Jiang, Z., Remsing, R. C., Rego, N. B., & Patel, A. J. (2019). Characterizing solvent density fluctuations in dynamical observation volumes. The Journal of Physical Chemistry B, 123(7), 1650–1661. https://doi.org/10.1021/acs.jpcb.8b11423
Computational Methods and Models
Developing Novel Simulation Techniques and Theoretical Models
We make extensive use of enhanced sampling techniques (both configurational and path sampling techniques), in conjunction with explicit-solvent molecular dynamics simulations, and when necessary, we develop new simulation techniques. We also develop highly efficient coarse-grained theoretical models to study phenomena characterized by large length scales and/or long time scales. An example of a technique that we frequently use and improve upon is the INDUS (INDirect Umbrella Sampling) method, which has been used extensively (by us and others) to characterize the free energetics of solvent density fluctuations in the bulk and near diverse surfaces.
Relevant Publications
Jiang, H., Fialoke, S., Vicars, Z., & Patel, A. J. (2019). Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES). Soft Matter, 15(5), 860–869. https://doi.org/10.1039/C8SM02317D
Xi, E., Marks, S. M., Fialoke, S., & Patel, A. J. (2018). Sparse sampling of water density fluctuations near liquid-vapor coexistence. Molecular Simulation, 44(13–14), 1124–1135. https://doi.org/10.1080/08927022.2018.1457218
Xi, E., Remsing, R. C., & Patel, A. J. (2016). Sparse sampling of water density fluctuations in interfacial environments. Journal of Chemical Theory and Computation, 12(2), 706–713. https://doi.org/10.1021/acs.jctc.5b01037
Patel, A. J., Varilly, P., Chandler, D., & Garde, S. (2011). Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling. Journal of Statistical Physics, 145(2), 265–275. https://doi.org/10.1007/s10955-011-0269-9
Varilly, P., Patel, A. J., & Chandler, D. (2011). An improved coarse-grained model of solvation and the hydrophobic effect. The Journal of Chemical Physics, 134(7), 074109. https://doi.org/10.1063/1.3532939
Patel, A. J., Varilly, P., & Chandler, D. (2010). Fluctuations of water near extended hydrophobic and hydrophilic surfaces. The Journal of Physical Chemistry B, 114(4), 1632–1637. https://doi.org/10.1021/jp909048f