KMap
Research Opportunities
  • Graduate Research Assistant

    Grant: Evolving Quantum Mechanical Tunnelling in Enzymes

    I am always looking for talented graduate students....
  • Graduate Research Assistant

    Grant: Protein Dynamics from Femtoseconds to Milliseconds as Crafted by Natural and Laboratory Evolution: Towards Enzyme Design

    I am looking for talented graduate students for this project....
Courses
  • ST
    Statistical Thermodynamics

  • PC
    Physical Chemistry

  • GCL
    General Chemistry Lecture I: Quantitative

  • MMC
    Mathematical Methods for Chemists

  • QC
    Quantum Chemistry

  • GCL
    General Chemistry Lecture II: Quantitative Approach

Student Thesis/Dissertation
  • For Whom the Heart Tolls: Development of a Molecular Description for Cardiac Muscle Function

    2022

    doctoral
  • Determining the Dynamics and Function of the Cardiac Thin Filament

    2022

    doctoral
  • On the Origin of Protein Dynamics

    2021

    doctoral
  • The Effect of Mutations on Fast Protein Dynamics

    2020

    doctoral
  • Computational Studies of the Aggregation Properties of Microbially Produced Rhamnolipids

    2019

    doctoral
  • The Dynamics of Dehydrogenases - A Phase Space Odyssey

    2017

    doctoral
  • The Tell–Tale Cardiac Thin Filament Model: An Investigation into the Dynamics of Contraction and Relaxation

    2017

    doctoral
  • The Dynamics of Enzymatic Reactions: A Tale of Two Dehydrogenases

    2016

    doctoral
  • Theoretical Study of Selective Human Melanocortin Receptors Agonists and Antagonists

    2015

    bachelors
Grants
  • Funding agency logo
    Evolving Quantum Mechanical Tunnelling in Enzymes

    Principal Investigator (PI)

    2022

    $647.1K
    Active
    Opportunity
  • Funding agency logo
    Protein Dynamics from Femtoseconds to Milliseconds as Crafted by Natural and Laboratory Evolution: Towards Enzyme Design

    Principal Investigator (PI)

    2022

    $315.9K
    Active
    Opportunity
  • Funding agency logo
    Integrative Approach to Divergent Remodeling in Thin Filament Cardiomyopathies

    Key Personnel (KP)

    2021

    $1.1M
    Active
  • Funding agency logo
    CAS: Glyonic Liquids: Sugar-Based Ionic Liquids & Deep Eutectic Solvents from Sustainable Sources for Electrochemical Applications

    Co-Investigator (COI)

    2020

    $570.0K
    Active
  • Funding agency logo
    Structural Dynamics of Cardiac Myosin-Binding Protein C Regulation

    Co-Investigator (COI)

    2019

    $2.0M
    Active
  • Funding agency logo
    Rapid Protein Dynamics and Catalysis: Modulation by Laboratory Evolution, Designed Mutation, and Protein Control of Electric Field Environment

    Principal Investigator (PI)

    2019

    $1.4M
    Active
  • Funding agency logo
    Rapid Protein Dynamics and Catalysis: Modulation by Laboratory Evolution, Designed Mutation, and Protein Control of Electric Field Environment

    Principal Investigator (PI)

    2019

    $198.0K
    Active
  • Funding agency logo
    The Interaction of Myosin and The Thin Filament: How Mutations Cause Allosteric Dysfunction and Their Connection to Genetic Cardiomyopathy

    Multiple Principal Investigator (MPI)

    2020

    $3.0M
  • Funding agency logo
    Structural Dynamics of Cardiac Myosin-Binding Protein C Regulation

    Key Personnel (KP)

    2019

    $31.5K
  • Funding agency logo
    A New Paradigm to Incorporate Protein Dynamics into Targeted Small Molecule Design for Sarcomeric Cardiomyopathies: A Proof of Concept for Thin Filament Therapeutics

    Multiple Principal Investigator (MPI)

    2018

    $1.9M
News
  • Five UA Faculty Members Named Regents' Professors

    2018

Publications (124)
Recent
  • A Proposed Mechanism for the Initial Myosin Binding Event on the Cardiac Thin Filament: A Metadynamics Study

    2021

  • Inverse heavy enzyme isotope effects in methylthioadenosine nucleosidases

    2021

  • Investigation of the Recovery Stroke and ATP Hydrolysis and Changes Caused Due to the Cardiomyopathic Point Mutations in Human Cardiac β Myosin

    2021

  • Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament

    2021

  • Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts

    2020

  • Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction

    2020

  • Directed Evolution's Influence on Rapid Density Fluctuations Illustrates How Protein Dynamics Can Become Coupled to Chemistry

    2020

  • Role of Protein Motions in Catalysis by Formate Dehydrogenase

    2020

  • Mechanochemical Function of Myosin II: Investigation into the Recovery Stroke and ATP Hydrolysis

    2020

  • A Classical Molecular Dynamics Simulation Study of Interfacial and Bulk Solution Aggregation Properties of Dirhamnolipids

    2020

  • FRET-based analysis of the cardiac troponin T linker region reveals the structural basis of the hypertrophic cardiomyopathy-causing Δ160E mutation

    2019

  • Optimization of the Turnover in Artificial Enzymes via Directed Evolution Results in the Coupling of Protein Dynamics to Chemistry

    2019

  • Examining the Origin of Catalytic Power of Catechol O-Methyltransferase

    2019

  • Proof of Principle that Molecular Modeling Followed by a Biophysical Experiment Can DeveloSmall Molecules that Restore Function to the Cardiac Thin Filament in the Presence of Cardiomyopathic Mutations

    2019

  • Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels

    2018

  • Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence

    2018

  • Unraveling the Differential Aggregation of Anionic and Nonionic Monorhamnolipids at the Interfaces: A Classical Molecular Dynamics Simulation Study

    2018

  • Molecular Dynamics Simulation of the Oil Sequestration Properties of a Nonionic Rhamnolipid

    2018

  • Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change

    2018

  • Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

    2018

  • Mechanism of Cardiac Tropomyosin Transitions on Filamentous Actin As Revealed by All-Atom Steered Molecular Dynamics Simulations

    2018

  • Structurally Linked Dynamics in Lactate Dehydrogenases of Evolutionarily Distinct Species

    2017

  • Electric Fields and Fast Protein Dynamics in Enzymes

    2017

  • Structural Properties of Nonionic Monorhamnolipid Aggregates in Water Studied by Classical Molecular Dynamics Simulations

    2017

  • Clinically Divergent Mutation Effects on the Structure and Function of the Human Cardiac Tropomyosin Overlap

    2017

  • Evolution of aggregate structure in solutions of anionic monorhamnolipids: experimental and computational results

    2017

  • Incorporating Fast Protein Dynamics into Enzyme Design: A Proposed Mutant Aromatic Amine Dehydrogenase

    2017

  • Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase

    2017

  • Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models

    2016

  • Phase Space Bottlenecks in Enzymatic Reactions

    2016

  • Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

    2016

  • Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics

    2016

  • Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations

    2016

  • Atomic resolution probe for allostery in the regulatory thin filament

    2016

  • Targeting a Rate-Promoting Vibration with an Allosteric Mediator in Lactate Dehydrogenase

    2016

  • Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies

    2016

  • Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations

    2015

  • Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling

    2015

  • Evolution alters the enzymatic reaction coordinate of dihydrofolate reductase

    2015

  • Azepinone-Containing Tetrapeptide Analogues of Melanotropin Lead to Selective hMC4R Agonists and hMC5R Antagonist

    2015

  • Enzyme Homologues Have Distinct Reaction Paths through Their Transition States

    2015

  • The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path,

    2014

  • Changes in protein architecture and subpicosecond protein dynamics impact the reaction catalyzed by lactate dehydrogenase

    2013

  • Conformational freedom in tight binding enzymatic transition-state analogues

    2013

  • Protein dynamics and the enzymatic reaction coordinate

    2013

  • Barrier crossing in dihydrofolate reductase does not involve a rate-promoting vibration

    2012

  • Mass modulation of protein dynamics associated with barrier crossing in purine nucleoside phosphorylase

    2012

  • Protein dynamics and enzymatic chemical barrier passage

    2011

  • The promoting vibration in human heart lactate dehydrogenase is a preferred vibrational channel

    2011

  • A model of calcium activation of the cardiac thin filament

    2011

  • Reply to comment on Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method

    2011

  • Finite temperature application of the corrected propagator method to reactive dynamics in a condensed-phase environment

    2011

  • Dissipative dynamics with the corrected propagator method. Numerical comparison between fully quantum and mixed quantum/classical simulations

    2010

  • On the origin of the chemical barrier and tunneling in enzymes

    2010

  • Slow conformational motions that favor sub-picosecond motions important for catalysis

    2010

  • Comparison studies of the human heart and bacillus stearothermophilus lactate dehydrogreanse by transition path sampling

    2009

  • The stochastic separatrix and the reaction coordinate for complex systems

    2009

  • Approximate inclusion of quantum effects in transition path sampling

    2009

  • Enzymatic transition states and dynamic motion in barrier crossing

    2009

  • Modeling vibrational resonance in linear hydrocarbon chain with a mixed quantum-classical method

    2009

  • Transition path sampling study of the reaction catalyzed by purine nucleoside phosphorylase

    2008

  • Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase

    2008

  • Atomic detail of chemical transformation at the transition state of an enzymatic reaction

    2008

  • Tryptophan-free human PNP reveals catalytic site interactions

    2008

  • Tunneling dynamics with a mixed quantum-classical method: Quantum corrected propagator combined with frozen Gaussian wave packets

    2008

  • Computational characterization of mutations in cardiac troponin T known to cause familial hypertrophic cardiomyopathy

    2007

  • The Quantum Kramers Approach to Enzymatic Hydrogen Transfer Protein Dynamics as it Couples to Catalysis

    2007

  • New mixed quantumsemiclassical propagation method

    2007

  • Ligand binding and protein dynamics in lactate dehydrogenase

    2007

  • Reaction coordinate of an enzymatic reaction revealed by transition path sampling

    2007

  • Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis

    2006

  • Protein dynamics and catalysis: The problems of transition state theory and the subtlety of dynamic control

    2006

  • Insight into catalytically relevant correlated motions in human purine nucleoside phosphorylase

    2006

  • Effect of enzyme dynamics on catalytic activity

    2006

  • How enzyme dynamics helps catalyze a reaction in atomic detail: A transition path sampling study

    2005

  • A new semiclassical dynamics from the interaction representation

    2005

  • Changes in the chemical and dynamic properties of cardiac troponin T cause discrete cardiomyopathies in transgenic mice

    2005

  • Donor-acceptor distance and protein promoting vibration coupling to hydride transfer: A possible mechanism for kinetic control in isozymes of human lactate dehydrogenase

    2004

  • Transition path sampling study of classical rate-promoting vibrations

    2004

  • Rate-promoting vibrations and coupled hydrogen-electron transfer reactions in the condensed phase: A model for enzymatic catalysis

    2004

  • Coupling protein dynamics to reaction center electron density in enzymes: An electronic protein promoting vibration in human purine nucleoside phosphorylase

    2004

  • Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study

    2004

  • A computational method to identify residues important in creating a protein promoting vibration in enzymes

    2003

  • Protein promoting vibrations in enzyme catalysis A conserved evolutionary motif

    2003

  • Langevin equation in momentum space

    2003

  • Barrier passage and protein dynamics in enzymatically catalyzed reactions

    2002

  • Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase

    2002

  • Effect of active site mutation Phe 93 → Trin the horse liver alcohol dehydrogenase enzyme on catalysis: A molecular dynamics study

    2002

  • Nonequilibrium solvation and the quantum kramers problem: Proton transfer in aqueous glycine

    2001

  • Harmonic collective modes in atomic liquids

    2001

  • Internal enzyme motions as a source of catalytic activity: Rate-promoting vibrations and hydrogen tunneling

    2001

  • Computational method to discover the existence of promoting vibrations for chemical reactions in condensed phases

    2001

  • Neural network methods for identification and optimization of quantum mechanical features needed for bioactivity

    2000

  • Quantum dynamics in condensed phases via extended modes and exact interaction propagator relations

    2000

  • The effect of coupled nonreactive modes on laser control of quantum wave packet dynamics

    1999

  • A molecular dynamics quantum Kramers study of proton transfer in solution

    1999

  • Quantum proton transfer coupled to a quantum anharmonic mode

    1999

  • Prediction of inhibitor binding free energies by quantum neural networks. Nucleoside analogues binding to trypanosomal nucleoside hydrolase

    1999

  • Quantum proton transfer with spatially dependent friction: Phenol-amine in methyl chloride

    1999

  • Proton transfer in benzoic acid crystals: Another look using quantum operator theory

    1998

  • Activated chemistry in the presence of a strongly symmetrically coupled vibration

    1998

  • External field control of condensed phase reactions

    1998

  • Temperature dependent spectral densities and quantum activated rate theory

    1998

  • Large kinetic isotope effects in enzymatic proton transfer and the role of substrate oscillations

    1997

  • Quantum reaction in a condensed phase: Turnover behavior from new adiabatic factorizations and corrections

    1997

  • Quantum activated rates An evolution operator approach

    1996

  • A mixed momentum-position space representation to study quantum vibrational energy transfer

    1996

  • Quantitative measures of molecular similarity: Methods to analyze transition-state analogs for enzymatic reactions

    1996

  • Molecular electrostatic potential analysis for enzymatic substrates, competitive inhibitors, and transition-state inhibitors

    1996

  • Nonadiabatic effects in a method that combines classical and quantum mechanics

    1996

  • The interaction representation and nonadiabatic corrections to adiabatic evolution operators

    1996

  • Enzymatic transition states and inhibitor design from principles of classical and quantum chemistry

    1996

  • Vibrational energy transfer in linear hydrocarbon chains: New quantum results

    1995

  • Vibrational energy transfer from resummed evolution operators

    1994

  • Accurate quantum mechanics from high order resummed operator expansions

    1994

  • Operator expansions for multidimensional problems: New developments and applications

    1992

  • Effective Feynman propagators and Schrödinger equations for processes coupled to many degrees of freedom

    1992

  • A density matrix formulation for potential scattering in an oscillating/controlled potential: a model for some biophysical systems

    1991

  • Traffic control architectures for integrated broadband networks

    1990

  • Propagator expansions for softly coupled potentials: A model for complex reaction dynamics

    1989

  • Quantum mechanical rate constants for bimolecular reactions

    1983

  • System-bath decomposition of the reaction path Hamiltonian. II. Rotationally inelastic reactive scattering of H+H sub 2 sub in three dimensions

    1983

  • System-bath decomposition of the reaction path Hamiltonian for polyatomic scattering: Quantum perturbative treatment

    1982

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