Machine learning, Monte Carlo and MD
The prediction of thermodynamic properties at the molecular level using Monte Carlo and molecular dynamics simulations is an active research area in our group. Current work includes collaboration with Mark Tuckerman (New York U), focused on the application of machine learning techniques to molecular dynamics simulations of free energy surfaces.
(1) J.R. Cendagorta, J. Tolpin*, E. Schneider, R.Q. Topper and M.E. Tuckerman, Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables, J. Phys. Chem. B,124(18), pp.3647-3660(2020).
(2) E. Schneider, L. Dai***, R.Q. Topper, C. Drechsel-Grau and M.E. Tuckerman, Stochastic neural network approach for learning high-dimensional free energy surfaces, Physical Review Letters 119, 150601 (2017).
(3) R.Q. Topper, D.L. Freeman, D. Bergin* and K. LaMarche**, Computational techniques and strategies for Monte Carlo thermodynamic calculations with applications to nanoclusters, invited book chapter, Reviews in Computational Chemistry, Vol. 19, pp. 1-41, K.B. Lipkowitz, R. Larter and T.R. Cundari, Eds., Wiley-VCH/John Wiley and Sons, New York (2003). ISBN 0-471-23585-7.
(4) R.Q. Topper, Adaptive path-integral Monte Carlo methods for accurate computation of molecular thermodynamic properties, invited book chapter, Monte Carlo Methods in Chemical Physics, Advances in Chemical Physics105, Chapter 5, pp. 117-170, D. Ferguson, I. Siepmann, and D.G. Truhlar, Eds., John Wiley & Sons, Inc., New York (1999).
(5) R.Q. Topper, Q. Zhang, Y.-P. Liu, and D.G. Truhlar, Quantum steam tables. Free energy calculations for H2O,D2O, H2S, and H2Se by adaptively optimized Fourier path integrals, Journal of Chemical Physics98, 4991 (1993).
(6) R.Q. Topper, G.J. Tawa, and D.G. Truhlar, Quantum free-energy calculations: A three-dimensional test case, Journal of Chemical Physics97, 3648 (1992).
(7) R.Q. Topper and D.G. Truhlar, Quantum free-energy calculations: Optimized Fourier path-integral Monte Carlo computation of coupled vibrational partition functions,Journal of Chemical Physics97, 3648 (1992).
* = Undergraduate / graduate student researcher.
**=Undergraduate student researcher.
***=High school student researcher.