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Scholarly Interest Report
         
Anatoly B. Kolomeisky
Professor
Professor of Chemistry and Professor of Chemical and Biomolecular Engineering
 
e-mail:tolya@rice.edu
 
  • M.S. Chemistry (1991) Moscow State University, Moscow, Russia
  • M.S. Chemistry (1996) Cornell University, Ithaca, NY
  • Ph.D. Chemistry (1998) Cornell University, Ithaca, NY
 
Primary Department
   Department of Chemistry
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Department Affiliations
 
  • Center for Theoretical Biological Physics
  • Department of Chemical and Biomolecular Engineering
  • Institute of Biosciences and Bioengineering
  • Rice Quantum Institute
  •  
    Websites
     Anatoly Kolomeisky
     Kolomeisky Research Group
     Kolomeisky Research Group
     
    Research Areas
     Theoretical Physical Chemistry. Theoretical Biophysics. Statistical Mechanics of Complex Systems. Biological Transport. Thermodynamics of Electrolytes. Random Walks. Theory of Hydrophobicity.
     

    Kolomeisky Current Research

     

    Theoretical investigation of complex chemical and biophysical processes using the methods of statistical mechanics. Specific projects: 1) motor proteins; 2) cytoskeleton filaments; 3) polymer translocation through nanopores; 4) facilitated diffusion; 5) transport through membrane pores; 6) multi-partical non-equilibrium dynamics; 6) protein nucleation and crystallizations; 7) viscosity in biological systems, 8) protein-DNA interactions, 9) modeling of dynamics of nanocars.

     
    Teaching Areas
     Physical Chemistry
     
    Selected Publications
     Refereed articles
     

    Sequence Heterogeneity Accelerates Protein Search for Targets on DNA, (A.A. Shvets and A.B.K.), submitted to J. Chem. Phys. (2015).

     
     

    The Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA
    (A.A. Shvets, M. Kochugaeva and A.B.K.), to appear in J. Phys. Chem. B (2015).

     
     

    Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy,
    (A.B.K.), Biophys. J. 109, 459-460 (2015).

     
     

    Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015).

     
     

    Development of Morphogen Gradients with Spatially Varying Degradation Rates, (B. Bozorgui, H. Teimouri and A.B.K.), submitted to J. Phys. Chem. B (2015).

     
     

    Theoretical Analysis of Degradation Mechanisms in the Formation of Morphogen Gradients,
    (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 143, 025102 (2015).

     
     

    Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors,
    (D. Celis-Garza, H. Teimouri and A.B.K.), J. Stat. Mech. P04013 (2015).

     
     

    The Role of Source Delocalization in the Development of Morphogen Gradients, (H. Teimouri and A.B.K.), Phys. Biol. 12, 026006 (2015).

     
     

    Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors, (H. Teimouri, A.B.K. and K. Mehrabiani), J. Phys. A 48, 065001 (2015).

     
     

    Dynamics of the Protein Search for Targets on DNA in the Presence of Traps, (M. Lange, M. Kochugaeva and A.B. K.), J. Phys. Chem. B 119, 12410-12416 (2015).

     
     

    Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.),
    J. Chem. Phys. 143, 105102 (2015).

     
     

    Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanisms and Kinetic Scheme, (M.G. Khrenova, B.L. Grigorenko, A.B.K., and A.V. Nemukhin), J. Phys. Chem. B 119, 12838-12845 (2015).

     
     

    Collective Dynamics of Cytoskeletal Processive Motor Proteins, (R.T. McLaughlin, M.R. Diehl and A.B. Kolomeisky), Soft Matter, (2015).

     
     

    Theoretical Analysis of Selectivity Mechanisms in Molecular Transport Through Channels and Nanopores, (S. Agah, M. Pasquali and A.B.K.), J. Chem. Phys. 142, 044705 (2015).

     
     

    Unimolecular Submersible Nanomachines. Synthesis, Actuation, and Monitoring (V. Garcia-Lopez, P.-T. Chiang, F. Chen, G. Ruan, A.A. Marti, A.B.K., G. Wang and J.M. Tour), to appear in Nano Lett. (2015).

     
     

    The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies, (X. Li and A.B.K.), J. Phys. Chem. B 119, 4653 (2015).

     
     

    Positive and Negative Impacts of Nonspecific Sites During Target Location by a Sequence-Specific DNA-binding Protein: Origin of the Optimal Search at Physiological Ionic Strength, A. Esadze, A.B. Kolomeisky and J. Iwahara, Nucl. Acids Res. 42, 7039-7046 (2014).

     
     

    Unveling the Hidden Structure of Complex Stochastic Biochemical Networks, A. Valleriani, X. Li and A.B. Kolomeisky, J. Chem. Phys. 140, 064101 (2014). 

     
     

    A Simple Kinetic Model for Singlet Fission: A Role of Electronic and Entropic Contributions to Macroscopic Rates, A.B. Kolomeisky, X. Feng and A.I. Krylov, J. Phys. Chem. C 118, 5188-5195 (2014). 

     
     

    Development of Morphogen Gradient: The Role of Dimension and Discreteness, H. Teimouri and A.B. Kolomeisky, J. Chem. Phys. 140, 085102 (2014).

     
     

     Dissecting the Effect of Morphology on the Rates of Singlet Fission: Insights from Theory, X. Feng, A.B. Kolomeisky and A.I. Krylov, J. Phys. Chem. C, 118, 19607-19617 (2014).

     
     

    A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins, X. Li and A.B. Kolomeisky, J. Phys. Chem. B 118, 2966-2972 (2014).

     
     

    Pathway Structure Determination of Complex Stochastic Networks with Non-Exponential Dwell Times, X. Li, A.B. Kolomeisky and A. Valleriani, J. Chem. Phys. 140, 184102 (2014).

     
     

    Stochastic Kinetics on Networks: When Slow is Fast, X. Li, A.B. Kolomeisky and A. Valleriani, J. Phys. Chem. B, 118, 10419-10425 (2014).

     
     

    Bulk Induced Phase Transitions in Driven Diffusive Systems, Y.-Q. Wang, R. Jiang, A.B. Kolomeisky and M.-B. Hu, Sci. Rep. 4, 5459 (2014).  

     
     

    A. B. Kolomeisky "Mechanisms of Protein Binding to DNA: Statistical Interactions are Important." Biophys. J., 104 (2013) : 966-967.

     
     

    A. B. Kolomeisky "Motor Proteins and Molecular Motors: How to Operate Machines at the Nanoscale." J. Phys.: Condens. Matter, 25 (2013) : 463101.

     
     

    A. B. Kolomeisky "Physics of Protein Motility and Motor Proteins. ." J. Phys.: Condens. Matter, 25 (2013) : 370301.

     
     

    A. Veksler and A. B. Kolomeisky "Speed-Selectivity Paradox in the Protein Search for Targets on DNA: Is It Real or Not?." J. Phys. Chem. B, 117 (2013) : 12695-12701.

     
     

    B. Farrell, F. Qian, A. B. Kolomeisky, B. Anwari and W. E. Brownell "Measuring Forces at the Leading Edge: A Force Assay for Cell Motility." Integr. Biol., 5 (2013) : 204-214.

     
     

    D. Panja, G. T. Barkema and A. B. Kolomeisky "Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation." J. Phys.: Condens. Matter, 25 (2013) : 413101.

     
     

    H. Teimouri and A. B. Kolomeisky "All-Time Dynamics in Complex Continuous-Time Random Walk Models." J. Chem. Phys., 138 (2013) : 084110.

     
     

    K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky "Analysis of Cooperative Behavior in Multiple Kinesins Motor Protein Transport by Varying Structural and Chemical Properties ." Cell. Mol. Bioeng., 6 (2013) : 38-47.

     
     

    P.-L. E. Chu, L.-Y. Wang, S. Khatua, A. B. Kolomeisky, S. Link and J. M. Tour "Synthesis and Single-Molecule Imaging of Highly Mobile Adamantane-Wheeled Nanocars." ACS Nano, 7 (2013) : 35-41.

     
     

    R. Jiang, Y.-Q. Wang, A. B. Kolomeisky, W. Huang, M.-B. Hu and Q.-S. Wu "Phase Diagram Structures in a Periodic One-Dimensional Exclusion Process." Phys. Rev. E, 87 (2013) : 012107.

     
     

    X. Banquy, G. W. Greene, B. Zappone, A. B. Kolomisky and J. N. Israelachvili "Dynamics of Force Generation by Confined Actin Filaments." Soft Matter, 9 (2013) : 2389-2392.

     
     

    X. Li and A. B. Kolomeisky "Mechanisms and Topology Determination of Complex Chemical and Biological Network Systems from First-Passage Theoretical Approach." J. Chem. Phys., 139 (2013) : 144106.

     
     

    X. Li and A. B. Kolomeisky "Theoretical Analysis of Microtubules Dynamics Using a Physical-Chemical Description of Hydrolysis." J. Phys. Chem. B, 117 (2013) : 9217-9223.

     
     

    A. B. Kolomeisky and A. Veksler "How to Accelerate Protein Search on DNA: Location and Dissociation." J. Chem. Phys., 136 (2012) : 12501.

     
     

    A. B. Kolomeisky and D. Lacoste "Random Hydrolysis Controls the Dynamic Instability of Microtubules." Biophys. J., 102 (2012) : 1274-1283.

     
     

    A. V. Akimov and A. B. Kolomeisky "Unidirectional Rolling of Nanocars Induced by Electric Field." J. Phys. Chem. C, 116 (2012) : 22595-22601.

     
     

    A. V. Akimov, C. Williams and A. B. Kolomeisky "Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars." J. Phys. Chem. C, 116 (2012) : 13816-13826.

     
     

    K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky "How the Interplay between Mechanical and Nonmechanical Interactions Affects Multiple Kinesin Dynamics." J. Phys. Chem. B, 116 (2012) : 8846-8855.

     
     

    A. B. Kolomeisky "Formation of a Morphogen Gradient: Acceleration by Degradation." J. Phys. Chem. Lett., 2 (2011) : 1502-1505.

     
     

    A. B. Kolomeisky "Michaelis-Menten Relation for Complex Enzymatic Networks." J. Chem. Phys., 134 (2011) : 155101.

     
     

    A. B. Kolomeisky "Physics of Protein-DNA Interactions: Mechanisms of Facilitated Diffusion." Phys. Chem. Chem. Phys., 13 (2011) : 2088-2095.

     
     

    A. B. Kolomeisky and K. Uppulury "How Interactions Control Molecular Transport in Channels." J. Stat. Phys., 142 (2011) : 1268-1276.

     
     

    A. V. Akimov and A. B. Kolomeisky "Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions and Molecular Sizes." J. Phys. Chem. C, 115 (2011) : 125-131.

     
     

    A. V. Akimov and A. B. Kolomeisky "Molecular Dynamics Study of Crystalline Molecular Gyroscopes." J. Phys. Chem. C, 115 (2011) : 13584-13591.

     
     

    A. V. Akimov and A. B. Kolomeisky "Recursive Taylor Series Expansion Method for Rigid-Body Molecular Dynamics." J. Theor. Chem. Comp., 7 (2011) : 3062-3071.

     
     

    I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin and A.B.Kolomeisky "On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface." J. Phys. Chem. C, 115 (2011) : 108-111.

     
     

    J. H. P. Schulz, A. B. Kolomeisky and E. Frey "Current Reversal ad Exclusion Processes with History-Dependent Random Walks." Europhys. Lett., 95 (2011) : 30004.

     
     

    J. W. Driver, D. K. Jamison, K. Uppulury, A. R. Rogers, A. B. Kolomeisky and M. R. Diehl "Productive Cooperation among Processive Motors Depends Inversely on Their Mechanochemical Efficiency." Biophys. J., 101 (2011) : 386-395.

     
     

    R. Wang, A. B. Kolomeisky, and M. Liu "Spontaneous Symmetry Breaking on a Multiple-Channel Hollow Cylinder." Phys. Rev. A, 375 (2011) : 318-323.

     
     

    A. Mohan, A. B. Kolomeisky and M. Pasquali "Polymer Translocation through Pores with Complex Geometry." J. Chem. Phys., 133 (2010) : 024902.

     
     

    J. Lin, A.B.Kolomeisky and A. Meller, "Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel,"   Phys. Rev. Lett. 104, 158101 (2010).

     
     

    J. W. Driver, A. R. Rogers, D. K. Jamison, R. K. Das, A. B. Kolomeisky and M. R. Diehl "Coupling between Motor Proteins Determines Dynamic Behaviors of Motor Protein Assemblies." Phys. Chem. Chem. Phys., 12 (2010) : 10398-10405.

     
     

    M.N. Artyomov, A.Y. Morozov and A.B.Kolomeisky, "Dynamics of Molecular Motors in Reversible Burnt-Bridge Models,"  Condens. Matter Phys. 13, 23801 (2010).

     
     

    R.K. Das and A.B. Kolomeisky, "Facilitated Search of Proteins on DNA: Correlations are Important," Phys. Chem.-Chem. Phys. 12, 2999-3004 (2010).

     
     

    S. S. Konyukhov, I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin, A. V. Akimov and A. B. Kolomeisky "Rigid-Body Molecular Dynamics of the Fullerene-Based Nanocars on the Metallic Surfaces." J. Chem. Theory Comput., 6 (2010) : 2581-2590.

     
     

    A. B. Kolomeisky "Continuous-Time Random Walks at All Times." J. Chem. Phys., 131 (2009) : 23414.

     
     

    C. H. Sykes, A. Akimov and A. B. Kolomeisky "Dynamics of Thioethers Molecular Rotors: Effect of Surface Interactions and Chain Flexibility ." J. Phys. Chem. C, 113 (2009) : 10913-10920.

     
     

    D. Panja, G. T. Barkema and A. B. Kolomeisky "Non-Equilibrium Dynamics of Single Polymer Adsorption to Solid Surfaces." J. Phys. Condens. Matter, 21 (2009) : 242101.

     
     

    R. K. Das and A. B. Kolomeisky "Dynamic Properties of Molecular Motors in the Divided-Pathway Model." Phys. Chem. Chem. Phys., 11 (2009) : 4815-4820.

     
     

    S.Khatua, J.M. Guerrero, K. Claytor, G. Vives, A.B. Kolomeisky, J.M. Tour and S. Link "Micrometer-Scale Translation and Monitoring of Individual Nanocars on Glass ." ACS Nano, 3 (2009) : 351-356.

     
     

    A. Akimov, A. V. Nemukhin, A. Moskovsky, A. B. Kolomeisky, J. M. Tour "Molecular Dynamics of Surface-Moving Thermally Driven Nanocars." J. Chem. Theor. Comp., 4 (2008) : 652-656.

     
     

    A. B. Kolomeisky "How Proteins Translate Through Pores: Memory is Important." Biophys. J., 94 (2008) : 5547-1548.

     
     

    A. B. Kolomeisky, S. Kotsev "Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport across Membrane Channels." J. Chem. Phys., 128 (2008) : 085101-1:185101-6.

     
     

    A. G. Cherstvy, A. B. Kolomeisky, A. A. Kornyshev "Protein-DNA Interactions: Reaching and Recognizing the Targets." J. Phys. Chem. B, 112 (2008) : 4741-4750.

     
     

    A. Mohan, A. B. Kolomeisky, M. Pasquali "Effect of Charge Distribution on the Translocation of an Imhomogeneously Charged Polymer Through a Nanopore." J. Chem. Phys., 128 (2008) : 125104-1:125104-7.

     
     

    A.B. Kolomeisky "How Proteins Translocate Through Pores: Memory is Important." Biophys. J., 94: 1547-1548.

     
     

    D.A. Tsyboulski, S. M. Bachilo, A. B. Kolomeisky, R. B. Weisman "Translational and Rotational Dynamics of Individual Single-Walled Carbon Nanotubes in Aqueous Suspensions." ACS Nano, 2 (2008) : 1770-1776.

     
     

    K. Tsekouras and A. B. Kolomeisky "Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes." J. Phys. A: Math Theor., 41 (2008) : 095002.

     
     

    M. N. Artyomov, A. Y. Morozov, A. B. Kolomeisky "Molecular Motors Interacting with Their Own Tracks." Phys. Rev. E, 77 (2008) : 040901(R).

     
     

    R. K. Das, A. B. Kolomeisky "Interaction between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins." Phys. Rev. E, 77 (2008) : 061912.

     
     

    R. K. Das, A. B. Kolomeisky "Spatial Fluctuations Affect the Dynamics of Motor Proteins." J. Phys. Chem. B, 112 (2008) : 11112-11121.

     
     

    A. Morozov, E. Pronina, A.B.Kolomeisky and M.N. Artyomov "Solutions of Burnt-Bridge Model for Molecular Motors Transport." Phys. Rev. E, 75 (2007) : 031910.

     
     

    A.B. Kolomeisky "Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry." Phys. Rev. Lett., 98 (2007) : 048105.

     
     

    A.B. Kolomeisky and S. Kotsev "Translocation of Polymers with Folded Configurations across Nanopores." J. Chem. Phys., 127 (2007) : 185103.

     
     

    B. Hornblower, A. Combs, R. Whitaker, A.B.Kolomeisky, A. Meller and M. Akeson "Direct Measurement of the Dissociation Kinetics of Escherichia coli Exonuclease I from Single Stranded DNA Using a Nanopore." Nat. Methods, 4 (2007) : 315-317.

     
     

    E.Pronina and A.B.Kolomeisky "Spontaneous Symmetry Breaking in Two-Channel Asymmetric Exclusion Processes with Narrow Entrances." J. Phys. A: Math. Theor., 40 (2007) : 2275-2286.

     
     

    M.N. Artyomov, A. Y. Morozov, E. Pronina and A.B.Kolomeisky "Dynamic Properties of Molecular Motors in Burnt-Bridge Models." J. Stat. Mech. (2007) : P08002.

     
     

    E. B. Stukalin and A. B. Kolomeisky "ATP Hydrolysis Stimulates Large Length Fluctuations in Single Actin Filaments." Biophys. J., 90 (2006) : 2673-2685.

     
     

    E. B. Stukalin and A. B. Kolomeisky "Dynamic transitions in coupled motor proteins." Phys. Rev. E, 73 (2006) : 031922.

     
     

    E. B. Stukalin and A. B. Kolomeisky "Transport of Single Molecules Along the Periodic Parallel Lattices with Coupling." J. Chem. Phys., 124 (2006) : 204901.

     
     

    E. Pronina and A. B. Kolomeisky "Asymmetric coupling in two-channel simple exclusion processes." Physica A, 372 (2006) : 12-21.

     
     

    S. Kotsev and A. B. Kolomeisky "Effect of orientation in translocation of polymers through nanopores." J. Chem. Phys., 125 (2006) : 084906.

     
     

    S. Matysiak, M. Montesi, M. Pasquali, A. B. Kolomeisky and C. Clementi "Dynamics of Polymer Translocation Through Nanopore: Theory Meets Experiments." Phys. Rev. Lett., 96 (2006) : 118103.

     
     

    A. B. Kolomeisky and H. Phillips III "Dynamic Properties of Motor Proteins with Two Subunits." J. Phys. Cond. Mat., 17 (2005) : S3887-S3899.

     
     

    A. B. Kolomeisky, E. B. Stukalin and A. A. Popov "Understanding Mechanochemical Coupling in Kinesins Using First-Passage Time Processes." Phys. Rev. E, 71 (2005) : 031902.

     
     

    D. Kashchiev, P. Vekilov and A. B. Kolomeisky "Kinetics of Two-Step Nucleation of Crystals." J. Chem. Phys., 22 (2005) : 244706.

     
     

    E. B. Stukalin and A. B. Kolomeisky "Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach." J. Chem. Phys., 122 (2005) : 104903/1-104903/9.

     
     

    E. B. Stukalin, H. Phillips III and A. B. Kolomeisky "Coupling of Two Motor Proteins: a New Motor Can Move Faster." Phys. Rev. Lett., 94 (2005) : 238101.

     
     

    E. Pronina and A. B. Kolomeisky "Theoretical Investigation of Totally Asymmetric Simple Exclusion Processes on Lattices with Junctions." J. Stat. Mech. (2005) : P07010.

     
     

    G. Lakatos, T. Chou and A. Kolomeisky "Steady-State Properties of a Totally Asymmetric Exclusion Process with Periodic Structure Rates." Phys. Rev. E, 71 (2005) : 011103.

     
     

    J. Son, G. Orkoulas and A. B. Kolomeisky "Monte Carlo Simulations of Rigid Biopolymer Growth Processes." J. Chem. Phys., 123 (2005) : 124902.

     
     

    M. Arya, A. B. Kolomeisky, G. M. Romo, M. A. Cruz, J. A. Lopez and B. Anvari "Dynamic Force Spectroscopy of Glycoprotein Ib-IX Mutants and von Willebrand Factor." Biophys. J., 88 (2005) : 4391-4401.

     
     

    M. N. Artyomov and A. B. Kolomeisky "Thermodynamics and Phase Transitions of Electrolytes on Lattices with Different Discretization Parameters." Mol. Phys., 103 (2005) : 2863-2872.

     
     

    W. Pan, A. B. Kolomeisky, P. G. Vekilov "Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach." J. Chem. Phys., 122 (2005) : 174905/1-174905/7.

     
     

    A. B. Kolomeisky and A. Drzewinski "Polymers Dynamics in Repton Model at Large Fields." J. Chem. Phys., 120 (2004) : 7784-7791.

     
     

    E. B. Stukalin and A. B. Kolomeisky "Simple Growth Models of Rigid Multifilament Biopolymers." J. Chem. Phys., 121 (2004) : 1097-1104.

     
     

    E. Pronina and A. B. Kolomeisky "Two-Channel Totally Asymmetric Exclusion Processes." J. Phys. A: Math. Gen., 37 (2004) : 9907-9918.

     
     

    L. B. Shaw, A. B. Kolomeisky and K. H. Lee "Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects." J. Phys. A: Math. Gen., 37 (2004) : 2105-2113.

     
     

    A. B. Kolomeisky and M. E. Fisher "A Simple Kinetic Model Describes the Processivity of Myosin V." Biophys. J., 84 (2003) : 1-9.

     
     

    E. Slonkina and A. B. Kolomeisky "Polymer translocation through a long nanopore." J. Chem. Phys., 118 (2003) : 7112-7118.

     
     

    M. N. Artyomov, V. Kobelev, and A. B. Kolomeisky "Lattice models of ionic systems with charge asymmetry." J. Chem. Phys., 118 (2003) : 6394-6402.

     
     

    N. Mirin and A. B. Kolomeisky "The Effect of Detachments in Asymmetric Simple Exclusion Processes." J. Stat. Phys., 110 (2003) : 811-823.

     
     

    V. Popkov, A. Rakos, G. M. Schutz, R. D. Willmann and A. B. Kolomeisky "Localized Shocks in Driven Diffusive Systems without Particle Number Conservation." Phys. Rev. E, 67 (2003) : 066117-1 - 066117-6.

     
     

    Kobelev, V., Kolomeisky, A. "Anisotropic Lattice Models of Electrolytes." J. Chem. Phys., 117 (2002) : 8879-8885.

     
     

    Kolbelev, V, Kolomeisky, A., Fisher, M.E. "Lattice Models for Ionic Systems." J. Chem. Phys., 116 (2002) : 7589-7598.

     
     

    Anatoly B. Kolomeisky "Exact Results for Parallel Chains Kinetic Models of Biological Transport ." J. Chem. Phys., 115 (2001) : 7253-7259.

     
     

    Anatoly B. Kolomeisky and Michael E. Fisher "Force-Velocity Relation for Growing Microtubules." Biophys. J. , 80 (2001) : 149-154.

     
     

    Anatoly B. Kolomeisky and Michael E. Fisher "Simple Mechanochemistry Describes the Dynamics of Kinesin Molecules ." Proc. Natl. Acad. Sci. USA, 98 (2001) : 7748-7753.

     
     

    A. B. Kolomeisky and M. E. Fisher "Extended Kinetic Models with Waiting-Time Distributions: Exact Results ." J. Chem. Phys., 113 (2000) : 10867-10877.

     
     Books
     

    A.B. Kolomeisky “Motor Proteins and Molecular Motors.” CRC, Taylor and Francis, 2015.

     
     Book chapters
     

    A. B. Kolomeisky "Channel-Facilitated Molecular Transport Across Membranes." Computational Modeling of Biological Systems: From Molecules to Pathways (2012)

     
     

    A. B. Kolomeisky "Molecular Motor Dynamics." Encyclopedia of Applied and Computational Physics (2012)

     
     

    A. B. Kolomeisky "Discrete-State Stochastic Models of Single-Molecule Motor Protein Dynamics." Theoretical and Numerical Approaches to Single-Molecule Data and Analysis (2008) In Press

     
    Presentations
     Invited Talks
     

    Dynamics of Assembly and Disassembly of Microtubule Protein Filaments: Theoretical Analysis, Francqui Symposium on Aggregation of Biological Molecules, Brussels, Belgium, June 2015.

     
     

    Dynamics of Assembly and Disassembly of Microtubule Protein Filaments: Theoretical Analysis, Telluride Workshop on Biophysical Dynamics, Telluride, Colorado, July 2015.

     
     

    How to Understand Mechanism of Protein Search for Targets on DNA, Physics Colloquium, Oxford University, Oxford, UK, October 2015.

     
     

    How to Understand Mechanism of Protein Search for Targets on DNA, Biophysics Seminar, Princeton University, Princeton, New Jersey, September 2015.

     
     

    How to Understand Mechanism of Protein Search for Targets on DNA, Free University of Brussels, Department of Physics, Brussels, Belgium, June 2015.

     
     

    How to Understand Molecular Transport through Channels: The Role of Interactions, Department of Physics, Cambridge University, Cambridge, UK, October 2015.

     
     

    The Mechanisms of Formation of Biological Signaling Profiles, Department of Chemistry, Imperial College, London, UK, November 2015.

     
     

    How to Understand Molecular Transport through Channels: The Role of Interactions, Lorentz Workshop on Nanothermodynamics, Leiden, Netherlands, December 2014.

     
     

    How to Understand the Formation of Morphogen Gradients during Biological Development, Mini-Symposium “Application of Statistical Physics in Quantitative Biology,” 9-th European Conference on Mathematical and Theoretical Biology, Goteborg, Sweden, June 2014. 

     
     

    How to Understand the Formation of Signaling Molecules Profiles in Biological Development, Center for Physics Studies in Brazil, Rio de Janeiro, Brazil, October 2014.

     
     

    Speed-Selectivity Paradox in the Protein Search for Targets on DNA, Is It Real or Not? University of Sao Paulo, Sao Paulo, Brazil, October 2014. 

     
     

    Speed-Selectivity Paradox in the Protein Search for Targets on DNA, Is It Real or Not? Federal University of Rio Grande du Sul, Porto Alegre, Brazil, October 2014. 

     
     

    How to Understand the Formation of Signaling Molecules Profiles in Biological Development, University of Texas Medical Branch, Galveston, TX, September 2014.

     
     

    "How Interactions Affect Multiple Kinesin Dynamics." American Physical Society Meeting, Baltimore, Maryland. (March, 2013) With M. R. Diehl

     
     

    "How to Understand Complex Processes in Chemistry, Physics and Biology Using Simple Models." Norway-Texas Collaborative Research Seminar, Trondheim, Norway. (October, 2013)

     
     

    "Mechanisms and Topography Determination of Complex Networks from First-Passage Theoretical Approach." Kavli Institute of Theoretical Physics in China Statphys Satellite Conference, Beijing, China. (July, 2013) With X. Li

     
     

    "Mechanisms and Topography Determination of Complex Networks from First-Passage Theoretical Approach." Southwest Regional Meeting of the American Chemical Society, Waco, Texas. (November, 2013) With X. Li

     
     

    "Mechanisms and Topography Determination of Complex Networks from First-Passage Theoretical Approach." International Conference on Multiscale Motility of Molecular Motors, Potsdam, Germany. (September, 2013) With X. Li

     
     

    "Random Hydrolysis Controls the Dynamic Instability in Microtubules." Society for Industrial and Applied Mathematics Conference on Applications of Dynamic Systems, Snowbird, Utah. (May, 2013) With D. Lacoste, R. Padinhateeri

     
     

    "Can We Understand Complex Dynamics of Motor Proteins Using Simple Models?." University of Barcelona, Barcelona, Spain. (May 23-26, 2012)

     
     

    "Can We Understand Complex Dynamics of Motor Proteins using Simple Models?." Multiscale Methods and Validation in Medicine and Biology I: Biomechanics and Mechanobiology Conference, San Francisco, California. (February 12-14, 2012)

     
     

    "Formation of Signaling Molecules Concentration Profiles." Department of Physics, Syracuse University, Syracuse, New York. (March, 2012)

     
     

    "Formation of a Morphogen Gradient: Acceleration by Dissociation." Department of Physics, University of Barcelona, Barcelona, Spain. (May, 2012)

     
     

    "Formation of a Morphogen Gradient: Acceleration by Dissociation." Department of Chemistry, Cornell University, Ithaca, New York. (March, 2012)

     
     

    "How Interactions Control Transport through Channels." Department of Chemistry, University of Utah, Salt Lake City, Utah. (October, 2012)

     
     

    "How Interactions Control Transport through Channels." CECAM Workshop "Polymer Translocation through Nanopores", Mainz, Germany. (September, 2012)

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Department of Chemistry, University of Rochester, Rochester, New York. (March, 2012)

     
     

    "How to Understand Mechanisms of Biological Development." University of Barcelona, Barcelona, Spain. (May 23-26, 2012)

     
     

    "How to Understand Signaling Mechanisms in Biological Development." Department of Chemistry, University of California, Irvine, California. (April, 2012)

     
     

    "Mechanism of Fast Protein Search for Targets on DNA: Strong Coupling between 1D and 3D Motions." Search and Stochastic Phenomena in Complex Physical and Biological Systems Conference, Instituto de Fisica Interdisciplinar y Sistemas Complejos, Palma de Mallorca, Spain. (May 28-June 1, 2012)

     
     

    "Mechanisms of Fast Protein Search for Targets on DNA: Strong Coupling between 1D and 3D Motions." Michael E. Fisher's Symposium, University of Maryland, College Park, Maryland. (October, 2012)

     
     

    "Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms?." Institute of Chemical Physics, Dalian, China. (December 2011) With A. V. Akimov

     
     

    "Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms?." Conference on Functional and Nanostructured Materials FNMA-11, Szczecin, Poland. (September 2011) With A. V. Akimov

     
     

    "Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms?

     ." Zheijang Gongshang University, Hangzhou, China. (December 2011) With A. V. Akimov

     
     

    "Formation of Signaling Molecules Concentration Profiles." Department of Chemistry, Peking University, Beijing, China. (December 2011)

     
     

    "Formation of a Morphogen Gradient ." Nordic Institute for Theoretical Physics, Stockholm, Sweden. (October 2011)

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Zheijang University, Hangzhou, China. (December 2011)

     
     

    "How Proteins Find and Recognize Their Targets on DNA ." University of Science and Technology of China, Hefei, China. (November 2011)

     
     

    "How Proteins Find and Recognize Their Targets on DNA ." Department of Chemistry, Nanjing University, Nanjing, China. (December 2011)

     
     

    "How to Accelerate Protein Search for Targets on DNA: Location and Dissociation ." DNA Search: From Biophysics to Cell Biology Conference, Safed, Israel. (September 2011) With A. Veksler

     
     

    "Physical-Chemical Aspects of Protein-DNA Interactions: Mechanisms of Facilitated Target Search." CECAM Workshop "Dynamics of Protein-Nucleic Acid Interactions: Integrating Simulations with Experiments", Zurich, Switzerland. (September 2011) With A. Veksler

     
     

    "What Are Fundamental Mechanisms for the Motion of Nanocars and Molecular Rotors on Surfaces?." 43rd International Union of Pure and Applied Chemistry World Chemistry Congress, San Juan, Puerto Rico. (July 2011) With A. V. Akimov

     
     

    "Can We understand the Complex Dynamics of Molecular Motors Using Simple Models?." Thermodynamics and Kinetics of Molecular Motors Conference, Santa Fe, New Mexico. (May 2010) With M. E. Fisher, R. K. Das, M. Diehl

     
     

    "Channel-Facilitated Molecular Motor Transport Across Cellular Membranes." École supérieure de physique et de chimie industrielles de la ville de Paris, Paris, France. (June, 2010) With K. Uppulury

     
     

    "Channel-Facilitated Molecular Transport Across Cellular Membranes." Mathematical Biosciences Workshop, The Ohio State University, Columbus, Ohio. (April, 2010) With K. Uppulury

     
     

    "Dynamic Properties of Motor Proteins in the Divided-Pathway Model." Society for Industrial and Applied Mathematics Conference, Pittsburgh, Pennsylvania. (July, 2010) With R. K. Das

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Indian Institute of Science, Bangalore, India. (January, 2010) With A. A. Kornyshev, A. Cherstvy, R. K. Das

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Tata Institute for Fundamental Research, Mumbai, India. (February, 2010) With A. A. Kornyshev, A. Cherstvy, R. K. Das

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Center for Biological Physics, Arizona State University, Tempe, Arizona. (March, 2010) With A. A. Kornyshev, A. Cherstvy, R. K. Das

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Department of Material Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois. (November, 2010) With A. A. Kornyshev, A. Cherstvy, R. K. Das

     
     

    "How Proteins Find and Recognize Their Targets on DNA ." Joseph Fourier University, Grenoble, France. (June, 2010) With A. A. Kornyshev, A. Cherstvy, R. K. Das

     
     

    "Interactions between Motor Proteins can Explain Collective Transport of Kinesins." Biophysical Society Meeting, San Francisco, California. (February, 2010) With M. Diehl, J. Driver, R. K. Das

     
     

    "Spatial Fluctuations Affect Dynamics of Motor Proteins." Indian Institute of Technology Golden Jubilee Conference on Interaction, Stability, Transport and Kinetics, Kanpur, India. (February, 2010) With R. K. Das

     
     

    "Theoretical Studies of Coupled Parallel Exclusion Processes ." Indian Institute of Technology Golden Jubilee Conference on Non-Equilibrium Statistical Physics, Kanpur, India. (January, 2010) With E. Pronina, K. Tsekouras

     
     

    "Complex Dynamics of Motor Proteins: A Theorist's View." University of Texas, Austin, Texas. (November 2009)

     
     

    "Complex Dynamics of Motor Proteins: A Theorist's View." Laboratory of Statistical Physics, Ecole Normale Superieure, Paris, France. (July 2009)

     
     

    "Complex Dynamics of Motor Proteins: A Theorist's View." Department of Physics, University of Illinois, Chicago, Illinois. (September 2009)

     
     

    "How Proteins Find Targets on DNA." International Centre for Theoretical Physics, Trieste, Italy. (June 2009)

     
     

    "How Proteins Find and Recognize Their Targets on DNA." XIV Statistical Physics Minisymposium, Institute of Mathematics, Czestochowa University of Technology, Czestochova, Poland. (June 2009)

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Laboratoire de Physique Stastique, Ecole Normale Superieure, Paris, France. (May 2009)

     
     

    "How Proteins Find and Recognize Their Targets on DNA." Department of Chemistry, University of Illinois, Chicago, Illinois. (September 2009)

     
     

    "Spatial Fluctuations Affect Dynamics of Motor Proteins." Max-Planck Institute for Physics of Complex Systems, Dresden, Germany. (May 2009) With R. Das

     
     

    "Thermally-Driven Nanocars and Molecular Rotors: What Can We Learn from Molecular Dynamics Simulations?." Department of Physics, University of Zielona Gora, Zielona Gora, Poland. (June 2009) With A. Akimov

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." Research Center Julich, Julich, Germany. (November, 2008)

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts. (September, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Department of Chemistry, Harvard University, Cambridge, Massachusetts. (September, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Department of Physics, University of Munich, Munich, Germany. (December, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Max-Planck Institute, Potsdam, Germany. (December, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Max-Planck Institute of Polymer Sciences, Mainz, Germany. (November, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Department of Physics Colloquium, Syracuse University, Syracuse, New York. (September, 2008)

     
     

    "How Proteins Find Their Targets on DNA: Mechanism of Facilitated Diffusion." Department of Physics, University of Stuttgart, Stuttgart, Germany. (November, 2008)

     
     

    "Molecular Motors Interacting with Their Own Tracks." Society for Industrial and Applied Mathematics Annual Meeting, San Diego, California. (July 7, 2008) With Max Artyomov, Alexander Morozov

     
     

    "Molecular Motors Interacting with Their Own Tracks." International Conference on Statistical Physics, Crete, Greece. (July 14-18, 2008)

     
     

    "Molecular Motors Interacting with Their Own Tracks." 236th National Meeting of the American Chemical Society, Philadelphia, Pennsylvania. (August 16-21, 2008)

     
     

    "Motor Proteins: A Theorist's View." Center for Nanosciences, University of Munich, Munich, Germany. (December, 2008)

     
     

    "Burnt-Bridge Model of Molecular Motor Transport." SIAM Conference on Applications of Dynamical Systems, Snowbird, Utah. (May 2007)

     
     

    "Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry." Statistical Physics Conference, Genoa, Italy. (July 2007)

     
     

    "Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry." Telluride Research Workshop: "Nonequilibrium Phenomena, Nonadiabatic Dynamics and Spectroscopy", Telluride, Colorado. (July 2007)

     
     

    "Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry." American Chemical Society, Boston. (August 2007)

     
     

    "How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion." Bar-Ilan University, Ramat-Gan, Israel. (November 2007)

     
     

    "Asymmetric Exclusion Processes on Parallel Channels." Indian Institute of Technology, Kanpur, India. (February, 2006)

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." International Workshop on on Stochastic Models in Biological Sciences, Warsaw, Poland. (May, 2006)

     
     

    "Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Symmetry." Rutgers Statistical Mechanics Meeting, Rutgers University, Piscataway, New Jersey. (December, 2006)

     
     

    "Coupling of Two Motor Proteins: A New Motor Can Move Faster." University of Wisconsin, Madison, WI. (March, 2006)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." University of Montreal, Montreal, Canada. (January, 2006)

     
     

    "Growth Dynamics of Cytoskeleton Proteins: Multiscale Theoretical Analysis." International Workshop on Multiscale Modeling of Complex Fluids, Prato, Italy. (July, 2006)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." Department of Chemistry, Cornell University, Ithaca, New York. (May 2005)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." 6th SIAM Conference on Control and its Applications, Symposium on Brownian Motors and Protein Dynamics, New Orleans, Louisiana. (July 2005)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." The Telluride Scientific Research Workshop: "Single-molecule measurements; kinetics, fluctuations, and non-equilibrium thermodynamics", Telluride, Colorado. (August 2005)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." Institute for Physical Science and Technology, University of Maryland, College Park, Maryland. (December 2005)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." McGovern Lecture in Biomedical Computing and Imaging, Texas Medical Center, Houston, Texas. (September 2005)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." University of Montreal, Montreal, Canada. (November 2005)

     
     

    "Growth Dynamics of Cytoskeleton Proteins: Multiscale Theoretical Analysis, Workshop I: Multiscale Modeling in Soft Matter and Bio-Physics." Institute for Pure and Applied Mathematics, University of California, Los Angeles, Los Angeles, California. (September 2005)

     
     

    "Can We Understand the Complex Dynamics of Motor Protein Using Simple Stochastic Models?." Boston University-Harvard-Massachusetts Institute of Technology Theoretical Chemistry Lecture Series, Boston, Massachusetts. (October, 2004)

     
     

    "Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments." International Conference on Biological Physics, Goteborg, Sweden. (August, 2004)

     
     

    "Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments." Department of Chemistry, Iowa State University, Ames, Iowa. (September, 2004)

     
     

    "Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments." Materials Research laboratory, University of California, Santa Barbara, Santa Barbara, California. (October, 2004)

     
     

    "Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments." Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania. (December, 2004)

     
     

    "Effect of Detachments in Asymmetric Simple Exclusion Processes." Fock School on Quantum and Computational Chemistry, Norgorod, Russia. (April, 2004)

     
     

    "Lattics Models of Electrolytes." Institute of Condensed Matter Physics, Ukranian Academy of Science, Lviv, Ukraine. (May, 2004)

     
     

    "Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach." Materials Research Society, San Francisco, California. (April, 2004)

     
     

    "Simple Models of Rigid Multifilament Biopolymer's Growth Dynamics." Department of Physics, Brandeis University, Waltham, Massachusetts. (October, 2004)

     
     

    "Simple Models of Rigid Multifilament biopolymer's Growth Dynamics." Department of Chemical Engineering, University of California, Los Angeles, Los Angeles, California. (Ocrober, 2004)

     
     

    "Simple Stochastic Models of Motor Protein Dynamics." SIAM Conference on Mathematical Aspects of Material Science, Los Angeles, California. (May, 2004)

     
     

    "Dynamics of Polymer Translocation Through a Long Nanopore." Department of Chemistry, University of Washington, Seattle, WA. (October, 2003)

     
     

    "Dynamics of Polymer Translocation Through a Long Nanopore." Department of Chemical Engineering, Princeton University, Princeton, NJ. (December, 2003)

     
     

    "Dynamics of Polymer Translocation Through a Long Nanopore." Department of Chemical Engineering, University of Houston, Houston, TX. (April, 2003)

     
     

    "Effect of Detachments in Asymmetric Simple Exclusion Processes." European Research Council Chemistry Committees Workshop on Computer Modeling of Chemical and Biological Systems, Porto, Portugal. (May, 2003)

     
     

    "Lattice Models of Electrolytes." Department of Physics, University of Washington, Seattle, WA. (October, 2003)

     
     

    "Phenomenological Model of Protein Nucleation." Institute for Physical Science and Technology, University of Maryland, College Park, MD. (November, 2003)

     
     

    "Physical-Chemical Analysis of the Factors Influencing the Behavior of Flasks During the Heating in Jewelry Casting Process." 2nd International Jewelry Symposium - Jewelry Manufacturing: Technologies, Main Problems and Prospects, Saint Petersburg, Russia. (July, 2003)

     
     

    "Simple Models of the Growth of Microtubules." 15th American Conference on Crystal Growth and Epitaxy, Keystone, CO. (July, 2003)

     
     

    "Stochastic Models with Waiting-Time Distributions for Translocatory Motor Proteins." American Chemical Society 225th National Meeting, New Orleans, LA. (March, 2003)

     
     

    "A Simple Stochastic Model Can explain the Mobility of Myosin V Molecules." 46th Annual Biophysical Society Meeting, San Fransisco, CA. (February 2002)

     
     

    "Lattice Models of Electrolytes." Department of Mathematics, Rice Univeristy, Houston, TX. (September 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." Statistical Mechanics Meeting, Rutgers University, Rutgers, NJ. (December 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." Department of Chemistry, Moscow State University, Moscow, Russia. (December 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." 19th Southwestern Theoretical Chemistry Conference, Univ. of Houston, Houston, TX. (November 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." Institue for Physical Science and Technology, Univ. of Maryland, College Park, MA. (August 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." Department of Chemistry, Univ. of Southern California, Los Angeles, CA. (March 2002)

     
     

    "Polymer Translocation Through a Long Nanopore." Department of Chemistry, Univ. of California- Los Angeles, Los Angeles, CA. (March 2002)

     
     

    "Polymer Translocation Throuhh a Long Nanopore." Department of Chemistry, Univ. of California, Berkeley, Berkeley, CA. (February 2002)

     
     

    "Simple Stochastic Models Can Explain the Dynamics of Motor Proteins." symposium COOPERATIVITY IN BIOPHYSICAL SYSTEMS, Institute fur Festkorperforschung at the Forschungzentrum, Julich, Germany. (October 2002)

     
     

    "Stochastic Models of Biological Transport." Department of Chemistry, Moscow State University, Moscow, Russia. (May 2002)

     
     Lectures
     

    "How Chain Flexibiliity and Surface Interaction Affect the Properties of Surface-mounted Molecular Rotors: Molecular Dynamics of Thioethers." Southwest Theoretical Chemistry Conference, University of Houston, Houston, Texas. (October 2009) With A. Akimov

     
     

    "Thermally-Driven Nanocars and Molecular Rotors: What Can We Learn from Molecular Dynamics Simulations?." 237th National Meeting of the American Chemical Society, Salt Lake City, Utah. (March 2009) With A. Akimov

     
     

    "Effect of charge distribution on the translocation of an inhomogeneously charged polymer through a nanopore." 2008 American Physical Society March Meeting, New Orleans, Louisiana. (March 13, 2008) With A. Mohan, M. Pasquali

     
     

    "Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach." Gordon Research Conference on "Thin Films and Growth Mechanisms", Mount Holyoke College, South Hadley, Massachusetts. (June 2007)

     
     

    "Nucleation of Ordered Solid Phases of Proteins via Unstable and Metal Stable High-Density States: Phenomenological Approach." Rutgers University, Piscataway, NJ. (December, 2003)

     
     Other
     

    "Undirectional rolling motion of nanocars induced by electric field." 246th National Meeting of the American Chemical Society, Indianapolis, Indiana. (September 10, 2013) With A. V. Akimov

     
     

    Contributed talk.  "How Proteins Find and Recognize Their Targets on DNA." 52nd Annual Meeting of the Biophysical Society, Long Beach, California. (February, 2008)

     
     

    Contributed Talk.  "ATP Hydrolysis Stimulates Large Length Fluctuations in Single Actin Filaments." 50th Annual Biophysical Society Meeting, Salt Lake City, Utah. (February, 2006)

     
     

    "Description of Motor Protein Motility using Stochastic Models ." International Conference on Mathematical and Theoretical Biology , Hilo, Hawaii. (July, 2001)

     
     

    "Exact Results for Parallel-Chain Kinetic Models of Biological Transport." NANOBIOLOGY 2001 International Conference, Emory University, Atlanta, Georgia. (October, 2001)

     
     

    "Nanotechnology: What Can We Learn from Biology ." NANOSPACE 2001 International Conference, Galveston, Texas. (March, 2001)

     
     

    "Stochastic Models of Biological Transport." Department of Physics, Sam Houston State University , Huntsville, Texas. (September, 2001)

     
     

    "Stochastic Models of Biological Transport." Department of Chemistry, University of Houston , Houston, Texas. (October, 2001)

     
     

    "The Growth of Microtubules Against an External Force." 45th Annual Biophysical Society Meeting , Boston, Massachusetts. (February, 2001)

     
     

    "Describing Kinesin Dynamics Using Stochastic Models ." National Academy of Sciences Colloquium, Molecular Kinesis in Cellular Function and Plasticity, Irvine, California. (December 2000)

     
     

    "One-layer Model of the Growth of Microtubules." 84th Statistical Mechanics Meeting, Rutgers University, Piscataway, New Jersey. (December 2000)

     
     Panelist
     

    "Simple Models of the Growth of Microtubules.." 48th Annual Biophysical Society Meeting, Baltimore, Maryland. (February, 2004)

     
     

    "Thermodynamics and Phase Transitions of Electrolytes on Lattices with Different Discretization Parameters." Annual Meeting of the American Physical Society, Montreal, Canada. (March, 2004)

     
     Posters
     

    "Random Hydrolysis Controls Dynamic Instability of Microtubules." 56th Annual Meeting of the Biophysical Society, San Diego, California. (February 25-29, 2012)

     
     

    "Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores." Biophysical Spciety Meeting, Baltimore, Maryland. (March 2007)

     
     

    "Nucleation of Proteins via Intermediate States: Phenomenological Approach." Liquid Matter Conference, Utrecht, The Netherlands. (July, 2005)

     
     

    "Thermodynamics and Phase Transitions of Electrolytes on Lattices with Different Discretization Parameters." Liquid Matter Conference, Utrecht, The Netherlands. (July, 2005)

     
     

    "Understanding Mechanochemical Coupling in Kinesins Using First-Passage Time Processes." 49th Annual Biophysical Society Meeting, Long Beach, California. (February, 2005)

     
     

    "Dynamics of Polymer Translocation Through a Long Nanopore." 47th Annual Biophysical Society Meeting, San Antonio, TX. (March, 2003)

     
     Seminar Speaker
     
    1. How to Understand Signaling Mechanisms in Biological Development, Department of Chemistry, University of Southern California, Los Angeles, CA, April 2014. 
     
     
    1. Speed-Selectivity Paradox in the Protein Search for Targets on DNA, Is It Real or Not? Biomedical Center, Uppsala University, Sweden, June 2014. 
     
     

    "How to Understand Signaling Mechanisms in Biological Development." Department of Chemical Engineering, Stanford University, Stanford, California. (September, 2013)

     
     

    "Nanocars and Molecular Rotors: What are Fundamental Mechanisms of Motion?." Department of Chemistry, University of California Los Angeles, Los Angeles, California. (May 2011) With A. V. Akimov

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." University of Texas Medical Branch, Galveston, Texas. (September 2007)

     
     

    "Coupling of Two Motor Proteins: a New Motor Can Move Faster." Department of Chemistry, University of Nevada Reno. (February 2007)

     
     

    "How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion." Technion, Haifa, Israel. (December 2007)

     
     

    "How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion." Department of Chemistry, University of Texas, Austin, Texas. (September 2007)

     
     

    "How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion." Department of Chemistry, University of Tel-Aviv, Tel-Aviv, Israel. (December 2007)

     
     

    "How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion." Weizmann Research Institute, Rehovot, Israel. (December 2007)

     
     Session Chair
     

    Co-organizer.  "Recent Advances in Biophysical Chemistry of Transport by Biomolecular Motors and Machines." 236th National Meeting of the American Chemical Society, Philadelphia, Pennsylvania. (August 16-21, 2008)

     
     Workshops
     

    "How Interactions Control Transport through Channels." Telluride Workshop on Nonequilibrium Phenomena, Nonadiabatic Dynamics and Spectroscopy, Telluride, Colorado. (July, 2013)

     
     

    "Speed-Selectivity Paradox in the Protein Search for Targets on DNA. Is It Real or Not?." Telluride Workshop on Biophysical Dynamics, Telluride, Colorado. (July, 2013) With A. Veksler

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." Telluride Research Workshop, Telluride, Colorado. (June 2009)

     
     

    "Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models?." Mesilla Workshop on Multi-Scale Modeling of Biological Systems, Las Cruces, New Mexico. (February 2009) With R. Das

     
     

    "Discrete Stochastic Models of Single-Molecule Motor Protein Dynamics." Workshop: Theory, Modeling and Evaluation of Single-Molecule Measurements, Lorentz Center, University of Leiden. (April 2007)

     
     

    "Understanding Mechanochemical Coupling in Kinesins Using First-Passage Times." Proteomics Workshop IV: Molecular Machines, Institute for Pure and Applied Mathematics, University of California, Los Angeles, Los Angeles, California. (May, 2004)

     
    Editorial Positions
     Editor, PLoS Comput. Biol. PLoS Computational Biology. (2009 - 2009)

     Associate Editor, PLoS Computational Biology. Public Library of Science. (2010 - 2010)

     Editor for Special Issue, Phys. Chem. Chem. Phys. Physical Chemistry - Chemical Physics. (2009 - 2009)

     Other, Guest Editor for Special Issue on Motor Proteins and Molecular Motors, J. Phys.: Condens. Matter. (2013 - 2013)

     Member of the Editorial Board, Journal of Physics D. (2015 - 2015)

     Member of the Editorial Board, Reports in Theoretical Chemistry. (2012 - 2012)

     Member of the Editorial Board, Reports in Theoretical Chemistry. Dovepress. (2011 - 2011)

     Member of the Editorial Board, Biophysical Journal. (2015 - 2015)

    Supervised Theses & Dissertations
     Ekaterina Pronina, PhD One-Dimensional Non-Equilibrium Processes. (2007) (Thesis Director)

     S. Matysiak, PhD Protein Folding Studies. (2007) (Thesis Committee Member)

     Oleg Vydrov, PhD Density-Functional Studies of Radicals. (2007) (Thesis Committee Member)

     Payel Das, PhD Minimalists models of protein folding. (2007) (Thesis Committee Member)

     Aliaksandr Krukau, PhD New approaches for incorporating the exact exchange energy density into density functional approximations. (2009) (Thesis Committee Member)

     Rahul Kumar Das, PhD Stochastic modeling of biological transport. (2010) (Thesis Director)

     Konstantinos Tsekouras, PhD Theoretical Investigations of Asymmetric Exclusion Processes. (2010) (Thesis Director)

     Carmen Reznik, Ph.D. Environmental Response, Mechanisms, and Orientation of Diffusing Molecular Ions in Polyelectrolyte Thin Films. (2011) (Thesis Committee Member)

     Paul Jay Ledbetter, M.S. Reaction Rates and Transition States: A New Perspective on an Old Problem. (2011) (Thesis Committee Member)

     Alexey Akimov, PhD Theoretical and Computational Investigations of Dynamics of Nanocars, Artificial Molecular Motors and Molecular Motors. (2011) (Thesis Director)

     Alexey V Akimov, Ph.D. Theoretical Studies of Molecular Machines. (2012) (Thesis Director)

     Karthik Uppulury, Ph. D. Theoretical investigation of biological transport processes using discrete state stochastic models and simulations. (2013) (Thesis Director)

     Carlos Jimenez-Hoyos, Ph.D. Variational approaches to the molecular electronic structure problem based on symmetry-projected Hartree-Fock configurations. (2013) (Thesis Committee Member)

     Wenwei Zheng, Ph.D. Multiscale Analysis of Macromolecular Systems. (Thesis Committee Member)

    Awards, Prizes, & Fellowships
     Elected Fellow of American Physical Society, (2015)

     International Union of Pure and Applied Chemistry Young Observer Award, (2011)

     Alexander von Humboldt Research Fellowship, Alexander von Humboldt Foundation (2008-2009)

     Alexander von Humboldt Research Fellowship, Alexander von Humboldt Foundation (Fall 2008 - Summer 2009)

     Hammill Innovation Award, Institute of Biosciences and Bioengineering, Rice University (April 30, 2006)

     Sloan Fellowship, Alfred P. Sloan Foundation (2004)