Overview
overview
- Bernard S. Gerstman is a Professor in Physics and the Biomolecular Sciences Institute, specializing in Theoretical Biophysics.
research interests
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Theoretical Biophysics
Non-Linear Dynamics and Protein Folding
Protein Aggregation
Laser Effects on Biological Tissue and Material Science
Scholarly & Creative Works
selected publications
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Article
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2022Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachmentFull Text via DOI: 10.1039/d2cp00169a Web of Science: 000779732000001
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2022Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact MethodFull Text via DOI: 10.1021/acssensors.1c02385 Web of Science: 000746813600001
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2021Lipid II Binding and Transmembrane Properties of Various Antimicrobial LanthipeptidesFull Text via DOI: 10.1021/acs.jctc.1c00666 Web of Science: 000730568600001
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2021Ebola virus protein VP40 binding to Sec24c for transport to the plasma membraneFull Text via DOI: 10.1002/prot.26221 Web of Science: 000692659700001
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2021Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351Full Text via DOI: 10.1021/acs.jpcb.1c01626 Web of Science: 000672740600004
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2020In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic feverFull Text via DOI: 10.1038/s41598-020-63640-1 Web of Science: 000534024000034
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2019Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix FilamentFull Text via DOI: 10.1021/acs.jpcb.9b04674 Web of Science: 000493865200001
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2019Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140Full Text via DOI: 10.1039/c9cp01558b Web of Science: 000478994100046
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2019Membrane pore formation and ion selectivity of the Ebola virus delta peptideFull Text via DOI: 10.1039/c8cp07323f Web of Science: 000461722800020
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2019Molecular Dynamics Simulations of Conformational Conversions in Transformer ProteinsFull Text via DOI: 10.1007/978-1-4939-9161-7_15 Web of Science: 000706398300016
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2018Domain rearrangement and denaturation in Ebola virus protein VP40Full Text via DOI: 10.1063/1.5063474 Web of Science: 000454615100058
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2018Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24-Human Keap1 ComplexFull Text via DOI: 10.1021/acsomega.8b02386 Web of Science: 000458439900046
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2018A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrixFull Text via DOI: 10.1038/s41598-018-28077-7 Web of Science: 000436398100001
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2018In Silico Investigations of Calcium Phosphate Mineralization in Extracellular VesiclesFull Text via DOI: 10.1021/acs.jpcb.8b00169 Web of Science: 000430641900011
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2017Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filamentsFull Text via DOI: 10.1016/j.bbrc.2017.09.052 Web of Science: 000413134200028
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2017Membrane association and localization dynamics of the Ebola virus matrix protein VP40Full Text via DOI: 10.1016/j.bbamem.2017.07.007 Web of Science: 000411419000026
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2017Cooperative structural transitions in amyloid-like aggregationFull Text via DOI: 10.1063/1.4979516 Web of Science: 000399073300052
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2017Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimerFull Text via DOI: 10.1039/c7ra02940c Web of Science: 000400338000016
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2016The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P-2 lipids in the plasma membraneFull Text via DOI: 10.1039/c6cp03776c Web of Science: 000386668200003
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2016Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localizationFull Text via DOI: 10.1002/pro.2969 Web of Science: 000383619100008
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2016Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675Full Text via DOI: 10.1021/acs.jpclett.6b01172 Web of Science: 000381236400029
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2016DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coliFull Text via DOI: 10.1038/srep19243 Web of Science: 000368157700001
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2015The Role of the Interdomain Interactions on RfaH Dynamics and Conformational TransformationFull Text via DOI: 10.1021/acs.jpcb.5b05681 Web of Science: 000362701900003
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2015Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulatorFull Text via DOI: 10.1002/pro.2646 Web of Science: 000353524700016
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2015Pairwise amino acid secondary structural propensitiesFull Text via DOI: 10.1103/PhysRevE.91.042709 Web of Science: 000352850200007
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2015Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleachingFull Text via DOI: 10.1039/c4ib00251b Web of Science: 000349668600011
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2014Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription FactorFull Text via DOI: 10.1021/jp502193v Web of Science: 000336199100013
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2014Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum VariantsFull Text via DOI: 10.1021/jp412371y Web of Science: 000333381800016
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2013Exploring the Diffusion of Molecular Oxygen in the Red Fluorescent Protein mCherry Using Explicit Oxygen Molecular Dynamics SimulationsFull Text via DOI: 10.1021/jp308366y Web of Science: 000315707900003
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2012Structural propensities and entropy effects in peptide helix-coil transitionsFull Text via DOI: 10.1103/PhysRevE.86.031915 Web of Science: 000308872700005
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2012Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerizationFull Text via DOI: 10.1063/1.4752247 Web of Science: 000309100400057
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2012Kinetics of peptide secondary structure conversion during amyloid beta-protein fibrillogenesisFull Text via DOI: 10.1016/j.jtbi.2012.02.012 Web of Science: 000303079500010
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2011Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectoriesFull Text via DOI: 10.1103/PhysRevE.83.061905 Web of Science: 000291437200003
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2010Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine DimerFull Text via DOI: 10.1021/jp909872a Web of Science: 000273405000015
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2008The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerizationFull Text via DOI: 10.1063/1.3006421 Web of Science: 000260777400053
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2008Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipperFull Text via DOI: 10.1063/1.2831513 Web of Science: 000252821200094
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2007Acoustical resonant absorption of pulsed laser radiation by a spherical absorberFull Text via DOI: 10.1063/1.2822247 Web of Science: 000251987600026
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2007Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptideFull Text via DOI: 10.1063/1.2757172 Web of Science: 000248905300035
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2007The emergence of chaos in a laser irradiated spherical absorberFull Text via DOI: 10.1063/1.2407262 Web of Science: 000245317300001
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2006Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptideFull Text via DOI: 10.1002/bip.20388 Web of Science: 000235041200003
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2005Self-organization in protein folding and the hydrophobic interactionFull Text via DOI: 10.1063/1.1990110 Web of Science: 000231168700071
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2004Excluded volume entropic effects on protein unfolding times and intermediary stabilityFull Text via DOI: 10.1063/1.1637032 Web of Science: 000188498400046
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2003Finite size scaling of structural transitions in a simulated protein with secondary and tertiary structureFull Text via DOI: 10.1063/1.1579673 Web of Science: 000183842500058
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2000Bubble dynamics and shock waves generated by laser absorption of a photoacoustic sphereFull Text via DOI: 10.1063/1.1288507 Web of Science: 000088796500029
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1999Activated rate processes and a specific biochemical mechanism for explaining delayed laser induced thermal damage to the retinaFull Text via DOI: 10.1117/1.429936 Web of Science: 000082189400010
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1999Photoacoustic generation for a spherical absorber with impedance mismatch with the surrounding mediaFull Text via DOI: 10.1103/PhysRevE.59.5772 Web of Science: 000080382900041
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1996Melanin granule model for laser-induced thermal damage in the retinaFull Text via DOI: 10.1007/bf02459483
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1996Melanin granule model for laser-induced thermal damage in the retinaFull Text via DOI: 10.1007/BF02460595 Web of Science: A1996UN90300006
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1996Laser induced bubble formation in the retinaFull Text via DOI: 10.1002/(SICI)1096-9101(1996)18:1<10::AID-LSM2>3.0.CO;2-U Web of Science: A1996TM76300002
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1995ELECTRONIC PARAMAGNETISM IN BIOMOLECULAR STRUCTURE AND FUNCTIONFull Text via DOI: 10.1119/1.18015 Web of Science: A1995TG79400011
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1995CONTROL OF LONG-TIME DEPENDENCE OF CO BINDING TO HEME SYSTEMS BY INHOMOGENEOUS SPREAD IN ELECTRONIC PREFACTORFull Text via DOI: 10.1063/1.468909 Web of Science: A1995QC35400015
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1992NONADIABATIC ELECTRONIC SPIN TRANSITION IN LIGAND-HEME PROTEIN-BINDING KINETICS AND THE INFLUENCE OF THE HEME FE MOLECULAR ENVIRONMENTFull Text via DOI: 10.1063/1.462475 Web of Science: A1992GY24900041
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1991CORRELATED DISTRIBUTIONS IN G AND A TENSORS AT A BIOLOGICALLY-ACTIVE LOW-SYMMETRY CUPRIC SITEFull Text via DOI: 10.1103/PhysRevA.44.5257 Web of Science: A1991GM06000054
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1991Hybrid atomic orbital model of low-symmetry cupric sitesFull Text via DOI: 10.1016/0162-0134(91)84215-u
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1991TIME-RESOLVED INFRARED STUDIES OF MOLECULAR-DIFFUSION IN MYOGLOBINFull Text via DOI: 10.1103/PhysRevLett.66.2673 Web of Science: A1991FM03600033
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1989HYPERFINE CONTRIBUTIONS TO THE LINEAR-ELECTRIC-FIELD EFFECT IN LOW-SYMMETRY CUPRIC SITESFull Text via DOI: 10.1103/PhysRevA.39.5903 Web of Science: A1989U881800053
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1988CO BINDING TO HEMOGLOBIN - SPIN-TUNNELING TEMPERATURE-DEPENDENCE, FE ELECTRONIC STATES, AND ELECTRONIC EFFECTS ON NONADIABATIC DYNAMICSFull Text via DOI: 10.1063/1.454461 Web of Science: A1988N555800024
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1988LINEAR ELECTRIC-FIELD EFFECT ON G-VALUES OF LOW-SYMMETRY CUPRIC SITESFull Text via DOI: 10.1103/PhysRevA.37.2151 Web of Science: A1988M525800035
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Book
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2020
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Conference
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2020
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2020
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2020Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide. 586A-587A.Web of Science: 000513023203666
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2020Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling. 305A-305A.Web of Science: 000513023202030
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2019Computational Study of Calcium Phosphate Mineralization in Extracellular Vesicles. 572A-572A.Full Text via DOI: 10.1016/j.bpj.2018.11.3075 Web of Science: 000460779802874
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2019Dynamics of the Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. 472A-472A.Full Text via DOI: 10.1016/j.bpj.2018.11.2549 Web of Science: 000460779802370
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2019Molecular Basis of the Marburg Virus Protein VP24 Interactions with Human Keap1. 182A-182A.Full Text via DOI: 10.1016/j.bpj.2018.11.1011 Web of Science: 000460779800901
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2019Molecular Dynamics Investigations of Enzyme Conformational Changes. 186A-186A.Full Text via DOI: 10.1016/j.bpj.2018.11.1031 Web of Science: 000460779800921
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2018A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40. 64A-64A.Web of Science: 000429315800331
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2018Conformational Changes in Marburg Virus VP40 upon Plasma Membrane Association. 459A-459A.Web of Science: 000430563200066
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2017Plasma membrane localization dynamics of the filovirus matrix protein VP40. S211-S211.Web of Science: 000416406201256
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2017Temperature Dependent Pair-Wise Amino Acid Structural Propensity in cc beta and Implications for alpha to beta Secondary Structural Conversion. 191A-191A.Full Text via DOI: 10.1016/j.bpj.2016.11.1059 Web of Science: 000402328000944
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2017Pi(4,5)P-2 Clustering by the Ebola Virus Matrix Protein VP40. 326A-326A.Full Text via DOI: 10.1016/j.bpj.2016.11.1765 Web of Science: 000402375600611
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2016Interdomain Interactions and the Mechanism of Structural Transformation in RfaH. 378A-378A.Full Text via DOI: 10.1016/j.bpj.2015.11.2040 Web of Science: 000375142200330
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2016On the Origin of the Extended Stoke's Shifts in Fluorescent Proteins. 377A-378A.Full Text via DOI: 10.1016/j.bpj.2015.11.2039 Web of Science: 000375142200329
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2015Hydrogen Bond Flexibility and Water Dynamics in the Far Red Fluorescent Protein TagRFP675. 469A-469A.Full Text via DOI: 10.1016/j.bpj.2014.11.2562 Web of Science: 000362849400778
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2014Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Protein Mplum. 649A-649A.Full Text via DOI: 10.1016/j.bpj.2013.11.3592 Web of Science: 000337000403623
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2007Analyzing chaos in the pressure generated by laser absorption by microparticlesFull Text via DOI: 10.1117/12.696482 Web of Science: 000246520100011
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2006Chaos in the pressure generated by laser absorption by microparticlesFull Text via DOI: 10.1117/12.644846 Web of Science: 000237158300004
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2006Resonant absorption in nanometer gold spherical particlesFull Text via DOI: 10.1117/12.644815 Web of Science: 000237158300003
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2005Stress confinement, shock wave formation and laser induced damage. 209-215.Full Text via DOI: 10.1117/12.589469
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2005Response to pulsed radiation by a spherical solid absorber immersed in a transparent fluid. 101-109.Full Text via DOI: 10.1117/12.589364 Web of Science: 000229364200012
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2004Ab-initio calculations for shock wave and bubble production with Gaussian temporal laser pulses. 217-223.Full Text via DOI: 10.1117/12.527878 Web of Science: 000223056000028
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2004Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles.. 277-286.Web of Science: 000189504700028
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2003Modeling laser generated shock damage and thermo-mechanical chaos in nanoparticles. 277-286.Full Text via DOI: 10.1557/proc-800-aa7.4
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2001Laser induced retinal shock waves and bubbles and their dependencies on the thermo-mechanical properties of melanosomes. 149-158.Full Text via DOI: 10.1117/12.434699 Web of Science: 000171276900019
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2000Theoretical modeling of laser induced explosive pressure generation and vaporization in pigmented cells. 41-53.Full Text via DOI: 10.1117/12.379340 Web of Science: 000086446600006
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1998Parameter sensitivity of the Thompson granular retinal damage model. 146-155.Full Text via DOI: 10.1117/12.308160
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1998Pressure generation in melanosomes by sub-nanosecond laser pulses. 156-167.Full Text via DOI: 10.1117/12.308161 Web of Science: 000074238700021
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1997Nanosecond 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
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1996Gruneisen equation of state for melanosomes irradiated by subnanosecond laser pulses. 449-459.Full Text via DOI: 10.1117/12.239606
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1995LASER INDUCED BUBBLE FORMATION IN THE RETINA. 60-73.Full Text via DOI: 10.1117/12.209929 Web of Science: A1995BD32D00006
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1988A NEW SPECTROSCOPY - SPIN-TUNNELING IN HEME-PROTEINS. A280-A280.Web of Science: A1988L864300784
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Other Scholarly Work
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2022Alternating access switching in molecular dynamics simulations of PfMATE transporter. 250A-251A.Web of Science: 000759523001484
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2021Effects of G198R Mutation in the Ebola VP40 Matrix Protein: A Molecular Dynamics Study. 303A-303A.Web of Science: 000629601401715
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2018Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets. 218A-218A.Full Text via DOI: 10.1016/j.bpj.2017.11.1217 Web of Science: 000430439600337
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2015Preface to Special Topic: Amyloid Aggregation: Characterization, Function and Molecular MechanismsFull Text via DOI: 10.1063/1.4932621 Web of Science: 000362562100001
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2012Preface: Physics of CancerFull Text via DOI: 10.1063/1.3699622 Web of Science: 000302225400002
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2007Investigating 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
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2000Shock wave generation and bubble formation in the retina by lasers. 154-165.Full Text via DOI: 10.1117/12.388041 Web of Science: 000088674300019
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1999Modeling of pressure generation by lasers in melanosomes; How to avoid stress confinement and blow up a melanosome. 43-54.Full Text via DOI: 10.1117/12.350044 Web of Science: 000081436500007
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Preprint
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Review
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2008Self-Organizing Dynamics in Protein Folding. 1-37.Full Text via DOI: 10.1016/S0079-6603(08)00401-7 Web of Science: 000263621700001
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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
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
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