Office: 226 Reiss Science
B.A. Physics Rice University
Ph.D. 1985 Biophysics, Harvard University
Postdoctoral associate 1985-1989 University of California, Berkeley
Assistant, Associate & Full Professor 1989-2003 Washington State University
Statistical Mechanics, Physical Chemistry II, Computational Methods for Biomacromolecules
Physical Chemistry, Biophysics, Extreme Conditions, Computational Chemistry
Our research involves computational and theoretical studies of biological macromolecules and their aqueous environment at a molecular level. We use a variety of computational tools including molecular dynamics simulations, electronic structure calculations, continuum dielectrics, and bioinformatics as well as statistical mechanical theory.
Extreme Biophysics. One research area is in the structure and function of enzymes in microbes under extremes of pressure, temperature, and chemical composition. Our focus is on extreme pressure because recent advances in high pressure instrumentation as well as in collection methods for high pressure environments make complementary computational and theoretical studies timely. One aim is to understand how enzymes from piezophilic (pressure-loving) microbes can function at high pressures found at the ocean bottom, and ultimately, to determine the “limits of life”, which can be used in the search for life both terrestrially and extra-terrestrially. Another aim is to understand how much pressure will destroy enzymes from mesophilic microbes, and ultimately, to determine the “limits for death”, which can be used in high-pressure preservation of food.
Water and Aqueous Solutions. Another research area is understanding water and aqueous solutions. Although water is the most common liquid on this planet and has been heavily studied for many years, its properties as a liquid are still not understood well at a molecular level. Our approach has been to understand water by creating new models that are based on the essential features of a water molecule and studying these models in computer simulations. Our focus has been on practical modeling for simulations of biological macromolecules in water and in aqueous solutions containing solutes found in the intracellular environment. This research is complementary to our “extreme biophysics” studies, since extreme conditions will affect the water surrounding an enzyme and the water affects the enzyme.
Selected Recent Publications
Niu, S., M.-L. Tan, and T. Ichiye. The large quadrupole of water molecules. J. Chem. Phys., 2011. 134: 134501. doi: 10.1063/1.3569563, PMID:21476758, PMCID: PMC3081860
Tan, M.-L., J.R. Cendagorta, and T. Ichiye. Effects of microcomplexity on hydrophobic hydration in amphiphiles. J. Am. Chem. Soc., 2013. 135: 4918-4921. doi: 10.1021/ja312504q; PMID: 23506339
Tan, M.-L., J.R. Cendagorta, and T. Ichiye. The molecular charge distribution, the hydration shell, and the unique properties of liquid water. J. Chem. Phys., 2014. 141: 244504. doi: 10.1063/1.4904263
Huang, Q., K.N. Tran, J.M. Rodgers, D.H. Bartlett, R.J. Hemley, and T. Ichiye. A molecular perspective on the limits of life: Enzymes under pressure. Cond. Matter. Phys., 2016. 19: 1-16. Anthony D. J. Haymet Festschrift. doi: 10.54488/CMP.19.20101
Ichiye, T. What makes proteins work: Exploring life in P-T-X. Physical Biology, 2016. in press: Kamal Shukla Festschrift
Tran, K.N., M.-L. Tan, and T. Ichiye. A single-site multipole model for liquid water. J. Chem. Phys., 2016. 145: 034501. doi: 10.1063/1.4958621