10th Anniversary of Computation—Computational Biology
A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".
Deadline for manuscript submissions: 30 June 2024 | Viewed by 31865
Special Issue Editors
Interests: data-driven modeling; system identification; mathematical immunology
Special Issues, Collections and Topics in MDPI journals
Interests: genomics; evolution; ancient DNA; population genetics; evolutionary biology
Interests: computational systems biology; bioinformatics; metabolomics; dynamic modelling; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
The Special Issue "10th Anniversary of Computation—Computational Biology" is a collection of papers that focus on the use of computational methods to analyze biological data and to understand biological systems at various levels. The papers cover a wide range of topics, including gene expression analysis, protein structure prediction, drug design, and systems biology.
The Special Issue includes papers that use different computational approaches, such as machine learning, data mining, network analysis, and optimization. The papers also cover a wide range of biological applications, such as cancer research, drug discovery, metabolic engineering, and microbiome analysis.
The Special Issue aims to provide a platform for researchers to share their latest findings and insights in the field of computational biology. The papers in the Special Issue are expected to provide new methods, tools, and insights that can help accelerate research in the field of computational biology and ultimately lead to new breakthroughs in biomedical research.
Prof. Dr. Gennady Bocharov
Dr. Fabrizio Mafessoni
Prof. Dr. Rainer Breitling
Guest Editors
Manuscript Submission Information
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Computation is an international peer-reviewed open access monthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
Keywords
- computational biology
- systems biology
- bioinformatics
- data analysis
- mathematical modeling
- genomics
- pharmacology
Planned Papers
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Stochastic modeling in immunology based on a stage-dependent model with non-Markov constraints for individuals
Authors: Pertsev N.V.; Loginov K.K.
Affiliation: Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences
Abstract: Several stochastic models in immunology are presented. The variables of the models are integer random variables that denote the quantity of individuals (cells and virions) and sets of unique types of individuals that take into account the current state and history of stay of individuals in some stages of their development. A probabilistic description of onestage stochastic model and a numerical simulation algorithm are formulated. The results of numerical simulation of the dynamics of two populations within a two-compartment system and the results of numerical modeling of dynamics of HIV-1 infection in the lymph node are given.
Title: Determination of cellulose fibrils structure and organization in the soil acidobacterium using synchrotron radiation as exemplified by cylindrical symmetry diffraction
Authors: Vlad Kovalenko
Affiliation: N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Moscow
Abstract: In stressful conditions, bacterial cells use various ways to save genetic material in order to continue dividing upon returning to a favorable environment. For the soil bacterium acidobacterium, such a method is the construction of a cellulose chamber. This paper presents a detailed structural study of this cellulose chamber using synchrotron radiation. The diffraction pattern from the 45-day culture of the bacterium acidobacterium was composed of symmetrical radial streaks intersecting in the center of the detector. Such scattering is an example of diffraction from a structure with cylindrical symmetry, according to our assumption, these are cellulose fibers that form a protective chamber envelope and bind neighboring cells into a single cluster. According to the intensity distribution depending on the azimuth angle, the distribution of the deflection angle of individual cellulose microfibers relative to the main direction was calculated. In addition, we have managed to calculate the diameter of a single microfiber forming the basis of the cell membrane and intercellular cluster by modelling the intensity decline along the streaks.
Title: A biomechanical model for joint functioning of neck and shoulder
Authors: A. Yurova; Yu. Vassilevski; A. Gladkov; E. Kalinskiy; A. Lychagin
Affiliation: Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, Gubkina str., 8, 119333 Moscow, Russia
Abstract: We present a biomechanical model of the joint functioning of shoulder and neck sections which includes anatomically correct geometries and appropriate parameters. Motion capture experiments for a patient were carried out for movements in both sections and tensions which appear in muscles during these movements were calculated.
Title: Data-driven anisotropic biomembrane simulation based on the Laplace stretch
Authors: Alexey Liogky; Victoria Salamatova
Affiliation: Sirius University, Russia
Abstract: Data-driven approaches are gaining popularity in the field of computational mechanics, particularly in hyperelasticity. These approaches, which use neural networks and other data-driven techniques, offer numerous advantages, including the ability to address the non-uniqueness of model parameters. However, the lack of interpretability associated with neural networks raises concerns. In this study, we propose an interpretable data-driven approach to hyperelasticity, which is based on finite element forward simulations. This approach employs Laplace stretch as the strain measure and utilizes response functions as constitutive equations. To validate the method, we apply it to anisotropic membranes using synthetic data derived from the Holzapfel-GasserOgden model. Our results demonstrate the applicability of the method and show good agreement with reference displacements, although some discrepancies are observed in the stress calculations. Despite these discrepancies, our proposed method demonstrates its potential usefulness in the field of hyperelasticity.