Prem Chapagain
- Associate Professor, Physics , College of Arts, Sciences & Education
Publications
selected publications
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Article
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2021The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection. JACC-BASIC TO TRANSLATIONAL SCIENCE. 6:1-8.Full Text via DOI: 10.1016/j.jacbts.2020.10.003 Web of Science: 000613908200001
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2020Identification of HMGA2 inhibitors by AlphaScreen-based ultra-high-throughput screening assays. SCIENTIFIC REPORTS. 10.Full Text via DOI: 10.1038/s41598-020-75890-0 Web of Science: 000589618700022
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2020EF-hands in Neuronal Calcium Sensor Downstream Regulatory Element Antagonist Modulator Demonstrate Submillimolar Affinity for Li+: A New Prospect for Li+ Therapy. ACS CHEMICAL NEUROSCIENCE. 11:2543-2548.Full Text via DOI: 10.1021/acschemneuro.0c00399 Web of Science: 000569269100010
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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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2020Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. CHEMMEDCHEM. 15:623-631.Full Text via DOI: 10.1002/cmdc.201900721 Web of Science: 000520292700001
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2020Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2. JOURNAL OF MEDICAL MICROBIOLOGY. 69:864-873.Full Text via DOI: 10.1099/jmm.0.001203 Web of Science: 000546951100013
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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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2019Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY. 33:60-65.Full Text via DOI: 10.1002/rcm.8367 Web of Science: 000516887600008
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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 dominant variant in the PDE1C gene is associated with nonsyndromic hearing lossFull Text via DOI: 10.1007/s00439-018-1895-y Web of Science: 000439463700002
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2018Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry. JOURNAL OF PHYSICAL CHEMISTRY B. 122.Full Text via DOI: 10.1021/acs.jpcb.7b12544 Web of Science: 000439002900001
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2018Investigating molecular interactions between oxidized neuroglobin and cytochrome c. SCIENTIFIC REPORTS. 8.Full Text via DOI: 10.1038/s41598-018-28836-6 Web of Science: 000438343600067
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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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2018Amino acid 118 in the deafness causing (DFNA20/26) ACTG1 gene is a mutational hot spotFull Text via DOI: 10.1016/j.genrep.2018.04.011 Web of Science: 000433193600041
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2018ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing lossFull Text via DOI: 10.1007/s00439-018-1885-0 Web of Science: 000431534200005
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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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2018Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. SCIENTIFIC REPORTS. 8.
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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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2016Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations. FEBS LETTERS. 590:2844-2851.
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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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2016Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS LETTERS. 590:613-618.
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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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2016Structures of the kinetically trapped i-motif DNA intermediates. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. 18:26691-26702.
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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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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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2012Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins. JOURNAL OF PHYSICAL CHEMISTRY B. 116:12426-12440.
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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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2011Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry. JOURNAL OF CHEMICAL PHYSICS. 135.
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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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2008The effect of heterogeneous infectious period and contagiousness on the dynamics of Salmonella transmission in dairy cattle. EPIDEMIOLOGY AND INFECTION. 136.Full Text via DOI: 10.1017/S0950268807000209 Web of Science: 000260750500008
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2008The importance of culling in Johne's disease control. JOURNAL OF THEORETICAL BIOLOGY. 254.Full Text via DOI: 10.1016/j.jtbi.2008.05.008 Web of Science: 000258938200015
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2008Simulation modeling to evaluate the persistence of Mycobacterium avium subsp paratuberculosis (MAP) on commercial dairy farms in the United States. PREVENTIVE VETERINARY MEDICINE. 83.Full Text via DOI: 10.1016/j.prevetmed.2007.09.006 Web of Science: 000254109000012
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2008A mathematical model of the dynamics of Salmonella Cerro infection in a US dairy herd. EPIDEMIOLOGY AND INFECTION. 136.Full Text via DOI: 10.1017/S0950268807008400 Web of Science: 000259337000015
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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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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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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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Book Chapter
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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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Meeting Abstract
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2020Calculating the Binding Free Energy Difference between Conformational Changes of AT-Rich DNA Sequences. BIOPHYSICAL JOURNAL. 218A-218A.Web of Science: 000513023201340
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2020Computational Study of the Molecular Details of Ebola Virus Matrix Protein VP40 and Human Sec24C Protein Interaction. BIOPHYSICAL JOURNAL. 506A-506A.Web of Science: 000513023203272
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2020Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide. BIOPHYSICAL JOURNAL. 586A-587A.Web of Science: 000513023203666
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2020Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling. BIOPHYSICAL JOURNAL. 305A-305A.Web of Science: 000513023202030
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2019Computational Investigations of a Complex Formation between Neuroglobin and Cytochrome C Ferric Heme Proteins. BIOPHYSICAL JOURNAL. 433A-433A.Web of Science: 000460779802174
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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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2019Molecular Basis of the Marburg Virus Protein VP24 Interactions with Human Keap1. BIOPHYSICAL JOURNAL. 182A-182A.Web of Science: 000460779800901
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2019Molecular Dynamics Investigations of Enzyme Conformational Changes. BIOPHYSICAL JOURNAL. 186A-186A.Web of Science: 000460779800921
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2019Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Proteins mNeptune1, mNeptune2.5 and mCardinal2. BIOPHYSICAL JOURNAL. 475A-475A.Web of Science: 000460779802385
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2018Covalent Complex Model of DNA Topoisomerase and DNA for Molecular Dynamics Simulation. BIOPHYSICAL JOURNAL.Web of Science: 000430450000197
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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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2017Exploring Molecular Interactions between Escherichia coli RNA Polymerase and Topoisomerase I by Molecular Simulations. BIOPHYSICAL JOURNAL. 287A-287A.Full Text via DOI: 10.1016/j.bpj.2016.11.1555 Web of Science: 000402375600419
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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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Review
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2017Indispensable Role of Ion Channels and Transporters in the Auditory System. JOURNAL OF CELLULAR PHYSIOLOGY. 743-758.
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2017Zika Virus: An Emerging Global Health Threat. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY.
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2016Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. JOURNAL OF CELLULAR PHYSIOLOGY. 2599-2621.
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2016Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X(2) in the Auditory System. JOURNAL OF CELLULAR PHYSIOLOGY. 1656-1670.
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
Research
principal investigator on
Teaching
teaching activities
- PHY2048-RVC: General Physics Laboratory I Fall Term 2019
- PHY2048-RVC: Physics with Calculus I Fall Term 2019
- PHY2048-RVC: Physics with Calculus I Fall Term 2019
- PHY2048-U01: Physics with Calculus I Spring Term 2019
- PHY2048-U01: Physics with Calculus I Spring Term 2019
- PHY2053-RVC: Physics without Calculus I Fall Term 2019
- PHY2053-RVC: Physics without Calculus I Spring Term 2019
- PHY2053-RVD: Physics without Calculus I Spring Term 2019
- PHY2053-RVE: Physics without Calculus I Spring Term 2019
- PHY5936-U01: Special Topics Research Spring Term 2019
- PHY5936-U02: Special Topics Research Fall Term 2019
Contact
full name
- Prem Chapagain
Identifiers
ORCID iD
- https://orcid.org/0000-0002-0999-4975 (confirmed)
visualizations
Recent publications and grants in Scholars@FIU
publication subject areas
- Biochemistry & Molecular Biology
- Biophysics
- Cell Biology
- Chemistry
- Genetics & Heredity
- Immunology
- Infectious Diseases
- Life Sciences & Biomedicine - Other Topics
- Materials Science
- Mathematical & Computational Biology
- Microbiology
- Physics
- Physiology
- Public, Environmental & Occupational Health
- Science & Technology - Other Topics
- Veterinary Sciences