Kolomeisky Research Group Publications
Discover our groundbreaking research and published works that showcase our expertise.
Publications
Publications
2024
247. Stochastic Analysis of Human Ovarian Aging and Menopause Timing (A. Mondal, E. Tcherniak and A.B.K.), submitted to PNAS Nexus (2024).
246. How Dynamic Restructuring Impacts Intra-Particle Catalytic Cooperativity (B. Punia, S. Chaudhury and A.B.K.), submitted to J. Chem. Phys. (2024).
245. Oligomerization Can Enhance Synergistic Activity of Antimicrobial Peptides (A. Medvedeva, H. Teimouri and A.B.K.), to appear in Molecular Physics (2024).
244. Linear-Decoupling Enables Accurate Speed and Accuracy Predictions for Copolymerization Processes (T. Midha, A.B.K. and O.A. Igoshin), to ap-
pear in J. Phys. Chem. Lett. (2024).
243. How Transcription Factors Binding Stimulates Transcriptional Bursting Transcriptional Bursting (A. Mondal and A.B.K.), to appear in J. Phys. Chem. Lett. (2024).
242. 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).
241. Unraveling the Role of Physicochemical Differences in Predicting Protein-Protein Interactions (H. Teimouri, A. Medvedeva and A.B.K.), J. Chem. Phys. 161 045102 (2024).PDF - download
240. Molecular Mechanisms of Precise Timing in Cell Lysis (A. Mondal, H. Teimouri and A.B.K.), Biophys. J. 123 3090-3099 (2024). PDF - download
239. Elucidating Physicochemical Features of Holin Proteins Responsible for Bacterial Cell Lysis (A. Mondal, H. Teimouri and A.B.K.), J. Phys. Chem. B 128 7129-7140 (2024). PDF - download
238. 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), Journal of Chemical Information and Modeling 64 5570-5579 (2024). PDF - download
237. Insights into Error Control Mechanisms in Biological Processes: Copolymerization and Enzyme-Kinetics revisited (T. Midha, A.B.K., and O. Igoshin, J. Phys. Chem. B 128 5612-5622 (2024). PDF - download
236. Theoretical Understanding of Dynamic Catalysis (P. Jangid, S. Chaudhury and A.B.K), J. Phys. Chem. C 128 9077-9089 (2024). PDF - download
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.), J. Phys. Chem. Lett. 15, 1828−1835 (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). ACS Nano 18, 3, 2446–2454 (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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Temporal Order of Mutations Influences Cancer Initiation Dynamics. (H. Teimouri and A.B.K.), Physical Biology 18, 056002 (2021). PDF – download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- A Mechanochemical Model of Transcriptional Bursting. (A. Klindziuk, B. Meadowcroft and A.B.K.), Biophys. J. 118, 1213-1220 (2020). PDF – download
- 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
- 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
- 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
- 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
- Target Search on DNA by Interacting Molecules: First-Passage Approach. (J. Shin and A.B.K.), J. Chem. Phys. 151, 125101 (2019). PDF – download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Interactions in nonconserving driven diffusive systems (T. Midha, A.B.K. and A.K. Gupta), Phys. Rev. E 98, 042119 (2018). PDF – download
- 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
- 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
- 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
- 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
- Physical-Chemical Mechanisms of Pattern Formation during Gastrulation (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 148, 123302 (2018). PDF – download
- 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
- Surface-Assisted Dynamic Search Processes (J. Shin and A.B.K.), J. Phys. Chem. B 122, 2243-2250 (2018). PDF – download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- How Viruses Enter Cells: A Story behind Bacteriophage T4 (A.B.K.), Biophys. J. 113, 3-4 (2017). PDF – download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015). PDF-download
- Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy, (Anatoly B. Kolomeisky), Biophys. J. 109, 459-460 (2015). PDF-download
- 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
- 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
- Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.), J. Chem. Phys. 143, 105102 (2015). PDF-download
- Sequence Heterogeneity Accelerates Protein Search for Targets on DNA,(A.A. Shvets and A.B.K.), J. Chem. Phys. 143, 245101 (2015). PDF-download
- 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
- 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
- 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
- The Role of Source Delocalization in the Development of Morphogen Gradients,(H. Teimouri and A.B.K), Phys. Biol. 12, 026006 (2015). PDF-download
- 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
- 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
- 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
- Development of Morphogen Gradient: The Role of Dimension and Discreteness, (H. Teimouri and A.B.K.), J. Chem. Phys. 140, 085102 (2014). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
- Theoretical Analysis of Microtubule Dynamics at All Times, (X. Li and A.B.K.), J. Phys. Chem. B 118, 13777-13784 (2014). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
- All-Time Dynamics in Complex Continuous-Time Random Walk Models, (H. Teimouri and A.B.K.), J. Chem. Phys. 138, 084110 (2013). PDF-download
- 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
- Mechanisms of Protein Binding to DNA: Statistical Interactions are Important, (A.B.K.), Biophys. J. 104, 966-967 (2013). PDF-download
- Physics of Protein Motility and Motor Proteins. PREFACE (A.B.K.)J. Phys.: Condens. Matter 25, 370301 (2013). PDF-download
- 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
- 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
- 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
- Random Hydrolysis Controls the Dynamic Instability of Microtubules, (R. Padinhateeri, A.B.K. and D. Lacoste), Biophysical J. 102, 1274-1283 (2012). PDF-download
- How to Accelerate Protein Search on DNA: Location and Dissociation, (A.B.K. and A. Veksler), J. Chem. Phys. 136, 125101 (2012). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
- How Interactions Control Molecular Transport in Channels, (A.B.K. and K. Uppulury), J. Stat. Phys. 142, 1268-1276 (2011). PDF-download
- 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
- Michaelis-Menten Relation for Complex Enzymatic Networks, (A.B.K.), J. Chem. Phys. 134, 155101 (2011). PDF-download
- 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
- 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
- Formation of a Morphogen Gradient: Acceleration by Degradation, (A.B.K.), J. Phys. Chem. Lett. 2, 1502-1505 (2011). PDF-download
- Molecular Dynamics Study of Crystalline Molecular Gyroscopes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 13584-13591 (2011). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Continuous-Time random Walks at All Times, (A.B.K.), J. Chem. Phys. 131, 234114 (2009). PDF-download
2008
- How Polymers Translocate Through Pores: Memory is Important (A.B.K.),Biophys. J. 94, 1547 (2008). PDF-download
- 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
- Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 095002 (2008). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Parallel Coupling of Symmetric and Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 465001 (2008). PDF-download
- 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
- 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
- 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
- Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry (A.B.K.), Phys. Rev. Lett. 98, 048105 (2007). PDF-download
- 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
- 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
- Translocation of Polymers with Folded Configurations across Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 127, 185103 (2007). PDF-download
- 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
- 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
- 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
- Dynamic Phase Transitions in Coupled Motor Proteins (E.B.Stukalin and A.B.K.), Phys. Rev. E 73, 031922 (2006). PDF-download
- 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
- Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 125, 084906 (2006). PDF-download
- Asymmetric Coupling in Two-Channel Simple Exclusion Processes (E. Pronina and A.B.K.), Physica A 372, 12-21 (2006). PDF-download
2005
- 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
- Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach (E.B.Stukalin and A.B.K.), J. Chem. Phys. 122, 104903 (2005). PDF-download
- 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
- 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
- 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
- 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
- Kinetics of Two-Step Nucleation of Crystals (D. Kashchiev, P. Vekilov and A.B.K.), J. Chem. Phys. 122, 244706 (2005). PDF-download
- 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
- 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
- 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
- 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
- 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
- Polymers Dynamics in Repton Model at Large Fields (A.B.K and A. Drzewinski), J. Chem. Phys. 120 7784-7791 (2004). PDF-download
- Simple Growth Models of Rigid Multifilament Biopolymers (E.B.Stukalin and A.B.K.), J. Chem. Phys. 121, 1097-1104 (2004). PDF-download
- 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
- The Effect of Detachments in Asymmetric Simple Exclusion Processes (N. Mirin and A.B.K.), J.Stat.Phys.,110,811-823 (2003). PDF-download
- 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
- 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
- Polymer Translocation Through a Long Nanopore (A.B.K. and E.Slonkina), J. Chem. Phys. 118, 7112-7118 (2003). PDF-download
- 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
- Thermodynamics of Electrolytes on Anisotropic Lattices (V. Kobelev, A.B.K and A.Z. Panagiotopoulos), Phys. Rev. E 68, 066110 (2003). PDF-download
2002
- Lattice Models of Ionic Systems ( V. Kobelev, A.B.K. and M.E.Fisher), J.Chem.Phys. 116, 7589-7598 (2002). PDF-download
- Anisotropic Lattice Models of Electrolytes (V.Kobelev and A.B.K.), J.Chem.Phys.,117,8879-8885 (2002). PDF-download
2001
- Exact Results for Parallel Chains Kinetic Models of Biological Transport (A.B.K.), J. Chem. Phys. 115 7253-7259 (2001). PDF-download
- 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
- Force-Velocity Relation for Growing Microtubules (A.B.K. and M.E.Fisher) Biophys. J. 80, 149-154 (2001). PDF-download
2000
- Periodic Sequential Kinetic Models with Jumping, Branching and Deaths (A.B.K. and M.E.Fisher), Physica A 279, 1-20 (2000). PDF-download
- 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
- 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
- Model of the Hydrophobic Interaction (A.B.K. and B.Widom), Faraday Discussion, 112, 81-89 (1999). PDF-download
- 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
- Asymmetric Simple Exclusion Model with Local Inhomogeneity (A.B.K.), J. Phys. A: Math. Gen., 31, 1153-1164 (1998). PDF-download
- 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
- A Simplified “Ratchet” Model of Molecular Motors (A.B.K. and B.Widom ), J. Stat. Phys., 93, 633-645 (1998).
1997
- 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
- Exact Solutions for a Partially Asymmetric Exclusion Model with Two Species (A.B.K.), Physica A, 245, 523-533 (1997). PDF-download
1996
- An Invariance Property of the Repton Model (A.B.K. and B.Widom), Physica A, 229, 53-60 (1996). PDF-download
1995
- 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
- 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
- Discrete-Stochastic Models of Single-Molecule Motor Proteins Dynamics (A.B.K.) in “Theory and Evaluation of Single-Molecule Signals”
- Molecular Motor Dynamics, Modelling (A.B.K.) in “Encyclopedia of Applied and Computational Mathematics” Springer-Verlag, 2012.
- 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.
- 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.
- 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.
- 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.
- 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
- Molecular Motors: A Theorist’s Perspective (A.B.K. and M.E. Fisher), Annual Reviews of Physical Chemistry 58, 675-695 (2007). PDF-download
- 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
- Motor Proteins and Molecular Motors: How to Operate Machines at the Nanoscale (A.B.K.), J. Phys.: Condens. Matter 25, 463101 (2013). PDF-download
- Collective Dynamics of Processive Cytoskeletal Motors (R.T. McLaughlin, M.R. Diehl and A.B.K.), Soft Matter, 12, 14-21. (2016). PDF-download
- 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
- 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
- Mechanisms of the Formation of Biological Signaling Profiles (H. Teimouri and A.B.K.), J.Phys.A: Math. Theor. 49, 483001 (2016). PDF-download
- 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
- 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
- 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
- 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
- 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
- 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
Create Your Own Website With Webador