of Work: The goal of this project is to improve the quality of molecular dynamics simulations, and to apply these methods to highly pertinent problems, both from the view of biomedical relevance and methodological challenge. In principle, molecular dynamics simulations offer a detailed atomic level description of the interactions between key biomolecules of significance to human health. Examples include the DNA metabolizing enzymes responsible for repair and replication of the human genome, and the enzymes involved in the coagulation cascade. In practice, this methodology is limited by the short simulation times (less than 100 nanoseconds) available with current computer technology, which translates into limited conformational sampling, and by the inaccuracies in the empirical force fields used in the simulations. While a number of groups are attempting to relieve the conformational sampling bottlenecks, we are focusing on improvements to the accuracy of representations, without sacrificing computational efficiency. The current focus is on accurate and efficient representations of electrostatic interactions between molecules. The long range goal is to do simulations from first principles, i.e. without resorting to empirical fitting procedures. - molecular dynamics, Ewald summation, Particle Mesh Ewald, free energy perturbation, homology modeling
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