Publications

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.

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, 2019.
  6. Organization of Intracellular Transport (Q. Wang and A.B.K.), in “Physics of Molecular and Cellular Processes”, Ed.: K. Blagoev and H. Levine, Springer Nature, 2022.
  7. How to Find Targets That are Always Hidden: Nucleosome-Covered DNA and Pioneer Transcription Factors (A. Mondal, C. Felipe and A.B.K.), in “The Target Problem”, Ed.: D.S. Grebenkov, R. Metzler and G. Oshanin, Springer Nature, 2023.

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 Processive Cytoskeletal Motors (R.T. McLaughlin, M.R. Diehl and A.B.K.), Soft Matter, 12, 14-21. (2016). PDF-download
  5. 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
  6. 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
  7. Mechanisms of the 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.), J. Phys. Chem B 124, 9289-9296 (2020). PDF-download
  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 23, 21399-21406 (2021). PDF-download
  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, e1612 (2022). PDF-download
  13. Can We Understand the Microscopic Mechanisms of Tumor Formation by Analyzing the Dynamics of Cancer Initiation? (H. Teimouri and A.B.K.), Feature Article, Europhysics Letters, 137, 27001 (2022). PDF-download

PUBLICATIONS

      1. 2024

      1. Molecular Mechanisms of Precise Timing in Cell Lysis (A. Mondal, H. Teimouri and A.B.K.) submitted to Proc. Natl. Acad. Sci. USA (2024).
      2. Theoretical Understanding of Dynamic Catalysis (P. Jangid, S. Chaud-
        hury and A.B.K) submitted to ACS Catalysis (2024).
      3. Physical-Chemical Approach to Desing Drugs with Multiple Targets (A.
        Medvedeva, S. Domakhina, C. Vasnetsov, V. Vasnetsov and A.B.K.), submited
        to J. Phys. Chem. Lett. (2024). PDF – download
      4. Brownian Diffusion of Hexagonal Boron Nitride Nanosheets and Graphene in Two Dimensions
        (U. Umezaki, A.D. Smith McWilliams, Z. Tang, Z.M. Sonia He, I.R. Siqueira,
        S.J. Corr, H. Ryu, A.B.K., M. Pasquali and A. Marti, to appear in ACS Nano
        (2024). PDF – download

        2023

      5. Differences in Relevant Physicochemical Properties Correlate with Synergistic Activity of Antimicrobial Peptides, (A. Medvedeva, H. Teimouri and A.B.K.), submitted to J. Theor. Chem. Comp. (2023). PDF – download

      6. Why Nucleosome Breathing Dynamics is Asymmetric? (A. Mondal and A.B.K.), submitted to PNAS Nexus (2023). PDF – download

      7. Increasing Heterogeneity in Antimicrobial Peptide Combinations Enhances Their Synergistic Activities (T.N. Nguyen, H. Teimouri and A.B.K.), J. Phys. Chem. Lett. 14 8405-8411 (2023). PDF – download

      8. How Heterogeneity Affects Cooperative Communications within Single Nanocatalysts, (B. Punia, S. Chaudhury and A.B.K.), J. Phys. Chem. Lett. 14 8227-8234 (2023). PDF – download

      9. Assembly of Synaptic Protein-DNA Complexes: Critical Role of Non-Specific Interactions, (S. Vemulapalli, M. Hashemi, A.B.K. and Y.L. Lyubchenko), Int. J. Mol Sci. 24, 9800 (2023). PDF – download

      10. The Role of Nucleosome Sliding in Protein Target Search for Covered DNA Sites, (A. Mondal and A.B.K.), J. Phys. Chem. Lett. 14, 7073-7082 (2023). PDF – download

      11. Predicting Antimicrobial Activity for Untested Peptide-Based Drugs Using Collaborative Filtering and Link Prediction, (A. Medvedeva, H. Teimouri and A.B.K.), J. Chem. Information and Modeling 63, 36973704 (2023). PDF – download

      12. Dynamics of Single-Base Editing: Theoretical Analysis, (V. Vardanyan, Q. Wang and A.B.K.), J. Chem. Phys. 158, 245101 (2023). PDF – download

      13. Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors, (A. Mondal, C. Felipe and A.B.K.), J. Phys. Chem. Lett. 14, 4096-4103 (2023). PDF – download

      14. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy, (T. Midha, J. Mallory, A.B.K. and O. Igoshin), J. Phys. Chem. Lett. 14, 3422-3429 (2023). PDF – download

      15. Theoretical Understanding of Evolutionary Dynamics on Inhomogeneous Networks, (H. Teimouri, D. Sattari Khavas, C. Spaulding, C. Li and A.B.K.), Phys. Biol. 20, 036003 (2023). PDF – download

      16. Dynamics of Chemical Reactions on Single Nanocatalysts with Heterogeneous Active Sites, (S. Chaudhury, P. Jangid and A.B.K.), J. Chem. Phys. 158, 074101 (2023). PDF – download

      17. Bacteria-Specific Features Selection for Enhanced Antimicrobial Peptide Activity Predictions Using Machine-Learning Methods, (H. Teimouri, A. Medvedeva and A.B.K.), J. Chem. Information and Modeling 66, 1723-1733 (2023). PDF – download

        2022

      18.  Microscopic Mechanisms of Cooperative Communications with Single Nanocatalysts. (B. Punia, S. Chaudhury and A.B.K.), Proceedings of the National Academy of Sciences 119 (3), e2115135119 (2022). PDF – download
      19. DLPacker: Deep Learning for Prediction of Aminoacid Side Chain Conformations in Proteins. (M. Misiura, R. Shroff, R. Thyer and A.B.K.), Proteins 90, 1278-1290 (2022). PDF – download
      20. Theoretical Study of Active Secondary Transport: Unexpected Differences in Molecular Mechanisms for Antiporters and Symporters. (A. Berlaga and A.B.K.), submitted to J. Chem. Phys. (2022). PDF – download
      21. The Energy Cost and Optimal Design of Networks for Biological Discrimination. (Q. Yu, A.B.K. and O.A. Igoshin), J. Roy. Soc. Interface 19, 20210883 (2022). PDF – download
      22. Formation of Cellular Close-Ended Tunneling Nanotubes through Mechanical Deformation. (M. Chang, O.C. Lee, G. Bu, J. Oh, N.O. Yunn, S.H. Ryu, H.B. Kwon, A.B.K., S.H. Shim,
        J. Doh, J.H. Jeon and J.B. Lee)        , Sci. Adv. 8, eabj3995 (2022). PDF – download
      23. The Role of Extended range of Interactions in the Dynamics of Interacting Molecular Motors. (C. Spaulding, H. Teimouri, S.L. Narasimhan and A.B.K), J. Phys. A. 55, 255601 (2022). PDF – download
      24. How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA. (C. Felipe, J. Shin and A.B.K.), J. Phys. Chem. B 126, 4061-4068 (2022). PDF – download
      25. Understanding Mechanisms of Secondary Active Transport by Analyzing the Effects of Mutations and Stoichiometry. (A. Berlaga and A.B.K.), J. Phys. Chem. Lett. 13, 5405-5412 (2022). PDF – download
      26. The Role of Spatial Structures of Tissues in Cancer Initiation Dynamics. (C. Spaulding, H. Teimouri and A.B.K.), Phys. Biol. 19, 056003 (2022). PDF – download
      27. Light-activated molecular machines are fast-acting broa.d-spectrum antibacterials that target the membrane (A.L. Santos, D.D. Liu, A.K. Reed, A.M. Wyderka,A. van Venrooy, J.T. Li, V.D. Li, M. Misiura, O. Samoylova, J.L. Beckham, C. Ayala-Orozco, A.B.K. Kolomeisky, L.B. Alemany, A. Oliver, G.P. Tegos and J.M. Tour), Sci. Adv. 8, eabm2055 (2022). PDF – download
      28. Optimal Pathways Control Fixation of Multiple Mutations during Cancer Initiation. (H. Teimouri, C. Spaulding and A.B.K.), Biophys. J. 121, 3698-3705 (2022). PDF – download
      29. Cooperativity in Bacterial Membrane Association Controls the Synergistic Activities of Antimicrobial Peptides, (T.N. Nguyen, H. Teimouri, A. Medvedeva and A.B.K.), J. Phys. Chem. B 126, 7365-7372 (2022). PDF – download
      30. Nanorings to Probe Mechanical Stress of Single-Stranded DNA Mediated by the DNA Duplex, (K. Zagorski, T. Stormberg, M. Hashemi, A.B.K. and Y.L. Lyubchenko), Int. J. Mol. Sci. 23, 12916 (2022). PDF – download
      31. Cation-π Interactions and Their Role in Assembling Collagen Triple Helices, (C.C. Cole, M. Misiura, S.A.H. Hulgan,C.M. Peterson, J.W. Williams, A.B.K., and J.D. Hartgerink), Biomacromolecules 23, 4645-4654 (2022). PDF – download
      32. Beyond Sequence: Internucleosomal Interactions Dominate Array Assembly, (Y. Wang, T. Stromberg, H. Mohtadin, A.B.K. and Y. Lyubchenko), J. Phys. Chem. B 126, 10813-10821 (2022).

        2021

      33. Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach. (B. Punia, S. Chaudhury and A.B.K.), J. Phys. Chem. Lett. 12, 11802-11810 (2021). PDF – download
      34. A General Theoretical Framework to Design Base Editors with reduced Bystander Effects. (Q. Wang, J. Yangs, Z. Zhong, J.A. Vanegas, X. Gao and A.B.K.), Nature Communications 12, 6529 (2021). PDF – download
      35. Surface-Facilitated Trapping by Active Sites: From Catalysts to Viruses. (M. Misiura, A.M. Berezhkovskii, S.M. Bezrukov and A.B.K.), J. Chem. Phys. 155, 184106 (2021). PDF – download
      36. Steady-State Dynamics of Exclusion Process with Local Reversible Association of Particles. (A. Jindal, A.B.K. and A.K. Gupta), J. Stat. Phys. 185, 17 (2021). PDF – download
      37. Molecular Mechanisms of Active Transport in Antiporters: Kinetic Constraints and Efficiency. (A. Berlaga and A.B.K.), J. Phys. Chem. Lett. 12, 9599-9594 (2021). PDF – download
      38. Single-Cell Stochastic Modeling of the Action of Antimicrobial Peptides on bacteria. (H. Teimouri, Thao N. Nguyen and A.B.K.), J. Roy. Soc. Inter. 18, 20210392 (2021). PDF – download
      39. Temporal Order of Mutations Influences Cancer Initiation Dynamics. (H. Teimouri and A.B.K.), Physical Biology 18, 056002 (2021). PDF – download
      40. 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
      41. 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
      42. 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
      43. 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
      44. 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
      45. 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
      46. 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

        2020

      47. 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
      48. 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
      49. 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
      50. 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
      51. 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
      52. 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
      53. 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
      54. 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
      55. 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
      56. 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
      57. 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
      58. 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
      59. 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
      60. A Mechanochemical Model of Transcriptional Bursting. (A. Klindziuk, B. Meadowcroft and A.B.K.), Biophys. J. 118, 1213-1220 (2020). PDF – download
      61. 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
      62. 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
      63. 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), J. Phys. Chem. B 124, 366-372
        (2020). PDF – download

        2019

      64. 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
      65. Target Search on DNA by Interacting Molecules: First-Passage Approach. (J. Shin and A.B.K.), J. Chem. Phys. 151, 125101 (2019). PDF – download
      66. 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
      67. 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
      68. 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
      69. 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
      70. 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
      71. 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
      72. 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
      73. 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
      74. 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
      75. 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

        2018

      76. 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
      77. 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
      78. 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
      79. Interactions in nonconserving driven diffusive systems (T. Midha, A.B.K. and A.K. Gupta), Phys. Rev. E 98, 042119 (2018). PDF – download
      80. Molecular Mechanism of the Inter-Head Coordination by  Inter-head  Tension in Cytoplasmic Dyneins (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
      81. 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
      82. 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
      83. 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
      84. Physical-Chemical Mechanisms of Pattern Formation during Gastrulation (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 148, 123302 (2018). PDF – download
      85. 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
      86. Surface-Assisted Dynamic Search Processes (J. Shin and A.B.K.), J. Phys. Chem. B 122, 2243-2250 (2018). PDF – download
      87. 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

        2017

      88. 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
      89. 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
      90. 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
      91. 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
      92. 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
      93. 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
      94. 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
      95. How Viruses Enter Cells: A Story behind Bacteriophage T4 (A.B.K.), Biophys. J. 113, 3-4 (2017). PDF – download
      96. 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
      97. 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
      98. 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
      99. 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

        2016

      100. 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
      101. 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
      102. 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
      103. 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
      104. 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
      105. Crowding on DNA in Protein Search for Targets (A.A. Shvets and A.B.K.), J. Phys. Chem. Lett. 7, 2502-2506 (2016). PDF – download
      106. 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
      107. 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
      108. 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
      109. 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
      110. 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

        2015

      111. 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
      112. Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015). PDF-download
      113. Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy, (Anatoly B. Kolomeisky), Biophys. J. 109, 459-460 (2015). PDF-download
      114. 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
      115. 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
      116. Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.), J. Chem. Phys. 143, 105102 (2015). PDF-download
      117. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA,(A.A. Shvets and A.B.K.), J. Chem. Phys. 143, 245101 (2015). PDF-download
      118. 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
      119. 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
      120. 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
      121. The Role of Source Delocalization in the Development of Morphogen Gradients,(H. Teimouri and A.B.K), Phys. Biol. 12, 026006 (2015). PDF-download
      122. 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
      123. 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

        2014

      124. 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
      125. Development of Morphogen Gradient: The Role of Dimension and Discreteness, (H. Teimouri and A.B.K.), J. Chem. Phys. 140, 085102 (2014). PDF-download
      126. 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
      127. 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
      128. 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
      129. 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
      130. 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
      131. 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
      132. Theoretical Analysis of Microtubule Dynamics at All Times, (X. Li and A.B.K.), J. Phys. Chem. B 118, 13777-13784 (2014). PDF-download
      133. 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
      134. 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

        2013

      135. 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
      136. 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
      137. 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
      138. 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
      139. All-Time Dynamics in Complex Continuous-Time Random Walk Models, (H. Teimouri and A.B.K.), J. Chem. Phys. 138, 084110 (2013). PDF-download
      140. 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
      141. Mechanisms of Protein Binding to DNA: Statistical Interactions are Important, (A.B.K.), Biophys. J. 104, 966-967 (2013). PDF-download
      142. Physics of Protein Motility and Motor Proteins. PREFACE (A.B.K.)J. Phys.: Condens. Matter 25, 370301 (2013). PDF-download
      143. 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
      144. 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
      145. 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

        2012

      146. Random Hydrolysis Controls the Dynamic Instability of Microtubules, (R. Padinhateeri, A.B.K. and D. Lacoste), Biophysical J. 102, 1274-1283 (2012). PDF-download
      147. How to Accelerate Protein Search on DNA: Location and Dissociation, (A.B.K. and A. Veksler), J. Chem. Phys. 136, 125101 (2012). PDF-download
      148. 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
      149. 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
      150. 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

        2011

      151. 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
      152. 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
      153. 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
      154. How Interactions Control Molecular Transport in Channels, (A.B.K. and K. Uppulury), J. Stat. Phys. 142, 1268-1276 (2011). PDF-download
      155. 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
      156. Michaelis-Menten Relation for Complex Enzymatic Networks, (A.B.K.), J. Chem. Phys. 134, 155101 (2011). PDF-download
      157. 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
      158. 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
      159. Formation of a Morphogen Gradient: Acceleration by Degradation, (A.B.K.), J. Phys. Chem. Lett. 2, 1502-1505 (2011). PDF-download
      160. Molecular Dynamics Study of Crystalline Molecular Gyroscopes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 13584-13591 (2011). PDF-download
      161. 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

        2010

      162. 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
      163. 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
      164. 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
      165. 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
      166. 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
      167. 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

        2009

      168. 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
      169. 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
      170. 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
      171. 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
      172. Continuous-Time random Walks at All Times, (A.B.K.), J. Chem. Phys. 131, 234114 (2009). PDF-download

        2008

      173. How Polymers Translocate Through Pores: Memory is Important (A.B.K.),Biophys. J. 94, 1547 (2008). PDF-download
      174. 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
      175. Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 095002 (2008). PDF-download
      176. 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
      177. 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
      178. 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
      179. 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
      180. 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
      181. 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
      182. 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
      183. Parallel Coupling of Symmetric and Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 465001 (2008). PDF-download
      184. 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

        2007

      185. 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
      186. 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
      187. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry (A.B.K.), Phys. Rev. Lett. 98, 048105 (2007). PDF-download
      188. 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
      189. 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
      190. Translocation of Polymers with Folded Configurations across Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 127, 185103 (2007). PDF-download
      191. Dynamic Properties of Molecular Motor Dimers in Burnt-Bridge Models (A. Y. Morozov and A.B.K.), J. Stat. Mech. P12008 (2007). PDF-download

        2006

      192. 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
      193. 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
      194. Dynamic Phase Transitions in Coupled Motor Proteins (E.B.Stukalin and A.B.K.), Phys. Rev. E 73, 031922 (2006). PDF-download
      195. 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
      196. Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 125, 084906 (2006). PDF-download
      197. Asymmetric Coupling in Two-Channel Simple Exclusion Processes (E. Pronina and A.B.K.), Physica A 372, 12-21 (2006). PDF-download

        2005

      198. 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
      199. Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach (E.B.Stukalin and A.B.K.), J. Chem. Phys. 122, 104903 (2005). PDF-download
      200. 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
      201. 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
      202. 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
      203. 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
      204. Kinetics of Two-Step Nucleation of Crystals (D. Kashchiev, P. Vekilov and A.B.K.), J. Chem. Phys. 122, 244706 (2005). PDF-download
      205. 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
      206. 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
      207. 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
      208. Monte Carlo Simulations of Rigid Biopolymer Growth Processes (Jenny Son, G. Orkoulas and A.B.K.), J. Chem. Phys. 123, 124902 (2005). PDF-download

        2004

      209. 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
      210. Polymers Dynamics in Repton Model at Large Fields (A.B.K and A. Drzewinski), J. Chem. Phys. 120 7784-7791 (2004). PDF-download
      211. Simple Growth Models of Rigid Multifilament Biopolymers (E.B.Stukalin and A.B.K.), J. Chem. Phys. 121, 1097-1104 (2004). PDF-download
      212. Two-Channel Totally Asymmetric Simple Exclusion Processes (E. Pronina and A.B.K.), J. Phys. A: Math. Gen. 37, 9907-9918 (2004). PDF-download

        2003

      213. The Effect of Detachments in Asymmetric Simple Exclusion Processes (N. Mirin and A.B.K.), J.Stat.Phys.,110,811-823 (2003). PDF-download
      214. 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
      215. 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
      216. Polymer Translocation Through a Long Nanopore (A.B.K. and E.Slonkina), J. Chem. Phys. 118, 7112-7118 (2003). PDF-download
      217. 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
      218. Thermodynamics of Electrolytes on Anisotropic Lattices (V. Kobelev, A.B.K and A.Z. Panagiotopoulos), Phys. Rev. E 68, 066110 (2003). PDF-download

        2002

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

        2001

      221. Exact Results for Parallel Chains Kinetic Models of Biological Transport (A.B.K.), J. Chem. Phys. 115 7253-7259 (2001). PDF-download
      222. 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
      223. Force-Velocity Relation for Growing Microtubules (A.B.K. and M.E.Fisher) Biophys. J. 80, 149-154 (2001). PDF-download

        2000

      224. Periodic Sequential Kinetic Models with Jumping, Branching and Deaths (A.B.K. and M.E.Fisher), Physica A 279, 1-20 (2000). PDF-download
      225. 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

        1999

      226. 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
      227. Model of the Hydrophobic Interaction (A.B.K. and B.Widom), Faraday Discussion, 112, 81-89 (1999). PDF-download
      228. 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

        1998

      229. Asymmetric Simple Exclusion Model with Local Inhomogeneity (A.B.K.), J. Phys. A: Math. Gen., 31, 1153-1164 (1998). PDF-download
      230. 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
      231. A Simplified “Ratchet” Model of Molecular Motors (A.B.K. and B.Widom ), J. Stat. Phys., 93, 633-645 (1998).

        1997

      232. 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
      233. Exact Solutions for a Partially Asymmetric Exclusion Model with Two Species (A.B.K.), Physica A, 245, 523-533 (1997). PDF-download

        1996

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

        1995

      235. 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

        1992

      236. 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