Professor Bernard S. GerstmanFIU Physics Logo


Prof. Bernard S. Gerstman Chairman-Department of Physics


Ph.D. (Physics) Princeton University


Theoretical and Computational



Department of Physics

Office: CP 232

Voice: (305) 348-3115

Florida International




University Park

Miami, FL  33199

Secretary: CP 204


Fax  305-348-6700


Post-Docs and

Graduate Students

CP 253   305-348-6661


Research         Publications            Teaching                 Service 


Pof. Bernard Gerstman
Gerstman Research Group

Prof. Gerstman with members of his Theoretical and Computational Biophysics research group.


Research: Theoretical and Computational Biophysics

·Non-Linear Dynamics and Protein Folding

·Protein Aggregation

·Amyloid Fibril Formation

·Laser Effects on Biological Tissue and Material Science





PHY 6524


PHZ 6255

Graduate Statistical Physics


Molecular Biophysics



PHY 6716

Advanced Biophysics



  • Executive Editor, Journal - AIP Advances
  • Past-Chairman, University Research Council



Recent Books and Book Chapters

Physics of CancerAIP Advances, 2, 010901, 2012 (with R. H. Austin).

“Computational Investigations of Protein Folding to Engineer Amino Acids to Encourage Desired Supersecondary Structure Formation”

In: Protein Supersecondary Structures, 191-204, Ed. Alexander E. Kister,

Methods in Molecular Biology 932, ISBN 978-1-62703-064-9, ISSN 1064-3745,

Human Press 2013, Springer New York.

“Self-Organizing Dynamics in Protein Folding”

In: Progress in Molecular Biology and Translational Science, Vol. 84, 1-38, ed.: P. Michael Conn

Elsevier Inc., Amsterdam, 2008; ISBN 978-0-12-374595-8 (with P. P. Chapagain).

Selected Publications

J. B. GC, Y. R. Bhandari, B. S. Gerstman, and P. P. Chapagain

“Molecular Dynamics Investigations of the α-Helix to β-barrel Conformational Transformation in the RfaH Transcription Factor”

The Journal of Physical Chemistry B, 118(19), 5101-8, 2014.

P. Konold, C. K. Regmi, P. P. Chapagain, B. S. Gerstman, R. Jimenez

“Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants",

The Journal of Physical Chemistry B, 118(11), 2940–2948, 2014.


C. K. Regmi, Y. R. Bhandari, B. S. Gerstman, and P. P. Chapagain

 “Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations”

The Journal of Physical Chemistry B, 117(8), 2247-53, 2013.


T. Steckmann, Z. Awan, B. S. Gerstman, and P. P. Chapagain,

“Kinetics of Peptide Secondary Structure Conversion During Amyloid β-Protein Fibrillogenesis”

Journal of Theoretical Biology, 301, 95–102, 2012.


Y. R. Bhandari, P. P. Chapagain, and B. S. Gerstman,

“Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization”

Journal of Chemical Physics, 137, 105103, 2012.


I. E. Chemmama, A. C. Pelea, Y. R. Bhandari, P. P. Chapagain, and B. S. Gerstman,

“Structural propensities and entropy effects in peptide helix-coil transitions”

Physical Review E, 86, 031915, 2012.  


P. P. Chapagain, B. S. Gerstman, Y. Bhandari, and D. Rimal,

“Free energy landscapes and thermodynamic parameters of complex molecules from non-equilibrium simulation trajectories”

Physical Review E, 83(6), 061905, 2011.


Y. Liu, P. P. Chapagain, and B. S. Gerstman,
“Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine Dimer 

The Journal of Physical Chemistry B, 114 (2), 796–803, 2010.


P. P. Chagagain, Y. Liu, and B. S. Gerstman

“The trigger sequence in the leucine zipper: a-helical propensity dependence of folding and dimerization”

The Journal of Chemical Physics, 129, 175103, 1-9, 2008.


Y. Liu, P. P. Chagagain, J. L. Parra, and B. S. Gerstman

“Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 leucine zipper”

The Journal of Chemical Physics, 128, 045106, 1-10, 2008.


E. Faraggi and B. S. Gerstman

“Resonant Absorption of Pulsed Laser Radiation by a Spherical Absorber”

Journal of Applied Physics, 102, 123505, 1-15, 2007


P. P. Chapagain, J. L. Parra, B. S. Gerstman and Y. Liu

“Sampling of states for estimating the folding funnel entropy and energy landscape

of a model alpha-helical hairpin peptide”

The Journal of Chemical Physics, 127, 075103, 1-7, 2007.


E. Faraggi, B. S. Gerstman, and J. Sun

“The Emergence of Chaos in a Laser Irradiated Spherical Absorber”

Chaos, 17, 013101, 2007


P. P. Chapagain and B. S. Gerstman

“Removal of Kinetic Traps and Enhanced Protein Folding by Strategic Substitution of Amino Acids in a Model a -helical Hairpin Peptide”

Biopolymers, 81(3), 167-178, 2006.


E. Faraggi, B.S. Gerstman, and J.M. Sun

“Biophysical Effects of Pulsed Lasers in the Retina and Other Biological Tissues With Strongly Absorbing Particles: Shockwave and Explosive Bubble Generation”

Journal of Biomedical Optics, 10(6), 064029, 2005.


B.S. Gerstman and P. P. Chapagain

“Self-Organization in Protein Folding and the Hydrophobic Interaction”

The Journal of Chemical Physics, 123, 054901, 1-6, 2005.


P. P. Chapagain and B. S. Gerstman

“Excluded Volume Entropic Effects on Protein Unfolding Times and Intermediary Stability”

The Journal of Chemical Physics, 120(5), 2475-2481, 2004.


P. P. Chapagain and B. S. Gerstman

“Finite Size Scaling of Structural Transitions in a Simulated Protein with Secondary and Tertiary Structure”

The Journal of Chemical Physics, 119(2), 1174-1180, 2003.


J. M. Sun, B. S. Gerstman, and B. Li,

“Bubble Dynamics and Shock Waves Generated by Laser Absorption of a Photoacoustic Sphere”

Journal of Applied Physics, 88(5), 2353-2362, 2000.


J. Sun and B. Gerstman,

Photoacoustic Generation for a Spherical Absorber with Impedance Mismatch with the Surrounding Media

Physical Review E, 59(5), 5772-5789, 1999.


B. S. Gerstman and R. D. Glickman,

“Activated Rate Processes and a Specific Biochemical Mechanism for Explaining Delayed Laser Induced Thermal Damage to the Retina”

Journal of Biomedical Optics, 4(3), 345-351, 1999.


B. Gerstman and Y. Garbourg,

“Structural Information Content and Lyapunov Exponent Calculation in Protein Unfolding” Journal of Polymer Science B: Polymer Physics, 36, 2761-2769, 1998.


B. S. Gerstman and N. Sungar,

"Non‑Adiabatic Electronic Spin Transition in Ligand‑Heme Protein Binding Kinetics and the Influence of the Heme Fe Molecular Environment"

Journal of Chemical Physics, 96, 387, 1992.


B. S. Gerstman,

"CO Binding to Hemoglobin: Spin Tunneling Temperature Dependence, Fe Electronic States,

and Electronic Effects on Non‑Adiabatic Dynamics" 

Journal of Chemical Physics, 88, 6228, 1988.


B. S. Gerstman and A. S. Brill,

"Magnetic Circular Dichroism of Low Symmetry Cupric Sites"

Journal of Chemical Physics, 32, 1212, 1985.


B. S. Gerstman, R. H. Austin, and J. J. Hopfield,

"Investigation of Spin‑Tunneling in Carbon Monoxide Recombination with ß‑Hemoglobin" 

Phys. Rev. Lett., 47, 1636, 1981.