The structural optimization of atomic and molecular microclusters using a genetic algorithm in real-valued space-fixed coordinates

This dissertation documents the development and application of the space-fixed modified genetic algorithm, SFMGA. The SFMGA is shown to be both portable and fast for the structural optimization of Lennard-Jones, silicon, water, benzene, naphthalene, and anthracene microclusters. We introduce the SFMGA and apply it to LJ atomic clusters. CPU times needed to obtain the global minimum are compared with similar methods. We then investigate a complicated potential representing silicon atoms. The results show that SFMGA is applicable to non-pairwise additive potentials. We demonstrate the use of SFMGA for clusters where the monomers are molecules. Water clusters are optimized and the relative performance of the genetic operators, for both LJ and H\sb2O clusters, is explored. Finally, we investigate benzene, naphthalene, and anthracene clusters. In these clusters the size and potential surface complexity can be varied independently

Genetic Algorithm Optimization of Point Charges in Force Field Development: Challenges and Insights

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA approach for the least-squares MEP point charge fitting, and show that the GA optimizations suffer from a magnified version of the classical buried atom effect, producing highly scattered yet correlated solutions. This effect can be understood in terms of the linearly independent, natural coordinates of the MEP fitting problem defined by the eigenvectors of the least-squares sum Hessian matrix, which are also equivalent to the eigenvectors of the covariance matrix evaluated for the scattered GA solutions. GAs quickly converge with respect to the high-curvature coordinates defined by the eigenvectors related to the leading terms of the multipole expansion, but have difficulty converging with respect to the low-curvature coordinates that mostly depend on the buried atom charges. The performance of the evolutionary techniques dramatically improves when the point charge optimization is performed using the Hessian or covariance matrix eigenvectors, an approach with a significant potential for the evolutionary optimization of the fixed-charge biomolecular force fields

The Application of Hybridized Genetic Algorithms to the Protein Folding Problem

The protein folding problem consists of attempting to determine the native conformation of a protein given its primary structure. This study examines various methods of hybridizing a genetic algorithm implementation in order to minimize an energy function and predict the conformation (structure) of Met-enkephalin. Genetic Algorithms are semi-optimal algorithms designed to explore and exploit a search space. The genetic algorithm uses selection, recombination, and mutation operators on populations of strings which represent possible solutions to the given problem. One step in solving the protein folding problem is the design of efficient energy minimization techniques. A conjugate gradient minimization technique is described and tested with different replacement frequencies. Baidwinian, Lamarckian, and probabilistic Lamarckian evolution are all tested. Another extension of simple genetic algorithms can be accomplished with niching. Niching works by de-emphasizing solutions based on their proximity to other solutions in the space. Several variations of niching are tested. Experiments are conducted to determine the benefits of each hybridization technique versus each other and versus the genetic algorithm by itself. The experiments are geared toward trying to find the lowest possible energy and hence the minimum conformation of Met-enkephalin. In the experiments, probabilistic Lamarckian strategies were successful in achieving energies below that of the published minimum in QUANTA

Optimization Of A Large Scale Industrial Reactor Towards Tailor Made Polymers Using Genetic Algorithm

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)This paper presents a computational procedure for producing tailor made polymer resins, satisfying customers' needs while operating with maximum profit. The case study is an industrial large-scale polymerization reactor. The molecular properties considered are melt index (MI), which measures the molecular weight distribution, and stress exponent (SE), which is related to polydispersity. An economic objective function is associated to a deterministic mathematical model and the resulting optimization problem is solved by genetic algorithm (GA), a stochastic method. The GA parameters for both binary and real codifications are tuned by means of the design of experiments. Attempting to achieve the global optimum, a hybrid method, which introduces process knowledge into GA random initial population, is proposed. The binary codification performs better than the real GA, especially with hybridization. Results show that the GA can satisfactorily predict tailor made polymer resins with profits up to 25% higher than the industrial practice.14259267CAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior)CNPq (Conselho Nacional de Pesquisa)FAPESB (Fundacao de Amaro a Pesquisa do Estado da Bahia)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Refined Genetic Algorithms for Polypeptide Structure Prediction

Accurate and reliable prediction of macromolecular structures has eluded researchers for nearly 40 years. Prediction via energy minimization assumes the native conformation has the globally minimal energy potential. An exhaustive search is impossible since for molecules of normal size, the size of the search space exceeds the size of the universe. Domain knowledge sources, such as the Brookhaven PDB can be mined for constraints to limit the search space. Genetic algorithms (GAs) are stochastic, population based, search algorithms of polynomial (P) time complexity that can produce semi-optimal solutions for problems of nondeterministic polynomial (NP) time complexity such as PSP. Three refined GAs are presented: A farming model parallel hybrid GA (PHGA) preserves the effectiveness of the serial algorithm with substantial speed up. Portability across distributed and MPP platforms is accomplished with the Message Passing Interface (MPI) communications standard. A Real-valved GA system, real-valued Genetic Algorithm, Limited by constraints (REGAL), exploiting domain knowledge. Experiments with the pentapeptide Met-enkephalin have identified conformers with lower energies (CHARMM) than the accepted optimal conformer (Scheraga, et al), -31.98 vs -28.96 kcals/mol. Analysis of exogenous parameters yields additional insight into performance. A parallel version (Para-REGAL), an island model modified to allow different active constraints in the distributed subpopulations and novel concepts of Probability of Migration and Probability of Complete Migration

An MINLP model to support the movement and storage decisions of the Indian food grain supply chain

This paper addresses the novel three stage food grain distribution problem of Public Distribution System (PDS) in India which comprises of farmers, procurement centers, base silos and field silos. The Indian food grain supply chain consists of various activities such as procurement, storage, transportation and distribution of food grain. In order to curb transportation and storage losses of food grain, the Food Corporation of India (FCI) is moving towards the modernized bulk food grain supply chain system. This paper develops a Mixed Integer Non-Linear Programming (MINLP) model for planning the movement and storage of food grain from surplus states to deficit states considering the seasonal procurement, silo capacity, demand satisfaction and vehicle capacity constraints. The objective function of the model seeks to minimize the bulk food grain transportation, inventory holding, and operational cost. Therein, shipment cost contains the fixed and variable cost, inventory holding and operational cost considered at the procurement centers and base silos. The developed mathematical model is computationally complex in nature due to nonlinearity, the presence of numerous binary and integer variables along with a huge number of constraints, thus, it is very difficult to solve it using exact methods. Therefore, recently developed, Hybrid Particle-Chemical Reaction Optimization (HP-CRO) algorithm has been employed to solve the MINLP model. Different problem instances with growing complexities are solved using HP-CRO and the results are compared with basic Chemical Reaction Optimization (CRO) and Particle Swarm Optimization (PSO) algorithms. The results of computational experiments illustrate that the HP-CRO algorithm is competent enough to obtain the better quality solutions within reasonable computational time

Bulk wheat transportation and storage problem of public distribution system

This research investigates the multi-period multi-modal bulk wheat transportation and storage problem in a two-stage supply chain network of Public Distribution System (PDS). The bulk transportation and storage can significantly curtail the transit and storage losses of food grains, which leads to substantial cost savings. A mixed integer non-linear programming model (MINLP) is developed after studying the Indian wheat supply chain scenario, where the objective is to minimize the transportation, storage and operational cost of the food grain incurred for efficient transfer of wheat from producing states to consuming states. The cost minimization of Indian food grain supply chain is a very complex and challenging problem because of the involvement of the many entities and their constraints such as seasonal procurement, limited scientific storages, varying demand, mode of transportation and vehicle capacity constraints. To address this complex and challenging problem of food grain supply chain, we have proposed the novel variant of Chemical Reaction Optimization (CRO) algorithm which combines the features of CRO and Tabu search (TS) and named it as a hybrid CROTS algorithm (Chemical reaction optimization combined with Tabu Search). The numerous problems with different sizes are solved using the proposed algorithm and obtained results have been compared with CRO. The comparative study reveals that the proposed CROTS algorithm offers a better solution in less computational time than CRO algorithm and the dominance of CROTS algorithm over the CRO algorithm is demonstrated through statistical analysis