Gerstman, Bernard

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Gerstman, Bernard Graduate Faculty

Positions

Professor, Physics , College of Arts, Sciences & Education

gerstman@fiu.edu

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

manager of

Machine Shop Facility

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. 649A-649A.
  Full Text via DOI: 10.1016/j.bpj.2013.11.3592 Web of Science: 000337000403623
- 2007
  
  Analyzing chaos in the pressure generated by laser absorption by microparticles. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII.
  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.
  Full Text via DOI: 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. 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012). 703-706.
  Web of Science: 000252158500167
- 2006
  
  Chaos in the pressure generated by laser absorption by microparticles. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII.
  Full Text via DOI: 10.1117/12.644846 Web of Science: 000237158300004
- 2006
  
  Resonant absorption in nanometer gold spherical particles. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII.
  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. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 101-109.
  Full Text via DOI: 10.1117/12.589364 Web of Science: 000229364200012
- 2004
  
  Ab-initio calculations for shock wave and bubble production with Gaussian temporal laser pulses. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 217-223.
  Full Text via DOI: 10.1117/12.527878 Web of Science: 000223056000028
- 2004
  
  Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles.. 277-286.
  Web of Science: 000189504700028
- 2003
  
  Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles. 277-286.
  Full Text via DOI: 10.1557/proc-800-aa7.4
- 2001
  
  Laser induced retinal shock waves and bubbles and their dependencies on the thermo-mechanical properties of melanosomes. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 149-158.
  Full Text via DOI: 10.1117/12.434699 Web of Science: 000171276900019
- 2000
  
  Theoretical modeling of laser induced explosive pressure generation and vaporization in pigmented cells. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 41-53.
  Full Text via DOI: 10.1117/12.379340 Web of Science: 000086446600006
- 1998
  
  Parameter sensitivity of the Thompson granular retinal damage model. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 146-155.
  Full Text via DOI: 10.1117/12.308160
- 1998
  
  Pressure generation in melanosomes by sub-nanosecond laser pulses. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 156-167.
  Full Text via DOI: 10.1117/12.308161 Web of Science: 000074238700021
- 1997
  
  Nanosecond laser pulses: From retinal damage to refined surgical treatment of congenital nevi and melanoma. 180-191.
  Full Text via DOI: 10.1117/12.275474 Web of Science: A1997BJ12Q00020
- 1996
  
  Gruneisen equation of state for melanosomes irradiated by subnanosecond laser pulses. 449-459.
  Full Text via DOI: 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
- 1994
  
  A working theory and experiments on photomechanical disruption of melanosomes to explain the threshold for minimal visible retinal lesions for sub-ns laser pulses.. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 54-65.
  Full Text via DOI: 10.1117/12.182967
- 1988
  
  A NEW SPECTROSCOPY - SPIN-TUNNELING IN HEME-PROTEINS. BIOPHYSICAL JOURNAL. A280-A280.
  Web of Science: A1988L864300784
Other Scholarly Work
- 2022
  
  Alternating access switching in molecular dynamics simulations of PfMATE transporter. 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. BIOPHYSICAL JOURNAL. 44-44.
  Web of Science: 000759523000209
- 2021
  
  Effects of G198R Mutation in the Ebola VP40 Matrix Protein: A Molecular Dynamics Study. BIOPHYSICAL JOURNAL. 303A-303A.
  Web of Science: 000629601401715
- 2018
  
  Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets. BIOPHYSICAL JOURNAL. 218A-218A.
  Full Text via DOI: 10.1016/j.bpj.2017.11.1217 Web of Science: 000430439600337
- 2015
  
  Preface to Special Topic: Amyloid Aggregation: Characterization, Function and Molecular Mechanisms. AIP ADVANCES.
  Full Text via DOI: 10.1063/1.4932621 Web of Science: 000362562100001
- 2015
  
  Pairwise amino acid secondary structural propensities (vol 91, 042709, 2015). PHYSICAL REVIEW E.
  Full Text via DOI: 10.1103/PhysRevE.91.049902 Web of Science: 000353463600018
- 2012
  
  Preface: Physics of Cancer. AIP ADVANCES.
  Full Text via DOI: 10.1063/1.3699622 Web of Science: 000302225400002
- 2008
  
  Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper (vol 128, art no 045106, 2008). JOURNAL OF CHEMICAL PHYSICS.
  Full Text via DOI: 10.1063/1.2898870 Web of Science: 000254537200086
- 2007
  
  Investigating the nanoparticle transition from bulk behavior to discrete atom/finite size behavior using laser induced pressure generation. 1025-1028.
  Full Text via DOI: 10.4028/www.scientific.net/SSP.121-123.1025 Web of Science: 000244739900240
- 2000
  
  Shock wave generation and bubble formation in the retina by lasers. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 154-165.
  Full Text via DOI: 10.1117/12.388041 Web of Science: 000088674300019
- 1999
  
  Modeling of pressure generation by lasers in melanosomes; How to avoid stress confinement and blow up a melanosome. ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS VII. 43-54.
  Full Text via DOI: 10.1117/12.350044 Web of Science: 000081436500007
- 1996
  
  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.
  Full Text via DOI: 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)P₂ 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

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

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

full name

Bernard Gerstman

ORCID iD

https://orcid.org/0000-0003-4258-529X (confirmed)

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