Special Issue "Multiscale Modeling and Simulation in Computational Biology"

Quicklinks

A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: closed (30 September 2014)

Special Issue Editors

Guest Editor
Prof. Dr. Werner Dubitzky (Website)

Professor of Bioinformatics, University of Ulster, Coleraine, UK
Guest Editor
Dr. Chong Wang

Research Associate in Computational Biology, Technische Hochschule Wildau, Technical University of Applied Sciences, Wildau, Germany
Interests: bioinformatics; modeling and simulation in biology; computational structural biology; systems biology; molecular docking and drug design; high performance computing in life sciences

Special Issue Information

Dear Colleagues,

Computational biology is concerned with the modeling and simulation of biological phenomena, processes and systems. Modeling refers to the process that creates a model representing some important features of a biological system. Simulation is the process that uses a model to determine the response of the modeled biological system to certain conditions, inputs or perturbations. In conventional monoscale modeling and simulation approaches, the scope and validity of a biological model is restricted to a specific time and space scale, and/or a particular level of biological organization (e.g., gene transcription). The scale focus of monoscale approaches provides an effective means to simplify the modeling and simulation process. As the need for a detailed mechanistic understanding of biological function grows, the single-scale limitation of conventional modeling and simulation approaches is no longer adequate. The realization that many biological problems of interest require a modeling and simulation approach spanning multiple levels of biophysical reality has led to a new methodology called multiscale modeling and simulation. Multiscale modeling and simulation in computational biology aims to describe and understand life phenomena at a global scale where biological function is recognized as a result of complex mechanisms that happen at several scales, from the molecular to the ecosystem level. Modeling and simulation concepts, methods and tools are invaluable for describing, understanding and predicting these mechanisms in a quantitative and integrative way. There is growing community of computational biologists that research, develop and use multiscale modeling and simulation concepts, methods, tools and systems. The aim of this special issue of Computation is to solicit contributions of original research in the area of multiscale modeling and simulation in computational biology. Specific topics include but are not limited to:

  • Multiscale modeling of biological and biomedical systems and processes.
  • Novel approaches for combining multiple models and scales.
  • Advanced numerical techniques for solving multiscale biological problems.
  • Automated techniques for reverse-engineering multiscale biological models.
  • Analysis, evaluation and validation of multiscale biological models and simulations.
  • Multiscale simulation/computing environments, frameworks and architectures.
  • Technologies supporting distributed multiscale computing using cloud- and grid-based computing environments.
  • E-infrastructures for distributed multiscale computing (computing, storage, networking).
  • Dedicated multiscale computing services and resources.
  • Technologies facilitating semantic interoperation of multiscale biological models and simulations, including model and data sharing.
  • Systematic analyses of emerging and future requirements for multiscale modeling and simulation in computational biology.

Prof. Dr. Werner Dubitzky
Dr. Chong Wang
Guest Editors

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • computational biology
  • systems biology
  • modeling
  • simulation
  • multiscale modeling and simulation
  • scale bridging
  • scale linking
  • multiscale dynamics
  • multiscale computing
  • complexity
  • complex systems
  • large-scale computing
  • bioinformatics

Published Papers (3 papers)

View options order results:
result details:
Displaying articles 1-3
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization
Computation 2015, 3(1), 29-57; doi:10.3390/computation3010029
Received: 20 August 2014 / Revised: 14 January 2015 / Accepted: 26 January 2015 / Published: 5 February 2015
PDF Full-text (5675 KB) | HTML Full-text | XML Full-text
Abstract
Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number [...] Read more.
Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number of atoms involved and the need to simulate over long time periods of biological interest, traditional computational tools, like molecular dynamics, are often infeasible for such systems. Hence, in the current review article, we present and discuss two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction-dominated regime: multiscale perturbation theory and multiscale factorization. These novel analytic foundations provide a self-consistent approach to yield accurate and feasible long-time simulations with atomic detail for a variety of multiscale phenomena, such as viral structural transitions and macromolecular self-assembly. As such, the accuracy and efficiency of the associated algorithms are demonstrated for a few representative biological systems, including satellite tobacco mosaic virus (STMV) and lactoferrin. Full article
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)
Open AccessArticle A 3-D Model of a Perennial Ryegrass Primary Cell Wall and Its Enzymatic Degradation
Computation 2014, 2(2), 23-46; doi:10.3390/computation2020023
Received: 23 December 2013 / Revised: 2 April 2014 / Accepted: 17 April 2014 / Published: 5 May 2014
Cited by 1 | PDF Full-text (3484 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We have developed a novel 3-D, agent-based model of cell-wall digestion to improve our understanding of ruminal cell-wall digestion. It offers a capability to study cell walls and their enzymatic modification, by providing a representation of cellulose microfibrils and non-cellulosic polysaccharides and [...] Read more.
We have developed a novel 3-D, agent-based model of cell-wall digestion to improve our understanding of ruminal cell-wall digestion. It offers a capability to study cell walls and their enzymatic modification, by providing a representation of cellulose microfibrils and non-cellulosic polysaccharides and by simulating their spatial and catalytic interactions with enzymes. One can vary cell-wall composition and the types and numbers of enzyme molecules, allowing the model to be applied to a range of systems where cell walls are degraded and to the modification of cell walls by endogenous enzymes. As a proof of principle, we have modelled the wall of a mesophyll cell from the leaf of perennial ryegrass and then simulated its enzymatic degradation. This is a primary, non-lignified cell wall and the model includes cellulose, hemicelluloses (glucuronoarabinoxylans, 1,3;1,4-β-glucans, and xyloglucans) and pectin. These polymers are represented at the level of constituent monosaccharides, and assembled to form a 3-D, meso-scale representation of the molecular structure of the cell wall. The composition of the cell wall can be parameterised to represent different walls in different cell types and taxa. The model can contain arbitrary combinations of different enzymes. It simulates their random diffusion through the polymer networks taking collisions into account, allowing steric hindrance from cell-wall polymers to be modelled. Steric considerations are included when target bonds are encountered, and breakdown products resulting from enzymatic activity are predicted. Full article
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)
Figures

Review

Jump to: Research

Open AccessReview Simulation Frameworks for Morphogenetic Problems
Computation 2015, 3(2), 197-221; doi:10.3390/computation3020197
Received: 24 October 2014 / Revised: 4 April 2015 / Accepted: 14 April 2015 / Published: 24 April 2015
Cited by 3 | PDF Full-text (5974 KB) | HTML Full-text | XML Full-text
Abstract
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has [...] Read more.
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has been discussed and used in a multitude of works, the realistic modelling of the tissue has only started on a larger scale in the last decade. Here, common tissue modelling techniques are reviewed. Besides the continuum approach, the principles and main applications of the spheroid, vertex, Cellular Potts, Immersed Boundary and Subcellular Element models are discussed in detail. In recent years, many software frameworks, implementing the aforementioned methods, have been developed. The most widely used frameworks and modelling markup languages and standards are presented. Full article
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)

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.

Type of Paper: Article
Authors: Stephen Pankavich et al.
Title: Multiscale Methods for the Simulation of Hierarchical and Mesoscopic Biological Systems
Abstract: Many N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. We present two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction dominated regime - Multiscale Perturbation Theory and Multiscale Factorization. These new analytic foundations also provide a self-consistent approach to yield long-time simulations with atomic detail for a variety of multiscale phenomena, such as structural transitions and self-assembly. As such, we demonstrate the accuracy and efficiency of the associated algorithms for a few representative biological systems, including Satellite Tobacco Mosaic Virus (STMV) and Lactoferrin.


Title: Simulation Frameworks for Morphogenetic Problems
Authors: Iber Dagmar, Tanaka Simon
Abstract: One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks – and how do they evolve? Morphogenesis provides an excellent model system to study how simple molecular networks robustly control complex pattern forming processes on the macroscopic scale in spite of molecular noise, and how important functional variants can evolve from small genetic changes. Recent advancements in 3D imaging technologies, computer algorithms, and computer power now allow us to develop and analyse increasingly realistic models of biological control. Here we review available simulation frameworks that permit the simulation of morphogenetic problems at different levels of detail, and we will provide an outlook to further developments in light of current limitations.

Journal Contact

MDPI AG
Computation Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
computation@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Computation
Back to Top