Hands-on Workshop on Computational Biophysics 2013
This workshop was presented by members of the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh and the members of the Theoretical and Computational Biophysics Group (www.ks.uiuc.edu) from the University of Illinois at Urbana-Champaign. It covered a wide range of physical models and computational approaches for the simulation of biological systems including ProDy, NAMD and VMD. The course was based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods were introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.
Welcome and Brief Overview
2013 MCell Workshop
This workshop was organized by the Center for Multiscale Modeling of Biological Systems and covered theory and practice for the design and simulation of models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks. The lastest version of the MCell simulation environment (www.mcell.org) were introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. During the workshop we they also introduced:
- Novel tools to incorporate rule-based modeling techniques into MCell simulations based on the BioNetGen Software (Faeder et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 113-167).
- Our new MCell model creation and visualization framework called CellBlender that builds on our previously developed model creation pipeline (Czech et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 237-287).