Computational

Department of Chemistry, University of Pittsburgh
Ph.D., Biophysics, University of California San Francisco, 2002
Summary:

Our research is focused on the use of molecular simulations to characterize the free energy landscapes and kinetics of a variety of biological processes, including large protein conformational transitions and protein binding. We have also been developing simulation strategies for aiding the design of protein-based conformational switches. Finally, we are developers of an upcoming AMBER force field and https://westpa.github.io/westpa/, a freely available, highly scalable software implementation of weighted ensemble path sampling strategies for the simulation of rare events (e.g. protein folding and protein binding).

Our research falls into the following main areas:

1) Development of weighted ensemble path sampling strategies and software for the efficient sampling of rare events (e.g. protein folding and binding) with rigorous kinetics.

2) Application of molecular simulations to investigate the mechanisms of protein conformational transitions, binding, and assembly processes.

3) Development of molecular simulation strategies for aiding the design of protein conformational switches.

4) Development of biomolecular force fields.

Selected Publications: 
  • "Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (Review)," Zuckerman, D.M.Chong, L.T., Annual Review of Biophysics 46, 43 (2017)
  • "Path-sampling strategies for simulating rare events in biomolecular systems," Chong, L.T., Saglam, A.S., Zuckerman, D.M., Current Opinion in Structural Biology 43, 88, (2017)  
  • "Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide," Zwier, M.C., Pratt, A.J., Adelman, J.L., Kaus, J.W., Zuckerman, D.M., Chong, L.T., J. Phys. Chem. Lett 7, 3440 (2016)
  • "Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model," Debiec, K.T., Cerutti, D.S., Baker, L.R., Gronenborn, A.M., Case, D.A., Chong, L.T., J. Chem. Theory Comput. 12, 3926 (2016)
  • "Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models," Saglam, A.S., Chong, L.T., J. Phys. Chem. B 120, 117 (2016)
Most Cited Publications
  1. "Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models"  Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
  2. "The Amber biomolecular simulation programs" Case, D.A., Cheatham III, T.E., Darden, T., (...), Wang, B., Woods, R.J. Journal of Computational Chemistry 26(16), pp. 1668-1688
  3. "GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit" Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
  4. "Docking and scoring in virtual screening for drug discovery: Methods and applications" Kitchen, D.B., Decornez, H., Furr, J.R., Bajorath, J. 2004 Nature Reviews Drug Discovery
  5. "Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model" Onufriev, A., Bashford, D., Case, D.A. Proteins: Structure, Function and Genetics
Recent Publications
  1. "Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields,"  K T Debiec, A M Gronenborn, and L T Chong Journal of Physical Chemistry B 123.19 (2019)
  2. "Large enhancement of response times of a protein conformational switch by computational design,"  Alex J. DeGrave, Jeung-Hoi Ha, Stewart N. Loh & Lillian T. Chong, Nature Commnications, 9, 1013 (2018).
  3. "Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein." Debiec, K.T., Whitley, M.J., Koharudin, L.M.I., Chong, L.T., Gronenborn, A.M.     Biophysical Journal 114(4), pp. 839-855. (2018).
  4. "WESTPA 2.0 Advances in Sampling, Storage, and Analysis of Weighted Ensemble Simulations,"  AJ Pratt, D M Zuckerman, and L T ChongBiophysical Journal 114.3 (2018)
  5. "Links between the charge model and bonded parameter force constants in biomolecular force fields." Cerutti, D.S., Debiec, K.T., Case, D.A., Chong, L.T.     Journal of Chemical Physics 147(16),161730. (2017).
Department of Physics, Carnegie Mellon University
Ph.D., Physics, University of Chicago, 1983
Summary:

Professor Widom's research focuses on theoretical modeling of novel materials in condensed matter and biological physics settings. Methods of statistical mechanics, quantum mechanics and computer simulation are used to investigate structure, stability and properties of these materials.

Metals in noncrystalline (nonperiodic) structures are a major focus of effort, including: Liquid metals, for example the liquid-liquid transition in supercooled silicon); Metallic glass es, which are multi-component alloys that freeze into a solid while maintaining a liquid-like structure; Quasicrystals, which are partially ordered and highly symmetric structures that are spatially quasiperiodic. These problems are addressed using first-principles total energy calculation coupled with statistical mechanics to model entire ensembles of probable structures.

Biological physics is the second major focus, including two specific projects. Virus capsids are highly symmetric protein shells that protect the viral genome. Methods of continuum mechanics and symmetry analysis are applied to identify soft modes of deformation. The RNA molecule plays many roles at the heart of gene expression, some of which such as microRNAs and riboswitches have only recently been discovered. A characteristic feature of RNA is its highly convoluted secondary structure, which are analyzed from both thermodynamic and kinetic points of view.

Most Cited Publications
  1. "Quasicrystal equilibrium state." Michael Widom, Katherine J Strandburg, Robert H Swendsen. Physical review letters.
  2. "Ductility improvement of amorphous steels: roles of shear modulus and electronic structure." XJ Gu, S Joseph Poon, Gary J Shiflet, Michael Widom. Acta Materialia.
  3. "Transfer-matrix analysis of a two-dimensional quasicrystal." M Widom, DP Deng, CL Henley. Physical review letters.
  4. "Radial fingering in a Hele-Shaw cell: a weakly nonlinear analysis." JoséA Miranda, Michael Widom. Physica D: Nonlinear Phenomena.
  5. "Signature of nearly icosahedral structures in liquid and supercooled liquid copper." P Ganesh, M Widom. Physical Review B.
Recent Publications
  1. "Mysterious SiB3: Identifying the Relation between α- and β-SiB3." Daniel Eklöf, Andreas Fischer, Annop Ektarawong, Aleksander Jaworski, Andrew J Pell, Jekabs Grins, Sergei I Simak, Björn Alling, Yang Wu, Michael Widom, Wolfgang Scherer, Ulrich Häussermann. ACS Omega.
  2. "First-principles study of the electronic structure and the Fermi surface in rare-earth filled skutterudites ." Gheorghe Lucian Pascut, Michael Widom, Kristjan Haule, Khandker F Quader. Physical Review B.
  3. "Spontaneous formation of thermodynamically stable Al--Cu--Fe icosahedral quasicrystal from realistic atomistic simulations." Marek Mihalkovic, Michael Widom. arXiv preprint arXiv:1908.03417.
  4. "Formation of Graphene atop a Si adlayer on the C-face of SiC." Jun Li, Qingxiao Wang, Guowei He, Michael Widom, Lydia Nemec, Volker Blum, Moon Kim, Patrick Rinke, Randall M Feenstra. arXiv preprint arXiv:1905.04234.
  5. "Coexistence of quantum spin hall edge state and proximity-induced superconducting gap in monolayer 1T'-WTe." Felix Lüpke, Dacen Waters, Sergio C de la Barrera, Michael Widom, David G Mandrus, Jiaqiang Yan, Randall M Feenstra, Benjamin M Hunt. arXiv preprint arXiv:1903.00493.
Pittsburgh Supercomputing Center
Ph.D., Physics, Florida Atlantic University
Summary:

Oak Ridge National Laboratory, Metals and Ceramics Division, Postdoctoral Researcher, Oak Ridge, TN, 1993 ~ 1996

  • Developed a linear scaling quantum mechanical simulation code to study electronic and magnetic structures of metals and alloys.  this code became the first scientific application package that exceeds the teraflop performance and won the first place of 1998 Gordon Bell Prize for high performance computing and the Year 2000 Smithsonian Computerworld Program Award.
  • Applied massively parallel supercomputing technology to alloy modeling and design.
Selected Publications: 
Most Cited Publications
  1. "Order-N Multiple Scattering Approach to Electronic Structure Calculations." Yang Wang, GM Stocks, WA Shelton, DMC Nicholson, Z Szotek, WM Temmerman. Physical review letters.
  2. "Order-N multiple scattering approach to electronic structure calculations." Yang Wang, GM Stocks, WA Shelton, DMC Nicholson, Z Szotek, WM Temmerman. Physical review letters.
  3. "Imaging columns of the light elements carbon, nitrogen and oxygen with sub Ångstrom resolution." C Kisielowski, CJD Hetherington, YC Wang, R Kilaas, MA O’keefe, A Thust. Ultramicroscopy.
  4. "Sub-Ångstrom high-resolution transmission electron microscopy at 300 keV." MA O’keefe, CJD Hetherington, YC Wang, EC Nelson, JH Turner, C Kisielowski, J-O Malm, R Mueller, J Ringnalda, M Pan, A Thust. Ultramicroscopy.
  5. "The Applications of Targeting Anti-Cancer Agents in Cancer Therapeutics." Guang-Chun Sun, Xu Yang, Yan Yu, Dai-Wei Zhao. Anti-Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry-Anti-Cancer Agents).
Recent Publications
  1. "Gata6 promotes hair follicle progenitor cell renewal by genome maintenance during proliferation." Alex B Wang, Ying V Zhang, Tudorita Tumbar. The EMBO journal.
  2. "Molecular regulation of hair follicle stem and progenitor cell homeostasis." Alex Bing Wang. Cornell University.
  3. "Imprinted DNA methylation reconstituted at a non-imprinted locus." David H Taylor, Chelsea M McLean, Warren L Wu, Alex B Wang, Paul D Soloway. Epigenetics & chromatin.
  4. "The relationship between atmospheric lead emissions and aggressive crime: an ecological study." Mark Patrick Taylor, Miriam K Forbes, Brian Opeskin, Nick Parr, Bruce P Lanphear. Environmental health.
  5. "Thermodynamic properties of refractory high entropy alloys." Hongquan Song, Fuyang Tian, Dongping Wang. Journal of Alloys and Compounds.
Department of Chemistry, Carnegie Mellon University
Ph.D., Chemistry, State University of New York at Stony Brook, 1988
Summary:

The main research goal of the Kim group is to gain theoretical understanding of condensed-phase chemical and electrochemical processes at the molecular level with proper account of solvation effects. They develop and apply analytic models and computational methods, viz., statistical mechanics theory, quantum chemistry tools and molecular dynamics simulations, to quantify solvation effects on free energetics and dynamics of chemical reactions and related spectroscopy in homogeneous and heterogeneous environments. Their primary focus is on solution systems that have important environmental, biological or energy implications. 

Our specific thrust areas include:

  • Solvation and chemical reactions in green solvents: The primary focus is on chemical reactions involving charge shift (e.g., SN1 and electron transfer reactions) and related dynamics (e.g., dielectric relaxation and vibrational energy relaxation) in environmentally benign green solvents, in particular, room-temperature ionic liquids and supercritical water.
  • Energy storage: Supercapacitors and pseudocapacitors: The main effort is directed towards quantitation of how electrode properties such as size and shape of carbon micropores and electrolyte properties, e.g., ion size, density and conductivity, control the energy and power densities of EDLCs.
  • Structure and dynamics of multi-domain proteins: The current thrust is to investigate specific bindings and interactions between domains of plasminogen using various simulation techniques.
Most Cited Publications
  1. "Mass spectrum of chiral ten-dimensional N=2 supergravity on S5,"  HJ Kim, LJ Romans, and P van Nieuwenhuizen.  Physical Rev D 32.2 (1985)
  2. "Nanoporous Carbon Supercapacitors in an Ionic Liquid: A Computer Simulation Study," Youngseon Shim and Hyung J. Kim, ACS Nano 4, 2345 (2010)
  3. "Equilibrium and nonequilibrium solvation and solute electronic structure I. Formulation," HJ Kim and JT Hynes.  Journal of Chemical Physics 93.7 (1990)
  4. "Equilibrium and nonequilibrium solvation and solute electronic structure.  III. Quantum theory," HJ Kim and JT Hynes.  Journal of Chemical Physics 96.7 (1992)
  5. "Solvation in molecular ionic liquids," Y SHim, J Duan, MY Choi, and HJ KimJournal of Chemical Physics 119.13 (2003)
Recent Publications
  1. "Vibrational spectroscopy of imidazolium-based ionic liquids: A combined MD/DFT study,"  J Liu, H Kim, NR Dhumal, and HJ KimJournal of Molecular Liquids 292 (2019)
  2. "Modeling neural circuit, blood-brain barrier, and myelination on a microfluidic 96 well plate," SR Lee, S Hyung, S Bang, Y Lee, J Ko, S Lee, HJ Kim, and NL Jeon, Biofabrication 11.3 (2019)
  3. "Gold-Paladium Nanoalloys Supported by Graphene Oxide and Lamellar TiO2 for Direct Synthesis of Hydrogen Peroxide," S Guo, S Zhang, Q Fang, H Abroshan, HJ Kim, M Haruta, and G Li.  ACS Applied Materials & Interfaces 10.47 (2018)
  4. "Theoretical Study of Alkylculfonic Acids: Force-Field Development and Molecular Dynamics Simulations."  Jiannan Liu, Nilesh R Dhumal, and Hyung J KimJournal of Phys. Chem. B 122.42 (2018)
  5. "Deconvolution of Conformational Equilibria in Methimazolium-Based Ionic Liquid Ion Pair: Infrared Spectroscopic and Computational Study." Nilesh R. Dhumal, Arsalan Mirjafari, and Hyung J KimJournal of Molecular Liquids 266 (2018)
Department of Chemistry, University of Pittsburgh
Ph.D., Physical Chemistry, Massachusetts Institute of Technology, 1974
Summary:

The Jordan group's research interests lie in several areas:

Accomodation of excess charge by water clusters: Excess electrons and protons in water are engaged in a wide range of important chemical, biological, and geochemical processes. Our group has been especially interested in understanding how these charged particles are accommodated by the water networks. Much of our work in this area is in collaboration with the Johnson group at Yale, which uses vibrational predissociation spectroscopy as a probe of the structure of the clusters. The resulting spectra tend to be highly anharmonic, providing a significant challenge to theory. Our group has been engaged in the development of model Hamiltonian approaches to characterize excess electrons in water and to understand the trends in the OH stretch spectra of protonated water clusters.

Long-range correlation effects: We are engaged in developing methods to describe long-range correlation effects in molecules, clusters, and at surfaces. This work includes extensions of the dispersion-correlated atomic potential (DCACP) procedure of Rothlesberger and co-workers, and the use of quantum Drude oscillators to describe long-range correlation effects between excess electrons and molecules and clusters.

Quantum Monte Carlo methods: The DMC method is highly parallel and can be run over tens of thousands of CPU cores enabling calculation of accurate energies for systems for which large basis set CCSD(T) calculations are not feasible. The main approximation of DMC calculations is the fixed-node approximation, which is made to maintain fermionic character of the wavefunction. Our research is focused on the development of improved nodal approximations via the use of multiconfigurational trial functions.

Sustainability: We are using computational methods to address a range of problems relevant to clean energy and sustainability. These include modeling heat transport in methane hydrate and other hydrates and elucidation of the role of water in the uptake of CO2 by clays. In these studies, we are using classical Monte Carlo and molecular dynamics simulation methods with classical force fields.

 

Most Cited Publications
  1. "Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer," K. Kim, K. D. JordanJ. Phys. Chem. 98, 10089 (1994)
  2. "Spectral Signatures of Hydrated Proton Vibrations in Water Clusters," Jeffrey M. Headrick, Eric G. Diken, Richard S. Walters, Nathan I. Hammer, Richard A. Christie, Jun Cui, Evgeniy M. Myshakin, Michael A. Duncan, Mark A. Johnson, Kenneth D. JordanScience 108, 1765 (2005)
  3. "Infrared Signature of Structures Associated with the H+(H2O)n (n = 6 to 27) Clusters," J.-W. Shin, N. I. Hammer, E. G. Diken, M. A. Johnson, R. S. Walters, T. D. Jaeger, M. A. Duncan, R. A. Christie, K. D. JordanScience 304, 1137 (2004)
  4. "Studies of the temporary anion states of unsaturated hydrocarbons by electron transmission spectroscopy," Kenneth D. Jordan, Paul D. Burrow, Acc. Chem. Res. 11, 341 (1978)
  5. "Role of water in electron-initiated processes and radical chemistry: Issues and scientific advances,"  KD Jordan et. al., Chemical Reviews 105.1 (2005)
Recent Publications
  1. "Prediction of a Non-Valence Temporary Anion State of  (NaCl)2," A Kairalapova, KD Jordan, MF Falcetta, DK Steiner, BL Sutter, and JS Gowen.  Journal Phys. Chem. B (2019)
  2. "Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface,"  J Denton, PJ Kelleher, MA Johnson, MD Baer, SM Kathmann, CJ Mundy, BA Wellen Rudd, HC Allen, TH Choi, and KD JordanProceedings of the National Academy of Sciences (2019)
  3. "Prediction of a Non-Valence Temporary Anion Shape Resonance for a Model (H 2 O) 4 System,"  A Kairalapova, KD Jordan, DN Maienshein, MC Fair, and MF Falcetta.  Journal of Physical Chemistry A 123.13 (2019)
  4. "Tag-Free and Isotopomer-Selective Vibrational Spectroscopy of the Cryogenically Cooled H9O4+ Cation with Two-Color, IR–IR Double-Resonance Photoexcitation: Isolating the Spectral Signature of a Single OH Group in the Hydronium Ion Core." Duong, Chinh H., Nan Yang, Patrick J. Kelleher, Mark A. Johnson, Ryan J. DiRisio, Anne B. McCoy, Qi Yu, Joel M. Bowman, Bryan V. Henderson, and Kenneth D. Jordan. The Journal of Physical Chemistry A (2018).
  5. "Accurate Predictions of Electron Binding Energies of Dipole-Bound Anions via Quantum Monte Carlo Methods." Hao, Hongxia, James Shee, Shiv Upadhyay, Can Ataca, Kenneth D. Jordan, and Brenda M. Rubenstein. The journal of physical chemistry letters 9, no. 21 (2018): 6185-6190.
Department of Chemistry, University of Pittsburgh
Ph.D., Chemistry, Northwestern University, 2004
Summary:

Our group develops new materials, as well as microscale and nanoscale functional devices literally from the bottom up. We focus on building electronic materials from molecular subunits, both organic and inorganic, using a variety of techniques to rationally design the desired properties. This encompasses chemical synthesis, characterization (both physical and chemical), combined with theoretical modeling and simulation.

Our group combines experimental and computational investigations to gain deep understanding of organic electronic materials.  The bottom line is to efficiently design novel molecular materials with improved properties.  Below are three areas we are currently studying in our lab.

1. Designer defects

2. Single-molecule piezoelectric springs

3. Organic solar cells

 

Most Cited Publications
  1. "Open Babel: An open chemical toolbox," Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison, Journal of Cheminformatics 3, 33 (2011)
  2. "Avogadro: an advanced semantic chemical editor, visualization, and analysis platform," Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison, Journal of Cheminformatics 4, 17 (2012)
  3. "Building Blocks for N-Type Molecular and Polymeric Electronics. Perfluoroalkyl- versus Alkyl-Functionalized Oligothiophenes (nTs; n = 2−6). Systematic Synthesis, Spectroscopy, Electrochemistry, and Solid-State Organization," Antonio Facchetti, Myung-Han Yoon, Charlotte L. Stern, Geoffrey R. Hutchison, Mark A. Ratner, and Tobin J. Marks, J. Am. Chem. Soc., 126, 13480 (2004)
  4. "Hopping Transport in Conductive Heterocyclic Oligomers:  Reorganization Energies and Substituent Effects," Geoffrey R. Hutchison, Mark A. Ratner, and Tobin J. Marks, J. Am. Chem. Soc. 127, 2339 (2005)
  5. "The Blue Obelisk - interoperability in chemical informatics," R Guha, MT Howard, GR Hutchison, P Murray-Rust, H Rzepa, C Steinbeck, J Wegner, and EL Willighagen.  Journal of chemical information and modeling 46.3 (2006)
Recent Publications
  1. "Fast, efficient fragment-based coordinate generation for Open Babel," Yoshikawa, Naruki, and Geoffrey R. Hutchison. Journal of cheminformatics 11, no. 1 (2019): 49.
  2. "Bayesian Optimization for Conformer Generation." Chan, Lucian, Geoffrey Hutchison, and Garrett Morris. (2018).
  3. "Polarizable Drude Model with s-type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields," Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, Carl Caleman, Geoffrey R. Hutchison, and David van der Spoel, ChemRxiv (2018).
  4. "A sobering assessment of small-molecule force field methods for low energy conformer predictions," IIana Y. Kanal, John A. Keith, Geoffrey R. Hutchison,International Journal of Quantum Chemistry (2017)
  5. "Interplay Among Sequence, Folding Propensity, and BioPiezoelectric Response in Short Peptides and Peptoids," Christopher W Marvin, Haley M. Grimm, Nathaniel C. Miller, W. Seth Horne, and Geoffrey R Hutchison, J. Phys. Chem. B (2017)
Department of Chemistry, University of Pittsburgh
Ph.D., Theoretical and Computational Chemistry, University of Tübingen, Germany, 2008
Summary:

The Lambrecht lab develops and applys electronic structure approaches to help guide discoveries in catalysis, spectroscopy, and materials chemistry. They develop electronic structure and embedding methods that yield an accurate and computationally feasible description of chemical reactions in solvent or solid environments. In cooperation with experiment, they aim at gaining insights into the thermodynamics, kinetics and spectral signatures along catalytic pathways. Another focus is to provide rationales for the improvement of catalysts. They are working on decomposition methods that allow us to extract correlations between electronic structure descriptors for ligands and solvents and thus ultimately allow to make recommendations for more active catalyst systems. Their research areas include:

  • Developing reduced-scaling first principles approaches for expedited predictions of molecular and materials properties: The aim is to enable calculations on larger systems than conventionally possible, which allows for more realistic chemical models. The scaling reduction is achieved by screening approaches exploiting the fact that some interactions between electrons (such as dispersion or vdW forces) are short-ranged and can therefore be neglected if the distance is big enough. Other approaches developed in the lab involve sparse matrix techniques, multi-scale approaches, as well as tensor decompositions.
  • Energy decomposition approaches to split infrared and other spectral signatures into chemically meaningful contributions and to facilitate force field development.
  • Simulating paramagnetic resonance spectra to identify the structures of metal binding sites in biological systems.
  • Metal nanoparticles (optical excitation and catalysis).
Most Cited Publications
  1. "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package," Y Shao, Z Gan, E Epifanovsky, ATB Gilbert, M Wormit, J Kussmann, ..., Daniel S Lambrecht, ..., Molecular Physics 113, 184 (2015)
  2. "Current status of the AMOEBA polarizable force field," Jay W Ponder, Chuanjie Wu, Pengyu Ren, Vijay S Pande, John D Chodera, Michael J Schnieders, Imran Haque, David L Mobley, Daniel S Lambrecht, Robert A DiStasio Jr, Martin Head-Gordon, Gary NI Clark, Margaret E Johnson, Teresa Head-Gordon, J. Phys. Chem. B 114, 2549 (2010)
  3. "Linear-scaling atomic orbital-based second-order Møller–Plesset perturbation theory by rigorous integral screening criteria" B Doser, DS Lambrecht, J Kussmann, C Ochsenfeld, J. Chem. Phys. 130, 064107 (2009)
  4. "Rigorous integral screening for electron correlation methods," DS Lambrecht, B Doser, C Ochsenfeld, J. Chem. Phys. 123, 184102 (2005)
  5. "Linear-scaling methods in quantum chemistry," C Ochsenfeld, J Kussmann, D S Lambrecht, Reviews in computational chemistry 23, 1 (2007)
Recent Publications
  1. "Generalizing energy decomposition analysis to response properties to inform expedited predictive models." Lambrecht, Daniel S. Computational and Theoretical Chemistry (2018).
  2. "A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions." Lambrecht, Daniel, and Eric Berquist. (2018).
  3. "Ligand−Substrate Dispersion Facilitates the Copper-Catalyzed Hydroamination of Unactivated Olefins", Gang Lu, Richard Y. Liu, Yang Yang, Cheng Fang, Daniel S. Lambrecht, Stephen L. Buchwald, and Peng Liu, J. Am. Chem. Soc., 139, 16548 (2017)
  4. "First-principles derived descriptors for rational design of functional molecular materials." Berquist, Eric, and Daniel Lambrecht. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 254. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, 2017.
  5. "Polymerization of silyl ketenes using alkoxide initiators: a combined computational and experimental study," Yuanhui Xiang, Daniel J. Burrill, Krista K. Bullard, Benjamin J. Albrecht, Lauren E. Tragesser, John McCaffrey, Daniel S. Lambrecht and Emily Pentzer, Polym. Chem. 8, 5381 (2017) 
Department of Chemical and Petroleum Engineering, University of Pittsburgh
Ph.D., Chemistry, California Institute of Technology, 2007
Summary:

The Keith group applies and develops computational chemistry to study and discover solutions to problems at the interface of engineering and basic science.  They are currently focused on modeling chemical reaction mechanisms and the atomic scale of materials to help develop renewable energy and sustainability technologies.

The group uses quantum chemistry-based multiscale modeling to predict and study the atomic scale of materials and chemical reactions. With electronic structure and atomistic methods, they can investigate fundamental reaction steps at different time- and length-scales that would otherwise be difficult or impossible to investigate with experiment. 

Notably, their studies are entirely carried out in silico (on a computer) and almost entirely free from artificial biases that are present when using experimental inputs. Whether doing so alone or in collaboration with experimentalists, the group provides deep perspective on the atomic-scale of catalytic environments to understand how they work and how to further improve them.

The 'ground-up' multiscale modeling approach uses appropriate levels of quantum chemistry (QC) theory (typically on up to ca. 200 atoms) to model reaction energiesbarrier heightspKas, and standard redox potentials. Using data obtained from QC theory, they can also develop analytic reactive forcefields, which are capable of modeling reaction dynamics on systems on the order of 100,000 atoms. Reactive forcefield data in turn can be used to generate rate constant libraries for kinetic Monte Carlo (kMC) simulations to model larger time-scale and length-scale phenomena such a nanoparticle/material growth and ripening.

Most Cited Publications
  1. "Water Oxidation on Pure and Doped Hematite (0001) Surfaces: Prediction of Co and Ni as Effective Dopants for Electrocatalysis," Peilin Liao, John A. Keith, and Emily A. Carter, J. Am. Chem. Soc. 134, 13296 (2012)
  2. "The Mechanism of the Wacker Reaction: A Tale of Two Hydroxypalladations," John A. Keith, Patrick M. Henry, Angew. Chem. Int. Ed. 48, 9038 (2009)
  3. "Theoretical Investigations of the Oxygen Reduction Reaction on Pt(111)," John A. Keith, Gregory Jerkiewicz, Timo Jacob, ChemPhysChem 11, 2779 (2010)
  4. "Elucidation of the selectivity of proton-dependent electrocatalytic CO2 reduction by fac-Re (bpy)(CO) 3CI," JA Keith, KA Grice, CP Kubiak, and EA Carter.  Journal of the American Chemical Society 135.42 (2013)
  5. "Theoretical Studies of Potential-Dependent and Competing Mechanisms of the Electrocatalytic Oxygen Reduction Reaction on Pt(111)," John A. Keith, Timo Jacob, Angew. Chem. Int. Ed. 49, 9521 (2010)
Recent Publications
  1. "Machine Learning Guided Approach for Studying Solvation Environments,"  Y Basdogan, MC Groenenboom, E Henderson, S De, S Rempe, and J KeithChemRxiv (2019)
  2. "Free Standing Nanoporous Palladium Alloys as CO Poisoning Tolerant Electrocatalysts for the Electrochemical Reduction of CO2 to Formate," S Chatterjee, CD Griego, J Hart, Y Li, M Taheri, J Keith, and J Snyder.  ACS Catalysis 9.6 (2019)
  3. "Benchmarking Computational Alchemy for Carbide, Nitride, and Oxide Catalysts." Griego, Charles D., Karthikeyan Saravanan, and John A. Keith. Advanced Theory and Simulations (2018): 1800142.
  4. "Mechanism of Isobutylene Polymerization: Quantum Chemical Insight into AlCl3/H2O‑Catalyzed Reactions," Minh Nguyen Vo, Yasemin Basdogan, Bridget S. Derksen, Nico Proust, G. Adam Cox, Cliff Kowall, John A. Keith, and J. Karl Johnson, ACS Catal., 8, 8006 (2018)
  5. "Oligomer Hydrate Crystallization Improves Carbon Nanotube Memory," Michael T. Chido, Peter Koronaios, Karthikeyan Saravanan, Alexander P. Adams, Steven J. Geib, Qiang Zhu, Hari B Sunkara, Sachin S. Velankar, Robert M. Enick, John A. Keith, and Alexander Star, Chemistry of Materials (2018).
Department of Mechanical Engineering and Materials Science, University of Pittsburgh
Ph.D., Mechanical Engineering, Carnegie Mellon University, 1984
Summary:

Dr. Givi’s areas of research interest are: turbulence, combustion, thermal-fluids, computational methods and stochastic processes.  He is currently the Deputy Editor of AIAA Journal and a member of the editorial boards of Computers & FluidsJournal of Applied Fluid Mechanics, and Open Aerospace Engineering Journal.  He is also the Book Review Editor of AIAA Journal, an Associate Editor of Journal of Combustion, and a past advisory board member of Progress in Energy and Combustion Science. Professor Givi is Fellow of AIAA, APS and ASME. 

Selected Publications: 
  • "Langevin simulation of turbulent combustion," Nouri A.G., Sammak S., Pisciuneri P.H., Givi, P., in Combustion for Power Generation and Transportation: Technology, Challenges and Prospects
  • "Model-free simulations of turbulent reactive flows," Peyman Givi, Progress in Energy and Combustion Science, Volume 15, 1 (1989)
  • "Filtered mass density function for large-eddy simulation of turbulent reacting flows," F. A. Jaberi, P. J. Colucci, S. James, P. Givi and S. B. Popoe, J. Fluid Mech. 401, 85 (1999)
  • "Large eddy simulation of a turbulent nonpremixed piloted methane jet flame (Sandia Flame D)," M.R.H. Sheikhi, T.G. Drozda, P. Givi, F.A. Jaberi, S.B. Pope, Proceedings of the Combustion Institute 30, 549 (2005)
  • "Velocity filtered density function for large eddy simulation of turbulent flows" L. Y. M. Gicquel, P. Givi, F. A. Jaberi and S. B. Pope, Phys. Fluids 14, 1196 (2002)
Most Cited Publications
  1. "Filtered density function for large eddy simulation of turbulent reacting flows" P. J. Colucci, F. A. Jaberi, and P. Givi, Physics of Fluids 10, 499 (1998)
  2. "Filtered mass density function for large-eddy simulation of turbulent reacting flows," F. A. Jaberi, P. J. Colucci, S. James, P. Givi and S. B. Pope, Journal of Fluid Mechanics  401, 85 (1999)
  3. "Model-free simulations of turbulent reactive flows," P. Givi, Progress in energy and combustion science 15, 1 (1989)
  4. "Large eddy simulation of a turbulent nonpremixed piloted methane jet flame (Sandia Flame D)," M R H Sheikhi, T G Drozda, P Givi, F A Jaberi, S B Pope, Proceedings of the Combustion Institute 30, 549 (2005)
  5. "Velocity filtered density function for large eddy simulation of turbulent flows," L. Y. M. Gicquel and P. Givi, Physics of Fluids 14, 1196 (2002)
Recent Publications
  1. "Quantum algorithm for the computation of the reactant conversion rate in homogeneous turbulence,"  G Xu, AJ Daley, P Givi, and RD Somma.  Combustion Theory and Modelling (2019)
  2. "Modeling and simulation of turbulent nuclear flames in Type Ia supernovae,"  AG Nouri, P Givi, and D Livescu.  Progress in Aerospace Sciences (2019)
  3. "Deep Learning of PDF Turbulence Closure,"  M Raissi, H Babaee, and P GiviBulletin of the American Physical Society (2018)
  4. "Sensitivity analysis of large eddy simulation data." Sammak, Shervin, Ling Miao, Peyman Givi, and Cyrus Madnia. Bulletin of the American Physical Society (2018).
  5. "Deep Learning of PDF Turbulence Closure." Raissi, Maziar, Hessam Babaee, and Peyman Givi. Bulletin of the American Physical Society (2018).
Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Computational and Theoretical Organic Chemistry, UCLA, 1990
Summary:

Our research program is driven by significant problems in organic, biochemistry, and physical chemistry. Our research in chemical theory and computation is fully integrated in strong collaboration with successful experimental chemists. We have a full range on interests, starting with the development of fundamental ideas on the theory of chemical bonding, and how this information can be used to understand the fundamentals of Lewis acidity and basicity, organic reaction catalysis, organometallic structures, and the bonding and reactions at surfaces. In the field of biochemistry, we investigate the energetics and mechanisms of phosphoryl transfer reactions, and design new antimicrobial agents to light the increasing risk of drug resistant bacterial fungal infections.

Selected Publications: 
  • "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  • "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  • "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)
  • "Hyperconjugation-Mediated Solvent Effects in Phosphoanhydride Bonds," Jean C. Summerton, Jeffrey D. Evanseck, and Michael S. Chapman, J. Phys. Chem. A 116 10209 (2012)
Most Cited Publications
  1. "All-atom empirical potential for molecular modeling and dynamics studies of proteins," A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B. 102, no. 18 (1998)
  2. "Transition structures of hydrocarbon pericyclic reactions," Houk, Kendall N., Yi Li, Jeffrey D. EvanseckAngewandte Chemie International Edition 31, no. 6 (1992)
  3. "Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin," Caves, Leo SD, Jeffrey D. Evanseck, Martin Karplus.,  Protein Science 7, no. 3 (1998)
  4. "Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study," Rovira, Carme, Brita Schulze, Markus Eichinger, Jeffrey D. Evanseck, Michele Parrinello,  Biophysical journal 81, no. 1 (2001)
  5. "Density functional theory study of aqueous-phase rate acceleration and endo/exo selectivity of the butadiene and acrolein Diels-Alder reaction," Kong, S., Evanseck, J.D., Journal of the American Chemical Society 122, no. 42 (2000)
Recent Publications
  1. "Chemistry REU Leadership Group: Support for the Chemistry Undergraduate Research Community"  Watkins, L.M., Evanseck, J.DACS Symposium Series 1295, pp. 73-83
  2. "Evolution of an AwESOME Chapter"  Cooper, E., Shaik, S., Bautista, D., (...), Gawalt, E.S., Evanseck, J.D. ACS Symposium Series 1278, pp. 55-71
  3. "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  4. "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  5. "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)

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