Theoretical Chemistry
The active areas of research in theoeretical and computational chemistry and biophysics include quantum dynamics, photo-ionization and electron-molecule scattering theory, classical statistical mechanics of dynamical processes in liquids, and protein structure and dynamics.
Associated Faculty
David Coker
Quantum dynamics and statistical mechanics
Coker's group develops semi-empirical methods to compute electronic excited
state potential energy surfaces for many-body systems. They are also
developing mixed quantum-classical and semi-classical molecular dynamics
methods which allow for electronic transitions. These methodologies are
combined in their work to study photodissociation dynamics in liquids,
solids and clusters, charge transfer reactions in different environments,
and various studies of how electronic states and electronic relaxation
dynamics are influenced by solvent.
Tom Keyes
Statistical mechanical mechanics of dynamical processes in liquids
The goal is to understand very slow and very fast dynamics. Relaxation
times vary by 17 decades in supercooled liquids between room temperature
and the glass transition, but theory and simulation are well established
for mild supercooling only. A description of deeply supercooled liquids
is sought via the ``potential energy landscape'' point of view and
the method of instantaneous normal modes, and through development of
new
accelerated molecular dynamics algorithms for slow systems. At the
other extreme, femtosecond time-resolved fifth and higher-order spectroscopy
can potentially provide new information on ultrafast dynamics, and
the
theories and simulations needed to interpret and explain the experiments
are under constrction.
John Straub
Protein structure and dynamics
The Straub group focuses on the theoretical and computational modeling
of biophysical systems. Particular areas of interest include ultrafast
dynamics and energy transfer in heme proteins, the development of computational
algorithms for structural optimization and sampling in proteins and organic
crystals, and the modeling of peptide and protein aggregation.
High-quality force fields and multi-scale molecular dynames and Monte Carlo simulations
The Wang group focuses on the development of high-quality force fields and
multi-scale molecular dynamics and Monte Carlo simulations. Systems of
particular interest include methane clathrate and metal hydrides. Projects
involve development of high quality force fields for methane clathrate and
metal hydrides and studies of the thermo-stability and the nucleation rate of
methane clathrate. A new method is being developed to study the escape
kinetics of methane from a clathrate lattice.
Brandon Xia
Protein bioinformatics
We apply computational techniques to study the structure, function, and evolution of complex bio-molecular systems, such as proteins and protein networks. Specific projects include: reconstruction of protein interaction and regulatory networks by genomic data integration; comparative and evolutionary analysis of proteins and protein networks; protein sequence-structure-function relationships; prediction of protein structure and function
Associated Graduate Courses
We offer the following graduate courses in Theoretical Chemisty:
GRS CH 651/652 - Molecular Quantum Mechanics
Prereq: CAS CH 351, CH 352, or equivalent. Suggested coreq: GRS CH 654. Introduction to quantum theory, atomic and molecular structure, spectroscopy. The chemical bond; Born-Oppenheimer approximation; electronic, vibrational, and rotational motion in molecules. NMR, ESR, microwave, IR, raman, visible, UV spectroscopy, computational ab initio methods for analyzing molecular structure and spectroscopy. Three hours lecture, two hours discussion. Coker, Ziegler. 4 cr, 1st & 2nd sem.
GRS CH 655 - Statistical Mechanics I
Prereq: CAS CH 352 or equivalent. Fundamental principles, including ensemble theory, Fermi-Dirac, Bose-Einstein, and classical statistics; phase transitions; classical applications, including the Mayer expansion, density expansion of the equation of state, and Debye-Huckel theory; time-dependent phenomena, including irreversible thermodynamics; scattering, spectroscopy, and time-correlation functions. Introduction to numerical methods of differentiation, integration, linear algebra, and solution of differential equations. Computational methods for Molecular Dynamics and Monte Carlo simulation of many-body systems. Three hours lecture. Keyes, Straub. 4 cr, 1st sem.
GRS CH 656 - Statistical Mechanics II
Prereq: GRS CH 655 or equivalent. Selected advanced topics may include theories of liquids, free energy perturbation theory, phase transitions, Ising model, Zimm-Bragg model of coil-to-helix transition; irreversible thermodynamics, scattering, linear response theory, time correlation functions, transport, models of diffusion, chemical reaction rate theory, and spectroscopy. Coker, Keyes, Straub. 4 cr, 2nd sem.
GRS CH 752 - Advanced Topics in Chemical Physics
Prereq: GRS CH 652. Current topics of research in theoretical, computational, and experimental chemical physics. Content varies with the instructor but may include material from such areas as advanced methods in molecular spectroscopy and magnetic resonance, nonlinear laser-induced phenomena, and photoionization and electron-molecule scattering. Coker, Keyes, Straub, Ziegler. 4 cr, either sem.