Positions

Overview

  • Research Interests
    Computational Biophysics, Biomolecular Simulations, Molecular Transport, Cell Signaling via Membrane Proteins
  • Publications

    Academic Article

    Year Title
    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 Genetics.  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.Journal of Physical Chemistry B Journal of Physical Chemistry B Materials.  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.Journal of Physical Chemistry B Journal of Physical Chemistry B Materials.  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 Genetics.  81:1017-1030. 2013
    2013 Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.Journal of Physical Chemistry B Journal of Physical Chemistry B Materials.  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 Structure with Folding & design.  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 The Scientific monthly.  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 Genetics.  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
    Functional mirror-image nanoassemblies templated by homochiral ssDNA scaffoldNature Communications
    Microsecond time-scale dynamics of insulin receptor and its componentsScience Advances
    Structure-based models to study RNA conformational transitionsJournal of Physical Chemistry B Journal of Physical Chemistry B Materials

    Conference Proceeding

    Year Title
    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 ProteinsFASEB 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 ExchangeFASEB 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 PeptideFASEB Journal. 2015
    2015 Regulators of G-protein Signaling Proteins: Conformational Dynamics and Allosteric ControlFASEB 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 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