Kolomeisky Research Group

THEORETICAL BIOPHYSICS
& Statistical Mechanics of Complex Systems

THESES


M.Sc.

Investigation of the Process of Synthesis of YBa2Cu3O6+x High-Tc Ceramics in the Presence of Silver (Moscow, 1991).

Ph.D.

One-Dimensional Non-Equilibrium Stochastic Models, Interface Models, and Their Applications (Cornell University, 1998).

BOOKS


  1. “Motor Proteins and Molecular Motors,” (A.B.K.), CRC Press, Taylor and Francis, 2015.
  2. Link to the publisher
    Link to Amazon

BOOK CHAPTERS


  1. Discrete-Stochastic Models of Single-Molecule Motor Proteins Dynamics (A.B.K.) in “Theory and Evaluation of Single-Molecule Signals”
  2. Molecular Motor Dynamics, Modelling (A.B.K.) in “Encyclopedia of Applied and Computational Mathematics” Springer-Verlag, 2012.
  3. Channel-Facilitated Molecular Transport Across Membranes (A.B.K.) in “Computational Modelling of Biological Systems: From Molecules to Pathways” Ed.: N. Dokholyan, Springer-Verlag, 2012.
  4. Discrete-State Stochastic Modelling of Morphogen Gradient Formation (H. Teimouri and A.B.K.) in “Methods in Molecular Biology - Morphogen Gradients” Ed.: J. Dubrulle. Springer-Verlag, 2018.
  5. Kinetics of Protein-DNA Interactions: First-Passage Analysis (M.P. Kochugaeva, A.A. Shvets and A,B.K.), in ”Chemical Kinetics beyond the Textbook”, Ed.: K. Lindenberg, R. Metzler, G. Oshanin, World Scientific, 2018.

INVITED REVIEW ARTICLES


  1. Molecular Motors: A Theorist’s Perspective (A.B.K. and M.E. Fisher), Annual Reviews of Physical Chemistry 58, 675-695 (2007). PDF-download
  2. Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation (D. Panja, G.T. Barkema and A.B.K.), J. Phys.: Condens. Matter 25, 413101 (2013). PDF-download
  3. Motor Proteins and Molecular Motors: How to Operate Machines at the Nanoscale (A.B.K.), J. Phys.: Condens. Matter 25, 463101 (2013). PDF-download
  4. Collective Dynamics of Cytoskeletal Motor Proteins (R.T. McLaughlin, M.R. Diehl and A.B.K.), Soft Matter, 12(1), 14-21. (2016). PDF-download
  5. DNA Sequencing by Nanopores: Advances and Challenges (S. Agah, M. Zheng, M. Pasquali and A.B.K.), J. Phys. D 49, 413001 (2016). PDF-download
  6. Entropy Production in Mesoscopic Stochastic Thermodynamics: Nonequilibrium Kinetic Cycles Driven by Chemical Potentials, Temperatures, and Mechanical Forces (H. Qian, S. Kjelstrup, A.B.K. and D. Bedeaux), J. Phys.: Condens. Matter 28, 153004 (2016). PDF-download
  7. Mechanisms of Formation of Biological Signaling Profiles (H. Teimouri and A.B.K.), J.Phys.A: Math. Theor. 49, 483001 (2016). PDF-download
  8. Mechanisms of Protein Search for Targets on DNA: Theoretical Insights (M.P. Kochugaeva, A.A. Shvets and A.B.K.), Molecules 23, 2106 (2018). PDF-download
  9. Do We Understand the Mechanisms of Error Correction Phenomena in Biological Systems? (J.D. Mallory, O.A. Igoshin and A.B.K.), Perspective Article, J. Phys. Chem B 124, 9289-9296 (2020).
  10. Discrete-State Stochastic Kinetic Models for Target DNA Search by Proteins: Theory and Experimental Applications (J. Iwahara and A.B.K.), Biophys. Chem. 106521 (2020). PDF-download
  11. Understanding the Molecular Mechanisms of Transcriptional Bursting (A. Klindziuk and A.B.K.), Perspective Article, Physical Chemistry Chemical Physics, to appear in 2022.
  12. Power of Chemical Kinetic Stochastic Models: From Biological Development to Cancer and Antibiotic Activitie (H. Teimouri and A.B.K.), Wiley Interdisciplinary Reviews Computational Molecular Science, to appear in 2022.

PUBLICATIONS


    2021


  1. DLPacker: Deep Learning for Prediction of Aminoacid Side Chain Conformations in Proteins. (M. Misiura, R. Shroff, R. Thyer and A.B.K.), submitted to Proteins (2021).
  2. Single-Cell Stochastic Modeling of the Action of Antimicrobial Peptides on bacteria. (H. Teimouri, Thao N. Nguyen and A.B.K.), to appear in J. Roy. Soc. Inter. (2021).
  3. Temporal Order of Mutations Influences Cancer Initiation Dynamics. (H. Teimouri and A.B.K.), Physical Biology 18, 056002 (2021). PDF - download
  4. Crowding Breaks the Forward/Backward Symmetry of Transition Times in Biased Random Walks. (J. Shin, A.M. Berezhkovskii and A.B.K.), J. Chem. Phys. 154, 204104 (2021). PDF - download
  5. Charge-free, stabilizing amide-pi interactions can be used to control collagen triple helix self-assembly. (D. Walker, A.A. Alizadehmojarad, A.B. K. and J. Hartgerink), Biomacromolecules 22, 2137-2147 (2021). PDF - download
  6. DNA Looping Mediated by Site-Specific SfiI-DNA Interactions. (S. Vemulapalli, M. Hashemi, A.B.K. and Y.L. Lyubchenko), J. Phys. Chem. B. 125, 4645-4653 (2021). PDF - download
  7. Long-Range Supercoiling-Mediated RNA Polymerase Cooperation in Transcription. (A. Klindziuk and A.B.K.), J. Phys. Chem. B 125, 4692-4700 (2021). PDF - download
  8. Theoretical Analysis Reveals the Cost and Benefit of Proofreading in Coronavirus Genome Replication. (J.D. Mallory, X.F. Mallory A.B.K. and O.A. Igoshin), J. Phys. Chem. Lett. 12, 2691-2698 (2021) PDF - download
  9. Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils. (D.S. Yang, A. Saeedi, A. Davtyan, M. Fathi, M.B. Sherman,M.S. Safari, A. Klindziuk, M.C. Barton, N. Varadarajan, A.B.K. and P.G. Vekilov), Proc. Natl. Acad. Sci. USA 118 e2015618118 (2021). PDF - download
  10. DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search. (C. Felipe, J. Shin and A.B.K.), J. Phys. Chem. B 125, 1727-1734 (2021) PDF - download
  11. 2020


  12. Dye Quenching of Carbon Nanotube Fluorescence Reveals Structure-Selective Coating Coverage. (Y. Zheng, A.A. Alizadehmojarad, S.M. Bachilo, A.B.K. and R.B. Weisman), ACS Nano 14, 12148-12158 (2020) PDF - download
  13. Effect of local dissociations in bidirectional transport of driven particles. (A. Jindal, A.B.K. and A.K. Gupta), J. Stat. Mech. P113202 (2020). PDF - download
  14. Asymmetry of forward/backward transition times as a non-equilibrium measure of complexity of microscopic mechanisms. (J. Shin and A.B.K.), J. Chem. Phys. 153, 124103 (2020). PDF - download
  15. Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects. (S.S. Lee, N. Ding, Y.D. Sun, T.L. Yuan, J. Li, Q.C. Yuan, L.Z. Liu, J. Yang, Q. Wang, A.B.K., I.B. Hilton, IB, E.W. Zuo, and X. Gao), Sci. Adv. 6, eaba1773 (2020). PDF - download
  16. Stochastic Mechanism of Cell-Size Regulation in Bacteria. (H. Teimouri, R. Mukherjee and A.B.K.), J. Phys. Chem. Lett. 11, 8777-8782 (2020). PDF - download
  17. Different Time Scales in Dynamic Systems with Multiple Exits. (G. Bel, A. Zilman and A.B.K.), J. Chem. Phys. 153, 054107 (2020). PDF - download
  18. Relaxation Times of Ligand-Receptor Complex Formation Control T Cell Activation. (H. Teimouri and A.B.K.), Biophys. J. 119, 1-8 (2020). PDF - download
  19. Direct Detection of Molecular Intermediates from First-Passage Times. (A.L. Thorneywork, J. Gladrow, Y. Qing, M. Rico-Pasto, F. Ritort, H. Bayley, A.B.K. and U.F. Keyser), Sci. Adv. 6, eaaz4642 (2020). PDF - download
  20. Biased Random Walk in Crowded Environment: Breaking Uphill/Downhill Symmetry of Transition Times. (J. Shin, A.M. Berezhkovskii and A.B.K.), J. Phys. Chem. Lett. 11, 4530-4535 (2020). PDF - download
  21. Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites. (S. Chaudhury, D. Singh and A.B.K.), J. Phys. Chem. Lett. 11, 2330-2335 (2020). PDF - download
  22. Trade-Offs between Speed, Accuracy and Dissipation in tRNAle Aminoacylation. (Q. Yu, J.D. Mallory, A.B.K., J. Ling and O.A. Igoshin), J. Phys. Chem. Lett. 11, 4001-4007 (2020). PDF - download
  23. The Role of Dynamic Defects in Transport of Interacting Molecular Motors. (A. Jindal, A.B.K. and A.K. Gupta), J. Stat. Mech. P043206 (2020). PDF - download
  24. Kinetic Control of Stationary Flux Ratios for a Wide Range of Biochemical Processes. (J.D. Mallory, A.B.K. and O.A. Igoshin), Proc. Natl. Acad. Sci. USA 117 (2020). PDF - download
  25. A Mechanochemical Model of Transcriptional Bursting. (A. Klindziuk, B. Meadowcroft and A.B.K.), Biophys. J. 118, 1213-1220 (2020). PDF - download
  26. The Effect of Obstacles in Multi-Site Protein Target Search with DNA Looping. (C. Felipe, J. Shin, Y. Loginova and A.B.K.), J. Chem. Phys. 152, 025101 (2020). PDF - download
  27. The Role of Intrinsically Disordered Regions in Acceleration of Protein-Protein Association. (M. Misiura and A.B.K.), J. Phys. Chem. B 124, 20 (2020). PDF - download
  28. 2019


  29. A Molecular Model of the Surface-Assisted Protein Aggregation Process. (Y. Pan, S. Banerjee, K. Zagorski, L.S. Shlyakhtenko, A.B.K. and Y.L. Lyubchenko), to appear in J. Phys. Chem. B (2019).
  30. Elucidating the Correlations between Cancer Initiation Times and Lifetime Cancer Risks. (H. Teimouri, M. Kochugaeva and A.B.K), Sci. Rep. 9, 18940 (2019). PDF - download
  31. Target Search on DNA by Interacting Molecules: First-Passage Approach. (J. Shin and A.B.K.), J. Chem. Phys. 151, 125101 (2019). PDF - download
  32. Enhancing Silica Surface Deprotonation by Using Magnetic Nanoparticles as Heating Objects. (W. Wolak, A.B.K., M.R. Dudek and M. Narc), J. Phys. D 52, 465001 (2019). PDF - download
  33. Theoretical study of network junction models for totally asymmetric exclusion processes with interacting particles. (T. Midha, A.B.K. and A.K. Gupta), J. Stat. Mech. P083202 (2019). PDF - download
  34. Kinetic Network Model to Explain Gain-of-Function Mutations in ERK2 Enzyme. (M. Misiura and A.B.K.), J. Chem. Phys. 150, 155101 (2019). PDF - download
  35. Trade-Offs between Error, Speed, Noise, and Energy Dissipation in Biological Processes with Proofreading. (J.D. Mallory, A.B.K. and O.A. Igoshin), J. Phys. Chem. B 123, 4718 (2019). PDF - download
  36. Theoretical Analysis of Run length Distributions for Coupled Motor Proteins. (Qian Wang and A.B.K.), J. Phys. Chem. B 123, 5805 (2019). PDF - download
  37. The Effect of Local Dissociation on Dynamics of Interacting Molecular Motors. (L.V.F. Gomes, T. Midha, A.K. Gupta, and A.B.K.), J. Phys. A: Math. Theor. 52, 365001 (2019). PDF - download
  38. Facilitation of DNA Loop Formation by Protein-DNA Non-specific Interactions. (J. Shin and A.B.K.), Soft Matter 15, 5255-5263 (2019). PDF - download
  39. Theoretical Insights into Mechanisms of Channel-Facilitated Molecular Transport in the Presence of Stochastic Gating. (A. Davtyan and A.B.K.), J. Chem. Phys. 150, 124111 (2019). PDF - download
  40. Anomalous Dense Liquid Condensates Host the Nucleation of Tumor Suppressor p53 Fibrils. (M.S. Safari, Z. Wang, K. Tailor, A.B.K., J.C. Conrad and P.G. Vekilov), iScience 12, 342-355 (2019). PDF - download
  41. Theoretical investigation of stochastic clearance of bacteria: First-passage analysis. (H. Teimouri, and A.B.K.), J. Royal Soc. Interface 16, 20180765 (2019). PDF - download
  42. 2018


  43. Theoretical Investigation of the Transcriptional Bursting Mechanism: A Multi-State Approach (A. Klindziuk and A.B.K.), J. Phys. Chem. B 122, 11969-11977 (2018). PDF - download
  44. First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions (S. Ghosh, B. Mishra, A. B. K. and D. Chowdhury), J. Stat. Mech.12, 123209 (2018). PDF - download
  45. Molecular Search with Conformational Change: One-Dimentional Discrete-State Stochastic Model (J. Shin and A.B.K.), J. Chem. Phys. 149, 174104 (2018). PDF - download
  46. Interactions in nonconserving driven diffusive systems (T. Midha, A.B.K. and A.K. Gupta), Phys. Rev. E 98, 042119 (2018). PDF - download
  47. Molecular Mechanism of Inter-Head Coordination in Cytoplasmic Kinesins (Q. Wang, B. Jana, M.R. Diehl, M.S. Cheung, J. Onuchic and A.B.K.), Proc. Natl. Acad. Sci. USA 115, 10052–10057 (2018). PDF - download
  48. Theoretical Investigations of Asymmetric Simple Exclusion Processes for Interacting Oligomers (T. Midha, L.V.F. Gomes, A.B.K. and A.K. Gupta), J. Stat. Mech. 5, P053209 (2018). PDF - download
  49. Effect of Interactions for One-Dimentional Asymmetric Exclusion Processes under Periodic and Bath-Adapted Coupling Environment (T. Midha, A.B.K. and A.K. Gupta), J. Stat. Mech. 4, P043205 (2018). PDF - download
  50. Dynamics of Relaxation to a Stationary State for Interacting Molecular Motors (L.V.F. Gomes and A.B.K.), J. Phys. A: Math. Theor. 51, 015601 (2018). PDF - download
  51. Physical-Chemical Mechanisms of Pattern Formation during Gastrulation (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 148, 123302 (2018). PDF - download
  52. Theoretical Investigation of Distributions of Run Lengths for Biological Molecular Motors (Zhang, Y. and A.B.K.), J. Phys. Chem. B 122, 3272–3279 (2018). PDF - download
  53. Surface-Assisted Dynamic Search Processes (J. Shin and A.B.K.), J. Phys. Chem. B 122, 2243-2250 (2018). PDF - download
  54. Theoretical Investigations of the Role of Mutations in Dynamics of Kinesin Motor Proteins (Misiura M.M., Wang Q., Cheung M.S. and A.B.K.), J. Phys. Chem. B 122, 4653–4661 (2018). PDF - download
  55. 2017


  56. Mechanism of Genome Interrogation: How CRISPR RNA-guided Cas9 Proteins Locate Specific Targets on DNA (A.A. Shvets and A.B.K.), Biophys. J. 113, 1416-1424 (2017). PDF - download
  57. Optimal Length of Conformational Transitions Region in the Protein Search for Targets on DNA (M.P. Kochugaeva, A.A. Berezhkovskii and A.B.K.), J. Phys. Chem. Lett. 8, 4049-4054 (2017). PDF - download
  58. A Deterministic Model for One-Dimensional Excluded Flow with Local Interactions, (M. Margaliot, Y. Zarai and A.B.K.), PLOS ONE, e0182074 (2017). PDF - download
  59. Molecular Machines Open Cell Membranes (V. Garcia-Lopez, F. Chen, L.G. Nilewski, G. Duret, A. Alian, A.B.K., J.T. Robinson, G. Wang, R. Pal and J.M. Tour), Nature 548, 567-572 (2017). PDF - download
  60. Current-Generating ’Double Layer Shoe’ with a Porous Sole: Ion Transport Matters (A.A. Kornyshev, R. Twidale and A.B.K.), J. Phys. Chem C 121, 7584-7595 (2017). PDF - download
  61. Molecular Origin of the Weak Susceptibility of Kinesin Velocity to Loads and Its Relation to the Collective Behavior of Kinesins (Q. Wang, M.R. Diehl, B. Jana, M.S. Cheung, A.B.K. and J. Onuchic), Proc. Natl. Acad. Sci. USA 114, E8611-8617 (2017). PDF - download
  62. Current-Generating Double-Layer Shoe with a Porous Sole: Ion Transport Matters (Alexei A. Kornyshev, Rebecca M. Twidale, and Anatoly B. Kolomeisky), J. Phys. Chem. C 121, 7584-7595 (2017). PDF - download
  63. The Effect of Side Motion in the Dynamics of Interacting Molecular Motors, (T. Midha, A.K. Gupta and A.B.K.), J. Stat. Mech., P073201 (2017). PDF - download
  64. How Viruses Enter Cells: A Story behind Bacteriophage T4 (A.B.K.), Biophys. J. 113, 3-4 (2017). PDF - download
  65. Accuracy of Substrate Selection by Enzymes is Controlled by Kinetic Discrimination (K. Banerjee, A.B.K. and O. A. Igoshin), J. Phys. Chem. Lett. 8, 1552-1556 (2017). PDF - download
  66. Elucidating Interplay of Speed and Accuracy in Biological Error Correction (K. Banerjee, A.B.K. and O. A. Igoshin), Proc. Natl. Acad. Sci. USA 114, 5183-5188 (2017). PDF - download
  67. On the Mechanism of Homology Search by RecA Protein Filaments (M.P. Kochugaeva, A.A. Shvets and A.B.K.), Biophys. J. 112, 859-867 (2017). PDF - download
  68. Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate (A.M. Berezhkovskii, A. Szabo, T. Rotbart, M. Urbakh and A.B.K.), J. Phys. Chem. B 121, 3437-3442 (2017). PDF - download
  69. 2016


  70. Current-Generating ’Double Layer Shoe’ with a Porous Sole (A.B.K. and A.A. Kornyshev), J. Phys. Condens. Matter 28, 464009 (2016). PDF - download
  71. The Role of DNA Looping in the Search for Specific Targets on DNA by Multisite Proteins (Alexey A. Shvets and A.B.K.), J. Phys. Chem. Lett. 4, 5022-5027 (2016). PDF - download
  72. Theoretical Investigation of the Mecanisms of ERK2 Enzymatic Catalysis (Mikita M. Misiura and A.B.K.), J. Phys. Chem. B 120, 10508-10514 (2016). PDF - download
  73. A Two-Step Method for smFRET Data Analysis (Jixin Chen, Joseph R. Pyle Kurt Waldo Sy Piecco, Anatoly B. Kolomeisky, and Christy F. Landes) J. Phys. Chem. B 120, 7128-7132(2016). PDF - download
  74. How Conformational Dynamics Influences the Protein Search for Targets on DNA (M.P. Kochugaeva, A.A. Shvets and A.B.K.) to appear in J. Phys. A: Math. Theor. 49, 444004 (2016) PDF - download
  75. Crowding in Protein Search for Targets on DNA (A.A. Shvets and A.B.K.), J. Phys. Chem. Lett. 7, 2502-2506 (2016). PDF - download
  76. Channel-Facilitated Molecular Transport: The Role of Strength and Spatial Distribution of Interactions (K. Uppulury and A.B.K.), Chem. Phys. 481, 34-41(2016). PDF - download
  77. Turning On and Off Photoinduced Electron Transfer in Fluorescent Proteins by pi-Stacking, Halide Binding, and Tyr145 Mutations, (A.M. Bogdanov, A. Acharya, A.V. Titelmayer, A.V. Mamontova, K.B. Bravaya, A.B.K., K. A. Lukyanov and A.I. Krylov), J. Am. Chem. Soc. 138, 4807-4817 (2016). PDF - download
  78. Development of Morphogen Gradients with Spatially Varying Degradation Rates, (H. Teimouri, B. Bozorgui, and A.B.K.), J. Phys. Chem. B 120, 2745-2750 (2016). PDF - download
  79. New Model for Understanding Mechanism of Biological Signaling: Direct Transport via Cytonemes, (H. Teimouri and A. B. Kolomeisky), J. Phys Chem. Lett. 7 , 180-185 (2016). PDF - download
  80. The Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA (A.A. Shvets, M. Kochugaeva and A.B.K.), J. Phys. Chem. B 120 , 5802-5809 (2016). PDF-download
  81. 2015


  82. 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), Nano Lett. 15 , 8229-8239 (2015). PDF-download
  83. Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015). PDF-download
  84. Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy, (Anatoly B. Kolomeisky), Biophys. J. 109, 459-460 (2015). PDF-download
  85. 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). PDF-download
  86. 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). PDF-download
  87. Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.), J. Chem. Phys. 143, 105102 (2015). PDF-download
  88. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA,(A.A. Shvets and A.B.K.), J. Chem. Phys. 143, 245101 (2015). PDF-download
  89. Theoretical Analysis of Degradation Mechanisms in the Formation of Morphogen Gradients, (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 143, 25102 (2015). PDF-download
  90. 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). PDF-download
  91. 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, 4653-4661 (2015). PDF-download
  92. The Role of Source Delocalization in the Development of Morphogen Gradients,(H. Teimouri and A.B.K), Phys. Biol. 12, 026006 (2015). PDF-download
  93. 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). PDF-download
  94. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors, (H. Teimouri, A.B.K. and K. Mehrabiani), J. Phys. A 48, 065001 (2015). PDF-download
  95. 2014


  96. Unveiling the Hidden Structure of Complex Stochastic Biochemical Networks, (A. Valleriani, X. Li and A.B.K.), J. Chem. Phys. 140, 064101 (2014). PDF-download
  97. Development of Morphogen Gradient: The Role of Dimension and Discreteness, (H. Teimouri and A.B.K.), J. Chem. Phys. 140, 085102 (2014). PDF-download
  98. A Simple Kinetic Model for Singlet Fission: A Role of Electronic and Entropic Contributions to Macroscopic Rates,(A.B.K., X. Feng and A.I. Krylov), J. Phys. Chem. C 118, 5188-5195 (2014). PDF-download
  99. A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins, (X. Li and A.B.K.), J. Phys. Chem. B 118, 2966-2972 (2014). PDF-download
  100. Pathway Structure Determination of Complex Stochastic Networks with Non-Exponential Dwell Times, (X. Li, A.B.K. and A. Valleriani), J. Chem. Phys. 140, 184102 (2014). PDF-download
  101. 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.K. and J. Iwahara), Nucl. Acids Res. 42, 7039-7046 (2014). PDF-download
  102. Bulk Induced Phase Transitions in Driven Diffusive Systems, (Y.-Q. Wang, R. Jiang, A.B.K. and M.-B. Hu), Sci. Rep. 4, 5459 (2014). PDF-download
  103. Stochastic Kinetics on Networks: When Slow is Fast,(X. Li, A.B.K. and A. Valleriani), J. Phys. Chem. B 118, 10419-10425 (2014). PDF-download
  104. Theoretical Analysis of Microtubule Dynamics at All Times, (X. Li and A.B.K.), J. Phys. Chem. B 118, 13777-13784 (2014). PDF-download
  105. Dissecting the Effect of Morphology on the Rates of Singlet Fission: Insights from Theory,(X. Feng, A.B.K., and A.I. Krylov), J. Phys. Chem. C 118, 19608-19617 (2014). PDF-download
  106. Single-Molecule FRET Studies of HIV TAR-DNA Hairpin Unfolding Dynamics, (J. Chen, N.K. Poddar, L.J. Tauzin, D. Cooper, A.B.K. and C.F. Landes), J. Phys. Chem. B 118, 12130-12139 (2014). PDF-download
  107. 2013


  108. Measuring Forces at the Leading Edge: A Force Assay for Cell Motility, (B. Farrell, F. Qian, A.B.K., B. Anwari and W.E. Brownell), Integr. Biol. 5, 204-214 (2013). PDF-download
  109. Dynamics of Force Generation by Confined Actin Filaments, (X. Banquy, G.W. Greene, B. Zappone, A.B.K. and J.N. Israelachvili), Soft Matter 9, 2389-2392 (2013). PDF-download
  110. Synthesis and Single-Molecule Imaging of Highly Mobile Adamantane-Wheeled Nanocars, (P.-L. E. Chu, L.-Y. Wang, S. Khatua, A.B.K., S. Link and J.M. Tour), ACS Nano 7, 35-41 (2013). PDF-download
  111. Phase Diagram Structures in a Periodic One-Dimensional Exclusion Process, (R. Jiang, Y.-Q. Wang, A.B.K., W. Huang, M.-B. Hu and Q.-S. Wu), Phys. Rev. E 87, 012107 (2013). PDF-download
  112. All-Time Dynamics in Complex Continuous-Time Random Walk Models, (H. Teimouri and A.B.K.), J. Chem. Phys. 138, 084110 (2013). PDF-download
  113. Analysis of Cooperative Behavior in Multiple Kinesins Motor Protein Transport by Varying Structural and Chemical Properties, (K. Uppulury, A.K. Efremov, J.W. Driver, D.K. Jamison, M.R. Diehl and A.B.K.), Cell. Mol. Bioeng. 6, 38-47 (2013). PDF-download
  114. Mechanisms of Protein Binding to DNA: Statistical Interactions are Important, (A.B.K.), Biophys. J. 104, 966-967 (2013). PDF-download
  115. Physics of Protein Motility and Motor Proteins. PREFACE (A.B.K.)J. Phys.: Condens. Matter 25, 370301 (2013). PDF-download
  116. Theoretical Analysis of Microtubules Dynamics Using a Physical-Chemical Description of Hydrolysis(X. Li and A.B.K.), J. Phys. Chem. B 117, 9217-9223 (2013). PDF-download
  117. Mechanisms and Topology Determination of Complex Chemical and Biological Network Systems from First-Passage Theoretical Approach, (X. Li and A.B.K.), J. Chem. Phys. 139, 144106 (2013).PDF-download
  118. Speed-Selectivity Paradox in the Protein Search for Targets on DNA: Is It Real or Not?(A. Veksler and A.B.K.), J. Phys. Chem. B 117, 12695 (2013). PDF-download
  119. 2012


  120. Random Hydrolysis Controls the Dynamic Instability of Microtubules, (R. Padinhateeri, A.B.K. and D. Lacoste), Biophysical J. 102, 1274-1283 (2012). PDF-download
  121. How to Accelerate Protein Search on DNA: Location and Dissociation, (A.B.K. and A. Veksler), J. Chem. Phys. 136, 125101 (2012). PDF-download
  122. Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars, (A.V. Akimov, C. Williams and A.B.K.), J. Phys. Chem. C 116, 13816-13826 (2012). PDF-download
  123. How the Interplay between Mechanical and Nonmechanical Interactions Affects Multiple Kinesin Dynamics, (K. Uppulury, A.K. Efremov, J.W. Driver, D.K. Jamison, M.R. Diehl and A.B.K.), J. Phys. Chem. B 116, 8846-8855 (2012). PDF-download
  124. Unidirectional Rolling of Nanocars Induced by Electric Field, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 116, 22595-22601 (2012). PDF-download
  125. 2011


  126. Spontaneous Symmetry Breaking on a Multiple-Channel Hollow Cylinder, (R. Wang, A.B.K. and M. Liu), Phys. Lett. A 375, 318-323 (2011). PDF-download
  127. Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions and Molecular Sizes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 125-131 (2011). PDF-download
  128. On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface, (I.V. Kupchenko, A.A. Moskovsky, A.V. Nemukhin and A.B.K.), J. Phys. Chem. C 115, 108-111 (2011). PDF-download
  129. How Interactions Control Molecular Transport in Channels, (A.B.K. and K. Uppulury), J. Stat. Phys. 142, 1268-1276 (2011). PDF-download
  130. Physics of Protein-DNA Interactions: Mechanisms of Facilitated Target Search,(A.B.K.), Perspective article, Phys. Chem. Chem. Phys. 13, 2088-2095 (2011). PDF-download
  131. Michaelis-Menten Relation for Complex Enzymatic Networks, (A.B.K.), J. Chem. Phys. 134, 155101 (2011). PDF-download
  132. Productive Cooperation among Processive Motors Depends Inversely on Their Mechanochemical Efficiency, (J.W. Driver, D.K. Jamison, K. Uppulury, A.R. Rogers, A.B.K., and M.R. Diehl), Biophys. J. 101, 386-395 (2011). PDF-download
  133. Current Reversal and Exclusion Processes with History-Dependent Random Walks, (J.H.P. Schulz, A.B.K. and E. Frey), Europhys. Lett. 95, 30004 (2011). PDF-download
  134. Formation of a Morphogen Gradient: Acceleration by Degradation, (A.B.K.), J. Phys. Chem. Lett. 2, 1502-1505 (2011). PDF-download
  135. Molecular Dynamics Study of Crystalline Molecular Gyroscopes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 13584-13591 (2011). PDF-download
  136. Recursive Taylor Series Expansion Method for Rigid-Body Molecular Dynamics, (A.V. Akimov and A.B.K.), J. Theor. Chem. Comp. 7, 3062-3071 (2011). PDF-download
  137. 2010


  138. Facilitated Search of Proteins on DNA: Correlations are Important,(R.K. Das and A.B.K.), Phys. Chem.-Chem. Phys. 12, 2999-3004 (2010). PDF-download
  139. Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel, (J. Lin, A.B.K. and A. Meller), Phys. Rev. Lett. 104, 158101 (2010). PDF-download
  140. Dynamics of Molecular Motors in Reversible Burnt-Bridge Models (M.N. Artyomov, A.Y. Morozov and A.B.K.), Condens. Matter Phys. 13, 23801 (2010). PDF-download
  141. Polymer Translocation through Pores with Complex Geometry (A. Mohan, A.B.K. and M. Pasquali), J. Chem. Phys. 133, 024902 (2010). Selected by American Institute of Physics for press release. PDF-download
  142. Coupling between Motor Proteins Determines Dynamic Behaviors of Motor Protein Assemblies, (J.W. Driver, A.R. Rogers, D.K. Jamison, R.K. das, A.B. K. and M.R. Diehl), Phys. Chem. Chem. Phys. 12, 10398-10405 (2010). PDF-download
  143. Rigid-Body Molecular Dynamics of the Fullerene-Based Nanocars on the Metallic Surfaces, (S.S. Konyukhov, I.V. Kupchenko, A.A. Moskovsky, A.V. Nemukhin, A.V. Akimov and A.B.K.), J. Chem. Theor. Comp. 6, 2581-2590 (2010). PDF-download
  144. 2009


  145. Micrometer-Scale Translation and Monitoring of Individual Nanocars on Glass, (S. Khatua, J.M. Guerrero, K. Claytor, G. Vives, A.B.K., J.M. Tour and S. Link), ACS Nano 3, 351-356 (2009). PDF-download
  146. Dynamic Properties of Molecular Motors in the Divided-Pathway Model (R.K. Das and A.B.K.), Phys. Chem.-Chem. Phys. 11, 4815-4820 (2009). PDF-download
  147. Dynamics of Thioethers Molecular Rotors: Effect of Surface Interactions and Chain Flexibility, (H.L. Tierney, A.E. Baber, E.C.H. Sykes, A. Akimov and A.B.K.), J. Phys. Chem. C 113, 10913-10920 (2009). PDF-download
  148. Non-Equilibrium Dynamics of Single Polymer Adsorption to Solid Surfaces, (D. Panja, G.T. Barkema and A.B.K.), J. Phys. Condens. Matter 21, 242101 (2009). PDF-download
  149. Continuous-Time random Walks at All Times, (A.B.K.), J. Chem. Phys. 131, 234114 (2009). PDF-download
  150. 2008


  151. How Proteins Translocate Through Pores: Memory is Important (A.B.K.),Biophys. J. 94, 1547 (2008). PDF-download
  152. Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport across Membrane Channels(A.B.K. and S. Kotsev), J. Chem. Phys. 128, 085101 (2008). PDF-download
  153. Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 095002 (2008). PDF-download
  154. Protein-DNA Interactions: Reaching and Recognizing the Targets(A.G. Cherstvy, A.B.K. and A.A. Kornyshev ), J. Phys. Chem. B 112, 4741-4750 (2008). PDF-download
  155. Molecular Dynamics of Surface-Moving Thermally Driven Nanocars (A. Akimov, A.V. Nemukhin, A. Moskovsky, A.B.K. and J.M. Tour), J. Chem. Theor. Comp. 4, 652-656 (2008). PDF-download
  156. Effect of Charge Distribution on the Translocation of an Inhomogeneously Charged Polymer Through a Nanopore (A. Mohan, A.B.K. and M. Pasquali), J. Chem. Phys. 128, 125104 (2008). PDF-download
  157. Molecular Motors Interacting with Their Own Tracks(M.N. Artyomov, A.Y. Morozov and A.B.K.), Phys. Rev. E 77, 040901(R) (2008). PDF-download
  158. Interaction Between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins,(R.K. Das and A.B.K.), Phys. Rev. E 77, 061912 (2008). PDF-download
  159. Spatial Fluctuations Affect the Dynamics of Motor Proteins(R.K. Das and A.B.K.), J. Phys. Chem. B 112, 11112-11121(2008). PDF-download
  160. Translational and Rotational Dynamics of Individual Single-Walled Carbon Nanotubes in Aqueous Suspension , (D.A. Tsyboulski, S.M. Bachilo, A.B.K. and R.B. Weisman), ACS Nano 2, 1770-1776 (2008). PDF-download
  161. Parallel Coupling of Symmetric and Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 465001 (2008). PDF-download
  162. Investigation of Asymmetric Exclusion Processes with Disorder: Effect of Correlation, (M.E. Foulaadvand, A.B.K. and H. Teimouri), Phys. Rev. E 78, 061116 (2008). PDF-download
  163. 2007


  164. Direct Measurement of the Dissociation Kinetics of Escherichia coli Exonuclease I from Single Stranded DNA Using a Nanopore (B. Hornblower, A. Combs, R. Whitaker, A.B.K., A. Meller and M. Akeson), Nature Methods 4, 315-317 (2007). PDF-download
  165. Spontaneous Symmetry Breaking in Two-Channel Asymmetric Exclusion Processes with Narrow Entrances (E.Pronina and A.B.K.), J. Phys. A: Math. Theor. 40, 2275-2286 (2007). PDF-download
  166. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry (A.B.K.), Phys. Rev. Lett. 98, 048105 (2007). PDF-download
  167. Solutions of Burnt-Bridge Model for Molecular Motors Transport(A. Morozov, E. Pronina, A.B.K. and M.N. Artyomov), Phys. Rev. E 75, 031910 (2007). PDF-download
  168. Dynamic Properties of Molecular Motors in Burnt-Bridge Models (M.N. Artyomov, A. Y. Morozov, E. Pronina and A.B.K.), J. Stat. Mech. P08002 (2007). PDF-download
  169. Translocation of Polymers with Folded Configurations across Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 127, 185103 (2007). PDF-download
  170. Dynamic Properties of Molecular Motor Dimers in Burnt-Bridge Models (A. Y. Morozov and A.B.K.), J. Stat. Mech. P12008 (2007). PDF-download
  171. 2006


  172. Dynamics of Polymer Translocation Through Nanopore: Theory Meets Experiments (S. Matysiak, A. Montesi, M. Pasquali, A.B.K. and C. Clementi), Phys. Rev. Lett. 96, 118103 (2006). PDF-download
  173. ATP Hydrolysis Stimulates Large Length Fluctuations in Single Actin Filaments (E.B.Stukalin and A.B.K.), Biophys. J. 90, 2673-2685 (2006). PDF-download
  174. Dynamic Phase Transitions in Coupled Motor Proteins (E.B.Stukalin and A.B.K.), Phys. Rev. E 73, 031922 (2006). PDF-download
  175. Transport of Single Molecules Along the Periodic Parallel Lattices with Coupling (E.B.Stukalin and A.B.K.), J. Chem. Phys. 124, 204901 (2006). PDF-download
  176. Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 125, 084906 (2006). PDF-download
  177. Asymmetric Coupling in Two-Channel Simple Exclusion Processes (E. Pronina and A.B.K.), Physica A 372, 12-21 (2006). PDF-download
  178. 2005


  179. Steady-State Properties of a Totally Asymmetric Exclusion Process with Periodic Structure Rates( G. Lakatos, T. Chou and A.B.K.), Phys. Rev. E. 71, 011103 (2005). PDF-download
  180. Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach (E.B.Stukalin and A.B.K.), J. Chem. Phys. 122, 104903 (2005). PDF-download
  181. Understanding Mechanochemical Coupling in Kinesins Using First-Passage Time Processes (A.B.K., A. Popov and E.B. Stukalin), Phys. Rev. E 71, 031902 (2005). PDF-download
  182. Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach (W. Pan, A.B.K. and P.G. Vekilov), J. Chem. Phys. 122, 174905 (2005).PDF-download
  183. Dynamic Force Spectroscopy of Glycoprotein Ib-IX Mutants and von Wildebrand Factor (M. Arya, A.B.K., G.M. Romo, M.A. Cruz, J.A. Lopez and B. Anvari) , Biophys. J. 88, 4391-4401 (2005). PDF-download
  184. Coupling of Two Motor Proteins: a New Motor Can Move Faster (E.B. Stukalin, H. Phillips III and A.B.K.), Phys. Rev. Lett. 94, 238101 (2005) . PDF-download
  185. Kinetics of Two-Step Nucleation of Crystals (D. Kashchiev, P. Vekilov and A.B.K.), J. Chem. Phys. 122, 244706 (2005). PDF-download
  186. Theoretical Investigation of Totally Asymmetric Simple Exclusion Processes on Lattices with Junctions (E. Pronina and A.B.K.), J. Stat. Mech., P07010 (2005). PDF-download
  187. Thermodynamics and Phase Transitions of Electrolytes on Lattices with Different Discretization Parameters (M.N. Artyomov and A.B.K.), Mol. Phys. 103, 2863-2872 (2005). PDF-download
  188. Dynamic Properties of Motor Proteins with Two Subunits (A.B.K. and H. Phillips III), J. Phys. Cond. Matter 17, S3887-S3899 (2005). PDF-download
  189. Monte Carlo Simulations of Rigid Biopolymer Growth Processes(Jenny Son, G. Orkoulas and A.B.K.), J. Chem. Phys. 123, 124902 (2005). PDF-download
  190. 2004


  191. Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects ( L.B. Shaw, A.B.K. and K.H. Lee)), J. Phys. A: Math. Gen. 37 2105-2113 (2004). PDF-download
  192. Polymers Dynamics in Repton Model at Large Fields (A.B.K and A. Drzewinski), J. Chem. Phys. 120 7784-7791 (2004). PDF-download
  193. Simple Growth Models of Rigid Multifilament Biopolymers (E.B.Stukalin and A.B.K.), J. Chem. Phys. 121, 1097-1104 (2004). PDF-download
  194. Two-Channel Totally Asymmetric Exclusion Processes(E. Pronina and A.B.K.), J. Phys. A: Math. Gen. 37, 9907-9918 (2004). PDF-download
  195. 2003


  196. The Effect of Detachments in Asymmetric Simple Exclusion Processes(N. Mirin and A.B.K.), J.Stat.Phys.,110,811-823 (2003). PDF-download
  197. A Simple Kinetic Model Describes the Processivity of Myosin V(A.B.K. and M.E.Fisher), Biophys. J.,84,1642-1650 (2003). PDF-download
  198. Lattice Models of Ionic Systems with Charge Asymmetry(M.N.Artyomov, V.Kobelev and A.B.K.), J.Chem. Phys. 118, 6394-6402 (2003). PDF-download
  199. Polymer Translocation Through a Long Nanopore (A.B.K. and E.Slonkina), J. Chem. Phys. 118, 7112-7118 (2003). PDF-download
  200. Localized Shocks in Driven Diffusive Systems without Particle Number Conservation (V. Popkov, A. Rakos, G.M. Schutz, R.D. Willmann and A.B.K.), Phys. Rev. E 67, 066117 (2003). PDF-download
  201. Thermodynamics of Electrolytes on Anisotropic Lattices (V. Kobelev, A.B.K and A.Z. Panagiotopoulos), Phys. Rev. E 68, 066110 (2003). PDF-download
  202. 2002


  203. Lattice Models of Ionic Systems ( V. Kobelev, A.B.K. and M.E.Fisher), J.Chem.Phys. 116, 7589-7598 (2002). PDF-download
  204. Anisotropic Lattice Models of Electrolytes (V.Kobelev and A.B.K.), J.Chem.Phys.,117,8879-8885 (2002). PDF-download
  205. 2001


  206. Force-Velocity Relation for Growing Microtubules (A.B.K. and M.E.Fisher) Biophys. J. 80, 149-154 (2001). PDF-download
  207. Simple Mechanochemistry Describes the Dynamics of Kinesin Molecules (M.E.Fisher and A.B.K), Proc. Natl. Acad. Sci. USA, 98, 7748-7753 (2001). PDF-download
  208. Exact Results for Parallel Chains Kinetic Models of Biological Transport(A.B.K.), J. Chem. Phys. 115 7253-7259 (2001). PDF-download
  209. 2000


  210. Periodic Sequential Kinetic Models with Jumping, Branching and Deaths (A.B.K. and M.E.Fisher), Physica A 279, 1-20 (2000). PDF-download
  211. Extended Kinetic Models with Waiting-Time Distributions: Exact Results (A.B.K. and M.E.Fisher), J. Chem. Phys. 113, 10867-10877 (2000). PDF-download
  212. 1999


  213. The Force Exerted by a Molecular Motor (M.E.Fisher and A.B.K.), Proc. Natl. Acad. Sci. USA, 96, 6597-6602 (1999). PDF-download
  214. Model of the Hydrophobic Interaction(A.B.K. and B.Widom), Faraday Discussion, 112, 81-89 (1999). PDF-download
  215. Molecular Motors and the Forces they Exert(M.E.Fisher and A.B.K.), Proc. NATO Advanced Research Workshop, May 1999, Budapest, Statistical Physics Applied to Practical Problems, (Elsevier, 1999), and Physica A 274, 241-266 (1999). PDF-download
  216. 1998


  217. Asymmetric Simple Exclusion Model with Local Inhomogeneity (A.B.K.), J. Phys. A: Math. Gen., 31, 1153-1164 (1998). PDF-download
  218. Phase Diagram of One-Dimensional Driven Lattice Gases with Open Boundaries (A.B.K., G.M.Schütz, E.B.Kolomeisky, and J.P.Straley), J. Phys. A: Math. Gen., 31, 6911-6919 (1998). PDF-download
  219. A Simplified ``Ratchet" Model of Molecular Motors(A.B.K. and B.Widom ), J. Stat. Phys., 93, 633-645 (1998).
  220. 1997


  221. Fluctuations in the Structure of Interfaces (D.J.Bukman, A.B.K., and B.Widom), Coll. Surf. A: Physicochem. Eng. Asp. 128, 119-128 (1997). PDF-download
  222. Exact Solutions for a Partially Asymmetric Exclusion Model with Two Species (A.B.K.), Physica A, 245, 523-533 (1997). PDF-download
  223. 1996


  224. An Invariance Property of the Repton Model(A.B.K. and B.Widom), Physica A, 229, 53-60 (1996). PDF-download
  225. 1995


  226. A High-Resolution Fourier Transform Infrared Study of the n3, n4, and n5 Bands of Deuterated Formyl Chloride (DCOCl) (D.-L.Joo, J.Laboy, A.B.K., Q.Zhuo, D.J.Clouthier, C.P.Chan, A.J.Merer, R.H.Judge), J. Mol. Spect. 170, 346-355 (1995). PDF-download
  227. 1992


  228. Replica-Scaling Analysis of Diffusion in Quenched Correlated Random Media (A.B.K. and E.B.Kolomeisky), Phys. Rev. A (Rapid Communication), 45(8), R5327-5330 (1992). PDF-download