Journal Publications
G. Ozer and T. Schlick, Unfolding heterogeneous chromatin fibers favors smoother transitions involving small nucleosome clusters, PLoS ONE, UNDER REVIEW.
A. Luque, G.Ozer, and T. Schlick, A sensitive interplay between nucleosome repeat length, linker histone concentration, and histone tail interactions, Biophys. J., 110, 2309–2319 (2016).
G.Ozer, A. Luque, and T. Schlick, The chromatin fiber: multiscale problems and approaches, Curr. Opin. Struct. Biol., 31, 124–139 (2015).
G. Ozer and T. Keyes, Classical Description of the Vibrational Spectroscopy, Structure, and Electrostatics of the Halide Solvation Shell with the POLIR Potential, J. Phys. Chem. B, 119 (29), 9312–9318 (2015).
G. Ozer, R. Collepardo-Guevara, and T. Schlick, Forced unraveling of chromatin fiber with nonuniform linker DNA lengths, J. Phys.: Condens. Matter, 27, 064113 (2015).
G. Ozer, T. Keyes, S. Quirk, and R. Hernandez, Multiple branched adaptive steered molecular dynamics, J. Chem. Phys., 141, 064101 (2014).
G. Ozer, S. Quirk, and R. Hernandez, Thermodynamics of decaalanine stretching in water obtained by adaptive steered Molecular dynamics simulations, J. Chem. Theory Comput., 8, 4837–4844 (2012).
G. Ozer, S. Quirk, and R. Hernandez, Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum, J. Chem. Phys., 136, 215104 (2012) [Selected for the June 15, 2012 issue of the Virtual Journal of Biological Physics Research, 23 (12)].
G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, Adaptive Steered Molecular Dynamics of the Long- Distance Unfolding of Neuropeptide Y, J. Chem. Theory Comput., 6, 3026–3038 (2010).
Conference Presentations
“Computational modeling of chromatin organization at the mesoscale level” (Postdocs Interdisciplinary Symposium • New York, NY. May 21, 2015)
“Enhanced sampling through the use of adaptive steered molecular dynamics and statistical temperature molecular dynamics” (From Computational Biophysics to Systems Biology • Knoxville, TN. June 3, 2012)
“Adaptive steered molecular dynamics” (Greater Boston Area Statistical Mechanics Meeting • Boston, MA. October 15, 2011)
“Sifting a massive virtual library of peptide ligands for an optimal binder to a given receptor” (55th Biophysical Society Meeting • Baltimore, MD. March 7, 2011)
“Novel checking function (D2) for secondary structure propensity of proteins at the residue level” (239th ACS National Meeting • San Francisco, CA. March 23, 2010)
“Adaptive steered molecular dynamics of the long-distance unfolding of neuropeptide Y” (239th ACS National Meeting • San Francisco, CA. March 21, 2010)
“Molecular dynamics simulation study of the unfolding of neuropeptide Y” (Frontiers in Macromolecular Simulations Symposium • Atlanta, GA. November 16, 2009)
“D2Check: A fully automated web server for the D2 analysis of protein structures” (239th ACS National Meeting • Atlanta, GA. March 30, 2006)