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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 480bffad8d352f88778e8806d1e84c23
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/employment.rst.txt

@@ -0,0 +1,28 @@
+Employment history
+------------------
+
+- 12.12.2023 - Today: Academic Lead for Software Engineering at `Yandex School of Data Analysis <https://shad.yandex.ru/>`_ (Moscow, Russia) 
+
+- 04.08.2022 -- 07.12.2023: Lead Researcher / Docent (Associate Professor) at `Sirius University <https://siriusuniversity.ru/>`_ (Sochi, Russia)
+
+- 16.03.2021 -- 31.08.2022 (on leave of absence since 07.03.2022): Research Software Engineer and Domain Expert in Life Sciences at `EuroCC National Competence Center Sweden (ENCCS) <https://enccs.se/>`_ (Stockholm, Sweden)
+
+- 01.11.2018 -- 31.08.2022 (on leave of absence since 07.03.2022): Researcher at `Science for Life Laboratory <https://www.scilifelab.se/>`_ (Stockholm, Sweden)
+
+- 01.11.2018 -- 31.08.2022 (on leave of absence since 07.03.2022): Core Developer of `the GROMACS molecular simulation toolkit <https://www.gromacs.org/>`_ (Stockholm, Sweden)
+
+- 01.11.2020 -- 31.12.2021: Application Expert / Researcher PDC, `KTH Royal Institute of Technology <https://www.kth.se/>`_ (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 <https://mipt.ru/>`_ (Dolgoprudny, Russia)
+
+- 01.09.2017 -- 31.08.2018: Docent (Associate Professor), Division of Informatics and Computational Mathematics, `Moscow Institute of Physics and Technology <https://mipt.ru/>`_ (Dolgoprudny, Russia)
+
+- 01.01.2012 -- 31.08.2017: Research/Teaching Associate, Division of Computational Mathematics, `Moscow Institute of Physics and Technology <https://mipt.ru/>`_ (Dolgoprudny, Russia)
+
+- 01.10.2014 -- 01.01.2016: Postdoctoral Fellow, Laboratory of Human Physiology, `Moscow Institute of Physics and Technology <https://mipt.ru/>`_ (Dolgoprudny, Russia)
+
+- 01.09.2006 -- 01.06.2010: Research/Teaching Assistant, `University of Massachusetts at Lowell <https://www.uml.edu/>`_ (Lowell, MA, USA)
+
+- 01.11.2005 -- 31.12.2006: Web-developer, `ESTER Solutions <http://www.estersolutions.ru/en/>`_ (Moscow, Russia)
+
+

_sources/funding.rst.txt

@@ -0,0 +1,18 @@
+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".

_sources/index.rst.txt

@@ -0,0 +1,42 @@
+
+Artem Zhmurov
+=============
+
+EMail: zhmurov@gmail.com
+
+This CV: `https://artemzhmurov.gitlab.io/webpage/ <https://artemzhmurov.gitlab.io/webpage/>`_ or `https://zhmurov.github.io/webpage/ <https://zhmurov.github.io/webpage/>`_
+
+Research profiles:
+`Google Scholar <http://scholar.google.ru/citations?user=5t0deUYAAAAJ>`_, 
+`Researcher ID <http://www.researcherid.com/rid/F-4455-2012>`_, 
+`Scopus <http://www.scopus.com/authid/detail.url?authorId=36524431100>`_.
+
+GitLab:
+`@artemzhmurov <https://gitlab.com/artemzhmurov>`_.
+
+GitHub:
+`@zhmurov <https://github.com/zhmurov>`_.
+
+Education
+---------
+
+- 2014, PhD in Chemistry, Biochemistry Option, 
+  University of Massachusetts at Lowell 
+  (advisers: `Valeri Barsegov <http://faculty.uml.edu/vbarsegov/>`_ and 
+  `Kenneth Marx <http://www.uml.edu/Sciences/chemistry/faculty/marx-kenneth.aspx>`_)
+
+- 2012, PhD in Mathematics and Physics (к.ф.-м.н.),
+  Moscow Institute of Physics and Technolody
+  (advisers: Yaroslav Kholodov and `Valeri Barsegov <http://faculty.uml.edu/vbarsegov/>`_)
+
+- 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)
+
+.. include:: employment.rst
+
+.. include:: teaching.rst
+
+.. include:: publications.rst
+
+.. include:: funding.rst

_sources/publications.rst.txt

@@ -0,0 +1,130 @@
+Publications
+------------
+
+32. 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 <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010165>`_",
+    *PLOS Comput. Biol.*, **18:** e1010165 (2022).
+
+31. 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 <https://www.sciencedirect.com/science/article/pii/S2473952922003317>`_",
+    *Blood Advances*, **6:** 4015-4027 (2022).
+
+30. 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 <https://www.sciencedirect.com/science/article/pii/S2001037022000356>`_",
+    *Comput. Struct. Biotech. J.*, **20:** 953-974 (2022).
+
+29. 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 <https://superfri.org/superfri/article/view/337>`_",
+    *Supercomp. Frontiers Innovat.*, **7:** 62-67 (2020).
+
+28. 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 <https://aip.scitation.org/doi/full/10.1063/5.0018516>`_",
+    *J. Chem. Phys.*, **153:** 134110 (2020).
+
+27. 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 <https://pubs.rsc.org/en/content/articlehtml/2020/sm/d0sm00916d>`_",
+    *Soft Matter*, **16:** 8272-8283 (2020).
+
+26. 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 <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00665>`_",
+    *J. Chem. Inform. Modeling*, **59:** 40930-4099 (2019).
+
+25. 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 <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007327>`_",
+    *PLoS Comp. Biol.*, **15:** e1007327 (2019).
+
+24. 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 <https://superfri.org/superfri/article/view/249>`_",
+    *Supercomp. Frontiers Innovat.*, **6:** 19-22 (2019).
+
+23. 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 <http://www.pnas.org/content/115/34/8575>`_",
+    *Proc. Natl. Acad. Sci. USA*, **115:** 8575-8580 (2018).
+
+22. A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, J.W. Weisel, and V. Barsegov,
+    "`Atomic structural models of fibrin oligomers <https://www.cell.com/structure/fulltext/S0969-2126(18)30130-8>`_",
+    *Structure*, **26:** 857-868 (2018).
+
+21. 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 <http://pubs.acs.org/doi/10.1021/jacs.7b06883>`_",
+    *J. Am. Chem. Soc.*, **139:** 16168-16177 (2017).
+
+20. 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 <http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b05654>`_",
+    *J. Phys. Chem. B*, **121:** 7833-7843 (2017).
+
+19. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova and R.I. Litvinov,
+    "`An anti-DNA antibody prefers damaged dsDNA over native <http://www.tandfonline.com/doi/abs/10.1080/07391102.2015.1128979>`_",
+    *J. Biomol. Struct. Dyn.*, **35:** 219-232 (2017).
+
+18. O. Kononova, A. Zhmurov, K.A. Marx, and V. Barsegov, 
+    "`Mechanics of viruses, <https://www.crcpress.com/Coarse-Grained-Modeling-of-Biomolecules/Papoian/p/book/9781466576063>`_",
+    in Series of Computational Biophysics: Coarse-grained Modeling of Biomolecules, Editors: N. Dokholyan and G. Papoian, Taylor & Francis Publishers (2017).
+
+17. 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 <http://www.cell.com/structure/pdf/S0969-2126(16)30242-8.pdf>`_", 
+    *Structure*, **24:** 1907-1917 (2016).
+
+16. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov, 
+    "`Essential dynamics of DNA-antibody complexes <http://link.springer.com/article/10.1007/s12668-016-0284-z>`_", 
+    *BioNanoScience*, **6:** 543-549 (2016).
+
+15. 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 <https://link.springer.com/article/10.1134%2FS0026893316020023>`_",
+    *Mol. Biol.*, **50:** 442-451 (2016).
+
+14. 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 <http://www.tandfonline.com/doi/abs/10.1080/07391102.2013.791878>`_",
+    *J. Biomol. Struct. Dyn.*, **32:** 804-815 (2014).
+
+13. 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 <http://www.tandfonline.com/doi/abs/10.1080/07391102.2012.698381>`_",
+    *J. Biomol. Struct. Dyn.*, **31:** 174-194 (2013).
+
+12. 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 <http://www.jbc.org/content/288/31/22681.long>`_", 
+    *J. Biol. Chem.*, **288:** 22681-22692 (2013).
+
+11. A. Zhmurov, O. Kononova, Y. Kholodov, and V. Barsegov, 
+    "`Force-induced phase transition from α-helices to β-sheets in fibrous proteins <http://crm.ics.org.ru/journal/article/2077/>`_", (in Russian) 
+    *Computational Research and Modelling*, **5:** 705-725 (2013).
+
+10. 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) <http://pubs.acs.org/doi/abs/10.1021/ja3076428>`_", 
+    *J. Am. Chem. Soc.*, **134:** 20396-20402 (2012).
+
+9.  K. Theisen, A. Zhmurov, M. Newberry, V. Barsegov, and R. Dima, 
+    "`Multiscale modeling of the nanomechanics of microtubule protofilaments <http://pubs.acs.org/doi/abs/10.1021/jp212608f>`_", 
+    *J. Phys. Chem. B*, **116:** 8545-8555 (2012).
+
+8.  L. Duan, A. Zhmurov, V. Barsegov, and R.I. Dima, 
+    "`Exploring the mechanical stability of the C2 domains in human synaptotagmin 1 <http://pubs.acs.org/doi/abs/10.1021/jp2025945>`_", 
+    *J. Phys. Chem. B*, **115:** 10133-10146 (2011).
+
+7.  A. Zhmurov, K. Rybnikov, Y. Kholodov and V. Barsegov, 
+    "`Generation of random numbers on graphics processors: Forced indentation *in silico* of the bacteriophage HK97 <http://pubs.acs.org/doi/abs/10.1021/jp109079t>`_", 
+    *J. Phys. Chem. B*, **115:** 5278-5288 (2011).
+
+6.  A. Zhmurov, A.E.X. Brown, R.I. Litvinov, R.I. Dima, J.W. Weisel and V. Barsegov, 
+    "`Mechanism of fibrin(ogen) forced unfolding <http://www.cell.com/structure/abstract/S0969-2126(11)00311-X>`_", 
+    *Structure*, **19:** 1615-1624 (2011).
+
+5.  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 <http://crm.ics.org.ru/journal/article/1809/>`_", (in Russian)
+    *Computational Research and Modelling*, **3:** 296-311 (2011).
+
+4.  A.A. Zhmurov, V.A. Barsegov, S.V. Trifonov, Y.A. Kholodov and A.S. Kholodov, 
+    "`Modeling micromechanics on graphics processors using Langevin dynamics <http://www.mathnet.ru/php/archive.phtml?wshow=paper&jrnid=mm&paperid=3170>`_", (in Russian)
+    *Mathematical Modeling*, **23:** 133-156 (2011).
+
+3.  A. Zhmurov, R.I. Dima and V. Barsegov, 
+    "`Order Statistics theory of unfolding of multimeric proteins <http://www.cell.com/biophysj/abstract/S0006-3495(10)00857-X>`_", 
+    *Biophys. J.*, **99:** 1959-1968 (2010).
+
+2.  A. Zhmurov, R.I. Dima, Y. Kholodov and V. Barsegov, 
+    "`SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale on graphics processors <http://onlinelibrary.wiley.com/doi/10.1002/prot.22824/abstract>`_", 
+    *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 <http://scitation.aip.org/content/aip/journal/jcp/130/1/10.1063/1.3050095>`_", 
+    *J. Chem. Phys.*, **130:** 015102-015117 (2009).

_sources/teaching.rst.txt

@@ -0,0 +1,12 @@
+Teaching
+--------
+
+- `Molecular simulations (MIPT, Sirius) <https://zhmurov.github.io/mdcourse/>`_.
+
+- `CUDA training <https://enccs.github.io/cuda/>`_.
+
+- `GROMACS GPU performance workshop <https://enccs.github.io/gromacs-gpu-performance/>`_.
+
+- `GROMACS tutorials <https://tutorials.gromacs.org/>`_.
+
+- `Computational mathematics (MIPT) <teaching/compmath/index.html>`_.

_sources/teaching/compmath/index.rst.txt

@@ -0,0 +1,32 @@
+Вычислительная математика
+-------------------------
+
+Контрольные прошлых лет
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Осенний семестр, промежуточные:
+`2012(docx) <files/exams/2012-fall-1.docx>`_,
+`2013 <files/exams/2013-fall-1.pdf>`_,
+`2014 <files/exams/2014-fall-1.pdf>`_,
+`2016 <files/exams/2016-fall-1.pdf>`_,
+`2017 <files/exams/2017-fall-1.pdf>`_.
+
+Осенний семестр, итоговые:
+`2012(docx) <files/compmath/exams/2012-fall-2.docx>`_,
+`2013 <files/compmath/exams/2013-fall-2.pdf>`_,
+`2014 <files/compmath/exams/2014-fall-2.pdf>`_,
+`2015 <files/compmath/exams/2015-fall.pdf>`_,
+`2016 <files/compmath/exams/2016-fall-2.pdf>`_.
+
+Весенний семестр, промежуточные:
+`2013 <files/compmath/exams/2013-spring-1.pdf>`_,
+`2014(docx) <files/compmath/exams/2014-spring-1.docx>`_,
+`2015 <files/compmath/exams/2015-spring-1.pdf>`_,
+`2016 <files/compmath/exams/2016-spring-1.pdf>`_,
+`2017 <files/compmath/exams/2017-spring-1.pdf>`_.
+
+Весенний семестр, итоговые:
+`2014 <files/compmath/exams/2014-spring-2.pdf>`_,
+`2015 <files/compmath/exams/2015-spring-2.pdf>`_,
+`2016 <files/compmath/exams/2016-spring-2.pdf>`_,
+`2017 <files/compmath/exams/2017-spring-2.pdf>`_.