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Research Publications
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Prof. Gerstman with members of his Theoretical and Computational Biophysics research group. |
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Research: Theoretical and Computational Biophysics
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· Non-Linear Dynamics and Protein Folding · Protein Aggregation
· Laser Effects on Biological Tissue and Material Science |
Teaching
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PHZ
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Recent Books and Book Chapters
Physics of Cancer, AIP 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,
“Self-Organizing Dynamics in Protein Folding”
In: Progress in Molecular Biology and Translational Science, Vol. 84, 1-38, ed.: P. Michael Conn
Elsevier Inc.,
Selected Publications
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"
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.