个人简介

2011 Visiting Fellow, Princeton University 2009–present Associate Professor of Chemistry, Carnegie Mellon University 2005 Visiting Researcher, Arizona State University 2003–2009 Assistant Professor of Chemistry, Carnegie Mellon University 2002 Visiting Researcher, Michigan State University 2001–2003 Assistant Professor, Marquette University 1999–2001 Research Associate, University of Pittsburgh 1999–2000 Guest Researcher, National Institute of Standards and Technology (NIST) 1998–1999 Postdoctoral Fellow, University of Tel-Aviv, Israel 1998 Ph.D., Theoretical Chemistry, University of Pittsburgh M.S. Applied Physics and Mathematics, Moscow Physical and Technical Institute, Russia

研究领域

Biophysical/Theoretical & Computational

The approach my research group is taking includes a combination of physics-based computational methodologies, such as molecular dynamics simulations, continuum electrostatics and quantum chemistry. The name of the game in this field is Statistical Mechanics, which is the corner-stone theory for understanding behavior of large molecular ensembles. Huge computational resources are needed to obtain correct statistics in biomolecular modeling, thus, we are active users of the national super-computer facilities sponsored by NSF and NIH, such as for example Pittsburgh Super Computer Center. Another challenge in this field is to develop models of intermolecular interactions that account for the properties of the system on a quantitative level, yet are simple enough computationally to be evaluated effectively. Finding a right balance between the complexity of the model and an effectiveness of it in the simulation — is a significant and yet unsolved intellectual challenge for many biologically important systems and processes. The educational background and interests needed to succeed in this field is physical chemistry, soft condensed matter physics and biophysics.

近期论文

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Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment . J.C. Flores-Canales, M. Vargas-Uribe, A.S. Ladokhin, M. Kurnikova Journal of Membrane Biology, In Press (2015) Crosslinking Constraints and Computational Models as Complementary Tools in Modeling the Extracellular Domain of the Glycine Receptor . Z. Liu, A. Szarecka, M. Yonkunas, K. Speranskiy, M. Kurnikova, M. Cascio PLOS ONE Vol 9, 7, pp e102571 (2014) Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels . N.A. Simakov, M.G. Kurnikova Molecular Based Mathematical Biology Vol 1, pp 151-163 (2013) pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines . I.V. Kurnikov, A. Kyrychenko, J.C. Flores-Canales, M.V. Rodnin, N. Simakov, M. Vargas-Uribe, Y.O. Posokhov, M. Kurnikova, and A.S. Ladokhin J. Molecular Biology Vol 425 (15), pp2752-64 (2013) Stability and Rigidity/Flexibility - Two Sides of the Same Coin? . T.Mamonova, A.Glyakina, O.Galzitskaya, and M.Kurnikova BBA - Proteins and Proteomics, Vol 1834, pp 854-866 (2013) Structural Basis for NERF1 PDZ Domain Binding . T. Mamonova, M. Kurnikova and P. Friedman Biochemistry, Vol 50(14), pp 3110-3120 (2012) Characterizing the Energetic States of the GluR2 Ligand Binding Domain Core-Dimer. . M. Yonkunas and M. Kurnikova Biophys. J., Vol 100(2), pp L5-L7 (2011) Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin . N. Simakov and M. Kurnikova J. Phys. Chem., Vol. 114(46), pp 15180-15190 (2010) Flexibility and Mobility in Mesophilic and Thermophilic Homologous Proteins from Molecular Dynamics and FoldUnfold Method . T. B. Mamonova, A.V. Glyakina, M. G. Kurnikova and O. G. Galzitskaya J. Bioinform. and Comp. Biol., Vol. 8(3), pp 377-394 (2010) An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations . A. Ramanathan, P. K. Agarwal, M. Kurnikova, C. J. Langmead J. Comp. Biol., Vol. 17, pp 309-324 (2010) (invited submission) Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations . A. Ramanathan, P. K. Agarwal, M. Kurnikova, C.J. Langmead 13th Annual International Conference on Research in Computational Molecular (RECOMB), pp 138-154 (2009) Biologically Relevant Motions of HIV-1 Reverse Transcriptase Investigated by Long-scale Molecular Dynamics . A. Ramathan, T. Mamonova, M. Madrid, M. Kurnikova Proceedings of the 3rd Annual TeraGrid ’08 conference.(2008) Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor . K. Speranskiy and M. Kurnikova Prot. Struct. Func. Bioinf., Vol. 76 (2), pp 271-280 (2009) Ion Channels, Computational approaches. . M. Kurnikova in Wiley Encyclopedia of Chemical Biology, ed. T. P. Begley, Wiley, ISBN: 978-0-471-75477-0 (2008) Overexpression and functional characterization of the extracellular domain of the human α1 glycine receptor . Z. Liu, G. Ramanoudjame, R. Fox, V. Jayaraman, M. Kurnikova and M. Cascio Biochemistry, Vol. 47, pp 9803-9810 (2008) Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain . T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry, Vol. 47(42), pp 11077-11085 (2008) Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2. . T. Mamonova, K. Speranskiy, and M. Kurnikova Prot.: Struct., Func., Bioinf., Vol. 73 (3), pp 656-671 (2008) Computational Prediction of Ion Permeation Characteristics in the Clycine Receptor Modifid by Photo-Sensitive Compounds . M. H. Cheng, R. D. Coalson, M. Cascio, and M. Kurnikova J. Comput. Aided Mol. Des., Vol. 22, pp. .563-570 (2008) Replica Exchange Molecular Dynamics Simulation of Poly(alkylthiophenes) . A. Widge, Y. Matsuoka, M. Kurnikova J. Mol. Graph. Model. Vol. 27, pp 34 (2008) Computational Modeling of Poly(alkylthiophene) Conductive Polymer Insertion Into Phospholipid Bilayers . A. Widge, Y. Matsuoka, M. Kurnikova Langmuir, Vol. 23, pp. 10672-10681 (2007)