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
- STStatistical Thermodynamics
- PCPhysical Chemistry
- GCLGeneral Chemistry Lecture I: Quantitative
- MMCMathematical Methods for Chemists
- QCQuantum Chemistry
- GCLGeneral 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
- Evolving Quantum Mechanical Tunnelling in Enzymes
Principal Investigator (PI)
2022
$647.1KActiveOpportunity - Protein Dynamics from Femtoseconds to Milliseconds as Crafted by Natural and Laboratory Evolution: Towards Enzyme Design
Principal Investigator (PI)
2022
$315.9KActiveOpportunity - Integrative Approach to Divergent Remodeling in Thin Filament Cardiomyopathies
Key Personnel (KP)
2021
$1.1MActive - CAS: Glyonic Liquids: Sugar-Based Ionic Liquids & Deep Eutectic Solvents from Sustainable Sources for Electrochemical Applications
Co-Investigator (COI)
2020
$570.0KActive - Structural Dynamics of Cardiac Myosin-Binding Protein C Regulation
Co-Investigator (COI)
2019
$2.0MActive - Rapid Protein Dynamics and Catalysis: Modulation by Laboratory Evolution, Designed Mutation, and Protein Control of Electric Field Environment
Principal Investigator (PI)
2019
$1.4MActive - Rapid Protein Dynamics and Catalysis: Modulation by Laboratory Evolution, Designed Mutation, and Protein Control of Electric Field Environment
Principal Investigator (PI)
2019
$198.0KActive - 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 - Structural Dynamics of Cardiac Myosin-Binding Protein C Regulation
Key Personnel (KP)
2019
$31.5K - 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
- Professor Links Gene Mutations With Heart Disease Precursors
2012
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
- 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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