Paper Citing NAMD - Abstract
Southern, James; Pitt-Francis, Joe; Whiteley, Jonathan; Stokeley, Daniel; Kobashi, Hiromichi; Nobes, Ross; Kadooka, Yoshimasa; Gavaghan, David
Multi-scale computational modelling in biology and physiology
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 96:60-89, JAN-APR 2008
Recent advances in biotechnology and the availability of ever more powerful computers have led to the formulation of increasingly complex models at all levels of biology. One of the main aims of systems biology is to couple these together to produce integrated models across multiple spatial scales and physical processes. In this review, we formulate a definition of multi-scale in terms of levels of biological organisation and describe the types of model that are found at each level. Key issues that arise in trying to formulate and solve multi-scale and multi-physics models are considered and examples of how these issues have been addressed are given for two of the more mature fields in computational biology: the molecular dynamics of ion channels and cardiac modelling. As even more complex models are developed over the coming few years, it will be necessary to develop new methods to model them (in particular in coupling across the interface between stochastic and deterministic processes) and new techniques will be required to compute their solutions efficiently on massively parallel computers. We outline how we envisage these developments occurring. (C) 2007 Elsevier Ltd. All rights reserved.
