Curriculum Vitae
Dmitri Klimov
Professor
School of Systems 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:
2014 - present: Professor, George Mason University
2008 - 2014: 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"
External funding:
R01 and R41 awards from the National Institure on Aging (NIH)
List of Publications:
- Honeycutt, J.D., Thirumalai, D., & Klimov, D.K. (1989) Polymer
chains in porous media. J. Phys. A22, L169-L175.
- Klimov, D.K. & Khokhlov, A. R. (1992) Study of polymer chain
in a solution of colloidal particles. Polymer 33, 2177-2181.
- Klimov, D.K. & Thirumalai, D. (1996) A criterion that
determines the foldability of proteins. Phys. Rev. Lett. 76, 4070-4073.
- Klimov, D.K. & Thirumalai, D. (1996) Factors governing the
foldability
of proteins. Proteins Struct. Funct. Gen. 26, 411-441.
-
Klimov, D. K. & Thirumalai, D. (1997) Viscosity dependence of folding rates of proteins. Phys. Rev. Lett. 79, 317-320.
- 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.
- 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.
- 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.
- 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.
- Klimov, D.K. & Thirumalai, D. (1998) Cooperativity in protein
folding: From lattice models with side chains to real proteins. Folding & Design 3, 127-139.
- Klimov, D.K. & Thirumalai, D. (1998) Lattice models for proteins
reveal
multiple folding nuclei for nucleation-collapse mechanism. J. Mol. Biol. 282, 471-492.
- Thirumalai, D. & Klimov, D. K. (1998) Fishing for folding nuclei in
lattice models and proteins. Folding & Design 3, R112-R118.
- 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.
- 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.
- 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.
- 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.
- 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).
- Klimov, D.K. & Thirumalai, D. (2000)
Native topology determines force-induced unfolding pathways in globular
proteins. Proc. Natl. Acad. Sci USA 97, 7254-7259.
- 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).
- 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.
- Thirumalai, D., Lee, N., Woodson, S.A., & Klimov. D.K. (2001)
Early events in RNA folding. Ann. Rev. Phys. Chem. 52,
751-762.
- Klimov, D.K. & Thirumalai, D. (2001)
Lattice Model studies of force-induced unfolding of proteins.
J. Phys. Chem. B 105, 6648-6654.
- 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.
- Klimov, D.K. & Thirumalai, D. (2002) Is there a unique melting
temperature for two-state proteins? J. Comp. Chem. 23,
161-165.
- 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.
- 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.
- 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.
- Li, M.S., Klimov, D.K. & Thirumalai, D. (2002) Folding in
lattice models with side chains. Comp. Phys. Comm. 147,
625-628.
- Li, M.S., Klimov, D.K. & Thirumalai, D. (2002)
Dependence of folding rates on protein length. J. Phys. Chem.
106, 8302-8305.
- 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).
- 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.
- Thirumalai, D., Klimov, D.K., & Lorimer, G.H. (2003) Caging
helps proteins fold. Proc. Natl. Acad. Sci. USA 100,
11195-11197.
- Li, M.S., Klimov, D.K. & Thirumalai, D. (2003)
Thermal denaturation and folding rates of single domain proteins:
size matters. Polymer 45, 573-579.
- 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.
- Klimov, D.K. & Thirumalai, D. (2004)
Progressing from folding
trajectories to transition state
ensemble in proteins. Chem. Phys. 307, 251-258.
- Klimov, D.K., Straub, J., & Thirumalai, D. (2004) Aqueous urea solution
destabilizes Abeta16-22 oligomers. Proc. Natl Acad. Sci. USA
101, 14760-14765.
- 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.
- 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.
- 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.
- Klimov, D.K. & Thirumalai, D. (2005)
Symmetric connectivity of secondary structure elements
enhances the diversity of folding pathways. J. Mol. Biol.
353, 1171-1186.
- 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.
- 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.
- Dong, X., Klimov, D.K., & Blaisten-Barojas, E. (2007)
Protein folding with the adaptive tempering Monte Carlo method.
Mol. Sim. 33, 577-582.
- Raman, E. P., Barsegov, V. & Klimov, D. K. (2007)
Folding of tandem-linked domains. Proteins: Struct. Funct. Bioinform.
67, 795-810.
- Takeda, T & Klimov, D. K. (2007) Dissociation of Abeta16-22 amyloid fibrils
probed by molecular dynamics. J. Mol. Biol. 368, 1202-1213.
- 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.
- 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.
- 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.
- Wang, P. & Klimov, D. K. (2008) Lattice simulations of cotranslational
folding of single domain proteins. Proteins: Struct. Funct. Bioinform.
70, 925-937.
- 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).
- Takeda, T. & Klimov, D. K. (2008) Temperature induced dissociation of Abeta monomers from amyloid
fibrils. Biophysical J. 95, 1758-1772.
- Takeda, T. & Klimov, D. K. (2009) Replica exchange simulations of the thermodynamics of Abeta
fibril growth. Biophysical J. 96, 442-452.
- 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).
- 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.
- Takeda, T., & Klimov, D.K. (2009) Probing the effect of
amino-terminal truncation for Abeta1-40 Peptides.
J. Phys. Chem. B 113, 6692-6702.
- 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 113, 11848-11857.
- Raman, E. P., Takeda, T., & Klimov, D.K. (2009)
Molecular dynamics simulations of ibuprofen binding to Abeta peptides.
Biophys. J. 97, 2070-2079.
- Takeda, T., & Klimov, D.K. (2010)
Computational backbone mutagenesis of Abeta peptides: Probing the role
of backbone hydrogen bonds in aggregation.
J. Phys. Chem. B 114, 4755-4762.
- Chang, W. E., Takeda, T., Raman, E. P., & Klimov, D.K. (2010)
Molecular dynamics simulations of anti-aggregation effect of ibuprofen.
Biophys. J. 98, 2662-2670.
- Kim, S., Takeda, T., & Klimov, D.K. (2010)
Globular state in the oligomers formed by Abeta peptides
J. Chem. Phys. (in press).
- Takeda, T., Chang, W. E., Raman, E. P., & Klimov, D.K. (2010)
Binding of non-steroidal anti-inflammatory drugs to Abeta fibril.
Proteins Str. Funct. Bioinform. 78, 2849-2860.
- Kim, S., Takeda, T., & Klimov, D.K. (2010)
Mapping conformational ensembles of Abeta oligomers in
molecular dynamics simulations.
Biophys. J.. 99, 1949-1958.
- Takeda, T., Kumar, R., Raman, E. P., & Klimov, D.K. (2010)
Non-steroidal anti-inflammatory drug naproxen destabilizes Abeta amyloid fibrils: A molecular dynamics investigation
J. Phys. Chem. B 114, 15394-15402.
- Kim, S., Chang, W., Kumar, R., & Klimov, D.K. (2011)
Naproxen interferes with the assembly of Abeta oligomers implicated in Alzheimer's disease.
Biophys. J. 100, 2024-2032.
- Lockhart, C., Kim, S., Kumar, R., & Klimov, D.K. (2011)
Does amino acid sequence determine the properties of Abeta dimer?
J. Chem. Phys. 135, 035103.
- Lockhart, C. & Klimov, D.K. (2012) Molecular interactions of Alzheimer's
biomarker FDDNP with Abeta peptide. Biophys. J. 103,
2341-2351.
- Lockhart, C., Kim, S., & Klimov, D.K. (2012) Explicit solvent molecular
dynamics simulations of Abeta peptide interacting with ibuprofen ligands.
J. Phys. Chem. B 116, 12922-12932.
- Kim, S. & Klimov, D.K. (2013) Binding to the lipid monolayer induces
conformational transition in Abeta monomer. J. Mol. Model.
19, 737-750.
- Lockhart, C. & Klimov, D.K. (2013)
Revealing hidden helix propensity in Abeta peptides by molecular dynamics
simulations.
J. Phys. Chem. B 117, 12030-12038.
- Lockhart, C. & Klimov, D.K. (2014) Alzheimer's Abeta10-40 Peptide Binds
and Penetrates DMPC Bilayer: An Isobaric-Isothermal Replica Exchange
Molecular Dynamics Study. J. Phys. Chem. B 118, 2638-2648.
- Lockhart, C. & Klimov, D.K. (2014) Binding of Abeta peptide creates
lipid density depression in DMPC bilayer.
BBA Biomembranes 1838, 2678-2688.
- Lockhart, C. & Klimov, D.K. (2015) Calcium enhances binding of
Abeta monomer to DMPC lipid bilayer.
Biophys. J. 108, 1807-1818.
- Lockhart, C., O'Connor, J., Armentrout, S.,& Klimov, D.K. (2015)
Greedy replica exchange algorithm improves performance on heterogeneous
computing grids. J. Mol. Model. , in press, doi
10.1007/s00894-015-2763-5
- Parikh, N. D. & Klimov, D.K. (2015) Molecular mechanisms of
Alzheimer's biomarker FDDNP binding to Abeta amyloid fibril.
J. Phys. Chem. B (accepted, DOI:
10.1021/acs.jpcb.5b06112).
- Lockhart, C. & Klimov, D.K. (2016) The Alzheimer's Disease
Abeta Peptide Binds to the Anionic DMPS Lipid Bilayer.
BBA Biomembranes, 1858, 1118–1128.
- Smith, A., Lockhart, C. & Klimov, D.K. (2016)
Does Replica Exchange with Solute Tempering efficiently sample Aβ
peptide conformational ensembles?" J. Chem. Theor. Comput.,
12, 5201–5214.
- Siwy, C. M., Lockhart, C., & Klimov, D. K. (2017)
Is the conformational ensemble of Alzheimer's Aβ10-40 peptide force
field dependent? PLOS Computational Biology, 13, e1005314.
- Parikh, N. and Klimov, D. K. (2017) Inclusion of lipopeptides into
the DMPC lipid bilayer prevents Abeta peptide insertion. Phys. Chem.
Chem. Phys., 19, 10087-10098.
- Lockhart, C. & Klimov, D. K. (2017) Cholesterol changes the
mechanism of Abeta peptide binding to the DMPC bilayer.
J. Chem. Inform. Model., 57, 2554–2565.
- Smith, A. & Klimov, D. K. (2018)
Binding of cytotoxic Abeta25-35 peptide to the DMPC lipid bilayer.
J. Chem. Inform. Model. 58, 1053–1065.
- Smith, A. & Klimov, D. K. (2018)
Molecular Dynamics Investigation of Ternary Bilayer Formed by Saturated
Phosphotidylcholine, Sphingomyelin, and Cholesterol.
J. Phys. Chem. B 122, 11311−11325.
- Lockhart, C., Smith, A. & Klimov, D. K. (2019)
Methionine Oxidation Changes the Mechanism of Abeta Peptide Binding to the
DMPC Bilayer. Sci. Reports 9, 5947.
- Smith, A. & Klimov, D. K. (2019) De novo aggregation of Alzheimer's
Aβ25-35 peptides in a lipid bilayer. Sci. Reports 9, 7161.
- Smith, A.K., Khayat, E., Lockhart, C., & Klimov, D. K. (2019)
Do Cholesterol and Sphingomyelin Change the Mechanism of Abeta25-35 Peptide
Binding to Zwitterionic Bilayer? J. Chem. Inform. Model. 59, 5207-5217.
- Lockhart, C., Smith, A. K., & Klimov, D. K. (2020) Three popular force fields
predict consensus mechanism of Abeta peptide binding to the DMPC bilayer.
J. Chem. Inform. Model. 60, 2282-2293.
- Siwy, C., Delfing, B.M., Smith, A.K., & Klimov, D. K. (2020) Partitioning of benzoic
acid into DMPC and blood-brain barrier mimetic bilayers. J. Chem. Inf. Model. 60, 4030-4046.
- Khayat, E., Klimov, D. K., & Smith, A. K. (2020) Phosphorylation promotes Aβ2535 peptide
aggregation within the DMPC bilayer ACS Chem. Neurosci. 11, 3430-3441.
- Siwy, C., Delfing, B.M., Lockhart, C., Smith, A.K., & Klimov, D. K. (2021)
Partitioning of Aβ peptide fragments into blood-brain barrier
mimetic bilayer J. Phys. Chem. B., 125, 2658-2676.
- McCoy, M.D., Hamre III, J., Klimov, D. K., Jafri, M. S. (2021)
Predicting Genetic Variation Severity Using Machine Learning to
Interpret Molecular Simulations. Biophys. J. 120, 189-204.
- Khayat, E., Lockhart, C., Delfing, B.M., Smith, A. K., & Klimov, D. K.
(2021) Met35 Oxidation Hinders Aβ25-35 Peptide
Aggregation within the DMPC Bilayer. ACS Chem. Neurosci.
12, 3225–3236.
- Bowers, S., Klimov, D. K., Lockhart, C. (2022)
Mechanisms of binding of antimicrobial peptide PGLa to DMPC/DMPG membrane
J. Chem. Inf. Model. doi.org/10.1021/acs.jcim.1c01518.
- Hamre III, J. R., Klimov, D. K., McCoy, M. D., Jafri, M. S. (2022) Machine
learning-based prediction of drug and ligand binding in BCL-2 variants
through molecular dynamics. Computers in Biol. Med. 140, 105060.
- Gurunathan, V., Hamre III, J., Klimov, D. K., Jafri, M. S. (2021) Data
Mining of Molecular Simulations Suggest Key Amino Acid Residues for
Aggregation, Signaling and Drug Action. Biomolecule 11, 1541.
- Vergilio, J., Lockhart, C., and Klimov, D. K. (2022) De novo transmembrane aggregation of Abeta10-40 peptides in anionic lipid bilayer.
J. Chem. Inf. Model. 62, 6228–6241.
- Khayat, E., Delfing, B., Laracuente, X., Olson, A., Lockhart, C., and Klimov, D. K. (2023) Lysine Acetylation Changes the
Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer.
ACS Chem. Neurosci. 14, 494–505.
- Delfing, B. M., Olson, A., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., and Klimov, D. K.
(2023) Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-alpha Receptors Explored with All-Atom Replica
Exchange Molecular Dynamics. J. Phys. Chem. B 127, 3175-3186.
- Lockhart, C., Luo, X., Olson, A., Delfing, B., Laracuente, X., Foreman, K., Paige, M., Kehn-Hall, K., Klimov, D. K. (2023)
Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites? J. Chem. Inf. Model.
63, 4791–4802.
- Delfing, B. M., Laracuente, X. E., Olson, A., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., and Klimov, D. K. (2023) Binding of Viral Nuclear Localization Signal Peptides
to Importin-𝛼 Nuclear Transport Protein. Biophys. J. 122, 3476-3488.
- Bowers, S. R., Lockhart, C., and Klimov, D. K. (2023) Replica Exchange with Hybrid Tempering Efficiently
Samples PGLa Peptide Binding to Anionic Bilayer. J. Chem. Theor. Comput.,
19, 6532–6550.
- Bowers, S. R., Lockhart, C., and Klimov, D. K. (2024) Binding and
dimerization of PGLa peptides in anionic lipid bilayer studied by
replica exchange molecular dynamics. Sci. Reports 14, 4972.
- Delfing, B. M., Laracuente, X. E., Jeffries, W., Luo, X., Olson, A., Foreman, K. W., Petruncio, G., Lee, K. H.,
Paige, M., Kehn-Hall, K., Lockhart, C., Klimov, D. K. (2024) Competitive Binding of Viral Nuclear Localization Signal
Peptide and Inhibitor Ligands to Importin-alpha Nuclear Transport Protein.
J. Chem. Inf. Model. 64, 5262-5272.
- Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Jeffries, W., Foreman, K. W.,
Paige, M., Kehn-Hall, K., Lockhart, C., Klimov, D. K. (2024) Binding of Inhibitors to Nuclear Localization
Signal Peptide from Venezuelan Equine Encephalitis Virus Capsid Protein Explored
with All-Atom Replica Exchange Molecular Dynamics.
ACS Omega (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.
Takeda, T. & Klimov, D. K. (2010) Side chain interactions can impede
amyloid fibril growth: Replica exchange simulations of Abeta peptide
mutant. Biophys. J. 98, 649.
Lockhart, C. & Klimov, D. K. (2013) Binding of FDDNP biomarker to Alzheimer's
disease Abeta peptide. Biophys. J. 104, 360a.
Lockhart, C. & Klimov, D. K. (2015) Binding of Abeta Monomer to DMPC
Bilayer using Isobaric-Isothermal Replica
Exchange Molecular Dynamics. Biophys. J. 108, 64a-65a.
Lockhart, C. and Klimov, D. K. (2017) Probing the Binding of Aβ
Peptides to Lipid Bilayers. Biophys. J. 112, 364a.
Research Presentations:
- Temperature-induced dissociation of amyloid fibrils.
Invited lecture at the 6th congress of the International Society
for Theoretical Chemical Physics, Vancouver, Canada, July 2008.
- Molecular dynamics simulations of force-induced unbinding of Abeta peptides from
amyloid fibrils. Biophysical Society meeting, Long Beach, CA, February 2008.
- Crowded Folding. IBM-SUR meeting,
College of Computer, Mathematical and Physical Sciences, University of
Maryland, January 2002.
- Computer Simulations of Protein Folding. IBM-SUR meeting,
College of Computer, Mathematical and Physical Sciences, University of
Maryland, August 2000.
- 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.
- Viscosity Dependence of the Folding Rates of Proteins. 12th Symposium
of The Protein Society, San Diego, July 1998.
Invited Talks:
- Molecular dynamics simulations of anti-aggregation effect of
ibuprofen. "From Computational Biophysics to Systems Biology" meeting,
Traverse City, MI, 2010.
- Replica exchange simulations of amyloid fibril growth.
American Chemical Society Meeting, Washington, DC, 2009.
- Temperature-induced dissociation of amyloid fibrils.
6th Congress of the International Society for Theoretical Chemical Physics,
Vancouver, Canada, 2008 (invited lecture).
- Molecular dynamics of biomolecules: Basics, Methodology, and Examples. Workshop on
Rigidity, Flexibility, and Motions in Biomolecules, Arizona State University, 2006.
- Blocking amyloid assembly with chemical denaturants.
American Chemical Society Meeting, San Diego, 2005.
- Assembly of Abeta16-22
oligomers: Role of sequence and environment.
Gordon Research Conference on Protein Folding Dynamics, Ventura,
California, January 2004.
- Assembly of Abeta16-22 amyloid peptides
into antiparallel beta-sheets.
Laboratory of Chemical Physics, NIDDK, National Institutes of
Health, April 2003.
- Aggregation of Abeta16-22
amyloid peptides: A molecular dynamics
study. CSCAMM Seminar, University of Maryland, October 2002.
- Stretching Proteins. Department of Physics Colloquia, Drexel University,
February 2002.
- Understanding Mechanical Unfolding of Proteins.
Scientific Computation Seminar, AMSC & CSCAMM, University of
Maryland, October 2001.
- Mechanism of beta-Hairpin Formation. Informal Statistical
Physics Seminar, Institute for Physical Science and Technology,
University of Maryland, April 2000.
- Mechanisms and Kinetics of beta-Hairpin Formation. Thomas
B. Woolf Laboratory, Department of Physiology, JHU Medical School,
January 2000.
- Studying protein folding with the help of simplified
models. Laboratory of Chemical Physics, NIDDK, National Institutes of
Health, February 1999.
- 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).