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Gerstman, Bernard
Graduate Faculty
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Professor
,
Physics
,
College of Arts, Sciences & Education
gerstman@fiu.edu
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Overview
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Overview
biography
Bernard S. Gerstman is a Professor in Physics and the Biomolecular Sciences Institute, specializing in Theoretical Biophysics.
research interests
Theoretical Biophysics
Non-Linear Dynamics and Protein Folding
Protein Aggregation
Laser Effects on Biological Tissue and Material Science
Affiliation
manager of
Machine Shop
Facility
Scholarly & Creative Works
selected scholarly works & creative activities
Article
2023
Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding
Full Text via DOI:
10.3390/ijms241612586
Web of Science:
001056249900001
2023
Exploring the dimer-dimer association of the ebolavirus matrix protein VP40 at the human plasma membrane
Full Text via DOI:
10.1016/j.bpj.2022.11.1194
2022
Immunoinformatic screening of Marburgvirus epitopes and computational investigations of epitope-allele complexes
.
INTERNATIONAL IMMUNOPHARMACOLOGY
. 111.
Full Text via DOI:
10.1016/j.intimp.2022.109109
Web of Science:
000862677800002
2022
Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachment
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
. 24:9123-9129.
Full Text via DOI:
10.1039/d2cp00169a
Web of Science:
000779732000001
2022
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane
.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
. 90:340-350.
Full Text via DOI:
10.1002/prot.26221
Web of Science:
000692659700001
2022
Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact Method
.
ACS SENSORS
. 7:555-563.
Full Text via DOI:
10.1021/acssensors.1c02385
Web of Science:
000746813600001
2021
Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides
.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
. 18:516-525.
Full Text via DOI:
10.1021/acs.jctc.1c00666
Web of Science:
000730568600001
2021
Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion
.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
. 574:14-19.
Full Text via DOI:
10.1016/j.bbrc.2021.08.036
Web of Science:
000687461600001
2021
Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop
Full Text via DOI:
10.3390/v13071375
Web of Science:
000677080900001
2021
Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 125:7101-7107.
Full Text via DOI:
10.1021/acs.jpcb.1c01626
Web of Science:
000672740600004
2021
Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly
.
JOURNAL OF BIOLOGICAL CHEMISTRY
. 296.
Full Text via DOI:
10.1016/j.jbc.2021.100796
Web of Science:
000674717300016
2020
In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever
.
SCIENTIFIC REPORTS
. 10.
Full Text via DOI:
10.1038/s41598-020-63640-1
Web of Science:
000534024000034
2020
A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation
Full Text via DOI:
10.3390/pathogens9050402
Web of Science:
000541443700085
2020
Mutation of Hydrophobic Residues in the C-Terminal Domain of the Marburg Virus Matrix Protein VP40 Disrupts Trafficking to the Plasma Membrane
Full Text via DOI:
10.3390/v12040482
Web of Science:
000539525300124
2019
Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 123:9045-9053.
Full Text via DOI:
10.1021/acs.jpcb.9b04674
Web of Science:
000493865200001
2019
Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
. 21:12530-12539.
Full Text via DOI:
10.1039/c9cp01558b
Web of Science:
000478994100046
2019
Membrane pore formation and ion selectivity of the Ebola virus delta peptide
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
. 21:5578-5585.
Full Text via DOI:
10.1039/c8cp07323f
Web of Science:
000461722800020
2019
Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins
Full Text via DOI:
10.1007/978-1-4939-9161-7_15
Web of Science:
000706398300016
2018
Domain rearrangement and denaturation in Ebola virus protein VP40
.
AIP ADVANCES
. 8.
Full Text via DOI:
10.1063/1.5063474
Web of Science:
000454615100058
2018
Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24-Human Keap1 Complex
.
ACS OMEGA
. 3:18639-18645.
Full Text via DOI:
10.1021/acsomega.8b02386
Web of Science:
000458439900046
2018
A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix
.
SCIENTIFIC REPORTS
. 8.
Full Text via DOI:
10.1038/s41598-018-28077-7
Web of Science:
000436398100001
2018
In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 122:3782-3789.
Full Text via DOI:
10.1021/acs.jpcb.8b00169
Web of Science:
000430641900011
2018
Referee acknowledgment for 2017
.
AIP ADVANCES
. 8:040201.
Full Text via DOI:
10.1063/1.5032191
2018
A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine
Full Text via DOI:
10.1074/jbc.M117.816280
Web of Science:
000426562800025
2017
Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments
.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
. 493:176-181.
Full Text via DOI:
10.1016/j.bbrc.2017.09.052
Web of Science:
000413134200028
2017
Membrane association and localization dynamics of the Ebola virus matrix protein VP40
.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
. 1859:2012-2020.
Full Text via DOI:
10.1016/j.bbamem.2017.07.007
Web of Science:
000411419000026
2017
Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry
Full Text via DOI:
10.1074/jbc.M116.758300
Web of Science:
000399538700009
2017
Cooperative structural transitions in amyloid-like aggregation
.
JOURNAL OF CHEMICAL PHYSICS
. 146.
Full Text via DOI:
10.1063/1.4979516
Web of Science:
000399073300052
2017
Referee acknowledgment for 2016
.
AIP ADVANCES
. 7:030201.
Full Text via DOI:
10.1063/1.4979606
2017
Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer
.
RSC ADVANCES
. 7:22741-22748.
Full Text via DOI:
10.1039/c7ra02940c
Web of Science:
000400338000016
2016
The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P-2 lipids in the plasma membrane
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
. 18:28409-28417.
Full Text via DOI:
10.1039/c6cp03776c
Web of Science:
000386668200003
2016
Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization
.
PROTEIN SCIENCE
. 25:1648-1658.
Full Text via DOI:
10.1002/pro.2969
Web of Science:
000383619100008
2016
Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675
.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
. 7:3046-3051.
Full Text via DOI:
10.1021/acs.jpclett.6b01172
Web of Science:
000381236400029
2016
Referee acknowledgment for 2015
.
AIP ADVANCES
. 6:060201.
Full Text via DOI:
10.1063/1.4953361
2016
DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli
.
SCIENTIFIC REPORTS
. 6.
Full Text via DOI:
10.1038/srep19243
Web of Science:
000368157700001
2015
The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 119:12750-12759.
Full Text via DOI:
10.1021/acs.jpcb.5b05681
Web of Science:
000362701900003
2015
Self-assembly dynamics for the transition of a globular aggregate to a fibril network of lysozyme proteins via a coarse-grained Monte Carlo simulation
.
AIP ADVANCES
. 5.
Full Text via DOI:
10.1063/1.4921074
Web of Science:
000362562100005
2015
Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator
.
PROTEIN SCIENCE
. 24:741-751.
Full Text via DOI:
10.1002/pro.2646
Web of Science:
000353524700016
2015
Pairwise amino acid secondary structural propensities
.
PHYSICAL REVIEW E
. 91.
Full Text via DOI:
10.1103/PhysRevE.91.042709
Web of Science:
000352850200007
2015
Referee acknowledgment for 2014
.
AIP ADVANCES
. 5:020201.
Full Text via DOI:
10.1063/1.4908041
2015
Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching
.
INTEGRATIVE BIOLOGY
. 7:263-273.
Full Text via DOI:
10.1039/c4ib00251b
Web of Science:
000349668600011
2014
Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription Factor
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 118:5101-5108.
Full Text via DOI:
10.1021/jp502193v
Web of Science:
000336199100013
2014
Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 118:2940-2948.
Full Text via DOI:
10.1021/jp412371y
Web of Science:
000333381800016
2014
Referee acknowledgment for 2013
.
AIP ADVANCES
. 4:030201.
Full Text via DOI:
10.1063/1.4869571
2013
Exploring the Diffusion of Molecular Oxygen in the Red Fluorescent Protein mCherry Using Explicit Oxygen Molecular Dynamics Simulations
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 117:2247-2253.
Full Text via DOI:
10.1021/jp308366y
Web of Science:
000315707900003
2013
Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation
Full Text via DOI:
10.1007/978-1-62703-65-6_12
2012
Structural propensities and entropy effects in peptide helix-coil transitions
.
PHYSICAL REVIEW E
. 86.
Full Text via DOI:
10.1103/PhysRevE.86.031915
Web of Science:
000308872700005
2012
Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization
.
JOURNAL OF CHEMICAL PHYSICS
. 137.
Full Text via DOI:
10.1063/1.4752247
Web of Science:
000309100400057
2012
Kinetics of peptide secondary structure conversion during amyloid beta-protein fibrillogenesis
.
JOURNAL OF THEORETICAL BIOLOGY
. 301:95-102.
Full Text via DOI:
10.1016/j.jtbi.2012.02.012
Web of Science:
000303079500010
2011
Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories
.
PHYSICAL REVIEW E
. 83.
Full Text via DOI:
10.1103/PhysRevE.83.061905
Web of Science:
000291437200003
2010
Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine Dimer
.
JOURNAL OF PHYSICAL CHEMISTRY B
. 114:796-803.
Full Text via DOI:
10.1021/jp909872a
Web of Science:
000273405000015
2008
The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization
.
JOURNAL OF CHEMICAL PHYSICS
. 129.
Full Text via DOI:
10.1063/1.3006421
Web of Science:
000260777400053
2008
Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper
.
JOURNAL OF CHEMICAL PHYSICS
. 128.
Full Text via DOI:
10.1063/1.2831513
Web of Science:
000252821200094
2007
Acoustical resonant absorption of pulsed laser radiation by a spherical absorber
.
JOURNAL OF APPLIED PHYSICS
. 102.
Full Text via DOI:
10.1063/1.2822247
Web of Science:
000251987600026
2007
Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide
.
JOURNAL OF CHEMICAL PHYSICS
. 127.
Full Text via DOI:
10.1063/1.2757172
Web of Science:
000248905300035
2007
The emergence of chaos in a laser irradiated spherical absorber
.
CHAOS
. 17.
Full Text via DOI:
10.1063/1.2407262
Web of Science:
000245317300001
2006
Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide
.
BIOPOLYMERS
. 81:167-178.
Full Text via DOI:
10.1002/bip.20388
Web of Science:
000235041200003
2005
Biophysical effects of pulsed lasers in the retina and other tissues containing strongly absorbing particles: shockwave and explosive bubble generation
.
JOURNAL OF BIOMEDICAL OPTICS
. 10.
Full Text via DOI:
10.1117/1.2139970
Web of Science:
000234859400031
2005
Self-organization in protein folding and the hydrophobic interaction
.
JOURNAL OF CHEMICAL PHYSICS
. 123.
Full Text via DOI:
10.1063/1.1990110
Web of Science:
000231168700071
2004
Excluded volume entropic effects on protein unfolding times and intermediary stability
.
JOURNAL OF CHEMICAL PHYSICS
. 120:2475-2481.
Full Text via DOI:
10.1063/1.1637032
Web of Science:
000188498400046
2003
Finite size scaling of structural transitions in a simulated protein with secondary and tertiary structure
.
JOURNAL OF CHEMICAL PHYSICS
. 119:1174-1180.
Full Text via DOI:
10.1063/1.1579673
Web of Science:
000183842500058
2000
Bubble dynamics and shock waves generated by laser absorption of a photoacoustic sphere
.
JOURNAL OF APPLIED PHYSICS
. 88:2352-2362.
Full Text via DOI:
10.1063/1.1288507
Web of Science:
000088796500029
1999
Activated rate processes and a specific biochemical mechanism for explaining delayed laser induced thermal damage to the retina
.
JOURNAL OF BIOMEDICAL OPTICS
. 4:345-351.
Full Text via DOI:
10.1117/1.429936
Web of Science:
000082189400010
1999
Photoacoustic generation for a spherical absorber with impedance mismatch with the surrounding media
.
PHYSICAL REVIEW E
. 59:5772-5789.
Full Text via DOI:
10.1103/PhysRevE.59.5772
Web of Science:
000080382900041
1999
Contributory presentations/posters
Full Text via DOI:
10.1007/bf02989373
1998
Structural information content and lyapunov exponent calculation in protein unfolding
.
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS
. 36:2761-2769.
Full Text via DOI:
10.1002/(SICI)1099-0488(19981115)36:15<2761::AID-POLB10>3.0.CO;2-5
1996
Melanin granule model for laser-induced thermal damage in the retina
.
BULLETIN OF MATHEMATICAL BIOLOGY
. 58:809-810.
Full Text via DOI:
10.1007/bf02459483
1996
Melanin granule model for laser-induced thermal damage in the retina
.
BULLETIN OF MATHEMATICAL BIOLOGY
. 58:513-553.
Full Text via DOI:
10.1007/BF02460595
Web of Science:
A1996UN90300006
1996
Laser induced bubble formation in the retina
.
LASERS IN SURGERY AND MEDICINE
. 18:10-21.
Full Text via DOI:
10.1002/(SICI)1096-9101(1996)18:1<10::AID-LSM2>3.0.CO;2-U
Web of Science:
A1996TM76300002
1995
ELECTRONIC PARAMAGNETISM IN BIOMOLECULAR STRUCTURE AND FUNCTION
.
AMERICAN JOURNAL OF PHYSICS
. 63:1096-1114.
Full Text via DOI:
10.1119/1.18015
Web of Science:
A1995TG79400011
1995
CONTROL OF LONG-TIME DEPENDENCE OF CO BINDING TO HEME SYSTEMS BY INHOMOGENEOUS SPREAD IN ELECTRONIC PREFACTOR
.
JOURNAL OF CHEMICAL PHYSICS
. 102:1225-1229.
Full Text via DOI:
10.1063/1.468909
Web of Science:
A1995QC35400015
1992
NONADIABATIC ELECTRONIC SPIN TRANSITION IN LIGAND-HEME PROTEIN-BINDING KINETICS AND THE INFLUENCE OF THE HEME FE MOLECULAR ENVIRONMENT
.
JOURNAL OF CHEMICAL PHYSICS
. 96:387-398.
Full Text via DOI:
10.1063/1.462475
Web of Science:
A1992GY24900041
1991
CORRELATED DISTRIBUTIONS IN G AND A TENSORS AT A BIOLOGICALLY-ACTIVE LOW-SYMMETRY CUPRIC SITE
.
PHYSICAL REVIEW A
. 44:5257-5271.
Full Text via DOI:
10.1103/PhysRevA.44.5257
Web of Science:
A1991GM06000054
1991
Hybrid atomic orbital model of low-symmetry cupric sites
.
JOURNAL OF INORGANIC BIOCHEMISTRY
. 43:223.
Full Text via DOI:
10.1016/0162-0134(91)84215-u
1991
TIME-RESOLVED INFRARED STUDIES OF MOLECULAR-DIFFUSION IN MYOGLOBIN
.
PHYSICAL REVIEW LETTERS
. 66:2673-2676.
Full Text via DOI:
10.1103/PhysRevLett.66.2673
Web of Science:
A1991FM03600033
1989
HYPERFINE CONTRIBUTIONS TO THE LINEAR-ELECTRIC-FIELD EFFECT IN LOW-SYMMETRY CUPRIC SITES
.
PHYSICAL REVIEW A
. 39:5903-5913.
Full Text via DOI:
10.1103/PhysRevA.39.5903
Web of Science:
A1989U881800053
1989
Enhancement of ligand binding to myoglobin by far-infrared excitation from a free-electron laser
.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS
. 6:1050-1057.
Full Text via DOI:
10.1364/JOSAB.6.001050
1988
CO BINDING TO HEMOGLOBIN - SPIN-TUNNELING TEMPERATURE-DEPENDENCE, FE ELECTRONIC STATES, AND ELECTRONIC EFFECTS ON NONADIABATIC DYNAMICS
.
JOURNAL OF CHEMICAL PHYSICS
. 88:6228-6232.
Full Text via DOI:
10.1063/1.454461
Web of Science:
A1988N555800024
1988
LINEAR ELECTRIC-FIELD EFFECT ON G-VALUES OF LOW-SYMMETRY CUPRIC SITES
.
PHYSICAL REVIEW A
. 37:2151-2164.
Full Text via DOI:
10.1103/PhysRevA.37.2151
Web of Science:
A1988M525800035
1986
Redox-insensitive molecular force constants
.
JOURNAL OF CHEMICAL PHYSICS
. 85:2227-2231.
Full Text via DOI:
10.1063/1.451117
1985
Magnetic circular dichroism of low symmetry cupric sites
.
JOURNAL OF CHEMICAL PHYSICS
. 82:1212-1230.
Full Text via DOI:
10.1063/1.448494
1983
Creationism still again
.
PHYSICS TODAY
. 36:11-88.
Full Text via DOI:
10.1063/1.2915565
1981
Hemoglobin-carbon monoxide binding rate. Low temperature magneto-optical detection of spin-tunneling
.
BIOPHYSICAL JOURNAL
. 35:471-484.
Full Text via DOI:
10.1016/S0006-3495(81)84803-5
1981
Investigation of spin tunneling in carbon monoxide recombination with hemoglobin
.
PHYSICAL REVIEW LETTERS
. 47:1636-1639.
Full Text via DOI:
10.1103/PhysRevLett.47.1636
Book
2020
Preface
2020
The physics of cancer: Research advances
Full Text via DOI:
10.1142/11915
2016
Research on the Physics of Cancer A Global Perspective
Conference
2020
Calculating the Binding Free Energy Difference between Conformational Changes of AT-Rich DNA Sequences
.
BIOPHYSICAL JOURNAL
. 218A-218A.
Web of Science:
000513023201340
2020
Computational Study of the Molecular Details of Ebola Virus Matrix Protein VP40 and Human Sec24C Protein Interaction
.
BIOPHYSICAL JOURNAL
. 506A-506A.
Web of Science:
000513023203272
2020
Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide
.
BIOPHYSICAL JOURNAL
. 586A-587A.
Web of Science:
000513023203666
2020
Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling
.
BIOPHYSICAL JOURNAL
. 305A-305A.
Web of Science:
000513023202030
2019
Computational Study of Calcium Phosphate Mineralization in Extracellular Vesicles
.
BIOPHYSICAL JOURNAL
. 572A-572A.
Full Text via DOI:
10.1016/j.bpj.2018.11.3075
Web of Science:
000460779802874
2019
Dynamics of the Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament
.
BIOPHYSICAL JOURNAL
. 472A-472A.
Full Text via DOI:
10.1016/j.bpj.2018.11.2549
Web of Science:
000460779802370
2019
Molecular Basis of the Marburg Virus Protein VP24 Interactions with Human Keap1
.
BIOPHYSICAL JOURNAL
. 182A-182A.
Full Text via DOI:
10.1016/j.bpj.2018.11.1011
Web of Science:
000460779800901
2019
Molecular Dynamics Investigations of Enzyme Conformational Changes
.
BIOPHYSICAL JOURNAL
. 186A-186A.
Full Text via DOI:
10.1016/j.bpj.2018.11.1031
Web of Science:
000460779800921
2018
A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40
.
BIOPHYSICAL JOURNAL
. 64A-64A.
Web of Science:
000429315800331
2018
Conformational Changes in Marburg Virus VP40 upon Plasma Membrane Association
.
BIOPHYSICAL JOURNAL
. 459A-459A.
Web of Science:
000430563200066
2017
Plasma membrane localization dynamics of the filovirus matrix protein VP40
.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
. S211-S211.
Web of Science:
000416406201256
2017
Pi(4,5)P-2 Clustering by the Ebola Virus Matrix Protein VP40
.
BIOPHYSICAL JOURNAL
. 326A-326A.
Full Text via DOI:
10.1016/j.bpj.2016.11.1765
Web of Science:
000402375600611
2017
Temperature Dependent Pair-Wise Amino Acid Structural Propensity in cc beta and Implications for alpha to beta Secondary Structural Conversion
.
BIOPHYSICAL JOURNAL
. 191A-191A.
Full Text via DOI:
10.1016/j.bpj.2016.11.1059
Web of Science:
000402328000944
2016
Picosecond hydrogen bond dynamics in proteins examined with femtosecond spectroscopy and molecular dynamics simulations
.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
.
Web of Science:
000431905705336
2016
Interdomain Interactions and the Mechanism of Structural Transformation in RfaH
.
BIOPHYSICAL JOURNAL
. 378A-378A.
Full Text via DOI:
10.1016/j.bpj.2015.11.2040
Web of Science:
000375142200330
2016
On the Origin of the Extended Stoke's Shifts in Fluorescent Proteins
.
BIOPHYSICAL JOURNAL
. 377A-378A.
Full Text via DOI:
10.1016/j.bpj.2015.11.2039
Web of Science:
000375142200329
2015
Hydrogen Bond Flexibility and Water Dynamics in the Far Red Fluorescent Protein TagRFP675
.
BIOPHYSICAL JOURNAL
. 469A-469A.
Full Text via DOI:
10.1016/j.bpj.2014.11.2562
Web of Science:
000362849400778
2014
Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Protein Mplum
.
BIOPHYSICAL JOURNAL
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10.1016/j.bpj.2013.11.3592
Web of Science:
000337000403623
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Analyzing chaos in the pressure generated by laser absorption by microparticles
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
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Full Text via DOI:
10.1117/12.696482
Web of Science:
000246520100011
2007
Investigating the nanoparticle transition from bulk behavior to discrete atom/finite size behavior using laser induced pressure generation
. 1025-1028.
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10.4028/3-908451-30-2.1025
2007
Using laser induced shock waves to investigate the nanoparticle tranistion from bulk behavior to discrete atom/finite size behavior
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11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012)
. 703-706.
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000252158500167
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Chaos in the pressure generated by laser absorption by microparticles
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
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Full Text via DOI:
10.1117/12.644846
Web of Science:
000237158300004
2006
Resonant absorption in nanometer gold spherical particles
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
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Full Text via DOI:
10.1117/12.644815
Web of Science:
000237158300003
2005
Stress confinement, shock wave formation and laser induced damage
. 209-215.
Full Text via DOI:
10.1117/12.589469
2005
Response to pulsed radiation by a spherical solid absorber immersed in a transparent fluid
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 101-109.
Full Text via DOI:
10.1117/12.589364
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000229364200012
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Ab-initio calculations for shock wave and bubble production with Gaussian temporal laser pulses
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 217-223.
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10.1117/12.527878
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000223056000028
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Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles.
. 277-286.
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000189504700028
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Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles
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Laser induced retinal shock waves and bubbles and their dependencies on the thermo-mechanical properties of melanosomes
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 149-158.
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10.1117/12.434699
Web of Science:
000171276900019
2000
Theoretical modeling of laser induced explosive pressure generation and vaporization in pigmented cells
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 41-53.
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10.1117/12.379340
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000086446600006
1998
Parameter sensitivity of the Thompson granular retinal damage model
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 146-155.
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10.1117/12.308160
1998
Pressure generation in melanosomes by sub-nanosecond laser pulses
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 156-167.
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10.1117/12.308161
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1997
Nanosecond laser pulses: From retinal damage to refined surgical treatment of congenital nevi and melanoma
. 180-191.
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10.1117/12.275474
Web of Science:
A1997BJ12Q00020
1996
Gruneisen equation of state for melanosomes irradiated by subnanosecond laser pulses
. 449-459.
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10.1117/12.239606
1995
LASER INDUCED BUBBLE FORMATION IN THE RETINA
. 60-73.
Full Text via DOI:
10.1117/12.209929
Web of Science:
A1995BD32D00006
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A working theory and experiments on photomechanical disruption of melanosomes to explain the threshold for minimal visible retinal lesions for sub-ns laser pulses.
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 54-65.
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A NEW SPECTROSCOPY - SPIN-TUNNELING IN HEME-PROTEINS
.
BIOPHYSICAL JOURNAL
. A280-A280.
Web of Science:
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Other Scholarly Work
2022
Alternating access switching in molecular dynamics simulations of PfMATE transporter
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BIOPHYSICAL JOURNAL
. 250A-251A.
Web of Science:
000759523001484
2022
Changes in the receptor-binding interface may cause immune evasion by the SARS-CoV-2 delta variant b.1.617.2
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BIOPHYSICAL JOURNAL
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Effects of G198R Mutation in the Ebola VP40 Matrix Protein: A Molecular Dynamics Study
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BIOPHYSICAL JOURNAL
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Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets
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BIOPHYSICAL JOURNAL
. 218A-218A.
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10.1016/j.bpj.2017.11.1217
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Preface to Special Topic: Amyloid Aggregation: Characterization, Function and Molecular Mechanisms
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AIP ADVANCES
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10.1063/1.4932621
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Pairwise amino acid secondary structural propensities (vol 91, 042709, 2015)
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PHYSICAL REVIEW E
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Preface: Physics of Cancer
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AIP ADVANCES
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Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper (vol 128, art no 045106, 2008)
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Investigating the nanoparticle transition from bulk behavior to discrete atom/finite size behavior using laser induced pressure generation
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Shock wave generation and bubble formation in the retina by lasers
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 154-165.
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10.1117/12.388041
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000088674300019
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Modeling of pressure generation by lasers in melanosomes; How to avoid stress confinement and blow up a melanosome
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ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII
. 43-54.
Full Text via DOI:
10.1117/12.350044
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Erratum: Melanin granule model for laser-induced thermal damage in the retina (Bulletin of Mathematical Biology (1996) 58 (513-553)
.
BULLETIN OF MATHEMATICAL BIOLOGY
. 809-810.
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10.1016/0092-8240(96)00054-7
Preprint
2022
Immunoinformatic Screening of Marburgvirus Epitopes and Computational Investigations of Epitope-Allele Complexes
Full Text via DOI:
10.2139/ssrn.4067188
2021
Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion
Full Text via DOI:
10.1101/2021.07.17.452576
2020
Lipid-specific protein oligomerization is regulated by two interfaces in Marburg virus matrix protein VP40
Full Text via DOI:
10.1101/2020.11.13.381350
2018
Mutation of Ebola Virus Matrix Protein Cysteine Residues Increases Binding to Phosphatidylserine through Increased Flexibility of a Lipid Binding Loop
Full Text via DOI:
10.1101/286120
2018
PI(4,5)P
2
Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding
Full Text via DOI:
10.1101/341248
2017
A superposition test for the emergence of nonlinearities in a laser irradiated spherical absorber
Full Text via DOI:
10.48550/arxiv.1711.02986
Mutation of Hydrophobic Residues in the C-Terminal Domain of the Marburg Virus Matrix Protein VP40 Disrupts Trafficking to the Plasma Membrane
Full Text via DOI:
10.20944/preprints202002.0467.v1
Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment
Full Text via DOI:
10.1101/2022.01.21.477244
The role of protonation in the PfMATE transporter protein structural transitions
Full Text via DOI:
10.22541/au.169645521.18264971/v1
Review
2008
Self-Organizing Dynamics in Protein Folding
. 1-37.
Full Text via DOI:
10.1016/S0079-6603(08)00401-7
Web of Science:
000263621700001
Works By Students
chaired theses and dissertations
GC, Jeevan,
Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins
2017
Steckmann, Timothy Michael,
Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins
2016
Regmi, Chola K,
Structural Flexibility and Oxygen Diffusion Pathways in Monomeric Fluorescent Proteins
2014
Bhandari, Yuba R,
Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins
2013
Chapagain, Prem P.,
The thermodynamics and statistical mechanics of protein folding
2005
Research
co-principal investigator on
Grant
FIU-JILA Partnership for Research and Education in AMO Physics
awarded by
National Science Foundation
2022 - 2025
investigator on
Computational modeling of lantibiotics interactions with lipid II and membrane
awarded by
Oragenics Inc.
2019 - 2021
Contact
full name
Bernard
Gerstman
Identifiers
ORCID iD
https://orcid.org/0000-0003-4258-529X
(confirmed)
visualizations
Co-author Network
Co-investigator Network
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publication subject areas
Biochemistry & Molecular Biology
Biophysics
Cell Biology
Chemistry
Dermatology
Life Sciences & Biomedicine - Other Topics
Materials Science
Mathematical & Computational Biology
Mathematics
Optics
Physics
Polymer Science
Radiology, Nuclear Medicine & Medical Imaging
Science & Technology - Other Topics
Surgery
Citation index-derived subject areas the researcher has published in