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John Weare
Physical chemistry: calculations of the dynamics of complex systems; theoretical geochemistry
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| Contact Information |
| Office: UH 3258 |
| Phone: (858) 534-3286 |
| Fax: (858) 534-7244 |
| Email: jweare@ucsd.edu |
| View group members
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| Education and Appointments |
| 1968 |
Ph.D., Johns Hopkins University
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| 1962 |
B.S., Harvey Mudd College
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| Awards and Academic Honors |
| 1976 |
Guggenheim Fellowship |
| 1968-1969 |
AFOSR Postdoctoral Fellow, Massachusetts Institute of Technology |
| 1968-1969 |
Postdoctoral position, Harvard University |
| Research Interests |
We are working in three areas: theoretical geochemistry and geophysics, theoretical biochemistry, and the development of computational methods for the first-principles simulation of nanoscale materials.
Our interests in geochemistry center around the production of accurate models of highly concentrated brines and their interactions with solid surfaces, reactions in silicate melts, and ion association in high temperature and pressure ore-forming fluids. Our objective in this work is the application of these models to the interpretation of field problems in geochemistry and geophysics. Recently in our program we have emphasized the use of first-principles simulations (ab-initio and conventional molecular dynamics) of the properties of natural fluids found in earth and planetary systems.
Our program in biochemistry is new and involves the simulation of complex biochemical reactions using large-scale quantum chemistry methods and ab-initio molecular dynamics. In our simulation approaches, we utilize powerful parallel computational strategies to allow us to treat systems of very large size. Our results show that, for many biochemical problems, it is necessary to describe a large part of the reactive region of the enzyme (100 or more atoms) with first-principles methods to accurately capture all the chemical interactions important to the catalytic activity of the enzyme. Recently we have had considerable success interpreting the mechanism of kinase reactions (see reference 1 below) important to cell signaling.
In our program, heavy emphasis is also placed on the development of methods of large-scale simulation. The students in the group are trained to develop their own computational methods as well as to learn to effectively implement methods on parallel computational platforms. Within the group, we have a fairly large parallel computer that is devoted to highly parallel computations giving our students an opportunity to have a "hands on" experience with all aspects of computational science.
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| Primary Research Area: |
Interdisciplinary Specialties: |
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Physical/Analytical Chemistry
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Computational and Theoretical
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| Selected Publications |
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The Role of the Putative Catalytic Base in the Phosphoryl Transfer Reaction in a Protein Kinase: First Principles Calculations, With M Valiev, J.H. Adams, R. Kawai. Journal of The American Chemical Society (in press).
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Parallel implementation of the projector augmented plane wave method for charged systems. With E.J. Bylaska, M. Kawai. Journal of Computational Physics and Computer Physics Communications, 14, 11-28, (2002).
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Ab Initio Molecular Dynamics Simulations of Aluminium Ion Solvation in Water Clusters. With M.I. Lubin and E.J. Bylaska. Chem Phys Lett. 322, 447 (2000).
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Accurate Prediction of the Thermodynamic Properties of Fluids in the System H2O-CO2-CH4-N-2 up to 2000 K and 100 kbar from a Corresponding States/one Fluid Equation of State. With Z.H. Duan and N. Moller. Geochim. Cosmochim. Ac. 64, 1069 (2000).
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From Small to Large Behavior: The Transition from the Aromatic to the Peierls Regime in Carbon Rings. With E.J. Bylaska and R. Kawai. J Chem Phys. 113, 6096 (2000).
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Software abstractions and computational issues in parallel structured adaptive mesh methods for electronic structure calculations. With S.R. Kohn, M.E.G. Ong, S.B. Baden. Ima Volumes In Mathematics And Its Application. 117, 75-95 (2000).
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The projector-augmented plane wave method applied to molecular bonding. With M. Valiev. Journal of Physical Chemistry A, 103:49, 10588-601 (1999).
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