James Stuart Newhouse
223 Maui Research and Technology Center, Building A (MRTC-A)
Kihei, Hawaii 96753
(808) 875-2626 (phone)
james.newhouse.ctr@mhpcc.hpc.mil

Education

Research Summary

My research since 2002 has been within a Computational Proteomics Project in collaboration with Prof. Maqsudul Alam of the University of Hawaii.   I have performed High level theoretical chemistry calculations on globular proteins (Ab Initio Molecular Dynamics characterizing ligand binding).   I have run extensive Molecular Dynamics simulations on globular proteins, helping to clarify their evolutionary development.   I have managed drug screening for dengue fever drugs in the envelope protein of flavivirus virion, both dimer and trimer.  I produced models of Gene Regulator proteins that are involved in a second messenger pathway.  This was achieved by a combination of homology modeling and threading—very complex structures were solved from sequence alone, advancing understanding of biofilm generation.

Drug Action Against Trimer: The docked drug molecule prevents the trimer from forming by getting in the way of contacts that the
virus has to have occur for the trimer to “zipper”.  The cd loop regions  (“fusion loop”) on each trimer section come together
for insertion  into the cell membrane, making the virus effective.

Publications

T.A.K. Freitas, S. Hou, E.M. Dioum, J.A. Saito, J. Newhouse, G. Gonzalez, M.A. Gilles-Gonzalez, & M. Alam.  2004.  Ancestral hemoglobins in Archaea.  Proc Natl Acad Sci USA.  101(17):6675-6680.

“Ab initio Calculations Characterizing an Effective Hamiltonian for Polymeric Photonic Muscles”, poster at Sanibel Symposium, 2002

J.S. Newhouse & R. Kopelman.  1988.  Steady-state Chemical Kinetics on Surface Clusters and Islands:  Segregation of Reactants.  J. Phys. Chem.  92:1538.

J.S. Newhouse, J. Hoshen, & R. Kopelman.  1987.  Refined Monte Carlo Simulations of Static Percolation.  J. Phys. Chem.  91:219.

J.S. Newhouse & R. Kopelman.  1986.  Reaction Kinetics on Clusters and Islands.  J. Chem. Phys.  85:6804.

J.S. Newhouse, "Critical Exponents and Random Walk Reactions on Percolation Clusters:  Simulation of Fractal Exciton Kinetics in Isotopically Mixed Molecular Crystals", Ph. D. thesis, University of Michigan, 1985