Kolomeisky Research Group Publications

Discover our groundbreaking research and published works that showcase our expertise.

Publications

 

2024

245. Linear-Decoupling Enables Accurate Speed and Accuracy Predictions for Copolymerization Processes (T. Midha, A.B.K. and O.A. Igoshin), submitted to J. Phys. Chem. Lett. (2024).

244. Theoretical Understanding on How Transcription factor Binding Stimulate Transcriptional Bursting (A. Mondal and A.B.K.), to appear in J. Phys. Chem. Lett. (2024)

243. Heterotrimeric Collagen Helix with High Specificity of Assembly Results in a Rapid Rate of Folding (Cole, C. C., Walker, D. R, Hulgan, S. A. H., Pogostin, B. H., Swain, J. W. R., Miller, M. D., Xu, W., Duella, R., Misiura, M., Wang, X., A.B.K., Philips, G. N. Jr and Hartgerink, J. D.), to appear in Nature Chemistry (2024).

242. Unraveling the Role of Physicochemical Differences in Predicting Protein-Protein Interactions (H. Teimouri, A. Medvedeva and A.B.K.), to appear in J. Chem. Phys. (2024).

241. Molecular Mechanisms of Precise Timing in Cell Lysis (A. Mondal, H. Teimouri and A.B.K.), to appear in Biophys. J. (2024).

240. Elucidating Physicochemical Features of Holin Proteins Responsible for Bacterial Cell Lysis (A. Mondal, H. Teimouri and A.B.K.), submitted to J. Phys. Chem. B (2024).

239. Chemoinformatics Insights on Molecular Jackhammers and Cancer Cells (C. Ayala-Orozco, H. Teimouri, A. Medvedeva, B. Li, A. Lathem, G. Li, A.B.K., and J.M. Tour), submitted to the Journal of Chemical Information and Modeling (2024).

238. Insights into Error Control Mechanisms in Biological Processes: Copolymerization and Enzyme-Kinetics revisited (T. Midha, A.B.K., and O.Igoshin, to appear in J. Phys. Chem. B (2024).

237. Molecular Mechanisms of Precise Timing in Cell Lysis (A. Mondal, H. Teimouri and A.B.K.) to appear in Biophys. J. (2024).

236. Theoretical Understanding of Dynamic Catalysis (P. Jangid, S. Chaudhury and A.B.K) to appear in J. Phys. Chem. C. (2024).

235. Morphology Transitions of SDS Coatings on Single-Wall Carbon Nanotubes (A. Alizadehmodjarad, S. Bachilo, A.B.K. and R.B. Weisman), J. Chem. Phys. C 128 6126-6132 (2024). PDF – download

234. How to Build Plasmon-Driven Molecular Jackhammers that Disassemble Cell Membranes and Cytoskeletons in Cancer (C. Ayala Orozco, G. Li, B. Li, V. Vardanyan, A.B.K. and J.M. Tour), Advanced Materials 2309910 (2024). PDF – download

234. Physical-Chemical Approach to Desing Drugs with Multiple Targets (A. Medvedeva, S. Domakhina, C. Vasnetsov, V. Vasnetsov and A.B.K.), (2024). PDF – download

233. 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, (2024). PDF – download


2023

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

231. Why Are Nucleosome Breathing Dynamics Asymmetric? (A. Mondal and A.B.K.), J. Phys. Chem. Lett. (2023). PDF – download

230. 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

229. 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

228. 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

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

226. 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

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

224. 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

223. 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

222. 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

221. 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

220. 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

  1.  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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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

  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. Temporal Order of Mutations Influences Cancer Initiation Dynamics. (H. Teimouri and A.B.K.), Physical Biology 18, 056002 (2021). PDF – download
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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

  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. A Mechanochemical Model of Transcriptional Bursting. (A. Klindziuk, B. Meadowcroft and A.B.K.), Biophys. J. 118, 1213-1220 (2020). PDF – download
  44. 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
  45. 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
  46. 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

  47. 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
  48. Target Search on DNA by Interacting Molecules: First-Passage Approach. (J. Shin and A.B.K.), J. Chem. Phys. 151, 125101 (2019). PDF – download
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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

  59. 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
  60. 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
  61. 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
  62. Interactions in nonconserving driven diffusive systems (T. Midha, A.B.K. and A.K. Gupta), Phys. Rev. E 98, 042119 (2018). PDF – download
  63. 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
  64. 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
  65. 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
  66. 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
  67. Physical-Chemical Mechanisms of Pattern Formation during Gastrulation (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 148, 123302 (2018). PDF – download
  68. 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
  69. Surface-Assisted Dynamic Search Processes (J. Shin and A.B.K.), J. Phys. Chem. B 122, 2243-2250 (2018). PDF – download
  70. 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

  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. How Viruses Enter Cells: A Story behind Bacteriophage T4 (A.B.K.), Biophys. J. 113, 3-4 (2017). PDF – download
  79. 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
  80. 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
  81. 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
  82. 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

  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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

  94. 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
  95. Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015). PDF-download
  96. Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy, (Anatoly B. Kolomeisky), Biophys. J. 109, 459-460 (2015). PDF-download
  97. 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
  98. 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
  99. Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.), J. Chem. Phys. 143, 105102 (2015). PDF-download
  100. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA,(A.A. Shvets and A.B.K.), J. Chem. Phys. 143, 245101 (2015). PDF-download
  101. 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
  102. 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
  103. 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
  104. The Role of Source Delocalization in the Development of Morphogen Gradients,(H. Teimouri and A.B.K), Phys. Biol. 12, 026006 (2015). PDF-download
  105. 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
  106. 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

  107. 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
  108. Development of Morphogen Gradient: The Role of Dimension and Discreteness, (H. Teimouri and A.B.K.), J. Chem. Phys. 140, 085102 (2014). PDF-download
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
  114. 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
  115. Theoretical Analysis of Microtubule Dynamics at All Times, (X. Li and A.B.K.), J. Phys. Chem. B 118, 13777-13784 (2014). PDF-download
  116. 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
  117. 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

  118. 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
  119. 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
  120. 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
  121. 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
  122. All-Time Dynamics in Complex Continuous-Time Random Walk Models, (H. Teimouri and A.B.K.), J. Chem. Phys. 138, 084110 (2013). PDF-download
  123. 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
  124. Mechanisms of Protein Binding to DNA: Statistical Interactions are Important, (A.B.K.), Biophys. J. 104, 966-967 (2013). PDF-download
  125. Physics of Protein Motility and Motor Proteins. PREFACE (A.B.K.)J. Phys.: Condens. Matter 25, 370301 (2013). PDF-download
  126. 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
  127. 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
  128. 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

  129. Random Hydrolysis Controls the Dynamic Instability of Microtubules, (R. Padinhateeri, A.B.K. and D. Lacoste), Biophysical J. 102, 1274-1283 (2012). PDF-download
  130. How to Accelerate Protein Search on DNA: Location and Dissociation, (A.B.K. and A. Veksler), J. Chem. Phys. 136, 125101 (2012). PDF-download
  131. 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
  132. 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
  133. 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

  134. 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
  135. 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
  136. 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
  137. How Interactions Control Molecular Transport in Channels, (A.B.K. and K. Uppulury), J. Stat. Phys. 142, 1268-1276 (2011). PDF-download
  138. 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
  139. Michaelis-Menten Relation for Complex Enzymatic Networks, (A.B.K.), J. Chem. Phys. 134, 155101 (2011). PDF-download
  140. 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
  141. 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
  142. Formation of a Morphogen Gradient: Acceleration by Degradation, (A.B.K.), J. Phys. Chem. Lett. 2, 1502-1505 (2011). PDF-download
  143. Molecular Dynamics Study of Crystalline Molecular Gyroscopes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 13584-13591 (2011). PDF-download
  144. 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

  145. 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
  146. 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
  147. 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
  148. 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
  149. 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
  150. 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

  151. 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
  152. 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
  153. 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
  154. 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
  155. Continuous-Time random Walks at All Times, (A.B.K.), J. Chem. Phys. 131, 234114 (2009). PDF-download

    2008

  156. How Polymers Translocate Through Pores: Memory is Important (A.B.K.),Biophys. J. 94, 1547 (2008). PDF-download
  157. 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
  158. Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 095002 (2008). PDF-download
  159. 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
  160. 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
  161. 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
  162. 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
  163. 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
  164. 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
  165. 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
  166. Parallel Coupling of Symmetric and Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 465001 (2008). PDF-download
  167. 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

  168. 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
  169. 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
  170. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry (A.B.K.), Phys. Rev. Lett. 98, 048105 (2007). PDF-download
  171. 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
  172. 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
  173. Translocation of Polymers with Folded Configurations across Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 127, 185103 (2007). PDF-download
  174. 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

  175. 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
  176. 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
  177. Dynamic Phase Transitions in Coupled Motor Proteins (E.B.Stukalin and A.B.K.), Phys. Rev. E 73, 031922 (2006). PDF-download
  178. 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
  179. Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 125, 084906 (2006). PDF-download
  180. Asymmetric Coupling in Two-Channel Simple Exclusion Processes (E. Pronina and A.B.K.), Physica A 372, 12-21 (2006). PDF-download

    2005

  181. 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
  182. Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach (E.B.Stukalin and A.B.K.), J. Chem. Phys. 122, 104903 (2005). PDF-download
  183. 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
  184. 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
  185. 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
  186. 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
  187. Kinetics of Two-Step Nucleation of Crystals (D. Kashchiev, P. Vekilov and A.B.K.), J. Chem. Phys. 122, 244706 (2005). PDF-download
  188. 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
  189. 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
  190. 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
  191. 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

  192. 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
  193. Polymers Dynamics in Repton Model at Large Fields (A.B.K and A. Drzewinski), J. Chem. Phys. 120 7784-7791 (2004). PDF-download
  194. Simple Growth Models of Rigid Multifilament Biopolymers (E.B.Stukalin and A.B.K.), J. Chem. Phys. 121, 1097-1104 (2004). PDF-download
  195. 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

  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

    2002

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

    2001

  204. Exact Results for Parallel Chains Kinetic Models of Biological Transport (A.B.K.), J. Chem. Phys. 115 7253-7259 (2001). PDF-download
  205. 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
  206. Force-Velocity Relation for Growing Microtubules (A.B.K. and M.E.Fisher) Biophys. J. 80, 149-154 (2001). PDF-download

    2000

  207. Periodic Sequential Kinetic Models with Jumping, Branching and Deaths (A.B.K. and M.E.Fisher), Physica A 279, 1-20 (2000). PDF-download
  208. 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

  209. 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
  210. Model of the Hydrophobic Interaction (A.B.K. and B.Widom), Faraday Discussion, 112, 81-89 (1999). PDF-download
  211. 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

  212. Asymmetric Simple Exclusion Model with Local Inhomogeneity (A.B.K.), J. Phys. A: Math. Gen., 31, 1153-1164 (1998). PDF-download
  213. 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
  214. A Simplified “Ratchet” Model of Molecular Motors (A.B.K. and B.Widom ), J. Stat. Phys., 93, 633-645 (1998).

    1997

  215. 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
  216. Exact Solutions for a Partially Asymmetric Exclusion Model with Two Species (A.B.K.), Physica A, 245, 523-533 (1997). PDF-download

    1996

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

    1995

  218. 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

  219. 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

 

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 and A.B.K.), in “The Target Problem”, Ed.: D.S. Grebenkov, R. Metzler and G. Oshanin, Springer Nature, 2024.

 

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

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