Positions

Research Areas research areas

Overview

  • Research Interests
    Computational Biophysics, Biomolecular Modeling and Simulations, Chemical Physics, Soft Matter and Self-assembly, Dynamics in biomolecular systems
  • Selected Publications

    Academic Article

    Year Title
    2024 Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.Biochemistry.  63:2692-2703. 2024
    2024 Theory and simulations of light-induced self-assembly in colloids with quantum chemistry derived empirical potentials.Soft Matter.  20:7367-7378. 2024
    2024 Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.bioRxiv2024
    2024 Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases.Proteins: Structure, Function, and Bioinformatics.  92:905-922. 2024
    2024 Conserved C-Terminal Tail Is Responsible for Membrane Localization and Function of Pseudomonas aeruginosa Hemerythrin.Biochemistry.  63:1795-1807. 2024
    2024 Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase.International Journal of Molecular Sciences.  25:5368. 2024
    2024 Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase.bioRxiv2024
    2024 Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.  128:3157-3166. 2024
    2024 Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface.Journal of Chemical Information and Modeling.  64:2068-2076. 2024
    2024 Interactions and Transport of a Bioconjugated Peptide Targeting the Mitomembrane.Bioconjugate Chemistry.  35:371-380. 2024
    2024 Porous Self-Assemblies Mediated by Dumbbell Particles as Cross-Linking Agents.Journal of Chemical Theory and Computation.  20:1590-1599. 2024
    2024 Self-Assembly in an Experimentally Realistic Model of Lobed Patchy Colloids.ACS Appl Bio Mater.  7:535-542. 2024
    2024 Structural and computational studies of HIV-1 RNA.RNA Biology.  21:1-32. 2024
    2023 Mechanism of Ligand Discrimination by the NMT1 Riboswitch.Journal of Chemical Information and Modeling.  63:4864-4874. 2023
    2023 Coupling of conformational dynamics and inhibitor binding in the phosphodiesterase-5 family.Protein Science.  32:e4720. 2023
    2023 Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA.Journal of Chemical Information and Modeling.  63:1002-1011. 2023
    2023 Structural models of viral insulin-like peptides and their analogs.Proteins: Structure, Function, and Bioinformatics.  91:62-73. 2023
    2022 Molecular interactions and inhibition of the SARS-CoV-2 main protease by a thiadiazolidinone derivative.Proteins: Structure, Function, and Bioinformatics.  90:1896-1907. 2022
    2022 Epitaxial Self-Assembly of Interfaces of 2D Metal-Organic Frameworks for Electroanalytical Detection of Neurotransmitters.ACS Nano.  16:13869-13883. 2022
    2022 Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides.Journal of Chemical Information and Modeling.  62:3381-3390. 2022
    2022 Self-Assembly in Mixtures of Charged Lobed ParticlesFrontiers in Physics.  10. 2022
    2022 Cover Image, Volume 90, Issue 3Proteins: Structure, Function, and Bioinformatics.  90. 2022
    2022 Structures and interactions of insulin-like peptides from cone snail venom.Proteins: Structure, Function, and Bioinformatics.  90:680-690. 2022
    2022 Progress in Simulation Studies of Insulin Structure and Function.Frontiers in Endocrinology.  13:908724. 2022
    2021 Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical Journal.  120:5060-5073. 2021
    2021 Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins.Physical Chemistry Chemical Physics.  23:24773-24779. 2021
    2021 Self-Assembly of Porous Structures From a Binary Mixture of Lobed Patchy ParticlesFrontiers in Physics.  9. 2021
    2021 Design of Functionalized Lobed Particles for Porous Self-AssembliesJournal of Metals.  73:2413-2422. 2021
    2021 Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin.BBA: Biomembranes.  1863:183637. 2021
    2021 Role of conformational heterogeneity in ligand recognition by viral RNA molecules.Physical Chemistry Chemical Physics.  23:11211-11223. 2021
    2021 Enhanced Porosity in Self-Assembled Morphologies Mediated by Charged Lobes on Patchy Particles.The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.  125:3208-3215. 2021
    2021 Reaction Coordinate and Thermodynamics of Base Flipping in RNA.Journal of Chemical Theory and Computation.  17:1914-1921. 2021
    2021 Allosteric Pathways Originating at Cysteine Residues in Regulators of G-Protein Signaling Proteins.Biophysical Journal.  120:517-526. 2021
    2021 Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes.Frontiers in Chemistry.  9:753635. 2021
    2020 Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway.Journal of Molecular Biology.  432:5765-5783. 2020
    2020 Self-assembly behavior of experimentally realizable lobed patchy particles.Soft Matter.  16:8101-8107. 2020
    2020 Role of Entropy in Colloidal Self-Assembly.Entropy: international and interdisciplinary journal of entropy and information studies.  22:E877. 2020
    2020 Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions.Journal of Physical Chemistry Letters.  11:5426-5432. 2020
    2020 Functional Nanoassemblies with Mirror-Image Chiroptical Properties Templated by a Single Homochiral DNA StrandChemistry of Materials.  32:2272-2281. 2020
    2020 Self-assembly of lobed particles into amorphous and crystalline porous structures.Soft Matter.  16:1142-1147. 2020
    2019 An Interhelical Salt Bridge Controls Flexibility and Inhibitor Potency for Regulators of G-protein Signaling Proteins 4, 8, and 19.Molecular Pharmacology.  96:683-691. 2019
    2019 Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes.Physical Chemistry Chemical Physics.  21:22711-22721. 2019
    2019 Phase space and collective variable based simulation methods for studies of rare eventsMolecular Simulation.  45:1273-1284. 2019
    2019 Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein.Proteins: Structure, Function, and Bioinformatics.  87:146-156. 2019
    2019 Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes.PLoS One.  14:e0214554. 2019
    2018 Diffusion network of CO in FeFe-Hydrogenase.Journal of Chemical Physics.  149:204108. 2018
    2018 Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins.The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.  122:9314-9323. 2018
    2018 Applications to water transport systems: general discussion.Faraday Discussions.  209:389-414. 2018
    2018 Biomimetic water channels: general discussion.Faraday Discussions.  209:205-229. 2018
    2018 Parameterization and atomistic simulations of biomimetic membranes.Faraday Discussions.  209:161-178. 2018
    2018 Structure and function of natural proteins for water transport: general discussion.Faraday Discussions.  209:83-95. 2018
    2018 The modelling and enhancement of water hydrodynamics: general discussion.Faraday Discussions.  209:273-285. 2018
    2018 Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes.Nature Communications.  9:2294. 2018
    2018 Differential Protein Dynamics of Regulators of G-Protein Signaling: Role in Specificity of Small-Molecule Inhibitors.Journal of the American Chemical Society.  140:3454-3460. 2018
    2017 Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase.The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.  121:10007-10017. 2017
    2017 Insulin mimetic peptide S371 folds into a helical structure.Journal of Computational Chemistry.  38:1158-1166. 2017
    2017 Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.Current Topics in Medicinal Chemistry.  17:2626-2641. 2017
    2016 All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.Frontiers in Endocrinology.  7:68. 2016
    2015 Theoretical and computational studies of peptides and receptors of the insulin family.Membranes.  5:48-83. 2015
    2014 Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor.Membranes.  4:730-746. 2014
    2014 Collective variable approaches for single molecule flexible fitting and enhanced sampling.Chemical Reviews.  114:3353-3365. 2014
    2013 Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule.ACS Chemical Biology.  8:2778-2784. 2013
    2013 All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.Proteins: Structure, Function, and Bioinformatics.  81:1017-1030. 2013
    2013 Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.  117:3738-3746. 2013
    2012 Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.Journal of Physical Chemistry Letters.  3:3379-3384. 2012
    2012 Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps.Structure.  20:1453-1462. 2012
    2012 "DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.Biophysical Journal.  102:1979-1987. 2012
    2011 Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.Science.  333:1449-1453. 2011
    2010 All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.Journal of Molecular Biology.  400:645-658. 2010
    2010 Docking of insulin to a structurally equilibrated insulin receptor ectodomain.Proteins: Structure, Function, and Bioinformatics.  78:1531-1543. 2010
    2008 Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex.Biophysical Journal.  95:4193-4204. 2008
    Characterization of water dynamics in sub-nm pore-size biomimetic membranesJournal of Physical Chemistry Letters
    Flux and pathways in model potentialsMolecular Simulation

    Conference Paper

    Year Title
    2022 Insulin analogs derived from venomous insulin-like peptidesBiophysical Journal. 49-49. 2022
    2022 Understanding viral RNA recognition by lab-evolved proteinsBiophysical Journal. 211A-211A. 2022
    2021 Rare Conformational Transition in Viral RNA upon Ligand BindingBiophysical Journal. 315A-315A. 2021
    2019 Enhanced sampling methods to resolve thermodynamics and kinetics of slow and rare biophysical processesACS National Meeting Book of Abstracts. 2019
    2019 A Salt Bridge between alpha 4 and alpha 5 Helices Drives Differences in Flexibility and Potency of Inhibition among Regulator of G-protein Signaling (RGS) ProteinsThe FASEB Journal. 2019
    2018 Atomically resolved simulation studies of RNA/small-molecule interactionsACS National Meeting Book of Abstracts. 2018
    2018 Computational studies of regulators of G-proteins signaling small-molecule inhibitorsACS National Meeting Book of Abstracts. 2018
    2018 Network of inhibitor diffusion pathways in hydrogenase enzymesACS National Meeting Book of Abstracts. 2018
    2018 Understanding permeability and selectivity in sub-nm pore-size synthetic water transport channelsACS National Meeting Book of Abstracts. 2018
    2018 Role of Protein Dynamics in Selectivity of Thiadiazolidinone Inhibition of RGS ProteinsThe FASEB Journal. 2018
    2018 Measuring Transport Kinetics of Light Driven Membrane Protein, HalorhodopsinBiophysical Journal. 146A-146A. 2018
    2017 Atomistic simulation studies of synthetic channels in biomimetic membranesACS National Meeting Book of Abstracts. 2017
    2017 Combining structure-based models and enhanced sampling methods to probe RNA conformational dynamicsACS National Meeting Book of Abstracts. 2017
    2017 Investigating Regulator of G-protein Signaling (RGS) Protein Dynamics by Hydrogen/Deuterium ExchangeThe FASEB Journal. 2017
    2017 Conformational Evolution of Three Regulator of G-Protein Signaling Proteins (RGS4, RGS8, RGS19) in Microsecond-Scale SimulationsBiophysical Journal. 353A-354A. 2017
    2016 All-Atom Structural Models of the Transmembrane Domains of Insulin Receptor and Type-1 Insulin-Like Growth Factor ReceptorBiophysical Journal. 58A-58A. 2016
    2015 All-atom Folding Simulations of Insulin B-chain and its Mimetic PeptideThe FASEB Journal. 2015
    2015 Regulators of G-protein Signaling Proteins: Conformational Dynamics and Allosteric ControlThe FASEB Journal. 2015
    2013 Enhanced Sampling Assisted Flexible Fitting of Atomic Structures into Electron Microscopy MapsBiophysical Journal. 35A-35A. 2013
    2012 Molecular Architecture of a Late 40S Ribosome Assembly IntermediateBiophysical Journal. 70A-70A. 2012
    2011 "DFG-flip" in the Insulin Receptor Kinase is Facilitated by a Helical Intermediate State of the Activation LoopBiophysical Journal. 533-533. 2011
    2010 Target-blind conformational sampling in all-atom protein simulations with temperature-accelerated molecular dynamicsACS National Meeting Book of Abstracts. 2010
    2010 How Insulin-Like Growth Factor Hormones, IGF1 And IGF2, Engage their Cognate ReceptorBiophysical Journal. 243A-243A. 2010
    2009 A Thermodynamic Study Of Ligand Access/escape From Protein CavitiesBiophysical Journal. 596A-596A. 2009
    2009 Docking of Insulin to its ReceptorBiophysical Journal. 673A-673A. 2009
    Atomistic Transport characteristics and stability of artificial water channels in lipid and biomimetic membranes
    Capturing Differences in Dynamics of Structurally Similar Signaling Proteins
    Mapping of Gas Diffusion Pathways in [FeFe]-Hydrogenase
    Predicting hydrogen-deuterium exchange rates in proteins using molecular dynamics simulations
    Role of protein dynamics in allosteric targeting of protein-protein interfaces

    Teaching Activities

  • Adv Chem Engg Thermodynamics Taught course
  • Advanced Research Experience Taught course
  • Advanced Research Experience Taught course
  • Computational Molecular Bioeng Taught course
  • Doctoral Research Taught course
  • Doctoral Research Taught course
  • Adv Chem Engg Thermodynamics Taught course 2024
  • Applied Math for Chem Engineer Taught course 2024
  • Chemical Engineering Project Taught course 2024
  • Doctoral Research Taught course 2024
  • Doctoral Research Taught course 2023
  • Seminar Taught course 2023
  • Adv Chem Eng Thermodynamics Taught course 2022
  • Doctoral Research Taught course 2022
  • Doctoral Research Taught course 2022
  • Adv Chem Eng Thermodynamics Taught course 2021
  • Appld Math for Chemical Engnrs Taught course 2021
  • Appld Math for Chemical Engnrs Taught course 2021
  • Doctoral Research Taught course 2021
  • Doctoral Research Taught course 2021
  • Appld Math for Chemical Engnrs Taught course 2020
  • Appld Math for Chemical Engnrs Taught course 2020
  • Doctoral Research Taught course 2020
  • Adv Chem Eng Thermodynamics Taught course 2020
  • Adv Rsrch Exp/Chemical Engr Taught course 2020
  • Chem Engnrng Thermodynamics Taught course 2020
  • Doctoral Research Taught course 2020
  • Rsrch Exp/Chemical Engr Taught course 2020
  • Computational Bioengineering Taught course 2019
  • Doctoral Research Taught course 2019
  • Adv Chem Eng Thermodynamics Taught course 2019
  • Adv Rsrch Exp/Chemical Engr Taught course 2019
  • Chem Engnrng Thermodynamics Taught course 2019
  • Chemical Engineering Project Taught course 2019
  • Doctoral Research Taught course 2019
  • Adv Rsrch Exp/Chemical Engr Taught course 2018
  • Appld Math for Chemical Engnrs Taught course 2018
  • Appld Math for Chemical Engnrs Taught course 2018
  • Doctoral Research Taught course 2018
  • Adv Chem Eng Thermodynamics Taught course 2018
  • Chem Engnrng Thermodynamics Taught course 2018
  • Doctoral Research Taught course 2018
  • Computational Bioengineering Taught course 2017
  • Computational Bioengineering Taught course 2017
  • Doctoral Research Taught course 2017
  • Adv Chem Eng Thermodynamics Taught course 2017
  • Chem Engnrng Thermodynamics Taught course 2017
  • Doctoral Research Taught course 2017
  • Appld Math for Chemical Engnrs Taught course 2016
  • Appld Math for Chemical Engnrs Taught course 2016
  • Doctoral Research Taught course 2016
  • Rsrch Exp/Chemical Engineering Taught course 2016
  • Chem Engnrng Thermodynamics Taught course 2016
  • Doctoral Research Taught course 2016
  • Rsrch Exp/Chemicial Engr Taught course 2016
  • Adv Chem Eng Thermodynamics Taught course 2015
  • Adv Rsrch Exp/Chemical Engr Taught course 2015
  • Appld Math for Chemical Engnrs Taught course 2015
  • Appld Math for Chemical Engnrs Taught course 2015
  • Rsrch Exp/Chemical Engineering Taught course 2015
  • Chem Engnrng Thermodynamics Taught course 2015
  • Doctoral Research Taught course 2015
  • Rsrch Exp/Chemical Engr Taught course 2015
  • Rsrch Exp/Chemicial Engr Taught course 2015
  • Adv Chem Eng Thermodynamics Taught course 2014
  • Adv Rsrch Exp/Chemical Engr Taught course 2014
  • Appld Math for Chemical Engnrs Taught course 2014
  • Appld Math for Chemical Engnrs Taught course 2014
  • Rsrch Exp/Chemical Engineering Taught course 2014
  • Chem Engnrng Thermodynamics Taught course 2014
  • Rsrch Exp/Chemicial Engr Taught course 2014
  • Education And Training

  • B.Tech. Chemical Engineering, National Instit of Tech
  • Ph.D. Chemical Engineering, Drexel University
  • Full Name

  • Harish Vashisth
  • Mailing Address

  • University of New Hampshire

    Chemical Engineering

    33 Academic Way S344B

    Durham, NH  03824

    United States