Applications of Modeling and Simulation in Computational Biology

Russell Schwartz, Celera Genomics

This talk will survey a variety of uses of modeling and simulation in understanding biological systems. The first part of the talk will cover applications of the local rules dynamics model, a simulation model which combined principles from the earlier local rules model of Berger et al. with techniques from molecular dynamics. Both models were originally developed to study virus protein shell self-assembly, although they were later applied to several other self-assembly systems including protein aggregates and amyloids. The second part of the talk will examine the use of a discrete lattice simulation model for studying sequence predictors of protein aggregate formation. It will also look at a statistical model of amino acid word distributions applied to protein sequence databases in order to confirm a prediction derived from the lattice model. The third part of the talk will examine a graph theoretic model and some associated combinatorial optimization problems formulated to aid in understanding the haplotype structure of sequenced genomes. For each type of system covered, we will examine the chosen methods of model building, the motivations for selecting them, and their specific applications.