Multi-scale Computer Simulations of Biological Systems: Extending Time- and Size-Limits of Molecular Resolution Models

Seminar

Title: Multi-scale Computer Simulations of Biological Systems: Extending Time- and Size-Limits of Molecular Resolution Models

Speaker: Michele Cascella

Affiliation: Department of Chemistry and Centre for Theoretical and Computational Chemistry (CTCC), University of Oslo, Norway

Host: António Baptista, Molecular Simulation Lab

Speaker's short biography

Abstract:

Since the beginning of the informatics revolution, major effort has been put in developing reliable mathematical and physical computational models of complex systems at different resolutions. In bottom-up approaches, the aim is to establish computational models based on fundamen-tai physical principles that are able to predict the behaviour of the system of interest. Even though atomistic simulations can now deal with systems as large as millions of atoms, and for simulation times reaching sometimes the millisecond, several biological processes involving large macromolecular complexes require description at time an sizes that go beyond even such di-mensionalities. In this seminar, I will present Coarse-Grained [1] and multi-scale computational strategies [2] aimed at reducing the intrinsic complexity in atomistic simulations. Such models make it possible to investigate systems composed by several hundred thousands to millions of atoms for several milliseconds on routinely available  computational architectures. In particular, I will present recent advances targeted at the study of polyelectrolyte multiphase systems like lipopolysaccharides.

References
[1] M Neri et al. Phys. Rev. Lett. 2005, 95, 218102; M Cascella et al. J. Chem. Theory Comput. 2008, 4, 1378; D Alemani et al. J. Chem. Theory Comput. 2010, 6, 315; E Spiga et al. J. Chem. Theory Comput. 2013, 9, 3515.
[2] G Milano et al. Phys. Biol. 2013, 10, 045007.