Special Issue

VOL 9, NO 2 (2022) "Supercomputing in Computational Biology and Molecular Modeling of Living Systems"

Submission Deadline: 30 June 2022

The use of molecular and mathematical modeling methods, along with the development of bioinformatics, has had an unprecedented impact on the study of the living world, understanding the principles of organization and functioning of biological systems and their components, down to the intimate details of molecular mechanisms. At the same time, we are now witnessing only the initial stage of this process, which allows us not only to understand the machinery of living systems at various levels of their structural organization, but also opens up fundamentally new opportunities for the practical use of this knowledge in medicine, pharmacology, biotechnology, agriculture, energy production as well as environmental protection and a number of other areas. Computational methods play an important role along these directions, thanks to which the implementation of molecular and mathematical modeling as well as bioinformatics methods approach a qualitatively new level. In this issue of the journal, we encourage authors to submit articles on various aspects of the application of high-performance computing in the study of living systems and their components, the development of the methods themselves, including those related to the big data analysis, the use of machine learning and artificial intelligence, devoted to technical and methodological aspects, as well as optimization of computing technologies themselves and their implementation using hybrid architectures.

This Special Issue on Supercomputing in Computational Biology  and Molecular Modeling of Living Systems (#2, 2022) of the scientific journal ''Supercomputing Frontiers and Innovations'' (indexed at ACM Digital Library and Scopus) is an open call for contributions seeking original, unpublished papers that present scientific contributions in the field of high-performance computing.

Topics of interest include, but are not limited to:

  • Applications of HPC in cutting-edge fundamental and applied research of studying living systems and their components;
  • Development of tools and novel hybrid architectures for HPC applications in the simulation of living systems;
  • Big data management and visualization in living systems modeling;
  • Fine tuning of computation performance and memory handling in software intended for modeling of living systems;
  • Application of machine learning and artificial intelligence to bioinformatics and modeling of living systems;
  • Development of numerical methods and algorithms for the high-performance computing in bioinformatics;
  • Approaches for the optimization of the training of AI models in bioinformatics and modeling of living systems using HPC systems;
  • New parameterizations of living systems as well as their components and related computational aspects;
  • Validation and calibration of models of living systems.

Mini-reviews are invited, representing a comprehensive analysis of publications related to the topics of the special issue, full-length articles (10-16 pages), presenting the results of a completed scientific research, as well as short communications (4-5 pages). Short communications as concise, independent reports representing a significant contribution may focus on hot topics or new findings that have a significant impact on current problems of supercomputing, and include, but are not limited to cutting-edge research or novelty in simulation and modeling. All manuscripts will be peer reviewed and accepted based on quality, originality, novelty, and relevance to the special issue.

Contributions should be written in good English and must meet Supercomputing Frontiers and Innovations standards. Please prepare your article according to the Author Guidelines before submitting a manuscript, and use JSFI's system to submit your manuscripts online (registration in the system). Plеase, do not forget to leave a comment for the Editorial Board, stating that the paper is submitted for the special 2/2022 journal issue.

Invited Editors:

  • Dr. Alexander Nemukhin, Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
  • Dr. Konstantin Shaitan, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
  • Dr. Vytas Švedas, Faculty of Bioengineering and Bioinformatics, Research Computing Center, Lomonosov Moscow State University, Moscow, Russia

All questions about submissions should be emailed to Prof. Vytas Švedas vytas@belozersky.msu.ru.