Lower-energy conformers search of TPP-1 polypeptide via hybrid particle swarm optimization and genetic algorithm

Low-energy conformation search on biological macromolecules remains a challenge in biochemical experiments and theoretical studies. Finding efficient approaches to minimize the energy of peptide structures is critically needed for researchers either studying peptide-protein interactions or designing peptide drugs. In this study, we aim to develop a heuristic-based algorithm to efficiently minimize a promising PD-L1 inhibiting polypeptide, TPP-1, and build its low-energy conformer pool to advance its subsequent structure optimization and molecular docking studies. Through our study, we find that, using backbone dihedral angles as the decision variables, both PSO and GA can outperform other existing heuristic approaches in optimizing the structure of Met-enkephalin, a benchmarking pentapeptide for evaluating the efficiency of conformation optimizers. Using the established algorithm pipeline, hybridizing PSO and GA minimized TPP-1 structure efficiently and a low-energy pool was built with an acceptable computational cost (a couple days using a single laptop). Remarkably, the efficiency of hybrid PSO-GA is hundreds-fold higher than the conventional Molecular Dynamic simulations running under the force filed. Meanwhile, the stereo-chemical quality of the minimized structures was validated using Ramachandran plot. In summary, hybrid PSO-GA minimizes TPP-1 structure efficiently and yields a low-energy conformer pool within a reasonably short time period. Overall, our approach can be extended to biochemical research to speed up the peptide conformation determinations and hence can facilitate peptide-involved drug development

Makespan Minimization in Re-entrant Permutation Flow Shops

Re-entrant permutation flow shop problems occur in practical applications such as wafer manufacturing, paint shops, mold and die processes and textile industry. A re-entrant material flow means that the production jobs need to visit at least one working station multiple times. A comprehensive review gives an overview of the literature on re-entrant scheduling. The influence of missing operations received just little attention so far and splitting the jobs into sublots was not examined in re-entrant permutation flow shops before. The computational complexity of makespan minimization in re-entrant permutation flow shop problems requires heuristic solution approaches for large problem sizes. The problem provides promising structural properties for the application of a variable neighborhood search because of the repeated processing of jobs on several machines. Furthermore the different characteristics of lot streaming and their impact on the makespan of a schedule are examined in this thesis and the heuristic solution methods are adjusted to manage the problem’s extension

Sessenta anos de Shop Scheduling : uma revisão sistemática da literatura

Orientador : Prof. Dr. Cassius Tadeu ScarpinDissertação (mestrado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduação em Engenharia de Produção. Defesa: Curitiba, 09/02/2017Inclui referências : f. 449-492Resumo: Desde o seminal artigo de Johnson em 1954, a Programação da Produção em Shop Scheduling tem se tornado uma área relevante dentro da Pesquisa Operacional e, atualmente, duzentos trabalhos tangentes à temática são publicados anualmente. Dentre os artigos aqui citados tem-se aqueles que se dedicam à apresentação e síntese do estado da arte desse assunto, intitulados artigos de revisão. Quando tais artigos são elaborados a partir de um conjunto objetivo de critérios, relativos à categorização dos artigos selecionados, tem-se a Revisão Sistemática da Literatura (RSL). O presente trabalho realiza uma RSL em Shop Scheduling, a partir da análise de cada ambiente fabril que o compõe. Fez-se o escrutínio de 560 artigos, à luz de um conjunto de métricas, que constitui a estrutura basilar da proposta de nova taxonomia do Shop Scheduling, complementar à notação de Graham, objetivo fulcral do presente trabalho. Além disso, utilizou-se uma representação em redes dos resultados obtidos em algumas das métricas empregadas, como a característica dos itens, algo outrora inaudito em estudos de revisão desse assunto. Ademais, outro ponto relevante desse estudo repousa na identificação de campos pouco explorados, de modo a colaborar com a pesquisa futura neste tomo. Palavras-chave: Shop Scheduling. Revisão Sistemática da Literatura. Taxonomia. Representação em Redes.Abstract: Since Johnson's seminal article in 1954, Shop Scheduling in Production Scheduling has become a relevant area within Operational Research, and currently hundreds of tangential works on the subject are published annually. Among the articles cited here are those dedicated to the presentation and synthesis of the state of the art of this subject, which are entitled review articles. When these articles are elaborated from an objective set of criteria, regarding the categorization of the selected articles, we have the Systematic Review of Literature (SLR). The present work performs a SLR in Shop Scheduling, based on the analysis of each manufacturing environment that composes it. There were 560 articles scrutinized based on a set of metrics, which is the basic structure of the proposed new Taxonomy of Shop Scheduling, complementary to Graham's notation, the main objective of this work. In addition to that a network representation of the results was obtained in some of the metrics used, such as the job characteristics, something previously unheard of in review studies of this subject. Moreover, another relevant point of this study lies in the identification of less explored fields in order to collaborate with future research in this matter. Keywords: Shop Scheduling. Systematic Literature Review. Taxonomy. Network Representation