Ivet Bahar John K. Vries Chair of Computational & Systems Biology

Computational Modeling of Biomolecular Systems

Keywords:  multiscale modeling, computer-aided design & discovery of biomolecular interaction

We are interested in gaining an understanding of the molecular basis of biological function by characterizing the molecular-to-cellular dynamics of biomolecular systems. We use computational and mathematical models of different complexities for simulating dynamic processes at different levels. At the molecular level, we focus on the conformational dynamics of proteins, including folding, domain movements, and/or local fluctuations, and their perturbation by ligand binding. Examples of our work in this area are the structural dynamics of enzyme-inhibitor interactions, the collective motions of viral capsids, or the ribosomal machinery. Direct computational assessment provides information on the collective dynamics of the enzyme and enables a better mechanistic understanding of how the inhibitors work. At the cellular level, we focus on the interactions involved in cell cycle regulation and signaling. We are interested not only in answering specific biological questions, but in developing new, widely applicable theories and computational tools, including in particular those based on network models, for improving our understanding of biomolecular machinery.

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