP3P和TIPS2模型水分子团簇(H2O)n结构的优化.在进行TIP3P模型水分子团簇结构的优化过程中,发现了能量比文献值更低的团簇结构,且执行效率有较大提高.把该方法应用到优化TIPS2模型的水分子团簇,发现最优结构和采用TTM2-F模型优化的水分子团簇结构在n < 17时完全相同,为全表面结构;而在n=17、19、22时为单中心水分子笼状结构;在n=25、27时为双中心水分子笼状结构.说明随着团簇中水分子个数的增加,采用TIPS2和TTM2-F势能函数优化的团簇最优结构有相同的变化趋势.     

不依赖于统计模型的手性毛细管电泳分离多指标同时优化

考虑到手性毛细管电泳分离机理的复杂性，提出了不依赖于统计模型的二进制编码遗传算法多目标优化策略。根据实验参数的多少及其重要性，采用均匀设计安排完成初步实验。并用Derringer功效函数作为多指标同时优化的评价指标，以取得较高的分离度和较快分离速度；通过对实验参数给予编码，转化为二进制字符串，根据得到的总功效函数值大小进行遗传算法操作，产生新的一组实验条件。重复上述过程直到得到最佳分离条件为止。此方法成功地应用于华法令对映体的毛细管电泳分离条件优化。     

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.     

Simple algorithm for isothermal-isobaric molecular dynamics

We review principles of non-Hamiltonian statistical mechanics and present a new set of equations and integration algorithm for isothermal-isobaric dynamics. The chief advantage of the present scheme is that it is somewhat simpler than previous methods. We perform numerical simulations to test the accuracy of the algorithm and compare its stability to that of a "gold standard," a symplectic integrator for Hamiltonian dynamics of the same system. The stability of the isothermal-isobaric algorithm is comparable to the stability of the symplectic integrator.     

两种计算吸光光度法同时测定钙镁

研究了在pH10．5的硼砂-氢氧化钾缓冲溶液和乙醇的增敏作用条件下，偶氮氯膦Ⅰ与钙、镁的吸收特性，建立了多波长光度法同时测定钙和镁的方法。采用两种矩阵算法对试验数据进行处理，并对结果进行比较和分析。钙和镁含量在0～25μg／25ml范围内用计算法Ⅱ能得到准确结果。