Professor Bernard S. GerstmanFIU Physics Logo


Prof. Bernard S. Gerstman 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

- Transformer Protein Dynamics

- Protein-Membrane Interactions and Membrane Pore Formation

- Amyloid Fibril Formation

- Laser Effects on Biological Tissue and Material Science





PHY 6524


PHZ 6255

Graduate Statistical Physics


Molecular Biophysics



PHY 6716

Advanced Biophysics



  • Editor-In-Chief, Springer-Nature Book Series - Biological and Medical Physics, Biomedical Engineering
  • Past-Chairman, Department of Physics
  • Past-Chairman, University Research Council



Recent Books and Book Chapters

Research on the Physics of Cancer: A Global Perspective

Bernard S. Gerstman

World Scientific Publishing Co.

ISBN: 978-981-4730-25-9 (hardcover), 2016.


Amyloid Aggregation: Characterization, Function and Molecular Mechanisms

Bernard S. Gerstman and Yifat Miller

AIP Advances 5, 092301, 2015;

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

Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins

In: Protein Supersecondary Structures - Second Edition, 297-312, Ed. Alexander E. Kister,

Methods in Molecular Biology 1958, ISBN 978-1-4939-9160-0, ISSN 1064-3745,

Springer-Nature Humana Press 2019, New York.

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,

Humana 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

Rudramani Pokhrel, Elumalai Pavadai, Bernard S. Gerstman, Prem P. Chapagain,

Membrane pore formation and ion selectivity of the Ebola virus delta peptide

Physical Chemistry Chemical Physics, 2019, 21, 5578-5585; DOI: 10.1039/c8cp07323f.


Elumalai Pavadai, Bernard S. Gerstman, Prem P. Chapagain,

A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix

Nature: Scientific Reports 8: 9776 (2018),


Rudramani Pokhrel, Bernard Gerstman, Joshua Hutcheson, Prem Chapagain,

In-Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles

The Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.8b00169, (2018).


Jeevan B. Gc, Rudramani Pokhrel, Nisha Bhattarai, Kristen A. Johnson, Bernard S. Gerstman, Robert V. Stahelin, Prem P. Chapagain,

Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments

Biochemical and Biophysical Research Communications, 493(1):176-181. doi: 10.1016/j.bbrc.2017.09.052. (2017).


Jeevan B GC, Bernard S Gerstman, Prem P. Chapagain,

Membrane Association and Localization dynamics of the Ebola Virus Matrix Protein VP40

Biochimica et Biophysica Acta 1859 (2017) 2012-2020,


Timothy Steckmann, Prem P. Chapagain, Yuba R. Bhandari, Bernard S. Gerstman,

Cooperative Structural Transitions in Amyloid-Like Aggregation

Journal of Chemical Physics, 146, 135103 (2017); doi: 10.1063/1.4979516,


K. J. Wijesinghe, S. Urata, N. Bhattarai, E. E. Kooijman, B. S. Gerstman, P. P. Chapagain, Sheng Li, R. V. Stahelin,

Detection of Lipid Induced Structural Changes of the Marburg Virus Matrix Protein VP40 Using Hydrogen/Deuterium Exchange Mass Spectrometry

Journal of Biological Chemistry, 292(15):6108-6122. 2017, doi: 10.1074/jbc.M116.758300,


J. B. GC, B. S. Gerstman, R. V. Stahelin, P. P. Chapagain,

The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane

Physical Chemistry Chemical Physics, 2016, 18, 28409-28417, DOI: 10.1039/c6cp03776c.


J. B. GC, K. A. Johnson, M. L. Husby, C. T. Frick, B. S. Gerstman, R. V. Stahelin, P. P. Chapagain,

Interdomain salt-bridges in Ebola virus protein VP40 and their role in domain association and plasma membrane localization

Protein Science, Sep; 25(9):1648-58. doi: 10.1002/pro.2969. Epub 2016 Jul 4. 2016.


F. Leng, G. Fulcrand, S. Dages, X. Zhi, P. Chapagain, B. S. Gerstman, and D. Dunlap, 

DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli

Nature: Scientific Reports, 6: 19243, 2016; doi:10.1038/srep19243.


I. E. Chemmama, P. P. Chapagain, B. S. Gerstman

Pairwise Amino Acid Secondary Structural Propensities

Physical Review E, 91, 042709, 2015.


J. B. GC, B. S. Gerstman, and P. P. Chapagain

The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation

The Journal of Physical Chemistry. B, 2015, DOI: 10.1021/acs.jpcb.5b05681.


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 �‑Hemoglobin

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