Artem Zhmurov

EMail: zhmurov@gmail.com

Phone: +7 965 714 50 31

Research profiles: Google Scholar, Researcher ID, Scopus.

GitLab: @artemzhmurov.

GitHub: @zhmurov.

Social: Twiter, Instagram.

Education

  • 2014, PhD in Chemistry, Biochemistry Option, University of Massachusetts at Lowell (advisers: Valeri Barsegov and Kenneth Marx)

  • 2012, PhD in Mathematics and Physics (к.ф.-м.н.), 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)

Current occupation (on leave of absence since 07.03.2022)

Employment history

  • 01.11.2020 – 31.12.2021: Application Expert / Researcher PDC, KTH Royal Institute of Technology (Stockholm, Sweden)

  • 01.10.2016 – 31.10.2018: Head of the Laboratory of Computer and Mathematical Modeling of Biological Systems, Moscow Institute of Physics and Technology (Dolgoprudny, Russia)

  • 01.09.2017 – 31.08.2018: Docent (Associate Professor), Division of Informatics and Computational Mathematics, Moscow Institute of Physics and Technology (Dolgoprudny, Russia)

  • 01.01.2012 – 31.08.2017: Research/Teaching Associate, Division of Computational Mathematics, Moscow Institute of Physics and Technology (Dolgoprudny, Russia)

  • 01.10.2014 – 01.01.2016: Postdoctoral fellow, Laboratory of Human Physiology, Moscow Institute of Physics and Technology (Dolgoprudny, Russia)

  • 01.09.2006 – 01.06.2010: Research/Teaching Assistant, University of Massachusetts at Lowell (Lowell, MA, USA)

  • 01.11.2005 – 31.12.2006: Web-developer, ESTER Solutions (http://www.estersolutions.ru/en/) (Moscow, Russia)

Teaching

Publications

  1. E. Kliuchnikov, A. Zhmurov, K.A. Marx, A. Mogilner, V. Barsegov “CellDynaMo-stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly”, PLOS Comput. Biol., 18: e1010165 (2022).

  1. N.L. Asquith, C. Duval, A. Zhmurov, S.R. Baker, H.R. McPherson, M.M. Domingues, S.D.A. Connell, V. Barsegov, R.A.S. Ariëns, “Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds”, Blood Advances, 6: 4015-4027 (2022).

  1. E. Kliuchnikov, E. Klyshko, M.S. Kelly, A. Zhmurov, R.I. Dima, K.A. Marx, V. Barsegov, “Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules’ Growth, Catastrophe, Shortening, and Rescue”, Comput. Struct. Biotech. J., 20: 953-974 (2022).

  1. V.A. Fedorov, E.G. Kholina, I.B. Kovalenko, N.B. Gudimchuk, P.S. Orekhov, A.A. Zhmurov, “Update on performance analysis of different computational architectures: Molecular Dynamics in application to protein-protein interactions”, Supercomp. Frontiers Innovat., 7: 62-67 (2020).

  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).

  1. K.A. Jansen, A. Zhmurov, B.E. Vos, G. Portale, D. Hermida-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).

  1. M. Abraham, R. Apostolov, J. Barnoud, P. Bauer, C. Blau, A.M.J.J. Bonvin, M. Chavent, J. Chodera, K. Čondić-Jurkić, L. Delemotte, H. Grubmüller, R.J. Howard, E.J. Jordan, E. Lindahl, O.H.S. Ollila, J. Selent, D.G.A. Smith, P.J. Stansfeld, J.K.S. Tiemann, M. Trellet, C. Woods, A. Zhmurov, “Sharing data from molecular simulations”, J. Chem. Inform. Modeling, 59: 40930-4099 (2019).

  1. V.A. Fedorov, P.S. Orekhov, E.G. Kholina, A.A. Zhmurov, F.I. Ataullakhanov, I.B. Kovalenko, 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).

  1. P.S. Orekhov, I.V. Kirillov, V.A. Fedorov, I.B. Kovalenko, N.B. Gudimchuk, A.A. Zhmurov, “Parametrization of the elastic network model using high-throughput parallel molecular dynamics simulations”, Supercomp. Frontiers Innovat., 6: 19-22 (2019).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov, “Essential dynamics of DNA-antibody complexes”, BioNanoScience, 6: 543-549 (2016).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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: 705-725 (2013).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. 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).

  1. A. Zhmurov, R.I. Dima and V. Barsegov, “Order Statistics theory of unfolding of multimeric proteins”, Biophys. J., 99: 1959-1968 (2010).

  1. 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).

  1. 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).

Funding

2017 – 2020: Grant #17-00-00479 from Russian Foundation for Basic Research, “A multi-scale molecular modeling study of tubulin and its complex with Ndc80”.

2017 – 2019: Grant #17-71-10202 from Russian Science Foundation, “Describing intra- and inter-protein interactions using co-evolution analisys”.

2016 – 2017: 5-100 Young Laboratories Grant from Moscow Institute of Physics and Technology, “Laboratory of Computer and Mathematical Modeling of Biological Systems”.

2015 – 2017: Grant #15-37-21027 from Russian Foundation for Basic Research, “A molecular modeling study of the protein fibers nanomechanics”.

2015 – 2016: Grant #15-01-06721 from Russian Foundation for Basic Research, “Multi-scale molecular modeling study of fibrin oligomers, protofibrils, fibrin fibers and fibrin gel”.

2014 – 2016: Post-doctoral fellowship from Moscow Institute of Physics and Technology, “From structural and molecular origins of fibrin to biomechanics of thrombosis and haemostasis”.

2012 – 2013: Grant #14.A18.21.1520 from Russian Ministry of Education and Science, “Modelling of large biomolecular comlexes using the combination of multi-level description and hybrid computational architecture”.

2012 – 2013: Grant #12-04-31861 from Russian Foundation for Basic Research, “Molecular modeling of DNA using chemically accurate coarse-grained model implemented on the GPU”.