Artem Zhmurov

Researcher in Biophysics
KTH Royal Institute of Technology

Email:  zhmurov@gmail.com
Google Scholar: http://scholar.google.ru/citations?user=5t0deUYAAAAJ

Projects: 

Education
2014 — PhD in Chemistry, Biochemistry Option, University of Massachusetts at Lowell (advisers: Valeri Barsegov and Kenneth Marx)
2012 — PhD in Mathematics and Physics, Moscow Institute of Physics and Technolody (advisers: Yaroslav Kholodov and Valeri Barsegov)
2006 — M.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technolody (adviser: Alexey Evdokimov)
2004 — B.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technolody (adviser: Andrey Galkin)

Publications:

  1. S. Páll, A. Zhmurov, P. Bauer, M. Abraham, M. Lundborg, A. Gray, B. Hess, E. Lindahl, “Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS”, J. Chem. Phys., 153: 134110 (2020).
  2. K.A. Jansen, A. Zhmurov, B.E. Vos, G. Portale, D.H. Merino, R.I. Litvinov, V. Tutwiler, N.A. Kurniawan, W. Bras, J.W. Weisel, V. Barsegov, G.H. Koenderink, “Molecular packing structure of fibrin fibers resolved by X-ray scattering and molecular modeling”, Soft Matter., 16: 8272-8283 (2020).
  3. M. Abraham, R. Apostolov, J. Barnoud, P. Bauer, C. Blau, A.M.J.J. Bonvin, M. Chavent, J. Chodera, K. Condic-Jurkic, L. Delemotte, H. Grubmüller, R.J. Howard, E.J. Jordan, E. Lindahl, O.H. Samuli Ollila, J. Selent, D.G.A. Smith, P.J. Stansfeld, J.K.S. Tiemann, M. Trellet, C. Woods, and A. Zhmurov, “Sharing data from molecular simulations”, J. Chem. Informat. Model., 59: 4093-4099 (2019).
  4. V.A. Fedorov, P.S. Orekhov, E.G. Kholina, A. Zhmurov, F.I. Ataullakhanov, I.B. Kovalenko, and N.B. Gudimchuk, “Mechanical properties of tubulin intra-and inter-dimer interfaces and their implications for microtubule dynamic instability”, PLoS Comp. Biol., 15: e1007327 (2019).
  5. P.S. Orekhov, I.V. Kirillov, V.A. Fedorov, I.B. Kovalenko, N.B. Gudimchuk, and A. Zhmurov, “Parametrization of the Elastic Network Model Using High-Throughput Parallel Molecular Dynamics Simulations”, Supercomp. Front. Innovat., 6: 19-22 (2019).
  6. R.I. Litvinov, O. Kononova, A. Zhmurov, K.A. Marx, D. Thirumalai, V. Barsegov, and J.W. Weisel,
    “A regulatory element in fibrin triggers tension-activated transition from catch to slip bonds“,
    Proc. Natl. Acad. Sci. USA, 115: 8575-8580 (2018).
  7. A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, J.W. Weisel, and V. Barsegov,
    “Atomic structural models of fibrin oligomers“,
    Structure, 26: 857-868 (2018).
  8. K.A. Minin, A. Zhmurov, K.A. Marx, P.K. Purohit, and V. Barsegov,
    “Dynamic transition from α-helices to β-sheets in polypeptide coiled-coil motifs“,
    J. Am. Chem. Soc., 139: 16168-16177 (2017).
  9. Y.F. Zuev, R.I. Litvinov, A.E. Sitnitsky, B.Z. Idiyatullin, D.R. Bakirova, D.K. Galanakis, A. Zhmurov, V. Barsegov, and J.W. Weisel,
    “Conformational flexibility and self-association of fibrinogen in concentrated solutions,“,
    J. Phys. Chem. B, 121: 7833-7843 (2017).
  10. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova and R.I. Litvinov,
    “An anti-DNA antibody prefers damaged dsDNA over native“,
    J. Biomol. Struct. Dyn., 35: 219-232 (2017).
  11. O. Kononova, A. Zhmurov, K.A. Marx, and V. Barsegov,
    “Mechanics of viruses,“, in Series of Computational Biophysics: Coarse-grained Modeling of Biomolecules, Editors: N. Dokholyan and G. Papoian, Taylor & Francis Publishers (2017).
  12. A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, A.R. Mukhitov, J.W. Weisel, and V. Barsegov,
    “Structural basis of interfacial flexibility in fibrin oligomers“,
    Structure, 24: 1907-1917 (2016).
  13. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov,
    “Essential dynamics of DNA-antibody complexes“,
    BioNanoScience, 6: 543-549 (2016).
  14. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov,
    “Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment“,
    Mol. Biol., 50: 442-451 (2016).
  15. R. Kumar, R.V. Kukreja, L. Li, A. Zhmurov, O. Kononova, S.W. Cai, S.A. Ahmed, V. Barsegov, and B.R. Singh,
    “Botulinum neurotoxin: Unique folding of enzyme domain of the most-poisonous poison“,
    J. Biomol. Struct. Dyn., 32: 804-815 (2014).
  16. R.A. Toubar, A. Zhmurov, V. Barsegov, and K.A. Marx,
    “Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides“,
    J. Biomol. Struct. Dyn., 31: 174-194 (2013).
  17. O. Kononova, R.I. Litvinov, A. Zhmurov, A. Alekseenko, C.H. Cheng, S. Agarwal, K.A. Marx, J.W. Weisel, and V. Barsegov,
    “Molecular mechanisms, thermodynamics, and dissociation kinetics of knob­-hole interactions in fibrin“,
    J. Biol. Chem., 288: 22681­-22692 (2013).
  18. A. Zhmurov, O. Kononova, Y. Kholodov, and V. Barsegov,
    “Force-induced phase transition from α-helices to β-sheets in fibrous proteins“, (in Russian)
    Computational Research and Modelling, 5: 705­725 (2013).
  19. A. Zhmurov, O. Kononova, R.I. Litvinov, R.I. Dima, V. Barsegov, and J.W. Weisel,
    “Mechanical transition from α-helical coiled-coils to β­-sheets in Fibrin(ogen)“,
    J. Am. Chem. Soc., 134: 20396-­20402 (2012).
  20. K. Theisen, A. Zhmurov, M. Newberry, V. Barsegov, and R. Dima,
    “Multiscale modeling of the nanomechanics of microtubule protofilaments“,
    J. Phys. Chem. B, 116: 8545-­8555 (2012).
  21. L. Duan, A. Zhmurov, V. Barsegov, and R.I. Dima,
    “Exploring the mechanical stability of the C2 domains in human synaptotagmin 1“,
    J. Phys. Chem. B, 115: 10133-­10146 (2011).
  22. A. Zhmurov, K. Rybnikov, Y. Kholodov and V. Barsegov,
    “Generation of random numbers on graphics processors: Forced indentation in silico of the bacteriophage HK97“,
    J. Phys. Chem. B, 115: 5278-­5288 (2011).
  23. A. Zhmurov, A.E.X. Brown, R.I. Litvinov, R.I. Dima, J.W. Weisel and V. Barsegov,
    “Mechanism of fibrin(ogen) forced unfolding“,
    Structure, 19: 1615-1624 (2011).
  24. A.A. Zhmurov, I.I. Morozov, Y.A. Kholodov, V.A. Barsegov and A.S. Kholodov,
    “Efficient generators of pseudorandom numbers for molecular modeling on graphics processors“, (in Russian)
    Computational Research and Modelling, 3: 296-­311 (2011).
  25. A.A. Zhmurov, V.A. Barsegov, S.V. Trifonov, Y.A. Kholodov and A.S. Kholodov,
    “Modeling micromechanics on graphics processors using Langevin dynamics“, (in Russian)
    Mathematical Modeling, 23: 133-­156 (2011).
  26. A. Zhmurov, R.I. Dima and V. Barsegov,
    “Order Statistics theory of unfolding of multimeric proteins“,
    Biophys. J., 99: 1959-1968 (2010).
  27. A. Zhmurov, R.I. Dima, Y. Kholodov and V. Barsegov,
    “SOP­-GPU: Accelerating biomolecular simulations in the centisecond timescale on graphics processors“,
    Proteins, 78: 2984-2999 (2010).
  28. E. Bura, A. Zhmurov and V. Barsegov,
    “Nonparametric density estimation and optimal bandwidth selection for protein unfolding and unbinding data“,
    J. Chem. Phys., 130: 015102-015117 (2009).