Bernard Gerstman
- Professor, Physics , College of Arts, Sciences & Education
Publications
selected publications
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Article
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2020In-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
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2020A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation. PATHOGENS. 9.Full Text via DOI: 10.3390/pathogens9050402 Web of Science: 000541443700085
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2020Mutation of Hydrophobic Residues in the C-Terminal Domain of the Marburg Virus Matrix Protein VP40 Disrupts Trafficking to the Plasma Membrane. VIRUSES-BASEL. 12.Full Text via DOI: 10.3390/v12040482 Web of Science: 000539525300124
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2019Conformational 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
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2019Molecular 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
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2019Membrane 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
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2018Domain rearrangement and denaturation in Ebola virus protein VP40. AIP ADVANCES. 8.Full 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 Complex. ACS OMEGA. 3.Full 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 matrix. SCIENTIFIC REPORTS. 8.Full Text via DOI: 10.1038/s41598-018-28077-7 Web of Science: 000436398100001
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2018A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine. JOURNAL OF BIOLOGICAL CHEMISTRY. 293:3335-3349.
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2018In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles. JOURNAL OF PHYSICAL CHEMISTRY B. 122:3782-3789.
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2017Cooperative structural transitions in amyloid-like aggregation. JOURNAL OF CHEMICAL PHYSICS. 146.
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2017Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry. JOURNAL OF BIOLOGICAL CHEMISTRY. 292:6108-6122.
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2017Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 493:176-181.
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2017Membrane association and localization dynamics of the Ebola virus matrix protein VP40. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES. 1859:2012-2020.
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2017Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer. RSC ADVANCES. 7:22741-22748.
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2016DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. SCIENTIFIC REPORTS. 6.
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2016Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675. JOURNAL OF PHYSICAL CHEMISTRY LETTERS. 7:3046-3051.
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2016Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization. PROTEIN SCIENCE. 25:1648-1658.
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2016The 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.
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2015Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator. PROTEIN SCIENCE. 24:741-751.
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2015Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. INTEGRATIVE BIOLOGY. 7:263-273.
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2015Self-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
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2015The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation. JOURNAL OF PHYSICAL CHEMISTRY B. 119:12750-12759.
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2014Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants. JOURNAL OF PHYSICAL CHEMISTRY B. 118:2940-2948.
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2014Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription Factor. JOURNAL OF PHYSICAL CHEMISTRY B. 118:5101-5108.
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2013Exploring 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.
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2012Kinetics of peptide secondary structure conversion during amyloid beta-protein fibrillogenesis. JOURNAL OF THEORETICAL BIOLOGY. 301:95-102.
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2012Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization. JOURNAL OF CHEMICAL PHYSICS. 137.
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2012Structural propensities and entropy effects in peptide helix-coil transitions. PHYSICAL REVIEW E. 86.
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2011Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories. PHYSICAL REVIEW E. 83.
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2010Stabilization 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.
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2008Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper. JOURNAL OF CHEMICAL PHYSICS. 128.
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2008The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization. JOURNAL OF CHEMICAL PHYSICS. 129.
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2007Acoustical 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
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2007Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide. JOURNAL OF CHEMICAL PHYSICS. 127.
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2005Biophysical effects of pulsed lasers in the retina and other tissues containing strongly absorbing particles: shockwave and explosive bubble generation. JOURNAL OF BIOMEDICAL OPTICS. 10.
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2005Self-organization in protein folding and the hydrophobic interaction. JOURNAL OF CHEMICAL PHYSICS. 123.
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2004Excluded volume entropic effects on protein unfolding times and intermediary stability. JOURNAL OF CHEMICAL PHYSICS. 120.Full 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 structure. JOURNAL OF CHEMICAL PHYSICS. 119.Full 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 sphere. JOURNAL OF APPLIED PHYSICS. 88.Full 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 retina. JOURNAL OF BIOMEDICAL OPTICS. 4.Full 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 media. PHYSICAL REVIEW E. 59.Full Text via DOI: 10.1103/PhysRevE.59.5772 Web of Science: 000080382900041
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1998Structural information content and Lyapunov exponent calculation in protein unfolding. JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS. 36.Full Text via DOI: 10.1002/(SICI)1099-0488(19981115)36:15<2761::AID-POLB10>3.0.CO;2-5 Web of Science: 000076664000010
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1996Melanin granule model for laser-induced thermal damage in the retina. BULLETIN OF MATHEMATICAL BIOLOGY. 58.Full Text via DOI: 10.1016/0092-8240(95)00360-6 Web of Science: A1996UN90300006
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1996Laser induced bubble formation in the retina. LASERS IN SURGERY AND MEDICINE. 18.Full 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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1995CONTROL OF LONG-TIME DEPENDENCE OF CO BINDING TO HEME SYSTEMS BY INHOMOGENEOUS SPREAD IN ELECTRONIC PREFACTOR. JOURNAL OF CHEMICAL PHYSICS. 102.Full 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 ENVIRONMENT. JOURNAL OF CHEMICAL PHYSICS. 96.Full 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 SITE. PHYSICAL REVIEW A. 44.Full Text via DOI: 10.1103/PhysRevA.44.5257 Web of Science: A1991GM06000054
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1991TIME-RESOLVED INFRARED STUDIES OF MOLECULAR-DIFFUSION IN MYOGLOBIN. PHYSICAL REVIEW LETTERS. 66.Full 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 SITES. PHYSICAL REVIEW A. 39.Full Text via DOI: 10.1103/PhysRevA.39.5903 Web of Science: A1989U881800053
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1989ENHANCEMENT 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.Full Text via DOI: 10.1364/JOSAB.6.001050 Web of Science: A1989U557300025
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1988CO BINDING TO HEMOGLOBIN - SPIN-TUNNELING TEMPERATURE-DEPENDENCE, FE ELECTRONIC STATES, AND ELECTRONIC EFFECTS ON NONADIABATIC DYNAMICS. JOURNAL OF CHEMICAL PHYSICS. 88.Full 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 SITES. PHYSICAL REVIEW A. 37.Full Text via DOI: 10.1103/PhysRevA.37.2151 Web of Science: A1988M525800035
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Book Chapter
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Conference
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1998Parameter sensitivity of the Thompson granular retinal damage modelFull Text via DOI: 10.1117/12.308160
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Correction
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2008Lattice 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
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Editorial Material
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2015Preface to Special Topic: Amyloid Aggregation: Characterization, Function and Molecular Mechanisms. AIP ADVANCES.Full Text via DOI: 10.1063/1.4932621 Web of Science: 000362562100001
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2012Preface: Physics of Cancer. AIP ADVANCES.Full Text via DOI: 10.1063/1.3699622 Web of Science: 000302225400002
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Meeting Abstract
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2019Computational Study of Calcium Phosphate Mineralization in Extracellular Vesicles. BIOPHYSICAL JOURNAL. 572A-572A.Web of Science: 000460779802874
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2019Dynamics of the Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. BIOPHYSICAL JOURNAL. 472A-472A.Web of Science: 000460779802370
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2018Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets. BIOPHYSICAL JOURNAL.Web of Science: 000430439600337
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2018A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40. BIOPHYSICAL JOURNAL. 64A-64A.Web of Science: 000429315800331
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2018Conformational Changes in Marburg Virus VP40 upon Plasma Membrane Association. BIOPHYSICAL JOURNAL. 459A-459A.Web of Science: 000430563200066
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2017Pi(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
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2017Plasma membrane localization dynamics of the filovirus matrix protein VP40. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. 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. BIOPHYSICAL JOURNAL. 191A-191A.Full Text via DOI: 10.1016/j.bpj.2016.11.1059 Web of Science: 000402328000944
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2016Interdomain 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
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2016On 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
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2015Hydrogen 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
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2014Temperature 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
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Proceedings Paper
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2007Analyzing chaos in the pressure generated by laser absorption by microparticles. COMPLEX DYNAMICS AND FLUCTUATIONS IN BIOMEDICAL PHOTONICS IV.Full Text via DOI: 10.1117/12.696482 Web of Science: 000246520100011
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2007Using laser induced shock waves to investigate the nanoparticle tranistion from bulk behavior to discrete atom/finite size behavior. SHOCK COMPRESSION OF CONDENSED MATTER - 2007, PTS 1 AND 2. 703-706.Web of Science: 000252158500167
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2006Chaos in the pressure generated by laser absorption by microparticles. OPTICAL INTERACTIONS WITH TISSUE AND CELLS XVII.Full Text via DOI: 10.1117/12.644846 Web of Science: 000237158300004
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2006Resonant absorption in nanometer gold spherical particles. OPTICAL INTERACTIONS WITH TISSUE AND CELLS XVII.Full Text via DOI: 10.1117/12.644815 Web of Science: 000237158300003
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2005Response to pulsed radiation by a spherical solid absorber immersed in a transparent fluid. COMPLEX DYNAMICS AND FLUCTUATIONS IN BIOMEDICAL PHOTONICS II. 101-109.Full Text via DOI: 10.1117/12.589364 Web of Science: 000229364200012
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2005Stress confinement, shock wave formation and laser induced damage. Optical Interactions with Tissue and Cells XVI. 209-215.Full Text via DOI: 10.1117/12.589469 Web of Science: 000229361500024
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2004Ab-initio calculations for shock wave and bubble production with Gaussian temporal laser pulses. LASER INTERACTION WITH TISSUE AND CELLS XV.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.. SYNTHESIS, CHARACTERIZATION AND PROPERTIES OF ENERGETIC/REACTIVE NANOMATERIALS.Web of Science: 000189504700028
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2001Laser induced retinal shock waves and bubbles and their dependencies on the thermo-mechanical properties of melanosomes. LASER-TISSUE INTERACTION XII: PHOTOCHEMICAL, PHOTOTHERMAL, AND PHOTOMECHANICAL.Full Text via DOI: 10.1117/12.434699 Web of Science: 000171276900019
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2000Shock wave generation and bubble formation in the retina by lasers. LASER-TISSUE INTERACTION XI: PHOTOCHEMICAL, PHOTOTHERMAL, AND PHOTOMECHANICAL.Full Text via DOI: 10.1117/12.388041 Web of Science: 000088674300019
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2000Theoretical modeling of laser induced explosive pressure generation and vaporization in pigmented cells. LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 1999.Full Text via DOI: 10.1117/12.379340 Web of Science: 000086446600006
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1999Modeling of pressure generation by lasers in melanosomes; How to avoid stress confinement and blow up a melanosome. LASER-TISSUE INTERACTION X: PHOTOCHEMICAL, PHOTOTHERMAL, AND PHOTOMECHANICAL, PROCEEDINGS OF.Full Text via DOI: 10.1117/12.350044 Web of Science: 000081436500007
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1998Pressure generation in melanosomes by sub-nanosecond laser pulses. LASER-TISSUE INTERACTION IX. PROCEEDINGS OF.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. LASER-TISSUE INTERACTION VIII, PROCEEDINGS OF.Full Text via DOI: 10.1117/12.275474 Web of Science: A1997BJ12Q00020
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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
Teaching
teaching activities
- IDH1001-U09: Honors Seminar I Fall Term 2019
- IDH1002-U09: Honors Seminar II: The Origin of Ideas and the Idea of Origins Spring Term 2019
- IDH1002-U10: Honors Seminar II: The Origin of Ideas and the Idea of Origins Spring Term 2019
- PHY2065-U01: Problem Solving in Physics without Calculus I Spring Term 2019
Contact
full name
- Bernard Gerstman
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