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Genetic science research
George Mason University

Faculty & Staff Directory

Dmitri Klimov

  • Professor

    Contact Info

    Klimov
    Name
    Dmitri Klimov
    Job Title
    Professor
    Phone Number
    703-993-8395
    Office Number
    Colgan Hall, Room 328B, MSN 5B3

    Affiliations

    Departments

    Education

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

    Current Research

    I have more than 30 years of experience in computer simulations, including all-atom molecular dynamics simulations of biomolecular systems and application of exhaustive sampling algorithms such as replica exchange. Over the years I performed computational studies of amyloid assembly. I used various molecular models and simulation methods to describe aggregation of Abeta peptides, to study binding and anti-aggregation action of non-steroidal anti-inflammatory drugs, and to explore binding of Abeta peptides to various lipid bilayers. Recently, I started work on computational design of antiviral inhibitors using free energy perturbation methods. My work has been funded by NIH through multiple R01, R41, and R56 grants awarded to me as PI. In all, I have published 100+ peer-reviewed papers on biomolecular modeling.

    Teaching Focus

    • BINF 641 "Biomolecular Modelling"
    • BINF 690 "Numerical Methods in Bioinformatics"
    • BINF 740 "Introduction to Biophysics"

     

    Selected Publications

    1. Bowers, S. R., Jeffries, W., Lockhart, C., Klimov, D. K.  (2026) Accelerating replica exchange molecular dynamics: A comparison of hydrogen mass repartitioning and light water models. J. Chem. Theor Comput. 22, 1187–1197.
    2. Jeffries, W., Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Foreman, K. W., Lee, K. H., Petruncio, G., De Benedictis, V., Paige, M., Kehn-Hall, K., Lockhart, C., Klimov, D. K.  (2025) Ligands binding diffusively to protein target act as inhibitors of protein-protein interactions. PLoS Comput Biol. 21, e1013495.
    3. Luo, X., Khayat, E., Bowers, S. R., Delfing, B. M., Lockhart, C., Klimov, D. K.  (2025) Free energy perturbation simulations measure the change in binding affinity of Abeta25-35 peptide to zwitterionic bilayer caused by oxidation. J. Chem. Inf. Model. 65, 12014–12026.
    4. Laracuente, X. E., Delfing, B. M., Luo, X., Olson, A., Jeffries, W., Bowers, S. R., Foreman, K. W., Lee, K. H., Paige, M., Kehn-Hall, K., Lockhart, C., Klimov, D. K.  (2025) Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands. J. Chem. Theor. Comput. 21, 4286–4298.
    5. 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.
    6. 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 9, 40259–40268.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. 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.
    12. 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.
    13. 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.
    14. 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.
    15. 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.

    The full list of publications includes 100+ peer-reviewed articles. 

    Contact Info

    Klimov
    Name
    Dmitri Klimov
    Job Title
    Professor
    Phone Number
    703-993-8395
    Office Number
    Colgan Hall, Room 328B, MSN 5B3

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