Novel methodologies for conformational sampling and QM/MM simulations in complex systems

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Mark E. Tuckerman of New York University is supported by the Theoretical and Computational Chemistry program to develop and implement methods based on specialized variable transformations that are capable of sampling the conformational equilibria of complex systems. This approach reduces the effects of energy barriers without altering thermodynamic and equilibrium properties. Applications of these methods include small peptides as test cases, and fast-folding proteins. A second theme of the research is to develop pseudopotentials appropriate for use in quantum mechanical/molecular mechanical (QM/MM) methods. An initial application of this method is to study the catalytic mechanism of the enzyme histone deacetylase, which is linked to various types of cancer. This work is having a broad impact in developing sampling and search algorithms for bio-simulations. Codes developed in this research, as well as a database of pseudopotentials, are freely available on the PI''s web site. Research results are incorporated into the classroom at the undergraduate and graduate level. Outreach to the community includes non-technical talks to students and faculty at regional middle schools, high school, colleges and universities.