Tom Keyes | Profiles RNS

Tom Keyes, PhD

Professor

Boston University College of Arts and Sciences

Chemistry

PhD, University of California, Los Angeles
BS, Yale University

Websites

Chemistry Faculty

Tom Keyes studies biomolecules and water using fundamental statistical mechanics and computer simulation, simultaneously developing algorithms for fast and efficient sampling of large systems. A passionate believer in “small science,” he keeps his research group small and informal and is involved in the details of his student’s research on a daily basis.

The Keyes Group pursues theoretical and computational biophysical chemistry. Collaborators include Professor Keyes’ postdoctoral advisor, Prof. Irwin Oppenheim (MIT), who visits every Thursday. Some current projects are:

-Creating replica exchange STMD for CHARMM and applying it to computationally challenging systems (application to checkpoint kinase with Alvaro Monteiro, University of South Florida).

-Energy landscape theory of chaperonin-assisted protein folding.

-Developing and applying the POLIR potential for aqueous spectroscopy and solvation (with Christian Burnham, University of Houston).

-Describing proteins, viruses and other nanostructures with coarse-grained, multiscale equations of motion (with Peter Ortoleva, Center for Cell and Virus Theory, Indiana University).

-Developing the idea that classical “electrostatic bonds” based on polarization energy can treat some ligand-protein formerly considered to require quantum mechanics.

Techniques & Resources: BU has superb computational resources, coordinated through the Center for Computational Science, of which Professor Keyes is a member. The Keyes Group is one of the most extensive users of supercomputer time.

BU Research

Combining Novel Simulation Methods and Nucleation Theory to Uncover the Secrets of Gas Hydrates
09/01/2012 - 11/30/2015 (PI)
Department of Energy
DE-SC0008810

RESTMD-CHARMM SIMULATION OF THE CHK2/PP2A INTERACTION IN DNA REPAIR
09/01/2009 - 08/31/2012 (PI)
NIH/National Institute of General Medical Sciences
5F31GM086166-03

Title

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Xu H, Baggioli M, Keyes T. A fresh look at the vibrational and thermodynamic properties of liquids within the soft potential model. J Chem Phys. 2023 Oct 21; 159(15). PMID: 37846955

Stelter D, Keyes T. Membrane Phase Transitions in Lipid-Wrapped Nanoparticles. J Phys Chem B. 2022 Apr 07; 126(13):2507-2512. PMID: 35349297

Jewett AI, Stelter D, Lambert J, Saladi SM, Roscioni OM, Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT, Shea JE, Jensen GJ, Goodsell DS. Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. J Mol Biol. 2021 05 28; 433(11):166841. PMID: 33539886; PMCID: PMC8119336; DOI: 10.1016/j.jmb.2021.166841;

Stelter D, Keyes T. Simulation of fluid/gel phase equilibrium in lipid vesicles. Soft Matter. 2019 Oct 28; 15(40):8102-8112. PMID: 31588466

Xu F, Bandara A, Akiyama H, Eshaghi B, Stelter D, Keyes T, Straub JE, Gummuluru S, Reinhard BM. Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways. Proc Natl Acad Sci U S A. 2018 09 25; 115(39):E9041-E9050.View Related Profiles.

Akiyama, Hisashi
Straub, John
Gummuluru, Suryaram
Keyes, Tom

PMID: 30190430; PMCID: PMC6166840; DOI: 10.1073/pnas.1804292115;

Stelter D, Keyes T. Lipid Packing in Lipid-Wrapped Nanoparticles. J Phys Chem B. 2018 07 05; 122(26):6755-6762. PMID: 29856621

Feizpour A, Stelter D, Wong C, Akiyama H, Gummuluru S, Keyes T, Reinhard BM. Membrane Fluidity Sensing on the Single Virus Particle Level with Plasmonic Nanoparticle Transducers. ACS Sens. 2017 Oct 27; 2(10):1415-1423.View Related Profiles.

Reinhard, Bjorn
Akiyama, Hisashi
Gummuluru, Suryaram
Keyes, Tom

PMID: 28933537; PMCID: PMC5781257; DOI: 10.1021/acssensors.7b00226;

Stelter D, Keyes T. Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers. J Phys Chem B. 2017 06 15; 121(23):5770-5780. PMID: 28530813

Malolepsza E, Keyes T. Pathways through Equilibrated States with Coexisting Phases for Gas Hydrate Formation. J Phys Chem B. 2015 Dec 31; 119(52):15857-65. PMID: 26624929; DOI: 10.1021/acs.jpcb.5b06832;

Malolepsza E, Keyes T. Water Freezing and Ice Melting. J Chem Theory Comput. 2015 Dec 08; 11(12):5613-23. PMID: 26642983; DOI: 10.1021/acs.jctc.5b00637;

Showing 10 of 48 results. Show More

Malolepsza E, Secor M, Keyes T. Isobaric Molecular Dynamics Version of the Generalized Replica Exchange Method (gREM): Liquid-Vapor Equilibrium. J Phys Chem B. 2015 Oct 22; 119(42):13379-84. PMID: 26398582; DOI: 10.1021/acs.jpcb.5b07614;

Malolepsza E, Kim J, Keyes T. Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases. Phys Rev Lett. 2015 May 01; 114(17):170601. PMID: 25978217; DOI: 10.1103/PhysRevLett.114.170601;

Ozer G, Keyes T. Classical Description of the Vibrational Spectroscopy, Structure, and Electrostatics of the Halide Solvation Shell with the POLIR Potential. J Phys Chem B. 2015 Jul 23; 119(29):9312-8. PMID: 25640952; DOI: 10.1021/jp509907v;

Ozer G, Keyes T, Quirk S, Hernandez R. Multiple branched adaptive steered molecular dynamics. J Chem Phys. 2014 Aug 14; 141(6):064101. PMID: 25134545; DOI: 10.1063/1.4891807;

Cho WJ, Kim J, Lee J, Keyes T, Straub JE, Kim KS. Limit of metastability for liquid and vapor phases of water. Phys Rev Lett. 2014 Apr 18; 112(15):157802.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 24785073

Ortoleva PJ, Keyes T, Tuckerman M. Macromolecular systems understood through multiscale and enhanced sampling techniques. J Phys Chem B. 2012 Jul 26; 116(29):8335-6. PMID: 22831487; DOI: 10.1021/jp304524b;

Kim J, Straub JE, Keyes T. Replica exchange statistical temperature molecular dynamics algorithm. J Phys Chem B. 2012 Jul 26; 116(29):8646-53.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 22540354; DOI: 10.1021/jp300366j;

Kumar R, Keyes T. The relation between the structure of the first solvation shell and the IR spectra of aqueous solutions. J Biol Phys. 2012 Jan; 38(1):75-83. PMID: 23277671; PMCID: PMC3285733; DOI: 10.1007/s10867-011-9243-7;

Burnham CJ, Hayashi T, Napoleon RL, Keyes T, Mukamel S, Reiter GF. The proton momentum distribution in strongly H-bonded phases of water: a critical test of electrostatic models. J Chem Phys. 2011 Oct 14; 135(14):144502. PMID: 22010722; PMCID: PMC3212866; DOI: 10.1063/1.3649679;

Kim J, Keyes T, Straub JE. Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables. J Chem Phys. 2011 Aug 14; 135(6):061103.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 21842919; PMCID: PMC3166335; DOI: 10.1063/1.3626150;

Kumar R, Keyes T. Classical simulations with the POLIR potential describe the vibrational spectroscopy and energetics of hydration: divalent cations, from solvation to coordination complex. J Am Chem Soc. 2011 Jun 22; 133(24):9441-50. PMID: 21545136; DOI: 10.1021/ja201695d;

Keyes T, Napoleon RL. Extending classical molecular theory with polarization. J Phys Chem B. 2011 Jan 27; 115(3):522-31. PMID: 21182320; DOI: 10.1021/jp105595q;

Sangha AK, Keyes T. Protein folding and confinement: inherent structure analysis of chaperonin action. J Phys Chem B. 2010 Dec 23; 114(50):16908-17. PMID: 21114309; DOI: 10.1021/jp107257b;

Kim J, Keyes T, Straub JE. Generalized replica exchange method. J Chem Phys. 2010 Jun 14; 132(22):224107.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 20550390; PMCID: PMC2896417; DOI: 10.1063/1.3432176;

Sangha AK, Keyes T. Proteins fold by subdiffusion of the order parameter. J Phys Chem B. 2009 Dec 03; 113(48):15886-94. PMID: 19902909; DOI: 10.1021/jp907009r;

Kim J, Keyes T, Straub JE. Replica exchange statistical temperature Monte Carlo. J Chem Phys. 2009 Mar 28; 130(12):124112.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 19334813; PMCID: PMC2736574; DOI: 10.1063/1.3095422;

Kim J, Keyes T, Straub JE. Relationship between protein folding thermodynamics and the energy landscape. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Mar; 79(3 Pt 1):030902.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 19391891

Mankoo PK, Keyes T. POLIR: polarizable, flexible, transferable water potential optimized for IR spectroscopy. J Chem Phys. 2008 Jul 21; 129(3):034504. PMID: 18647028; DOI: 10.1063/1.2948966;

Kim J, Keyes T. Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation. J Phys Chem B. 2008 Jan 24; 112(3):954-66. PMID: 18088107; DOI: 10.1021/jp072872u;

Kim J, Straub JE, Keyes T. Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jul; 76(1 Pt 1):011913.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 17677500

Kim J, Straub JE, Keyes T. Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models. J Chem Phys. 2007 Apr 7; 126(13):135101.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 17430069

Kim J, Keyes T. Inherent structure analysis of protein folding. J Phys Chem B. 2007 Mar 15; 111(10):2647-57. PMID: 17311447; DOI: 10.1021/jp0665776;

DeVane R, Space B, Jansen TL, Keyes T. Time correlation function and finite field approaches to the calculation of the fifth order Raman response in liquid xenon. J Chem Phys. 2006 Dec 21; 125(23):234501. PMID: 17190561; DOI: 10.1063/1.2403129;

Mankoo PK, Keyes T. Classical molecular electrostatics: recognition of ligands in proteins and the vibrational Stark effect. J Phys Chem B. 2006 Dec 14; 110(49):25074-9. PMID: 17149932; DOI: 10.1021/jp063971v;

Kim J, Straub JE, Keyes T. Statistical-temperature Monte Carlo and molecular dynamics algorithms. Phys Rev Lett. 2006 Aug 4; 97(5):050601.View Related Profiles.

Straub, John
Keyes, Tom

PMID: 17026089

Mankoo PK, Keyes T. Induction model for molecular electrostatics: application to the infrared spectroscopy of CO liquid. J Chem Phys. 2006 May 28; 124(20):204503. PMID: 16774349; DOI: 10.1063/1.2200692;

Kim J, Keyes T. On the breakdown of the Stokes-Einstein law in supercooled liquids. J Phys Chem B. 2005 Nov 17; 109(45):21445-8. PMID: 16853782; DOI: 10.1021/jp052338r;

Keyes T, Kim J. Qualitative features of the two-dimensional Raman spectrum in liquids. J Chem Phys. 2005 Jun 22; 122(24):244502. PMID: 16035777; DOI: 10.1063/1.1931627;

Kim J, Keyes T. On the mechanism of reorientational and structural relaxation in supercooled liquids: the role of border dynamics and cooperativity. J Chem Phys. 2004 Sep 01; 121(9):4237-45. PMID: 15332971; DOI: 10.1063/1.1776553;

Keyes T, Chowdhary J. Potential-energy-landscape-based extended van der Waals equation. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Apr; 69(4 Pt 1):041104. PMID: 15169005; DOI: 10.1103/PhysRevE.69.041104;

Kim J, Li WX, Keyes T. Probes of heterogeneity in rotational dynamics: application to supercooled liquid CS2. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Feb; 67(2 Pt 1):021506. PMID: 12636683; DOI: 10.1103/PhysRevE.67.021506;

Keyes T, Chowdhary J, Kim J. Random energy model for dynamics in supercooled liquids: N dependence. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov; 66(5 Pt 1):051110. PMID: 12513470; DOI: 10.1103/PhysRevE.66.051110;

Kim J, Keyes T. Generalized Langevin equation approach to higher-order classical response: second-order-response time-resolved Raman experiment in CS2. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jun; 65(6 Pt 1):061102. PMID: 12188698; DOI: 10.1103/PhysRevE.65.061102;

Keyes T, Chowdhary J. Potential energy landscape and mechanisms of diffusion in liquids. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr; 65(4 Pt 1):041106. PMID: 12005805; DOI: 10.1103/PhysRevE.65.041106;

Chowdhary J, Keyes T. Conjugate gradient filtering of instantaneous normal modes, saddles on the energy landscape, and diffusion in liquids. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Feb; 65(2 Pt 2):026125. PMID: 11863605; DOI: 10.1103/PhysRevE.65.026125;

Keyes T, Chowdhary J. Inherent-structure dynamics and diffusion in liquids. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Sep; 64(3 Pt 1):032201. PMID: 11580370; DOI: 10.1103/PhysRevE.64.032201;

Keyes T. Entropy, dynamics, and instantaneous normal modes in a random energy model Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec; 62(6 Pt A):7905-8. PMID: 11138073

Zürcher U, Keyes T. Configurational entropy and collective modes in normal and supercooled liquids. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Aug; 60(2 Pt B):2065-70. PMID: 11969999

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 48 publications over 22 distinct years, with a maximum of 5 publications in 2015