Keywords
Last Name

Tom Keyes, PhD

TitleProfessor
InstitutionBoston University College of Arts and Sciences
DepartmentChemistry
Address590 Commonwealth Avenue
Boston MA 02215
Phone(617) 353-4730
Fax(617) 353-6466
 Research Expertise & Professional Interests
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.

 Publications
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.
List All   |   Timeline
  1. 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.
    View in: PubMed
  2. Malolepsza E, Keyes T. Water Freezing and Ice Melting. J Chem Theory Comput. 2015 Dec 08; 11(12):5613-23. PMID: 26642983.
    View in: PubMed
  3. 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.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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.
    View in: PubMed
  6. 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.
    View in: PubMed
  7. 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. PMID: 24785073.
    View in: PubMed
  8. 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.
    View in: PubMed
  9. Kim J, Straub JE, Keyes T. Replica exchange statistical temperature molecular dynamics algorithm. J Phys Chem B. 2012 Jul 26; 116(29):8646-53. PMID: 22540354.
    View in: PubMed
  10. 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.
    View in: PubMed
  11. 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.
    View in: PubMed
  12. 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. PMID: 21842919.
    View in: PubMed
  13. 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.
    View in: PubMed
  14. Keyes T, Napoleon RL. Extending classical molecular theory with polarization. J Phys Chem B. 2011 Jan 27; 115(3):522-31. PMID: 21182320.
    View in: PubMed
  15. 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.
    View in: PubMed
  16. Kim J, Keyes T, Straub JE. Generalized replica exchange method. J Chem Phys. 2010 Jun 14; 132(22):224107. PMID: 20550390.
    View in: PubMed
  17. 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.
    View in: PubMed
  18. Kim J, Keyes T, Straub JE. Replica exchange statistical temperature Monte Carlo. J Chem Phys. 2009 Mar 28; 130(12):124112. PMID: 19334813.
    View in: PubMed
  19. 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. PMID: 19391891.
    View in: PubMed
  20. 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.
    View in: PubMed
  21. 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.
    View in: PubMed
  22. 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. PMID: 17677500.
    View in: PubMed
  23. 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. PMID: 17430069.
    View in: PubMed
  24. Kim J, Keyes T. Inherent structure analysis of protein folding. J Phys Chem B. 2007 Mar 15; 111(10):2647-57. PMID: 17311447.
    View in: PubMed
  25. 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.
    View in: PubMed
  26. 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.
    View in: PubMed
  27. Kim J, Straub JE, Keyes T. Statistical-temperature Monte Carlo and molecular dynamics algorithms. Phys Rev Lett. 2006 Aug 4; 97(5):050601. PMID: 17026089.
    View in: PubMed
  28. 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.
    View in: PubMed
  29. 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.
    View in: PubMed
  30. 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.
    View in: PubMed
  31. 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.
    View in: PubMed
  32. 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.
    View in: PubMed
  33. 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.
    View in: PubMed
  34. 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.
    View in: PubMed
  35. 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.
    View in: PubMed
  36. 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.
    View in: PubMed
  37. 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.
    View in: PubMed
  38. 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.
    View in: PubMed
  39. 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.
    View in: PubMed
  40. 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.
    View in: PubMed
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