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:
- 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).
- 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).
- 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).
- 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).
- 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).
- 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). - 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). - 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). - 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). - 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). - 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). - 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). - N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov,
“Essential dynamics of DNA-antibody complexes“,
BioNanoScience, 6: 543-549 (2016). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - 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). - A. Zhmurov, R.I. Dima and V. Barsegov,
“Order Statistics theory of unfolding of multimeric proteins“,
Biophys. J., 99: 1959-1968 (2010). - 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). - 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).
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