Drug Design, Protein Folding, and Molecular Modeling

In collaboration with the Walther Cancer Institute Center of Excellence in Cancer Research at Notre Dame, we will apply MD modeling to try to understand the binding of anti-breast-cancer drugs to estrogene and DNA. This may be helpful in screening potential drugs and thus guiding the design of better anti-cancer drugs. It will also add a computational component to their research methodology that is important for the training of biological scientists of the future, see Section 4.1. We will extend symplectic integrators for (bio)molecular systems in collaboration with Dr. Düsanka Janëzic, head of the Center for Molecular Modeling at the National Institute of Chemistry in Slovenia and Dr. David Chatfield, professor at Florida International University. He is interested in studying the folding of small proteins, and side-chain protein dynamics. This research will benefit from using faster methods and parallel computers, including perhaps massively parallel processors (MPPs). Systems of medicinal interest, like HIV-1 protease, will be addressed, see Section 4.2. Finally, in collaboration with the Nanotechnology center at Notre Dame we will characterize the charge screening of potential molecular quantum-dot cellular automata cells (QCAs) in different solvents. QCAs are the foundation of a transistor-less approach to nanoelectronics. See Section 4.3. Letters of support for all these subprojects are enclosed in the support documentation section of this proposal.