Dmitri Klimov, Associate Professor
Department of Bioinformatics and Computational Biology
           


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BINF690 Numerical Methods in Bioinformatics
BINF740 Introduction to Biophysics
BINF741 Introduction to Computer Simulations of Biomolecules
BINF841 Research topics in biomolecular simulations

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Curriculum Vitae

Dmitri Klimov

Associate Professor
Department of Bioinformatics and Computational Biology
College of Science

George Mason University
10900 University Boulevard, MS 5B3
Manassas, VA 20110

phone (703) 993-8395
fax (703) 993-8401
email dklimov@gmu.edu


Education:
Ph. D. (Physics), Moscow State University, 1992
M.Sc. (Physics), Moscow State University, 1989

Professional Experience:
2008 - present: Associate Professor, George Mason University
2004 - 2008: Assistant Professor, George Mason University
2001 - 2004: Assistant Research Scientist, IPST, University of Maryland
1994 - 2001: Research Associate, IPST, University of Maryland
1987: US-USSR Student Exchange Program, University of Maryland

Teaching Experience:
BINF 741 "Introduction to computer simulations of biomolecules"
BINF740/PHYS630 "Introduction to biophysics"
BINF690 "Numerical methods in bioinformatics"

List of Publications:

  1. Honeycutt, J.D., Thirumalai, D., & Klimov, D.K. (1989) Polymer chains in porous media. J. Phys. A22, L169-L175.

  2. Klimov, D.K. & Khokhlov, A. R. (1992) Study of polymer chain in a solution of colloidal particles. Polymer 33, 2177-2181.

  3. Klimov, D.K. & Thirumalai, D. (1996) A criterion that determines the foldability of proteins. Phys. Rev. Lett. 76, 4070-4073.

  4. Klimov, D.K. & Thirumalai, D. (1996) Factors governing the foldability of proteins. Proteins Struct. Funct. Gen. 26, 411-441.

  5. Klimov, D. K. & Thirumalai, D. (1997) Viscosity dependence of folding rates of proteins. Phys. Rev. Lett. 79, 317-320.

  6. Veitshans, T., Klimov, D. K., Thirumalai, D. (1997) Protein folding kinetics: Time scales, pathways, and energy landscapes in terms of sequence dependent properties. Folding & Design 2, 1-22.

  7. Thirumalai, D., Klimov, D. K., Woodson, S. A. (1997) Kinetic partitioning mechanism as unifying theme in the folding of biomolecules. Theor. Chem. Acct. 1, 23-30.

  8. Klimov, D.K. & Thirumalai, D. (1998) Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J. Chem. Phys. 109, 4119-4125.

  9. Thirumalai, D., Klimov, D.K., & Betancourt, M.R. (1998) Exploring the folding mechanisms of proteins using lattice models. In: Monte Carlo Approach to Biopolymers and Protein Folding. Edited by P. Grassberger, G. T. Barkema, W. Nadler. Singapore: World Scientific, pp. 19-28.

  10. Klimov, D.K. & Thirumalai, D. (1998) Cooperativity in protein folding: From lattice models with side chains to real proteins. Folding & Design 3, 127-139.

  11. Klimov, D.K. & Thirumalai, D. (1998) Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J. Mol. Biol. 282, 471-492.

  12. Thirumalai, D. & Klimov, D. K. (1998) Fishing for folding nuclei in lattice models and proteins. Folding & Design 3, R112-R118.

  13. Klimov, D.K., Betancourt, M.R., & Thirumalai, D. (1998) Virtual atom representation of hydrogen bonds in minimal off-lattice models of helices: Effect on stability, cooperativity and kinetics. Folding & Design 3, 481-496.

  14. Klimov, D.K. & Thirumalai, D. (1999) Stretching single domain proteins: phase diagram and kinetics of force-induced unfolding. Proc. Natl. Acad. Sci. USA 96, 6166-6170.

  15. Thirumalai, D. & Klimov, D.K. (1999) Deciphering the time scales and mechanisms of protein folding using minimal off-lattice models. Curr. Opin. Struct. Biol. 9, 197-207.

  16. Klimov, D.K. & Thirumalai, D. (1999) Mechanisms and kinetics of beta-hairpin formation (submitted for publication in Proc. Natl. Acad. Sci. USA 97, 2544-2549.

  17. Thirumalai, D. & Klimov, D.K. Emergence of stable and fast folding protein structures. In: Stochastic Dynamics and Pattern Formation in Biological Systems. Kim, S., Lee, K.J., & Sung, W. (eds.). American Institute of Physics, pp. 95-111 (2000).

  18. Klimov, D.K. & Thirumalai, D. (2000) Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl. Acad. Sci USA 97, 7254-7259.

  19. Thirumalai, D. & Klimov, D.K. Introducing protein folding using simple models. In: Encyclopedia of Chemical Physics and Protein Chemistry. Eds. J. Moore and N. Spencer, IoP Publishing, Bristol, UK (2001).

  20. Klimov, D.K. & Thirumalai, D. (2001) Multiple protein folding nuclei and the transition state ensemble in two-state proteins Proteins Struct. Funct. Gen. 43, 465-475.

  21. Thirumalai, D., Lee, N., Woodson, S.A., & Klimov. D.K. (2001) Early events in RNA folding. Ann. Rev. Phys. Chem. 52, 751-762.

  22. Klimov, D.K. & Thirumalai, D. (2001) Lattice Model studies of force-induced unfolding of proteins. J. Phys. Chem. B 105, 6648-6654.

  23. Thirumalai, D., Klimov, D. K., \& Dima, R. I. (2001) Insights into specific problems in protein folding using simple concepts. Adv. in Chem. Phys., v. 120, 35-76.

  24. Klimov, D.K. & Thirumalai, D. (2002) Is there a unique melting temperature for two-state proteins? J. Comp. Chem. 23, 161-165.

  25. Klimov, D.K. & Thirumalai, D. (2002) Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J. Mol. Biol. 315, 721-737.

  26. Massi, F., Klimov, D.K., Thirumalai, D., & Straub, J. (2002) Propensity for "beta-flickering" in the simulated dynamics of wildtype and E22Q "Dutch" mutant Alzheimer's amyloid peptides. Protein Sci. 11, 1639-1647.

  27. Klimov, D.K., Newfield, D., & Thirumalai, D. (2002) Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc. Natl. Acad. Sci. USA 99, 8019-8024.

  28. Li, M.S., Klimov, D.K. & Thirumalai, D. (2002) Folding in lattice models with side chains. Comp. Phys. Comm. 147, 625-628.

  29. Li, M.S., Klimov, D.K. & Thirumalai, D. (2002) Dependence of folding rates on protein length. J. Phys. Chem. 106, 8302-8305.

  30. Klimov, D.K. & Thirumalai, D. (2003) Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta-sheets. Structure 11, 295-307 (see also commentary, Structure 11, 242).

  31. Thirumalai, D., Klimov, D.K. & Dima, R.I. (2003) Emerging ideas in the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 13, 146-159.

  32. Thirumalai, D., Klimov, D.K., & Lorimer, G.H. (2003) Caging helps proteins fold. Proc. Natl. Acad. Sci. USA 100, 11195-11197.

  33. Li, M.S., Klimov, D.K. & Thirumalai, D. (2003) Thermal denaturation and folding rates of single domain proteins: size matters. Polymer 45, 573-579.

  34. Li, M.S., Klimov, D.K. & Thirumalai, D. (2004) Finite size effects on thermal denaturation of globular proteins. Phys. Rev. Lett. 93, 268107-1 - 268107-4.

  35. Klimov, D.K. & Thirumalai, D. (2004) Progressing from folding trajectories to transition state ensemble in proteins. Chem. Phys. 307, 251-258.

  36. Klimov, D.K., Straub, J., & Thirumalai, D. (2004) Aqueous urea solution destabilizes Abeta16-22 oligomers. Proc. Natl Acad. Sci. USA 101, 14760-14765.

  37. Cheung, M.S., Klimov, D.K., & Thirumalai, D. (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins Proc. Natl Acad. Sci. USA 102, 4753-4758.

  38. Li, M. S., Klimov, D.K., & Thirumalai, D. (2005) Finite size effects on calorimetric cooperativity of two-state proteins. Physica A: Statistical and Theoretical Physics 350, 38-44.

  39. Li, M. S., Hu, C.-K., Klimov, D.K., & Thirumalai, D. (2006) Multiple step wise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc. Natl Acad. Sci. USA 103, 93-98.

  40. Klimov, D.K. & Thirumalai, D. (2005) Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J. Mol. Biol. 353, 1171-1186.

  41. Dunlavy, D.M., O'Leary, D.P., Klimov, D.K. & Thirumalai, D. (2005) HOPE: A homotopy optimization method for protein structure prediction. Journal of Computational Biology 12, 1275-1288.

  42. Barsegov, V., Klimov, D.K., & Thirumalai, D. (2006) Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications. Biophys. J. 90, 3827-3941.

  43. Dong, X., Klimov, D.K., & Blaisten-Barojas, E. (2007) Protein folding with the adaptive tempering Monte Carlo method. Mol. Sim. 33, 577-582.

  44. Raman, E. P., Barsegov, V. & Klimov, D. K. (2007) Folding of tandem-linked domains. Proteins: Struct. Funct. Bioinform. 67, 795-810.

  45. Takeda, T & Klimov, D. K. (2007) Dissociation of Abeta16-22 amyloid fibrils probed by molecular dynamics. J. Mol. Biol. 368, 1202-1213.

  46. Bura, E., Klimov, D.K., & Barsegov, V. (2007) Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times. Biophys. J. 93, 1100-1115.

  47. Bura, E., Klimov, D.K and Barsegov, V. (2008) Analyzing forced unfolding of protein tandems by ordered aariates: 2. Dependent unfolding times. Biophys. J. 94, 2516-2528.

  48. Raman, E. P., Takeda, T., Barsegov, V. & Klimov, D. K. (2007) Mechanical unbinding of Abeta peptides from amyloid fibrils. J. Mol. Biol. 373, 785-800.

  49. Wang, P. & Klimov, D. K. (2008) Lattice simulations of cotranslational folding of single domain proteins. Proteins: Struct. Funct. Bioinform. 70, 925-937.

  50. Li, M.S., Klimov, D.K., Straub, J.E., & Thirumalai, D. (2008) Probing the mechanisms of fibril formation using lattice models. J. Chem. Phys. (in press).

  51. Takeda, T. & Klimov, D. K. (2008) Temperature induced dissociation of Abeta monomers from amyloid fibrils. Biophysical J. 95, 1758-1772.

  52. Takeda, T. & Klimov, D. K. (2009) Replica exchange simulations of the thermodynamics of Abeta fibril growth. Biophysical J. 96, 442-452.

  53. Takeda, T. & Klimov, D.K. (2009) Interpeptide interactions induce helix to strand structural transition in Abeta peptides. Proteins Struct. Funct. Bioinform. (accepted, doi 10.1002/prot.22406).

  54. Takeda, T., & Klimov, D.K. (2009) Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophys. J. doi:10.1016/j.bpj.2009.03.015.

  55. Takeda, T., & Klimov, D.K. (2009) Probing the effect of amino-terminal truncation for Abeta1-40 Peptides. J. Phys. Chem. B 113, 6692-6702.

  56. Takeda, T., & Klimov, D.K. (2009) Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of Abeta peptide mutant. J. Phys. Chem. B (in press).

  57. Raman, E. P., Takeda, T., & Klimov, D.K. (2009) Molecular dynamics simulations of ibuprofen binding to Abeta peptides. Biophys. J. (in press).

Other publications:

Raman, E. P., Takeda, T., Barsegov, V. & Klimov, D. K. (2008) Molecular dynamics simulations of force-induced unbinding of Abeta peptides from amyloid fibrils. Biophys. J. 94, 2818.

Research Presentations:

  1. Temperature-induced dissociation of amyloid fibrils. Invited lecture at the 6th congress of the International Society for Theoretical Chemical Physics, Vancouver, Canada, July 2008.

  2. Molecular dynamics simulations of force-induced unbinding of Abeta peptides from amyloid fibrils. Biophysical Society meeting, Long Beach, CA, February 2008.

  3. Crowded Folding. IBM-SUR meeting, College of Computer, Mathematical and Physical Sciences, University of Maryland, January 2002.

  4. Computer Simulations of Protein Folding. IBM-SUR meeting, College of Computer, Mathematical and Physical Sciences, University of Maryland, August 2000.

  5. Incorporating Hydrogen Bonds in Minimal Off-Lattice Models of Alpha-Helices: Effect on Stability, Cooperativity, and Kinetics. 13th Symposium of The Protein Society, Boston, July 1999.

  6. Viscosity Dependence of the Folding Rates of Proteins. 12th Symposium of The Protein Society, San Diego, July 1998.
Invited Talks:

  1. Temperature-induced dissociation of amyloid fibrils. 6th Congress of the International Society for Theoretical Chemical Physics, Vancouver, Canada, 2008 (invited lecture).

  2. Molecular dynamics of biomolecules: Basics, Methodology, and Examples. Workshop on Rigidity, Flexibility, and Motions in Biomolecules, Arizona State University, 2006.

  3. Blocking amyloid assembly with chemical denaturants. American Chemical Society Meeting, San Diego, 2005.

  4. Assembly of Abeta16-22 oligomers: Role of sequence and environment. Gordon Research Conference on Protein Folding Dynamics, Ventura, California, January 2004.

  5. Assembly of Abeta16-22 amyloid peptides into antiparallel beta-sheets. Laboratory of Chemical Physics, NIDDK, National Institutes of Health, April 2003.

  6. Aggregation of Abeta16-22 amyloid peptides: A molecular dynamics study. CSCAMM Seminar, University of Maryland, October 2002.

  7. Stretching Proteins. Department of Physics Colloquia, Drexel University, February 2002.

  8. Understanding Mechanical Unfolding of Proteins. Scientific Computation Seminar, AMSC & CSCAMM, University of Maryland, October 2001.

  9. Mechanism of beta-Hairpin Formation. Informal Statistical Physics Seminar, Institute for Physical Science and Technology, University of Maryland, April 2000.

  10. Mechanisms and Kinetics of beta-Hairpin Formation. Thomas B. Woolf Laboratory, Department of Physiology, JHU Medical School, January 2000.

  11. Studying protein folding with the help of simplified models. Laboratory of Chemical Physics, NIDDK, National Institutes of Health, February 1999.

  12. Thermodynamics and Kinetics of Protein Folding. Protein Folding Journal Club chaired by Dr. J. Bryngelson, NIH, December 1997.

Reviewing Activities:

Periodic review of research articles submitted to Physical Review Letters, Journal of American Chemistry Society, Journal of Biological Physics , Proteins: Structure, Function and Genetics and research grant proposals (NSF, Petrolium Research Fund).