The application of the genetic algorithm to the minimization of potential energy functions

We adapted the genetic algorithm to minimize the AMBER potential energy function. We describe specific recombination and mutation operators for this task. Next we use our algorithm to locate low energy conformation of three polypeptides (AGAGAGAGA, A9, and [Met]-enkephalin) which are probably the global minimum conformations. Our potential energy minima are –94.71, –98.50, and –48.94 kcal/mol respectively. Next, we applied our algorithm to the 46 amino acid protein crambin and located a non-native conformation which had an AMBER potential energy 150 kcal/mol lower than the native conformation. This is not necessarily the global minimum conformation, but it does illustrate problems with the AMBER potential energy function. We believe this occurred because the AMBER potential energy function does not account for hydration.     

C 1 surface interpolation with constraints

Givenn pairwise distinct and arbitrarily spaced pointsP _i in a domainD of thex–y plane andn real numbersf _i, consider the problem of computing a bivariate functionf(x, y) of classC ¹ inD whose values inP _i are exactlyf _i,i=1,,n, and whose first or second order partial derivatives satisfy appropriate equality and inequality constraints on a given set ofp pointsQ _l inD.In this paper we present a method for solving the above problem, which is designed for extremely large data sets. A step of this method requires the solution of a large scale quadratic programming (QP) problem.The main purpose of this work is to analyse an iterative method for determining the solution of this QP problem: such a method is very efficient and well suited for parallel implementation on a multiprocessor system.Work supported by MURST Project of Computational Mathematics, Italy.     

Analysis of grid file algorithms

Grid file algorithms were suggested in [12] to provide multi-key access to records in a dynamically growing file. We specify here two algorithms and derive the average sizes of the corresponding directories. We provide an asymptotic analysis. The growth of the indexes appears to be non-linear for uniform distributions:O(v ^c ) orO(v ), wherec=1+b^–1, =1+(s-1)/(sb+1),s is the number of attributes being used,v the file size, andb the page capacity of the system. Finally we give corresponding results for biased distributions and compare transient phases.     

Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

液相组合合成的纯化方法

综述了近8年来液相平行合成和组合合成中应用的不同技术, 包括可溶性载体、氟合成技术、离子液体、固相试剂树脂以及低聚乙烯二醇(OEG)衍生物的应用等几方面内容. 论述了它们的基本原理以及相关的应用实例, 并着重强调了目标化合物的分离纯化方法.     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

Selecting variables for k-means cluster analysis by using a genetic algorithm that optimises the silhouettes

The goal of present work is to analyse the effect of having non-informative variables (NIV) in a data set when applying cluster analysis and to propose a method computationally capable of detecting and removing these variables. The method proposed is based on the use of a genetic algorithm to select those variables important to make the presence of groups in data clear. The procedure has been implemented to be used with k-means and using the cluster silhouettes as fitness function for the genetic algorithm.The main problem that can appear when applying the method to real data is the fact that, in general, we do not know a priori what the real cluster structure is (number and composition of the groups).The work explores the evolution of the silhouette values computed from the clusters built by using k-means when non-informative variables are added to the original data set in both a literature data set as well as some simulated data in higher dimension. The procedure has also been applied to real data sets.     

A microcapillary system for simultaneous, parallel microwave-assisted synthesis

A continuous flow, microwave-assisted, parallel-capillary microreactor has been developed. Libraries of drug candidates were prepared on the milligram scale with this reactor by injecting plugs of reagents from separate syringes into common reaction capillaries, thereby producing discrete compounds in excellent yield and purity. Microwave irradiation provides the necessary energy that existing room-temperature microreactor technology lacks for higher activation barrier transformations, producing the required amounts of desired compounds in minutes or less.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.