Email: Click to Mail
Phone: (805) 284-8293
Fax: (805) 893-4731
Office Location: 3339 Engineering II
Address: Mail Code 5080
Chemical Engineering Dept.
University of California
Santa Barbara, CA 93106-5080 USA
Name: Allie Olympius
Email: Click to Mail
Phone: (805) 893-2214
Fax: (805) 893-4731
BS: Chemical Engineering, University of Missouri - Columbia (1999); B.S. Mathematics, University of Missouri - Columbia (1999)
PhD: Chemical Engineering, University of California - Berkeley (2004)
Honors: Camille Dreyfus Teacher-Scholar Award (2013)
NSF graduate fellowship (2000)
The kinetics of nucleation, electron transfer, and catalytic reactions depend on the properties of short-lived and rarely-visited transition states that cannot be directly observed in experiments. We gain insight into the properties of transition states using molecular simulation and electronic structure theory. Examples include the effects of solution additives on nucleation rates for crystallization, the dominant electron transfer conduits in realistic fluctuating environments, and catalytic reaction mechanisms. When applications pose new challenges beyond the scope of available techniques, we develop theories and algorithms to address those challenges. In particular, we specialize in path sampling methods for free energies and reaction coordinate identification, metrics for reaction coordinate error, methods to obtain accurate rate constants, and multiscale simulation approaches.
"p(TP|q) peak maximization: necessary but not sufficient for reaction coordinate accuracy," B. Peters, Chem. Phys. Lett. 494, 100 (2010)
"Transition state theory, dynamics, and narrow timescale separation in the rate promoting vibrations model of enzyme catalysis," B. Peters, J. Chem. Theory and Comp., 6, 1447 (2010).
[invited] "Direct simulation method for computing the interfacial free energy of nanoscale nuclei in solution," N. Duff, B. Peters, Molecular Simulation, 36, 498 (2010). [special AIChE issue]
[invited] "Recent advances in path sampling: accurate reaction coordinates, likelihood maximization, and diffusive barrier crossing dynamics," B. Peters, Molecular Simulation, (in press, special issue "Foundations of Modeling and Molecular Simulation" [FOMMS]).
"Estimating diffusivity along a reaction coordinate in the high friction limit: insights on pulse times in laser-induced nucleation," B. Knott, N. Duff, M.F. Doherty, B. Peters, J. Chem. Phys. 131, 224112 (2009).
[cover] "Nucleation in a Potts-Lattice gas model of crystallization from solution," N. Duff, B. Peters, J. Chem. Phys. 131, 184101 (2009).
"Competing nucleation pathways in a mixture of oppositely charged colloidal particles: out-of-equilibrium nucleation revisited," Baron Peters, J. Chem. Phys. 131, 224103, (2009)
"Path sampling calculation of methane diffusivity in gas hydrates by a water vacancy assisted mechanism," B. Peters, N.E.R. Zimmerman, G.T. Beckham, J.W. Tester, B.L.Trout, J. Am. Chem. Soc., 130 17342 (2008).
"Evidence for size dependent nucleation mechanism in solid state polymorph transformations," G. Beckham, B. Peters, B.L.Trout, J. Phys. Chem. B. 112 7460 (2008)
"Strictosidine Synthase: Mechanism of a Pictet-Spengler Catalyzing Enzyme," J.J. Maresh, L-A. Giddings, A. Friedrich, E.A. Loris, S. Panjikar, B.L. Trout, J. Stockigt, B. Peters, and S.E. O'Connor, J. Am. Chem. Soc., 130, 710, (2008)
"Extensions to the maximum likelihood approach for obtaining reaction coordinates," B. Peters, G. Beckham, B.L.Trout, J. Chem. Phys. 127, 034109 (2007)
"Surface mediated nucleation in the polymorph transformation of terephthalic acid," G. Beckham, B. Peters, N. Variankaval, C. Starbuck, B.L. Trout, J. Am. Chem. Soc. 129, 4714 (2007)
"New methods for computational chemistry in Q-Chem 3.0," J. Kong et al., Phys. Chem. Chem. Phys. 8, 1 (2006)
"Using the histogram test to quantify reaction coordinate error," B. Peters, J. Chem. Phys. 125, 241101 (2006)
"Asparagine deamidation: pH dependent mechanism from density functional theory," B. Peters, B.L. Trout, Biochemistry, 45, 5384 (2006)
"Obtaining reaction coordinates by likelihood maximization," B. Peters, B. L. Trout, J. Chem. Phys. 125, 054108 (2006)
"Comprehensive DFT Study of nitrous oxide decomposition over FeZSM5," A. Heyden, B. Peters, A. T. Bell, F.J. Keil, J. Phys. Chem. B, 109, 1857 (2005)
"Rate constants from the reaction path Hamiltonian II: non-separable semiclassical transition state theory," B. Peters, A.T. Bell, A. Chakraborty, J. Chem. Phys. 121, 4461 (2004)
"Rate constants from the reaction path Hamiltonian I: reactive flux simulations for dynamically correct rates," B. Peters, A.T. Bell, A. Chakraborty, J. Chem. Phys. 121, 4453 (2004)
"A growing string method for locating transition states: comparison to NEB and string methods," B. Peters, A. Heyden, A.T. Bell, A. Chakraborty, J. Chem. Phys. 120, 7877 (2004)
"Biasing a transition state search to locate multiple reaction pathways," B. Peters, W.Z. Liang, A.T. Bell, A. Chakraborty, J.Chem.Phys. 118, 9533 (2003)