Jeff Comer

Jeffrey Robert ComerAssociate Professor


B.S. Physics, University of Akron
Ph.D. Physics, University of Illinois at Urbana-Champaign


Phone: 785-532-6311


Molecular simulation of interactions between biological molecules and synthetic nanostructures. Particular focus on the thermodynamics and kinetics of binding, transmembrane transport of nanoparticles, and high-throughput screening.


Interaction between Biomolecules and Synthetic Nanomaterials

Comer J, Chen R, Poblete H, Vergara-Jaque A, Riviere JE (2015) Predicting adsorption affinities of small molecules on carbon nanotubes using molecular dynamics simulation. ACS Nano. DOI: 10.1021/acsnano.5b03592

Poblete H, Agarwal A, Thomas SS, Bohne C, Phospase J, Comer J, Alarcon EI (2015) Peptide–silver nanoparticle interaction: deciphering the role of cysteine and lysine on nanoparticle stability. Langmuir. DOI: 10.1021/acs.langmuir.5b03837

Vilos C, Morales FA, Solar PA, Herrera NS, Gonzalez-Nilo FD, Aguayo DA, Mendoza HL, Comer J, Bravo ML, Gonzalez PA, Kato S, Cuello MA, Alonso C, Bravo EJ, Bustamante EI, Owend GI, Velasquez LA (2013) Paclitaxel-PHBV nanoparticles and their toxicity to endometrial and primary ovarian cancer cells. Biomaterials 34(16):4098–4108. DOI: 10.1016/j.biomaterials.2013.02.034

Comer J, Dehez F, Cai W, Chipot C (2013) Water conduction through a peptide nanotube. J. Phys. Chem. C 117(50):26797–26803. DOI: 10.1021/jp4088223

Comer J, Ho A, Aksimentiev A (2012) Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations. Electrophoresis 33(23):3466–3479. DOI: 10.1002/elps.201200164

Passive Transport through Cell Membranes

Fu H, Comer J, Cai W, Chipot C (2015) Sonoporation at small and large length scales. effect of cavitation bubble collapse on membranes. J. Phys. Chem. Lett. 6:413–418. DOI: 10.1021/jz502513w

Comer J, Schulten K, Chipot C (2014) Diffusive models of membrane permeation with explicit orientational freedom. J. Chem. Theory Comput. 10(7):2710–2718. DOI: 10.1021/ct500209j

Comer J, Schulten K, Chipot C (2014) Calculation of lipid-bilayer permeabilities using an average force. J. Chem. Theory Comput. 10(2):554–564. DOI: 10.1021/ct400925s

Computational Methods for Determining Free Energies and Kinetics

Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C (2015) The adaptive biasing force method: everything you always wanted to know but were afraid to ask. J. Phys. Chem. B 119(3):1129–1151. DOI: 10.1021/jp506633n

Comer J, Phillips JC, Schulten K, Chipot C (2014) Multiple-walker strategies for free-energy calculations in NAMD: shared adaptive biasing force and walker selection rules. J. Chem. Theory Comput. 10(12):5276–5285. DOI: 10.1021/ct500874p

Comer J, Roux B, Chipot C (2014) Achieving ergodic sampling using replica-exchange free-energy calculations. Mol. Sim. 40(1-3):218-228. DOI: 10.1080/08927022.2013.841909

Comer J, Chipot C, Gonzalez-Nilo FD (2013) Calculating position-dependent diffusivity in biased molecular dynamics simulations. J. Chem. Theory Comput. 9(2):876–882. DOI: 10.1021/ct300867e

Membrane Protein Structure–Function

Poblete H, Oyarzún I, Olivero P, Comer J, Zuñiga M, Sepulveda RV, Báez-Nieto D, Leon CG, González-Nilo F, Latorre R (2015) Molecular determinants of phosphatidylinositol 4,5Bisphosphate (PI(4,5)P2) binding to transient receptor potential V1 (TRPV1) channels. J. Biol. Chem. 290(4):2086–2098. DOI: 10.1074/jbc.M114.613620

Zoonens M, Comer JR, Masscheleyn S, Pebay-Peyroula E, Chipot CJ, Miroux B, Dehez F (2013) Dangerous liaisons between detergents and membrane proteins. the case of mitochondrial uncoupling protein 2. J. Am. Chem. Soc. 135(40):15174–15182. DOI: 10.1021/ja407424v