Teaching

Teaching Experience:

• Rice University: Lecturer for graduate Classical and Statistical Thermodynamics, Spring 2001, Spring 2002, Spring 2003, Spring 2004, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2021, Spring 2024, Spring 2025.
• Rice University: Lecturer for undergraduate Physical Chemistry (Introduction to Quantum Mechanics), Fall 2001, Fall 2002, Fall 2003, Fall 2006.
• Rice University: Lecturer for undergraduate Physical Chemistry (Classical and Statistical Thermodynamics), Spring 2005, Spring 2006, Spring 2007, Spring 2008.
• Rice University: Lecturer for graduate Chemical Kinetics, Fall 2005, Fall 2007, Fall 2016, Fall 2017, Spring 2020.
• Rice University: Lecturer for graduate Biophysical Chemistry, Fall 2006, Spring 2009, Spring 2011, Spring 2019, Fall 2024.
• Rice University: Lecturer for graduate Quantum Mechanics, Fall 2009, Fall 2010, Fall 2014.
• Rice University: Lecturer for graduate Physical Organic Chemistry, Spring 2012, Spring 2013, Spring 2014.
• Rice University: Lecturer for graduate Chemical Physics of Condensed and Biological Matter, Fall 2012.

 

 

News

News

Jan 31 2020

We are in the news!

Awesome research paper by our PhD student Alena Klindziuk, visiting student Billie Meadowcroft and A.B.K. called “A Mechanochemical Model of Transcriptional Bursting” was featured in the news! In the paper the authors use chemical kinetics and first-passage method to show that the transcriptional bursting is observed when both the supercoiling and the mechanical stress-release due to gyrase are present in the system. They also show that the overall RNA production rate is not constant and depends on the number of previously synthesized RNA molecules. More details can be found on Rice’s website or on phys.org.

Congratulations to Masha Kochugaeva!

Masha is a PhD now! She will continue her research as a postdoc in Yale University!

We have a new postdoc!

Jaeoh Shin joined our group! Traditionally, we celebrated his arrival by having a lunch in Spanish restaraunt. Jaeoh, welcome to our group and good luck! (May, 2017)

Luiza is PhD candidate now!

Congratulations to Luiza, who passed qualifying exam and earned MA in Chemistry! (April 17, 2017)

Group memebers presented posters at NSF CTBP site visit.

As always we had a lot of fun discussing life and research! (April 17, 2017)

Media writes about us again!

Smalley-Curl Institute honors top posters, presentations at colloquium. Our graduate student won the prize! (August 17, 2016) – Read more

Alexey Shvets is MIT postdoc now!

Our group had a wonderful dinner in Sushi restaurant! Alex, good luck in your new life!

Media writes about us again!

It gets mighty crowded around your DNA, but don’t worry: According to Rice University researchers, your proteins are nimble enough to find what they need. (June 23, 2016) Image: Jeff Fitlow/Rice University – Read more

Celebration of Hamid’s defence!

Our group had a wonderful dinner in Iranian restaraunt. Everyone liked the food! (March 25, 2016)

Congratulations to Hamid Teimouri!

Hamid Teimouri, Rice graduate student, succesfully defended his thesis today and became a doctor. Congratulations, Dr. Teimouri! (March 11, 2016) Picture is taken from Studio-C.

New graduate student joined our group.

Mikita Misura, new Rice graduate student, joined our group for fruitful research. Welcome, Nikita! And please, enjoy statistical mechanics of biological systems! (January 7, 2016) Picture is taken from PhD comics(“Piled Higher and Deeper” by Jorge Cham).

Media writes about us!

Rice researchers’ theory finds blocked path sometimes speeds DNA sequence search. Proteins are little Olympians in the games of life, racing around cells to trigger critical processes through interactions with specific genes. Sometimes they’re sprinters, sometimes hurdlers. But they generally find their genetic targets, whatever the obstacles.(December 10, 2015) – Read more

Anatoly Kolomeisky named fellow of American Physical Society

Anatoly Kolomeisky, a professor of Chemistry and of Chemical and Biomolecular Engineering, has been named a fellow of the American Physical Society – Read more

New graduate student joined our group.

Luiza Ferreira, new Rice graduate student, started her research in our lab . Welcome to our group, Luiza! And please, enjoy molecular motors! (September 1, 2015)

Professor Kolomeisky Publishes New Textbook, Motor Proteins and Molecular Motors

Anatoly Kolomeisky, Professor of Chemistry and Chemical and Biomolecular Engineering, has just published a textbook for undergraduate and graduate students entitled “Motor Proteins and Molecular Motors”. (August 20, 2015) – Read more

Motor proteins prefer slow, steady movement

It takes at least two motor proteins to tango, according to Rice University scientists who discovered the workhorses that move cargo in cells are highly sensitive to the proximity of their peers. The study suggests that the collective behavior of motor proteins like kinesins keeps cellular transport systems robust by favoring slow and steady over maximum movement. (February 23, 2015) – Read more

Cell’s skeleton is never still

Rice University scientists model dynamic instability of microtubules

New computer models that show how microtubules age are the first to match experimental results and help explain the dynamic processes behind an essential component of every living cell, according to Rice University scientists. The results could help scientists fine-tune medications that manipulate microtubules to treat cancer and other diseases. Rice theoretical biophysicist Anatoly Kolomeisky and postdoctoral researcher Xin Li reported their results in the Journal of Physical Chemistry B. (November 24, 2014) –Read more

 

 

 

Publications

THESES

M.Sc.

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

Ph.D.

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

BOOKS

  1. “Motor Proteins and Molecular Motors,” (A.B.K.), CRC Press, Taylor and Francis, 2015.

Link to the publisher
Link to Amazon

BOOK CHAPTERS

  1. Discrete-Stochastic Models of Single-Molecule Motor Proteins Dynamics (A.B.K.) in “Theory and Evaluation of Single-Molecule Signals,” Ed.: E. Barkai, F. Brown, M. Orrit, H. Yang, World Scientific, 2008.
  2. Molecular Motor Dynamics, Modeling (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 Modeling of Biological Systems: From Molecules to Pathways,” Ed.: N. Dokholyan, Springer-Verlag, 2012.
  4. Discrete-State Stochastic Modeling of Morphogen Gradient Formation (H. Teimouri and A.B.K.) in “Methods in Molecular Biology- Morphogen Gradients”, Ed.: J. Dubrulle, Springer-Verlag, 2018.
  5. Kinetics of Protein-DNA Interactions: First-Passage Analysis (M.P. Kochugaeva, A.A. Shvets and A,B.K.), in ”Chemical Kinetics beyond the Textbook”, Ed.: K. Lindenberg, R. Metzler, G. Oshanin, World Scientific, 2019.
  6. Organization of Intracellular Transport (Q. Wang and A.B.K.), in “Physics of Molecular and Cellular Processes,” Ed.: K. Blagoev and H. Levine, Springer Nature, 2022.
  7. How to Find Targets That are Always Hidden: Nucleosome-Covered DNA and Pioneer Transcription Factors (A. Mondal, C. Felipe and A.B.K.), in “The Target Problem”, Eds.: D.S. Grebenkov, R. Metzler and G. Oshanin, Springer Nature, 2024.
  8. How I Met Michael Fisher and Started Working in Biophysics (Anatoly B. Kolomeisky), in ”50 Years of the Renormalization Group: Dedicated to the Memory of Michael E Fisher”. Eds.: A. Aharony, O. Entin-Wohlman, D.A. Huse and L. Radzihovsky, World Scientific, 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
  14. Microscopic origin of the spatial and temporal precision in biological systems (A. Mondal and A.B.K.), Biophysics Reports, 5, 100197 (2025). PDF-Download

PUBLICATIONS

_________________________________________________________________________________________________________________________________________________________________________________________________________

2025

256. Mind the Memory: Artefactual Scaling of Energy Dissipation Rate due to Inconsistent Time Reversal (T. Schwarz, A.B.K. and A. Godec), submitted to Phys. Rev. Lett. (2025).

255. How Transcription Bursting and mRNA Production Affect Precise Timing of Cell Lysis Phenomena (Z. Lyu, A. Mondal and A.B.K.), J. Phys. Chem. B. , 129, 15, 3807–3813 (2025). PDF – Download

254. Why Antiholins? Thermodynamic and Kinetic Arguments to Explain the Robustness of Bacteriophage Cell Lysis (A. Mondal and A.B.K.), 16 2920-2926 (2025). PDF – Download

253. Coarse-Graining Chemical Networks by Trimming to Preserve Energy Dissipation (O.A. Igoshin, A.B.K and D.E. Makarov), J. Phys. Chem. Lett., 16 1229-1237 (2025). PDF – Download 

252. Feature selection enhances peptide binding predictions for TCR-specific interactions (H. Teimouri, Z.S. Ghoreyshi, A.B.K. and J.T. George, Frontiers in Immunology, 15 1510435 (2025). PDF – Download 

251. Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states. (O.A. Igoshin, A.B.K and D.E. Makarov), J. Chem. Phys. 162, 034111 (2025).PDF – Download

250. Stochastic Analysis of Human Ovarian Aging and Menopause Timing (A. Mondal, E. Tcherniak and A.B.K.), Biophys. J. 124, 1095–1104 (2025). PDF – Download 

2024

249. Antimicrobial Peptides as Broad-Spectrum Therapeutics: Computational Analysis to Identify Universal Physical-Chemical Features Responsible for Multitarget Activity
(A. Medvedeva, C. Vasnetsov, V. Vasnetsov and A.B.K.) J. Phys. Chem. Lett. 15 12 416-12424 (2024). PDF – Download

248. Integration of Kinetic Data into Affinity-Based Models for Improved T cell Specificity Prediction (Z.S. Ghoreyshi, H. Teimouri, A.B.K. and J. T. George), Biophys. J. 123 4115-4123 (2024).  PDF – Download

247. How Dynamic Surface Restructuring Impacts Intra-Particle Catalytic Cooperativity (B. Punia, S. Chaudhury and A.B.K.), J. Chem. Phys. 161 194107 (2024). PDF – Download

246. Oligomerization Can Enhance Synergistic Activity of Antimicrobial Peptides (A. Medvedeva, H. Teimouri and A.B.K.), Molecular Physics e2445173 (2024).

245. Linear-Decoupling Enables Accurate Speed and Accuracy Predictions for Copolymerization Processes (T. Midha, A.B.K. and O.A. Igoshin), J. Phys. Chem. Lett. 15, 9361-9368 (2024). PDF – Download

244. How Transcription Factors Binding Stimulates Transcriptional Bursting Transcriptional Bursting (A. Mondal and A.B.K.), J. Phys. Chem. Lett. 15 8781-8789 (2024),. PDF – Download

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.), Nature Chemistry 16 1698-1704 (2024). PDF – Download

242. 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

241. Molecular Mechanisms of Precise Timing in Cell Lysis (A. Mondal, H. Teimouri and A.B.K.), Biophys. J. 123 3090-3099 (2024). PDF – download

240. 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

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), Journal of Chemical Information and Modeling 64 5570-5579 (2024). PDF – download 

238. 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

237. Theoretical Understanding of Dynamic Catalysis (P. Jangid, S. Chaudhury and A.B.K), J. Phys. Chem. C 128 9077-9089 (2024). PDF – download

236. 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

235. 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

219. 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

218. 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

217. 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

216. 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

215. 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

214. 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

213. 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

212. 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

211. 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

210. 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

209. 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

208. 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

207. 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

206. 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

205. 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

204. 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

203. 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

202. 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

201. 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

200. 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

199. 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

198. Temporal Order of Mutations Influences Cancer Initiation Dynamics. (H. Teimouri and A.B.K.), Physical Biology 18, 056002 (2021). PDF – download

197. 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

196. 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

195. 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

194. 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

193. 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

192. 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

191. 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

190. 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

189. 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

188. 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

187. 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

186. 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

185. 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

184. 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

183. 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

182. 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

181. 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

180. 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

179. 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

178. 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

177. A Mechanochemical Model of Transcriptional Bursting. (A. Klindziuk, B. Meadowcroft and A.B.K.), Biophys. J. 118, 1213-1220 (2020). PDF – download

176. 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

175. 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

174. 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

173. 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

172. Target Search on DNA by Interacting Molecules: First-Passage Approach. (J. Shin and A.B.K.), J. Chem. Phys. 151, 125101 (2019). PDF – download

171. 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

170. 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

169. 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

168. 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

167. 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

166. 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

165. 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

164. 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

163. 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

162. 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

161. 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

160. 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

159. 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

158. Interactions in nonconserving driven diffusive systems (T. Midha, A.B.K. and A.K. Gupta), Phys. Rev. E 98, 042119 (2018). PDF – download

157. 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

156. 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

155. 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

154. 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

153. Physical-Chemical Mechanisms of Pattern Formation during Gastrulation (B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 148, 123302 (2018). PDF – download

152. 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

151. Surface-Assisted Dynamic Search Processes (J. Shin and A.B.K.), J. Phys. Chem. B 122, 2243-2250 (2018). PDF – download

150. 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

149. 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

148. 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

147. 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

146. 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

145. 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

144. 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

143. 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

142. How Viruses Enter Cells: A Story behind Bacteriophage T4 (A.B.K.), Biophys. J. 113, 3-4 (2017). PDF – download

141. 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

140. 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

139. 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

138. 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

137. 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

136. 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

135. 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

134. 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

133. 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

132. 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

131. 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

130. 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

129. 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

128. 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

127. 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

126. 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

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

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

123. 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

122. 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

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

120. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA,(A.A. Shvets and A.B.K.), J. Chem. Phys. 143, 245101 (2015). PDF-download

119. 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

118. 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

117. 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

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

115. 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

114. 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

113. 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

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

111. 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

109. 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

108. 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

107. 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

106. 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

105. Theoretical Analysis of Microtubule Dynamics at All Times, (X. Li and A.B.K.), J. Phys. Chem. B 118, 13777-13784 (2014). PDF-download

104. 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

103. 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

102. 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

101. 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

100. 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

99. 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

98. All-Time Dynamics in Complex Continuous-Time Random Walk Models, (H. Teimouri and A.B.K.), J. Chem. Phys. 138, 084110 (2013). PDF-download

97. 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

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

95. Physics of Protein Motility and Motor Proteins. PREFACE (A.B.K.)J. Phys.: Condens. Matter 25, 370301 (2013). PDF-download

94. 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

93. 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

92. 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

91. Random Hydrolysis Controls the Dynamic Instability of Microtubules, (R. Padinhateeri, A.B.K. and D. Lacoste), Biophysical J. 102, 1274-1283 (2012). PDF-download

90. How to Accelerate Protein Search on DNA: Location and Dissociation, (A.B.K. and A. Veksler), J. Chem. Phys. 136, 125101 (2012). PDF-download

89. 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

88. 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

87. 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

86. 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

85. 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

84. 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

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

82. 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

81. Michaelis-Menten Relation for Complex Enzymatic Networks, (A.B.K.), J. Chem. Phys. 134, 155101 (2011). PDF-download

80. 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

79. 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

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

77. Molecular Dynamics Study of Crystalline Molecular Gyroscopes, (A.V. Akimov and A.B.K.), J. Phys. Chem. C 115, 13584-13591 (2011). PDF-download

76. 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

75. 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

74. 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

73. 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

72. 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

71. 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

70. 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

69. 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

68. 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

67. 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

66. 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

65. Continuous-Time random Walks at All Times, (A.B.K.), J. Chem. Phys. 131, 234114 (2009). PDF-download

2008

64. How Polymers Translocate Through Pores: Memory is Important (A.B.K.),Biophys. J. 94, 1547 (2008). PDF-download

63. 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

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

61. 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

60. 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

59. 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

58. 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

57. 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

56. 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

55. 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

54. Parallel Coupling of Symmetric and Asymmetric Exclusion Processes (K. Tsekouras and A.B.K.), J. Phys. A: Math. Theor. 41, 465001 (2008). PDF-download

53. 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

52. 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

51. 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

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

49. 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

48. 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

47. Translocation of Polymers with Folded Configurations across Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 127, 185103 (2007). PDF-downloadDynamic Properties of Molecular Motor

46. Dimers in Burnt-Bridge Models (A. Y. Morozov and A.B.K.), J. Stat. Mech. P12008 (2007). PDF-download

2006

45. 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

44. 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

43. Dynamic Phase Transitions in Coupled Motor Proteins (E.B.Stukalin and A.B.K.), Phys. Rev. E 73, 031922 (2006). PDF-download

42. 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

41. Effect of Orientation in Translocation of Inhomogeneous Polymers through Nanopores (S. Kotsev and A.B.K.), J. Chem. Phys. 125, 084906 (2006). PDF-download

40. Asymmetric Coupling in Two-Channel Simple Exclusion Processes (E. Pronina and A.B.K.), Physica A 372, 12-21 (2006). PDF-download

2005

39. 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

38. Polymerization Dynamics of Double-Stranded Biopolymers: Chemical Kinetic Approach (E.B.Stukalin and A.B.K.), J. Chem. Phys. 122, 104903 (2005). PDF-download

37. 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

36. 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

35. 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

34. 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

33. Kinetics of Two-Step Nucleation of Crystals (D. Kashchiev, P. Vekilov and A.B.K.), J. Chem. Phys. 122, 244706 (2005). PDF-download

32. 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

31. 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

30. 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

29. 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

28. 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

27. Polymers Dynamics in Repton Model at Large Fields (A.B.K and A. Drzewinski), J. Chem. Phys. 120 7784-7791 (2004). PDF-download

26. Simple Growth Models of Rigid Multifilament Biopolymers (E.B.Stukalin and A.B.K.), J. Chem. Phys. 121, 1097-1104 (2004). PDF-download

25. 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

24. The Effect of Detachments in Asymmetric Simple Exclusion Processes (N. Mirin and A.B.K.), J.Stat.Phys.,110,811-823 (2003). PDF-download

23. 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

22. 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

21. Polymer Translocation Through a Long Nanopore (A.B.K. and E.Slonkina), J. Chem. Phys. 118, 7112-7118 (2003). PDF-download

20. 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

19. Thermodynamics of Electrolytes on Anisotropic Lattices (V. Kobelev, A.B.K and A.Z. Panagiotopoulos), Phys. Rev. E 68, 066110 (2003). PDF-download

2002

18. Lattice Models of Ionic Systems ( V. Kobelev, A.B.K. and M.E.Fisher), J.Chem.Phys. 116, 7589-7598 (2002). PDF-download

17. Anisotropic Lattice Models of Electrolytes (V.Kobelev and A.B.K.), J.Chem.Phys.,117,8879-8885 (2002). PDF-download

2001

16. Exact Results for Parallel Chains Kinetic Models of Biological Transport (A.B.K.), J. Chem. Phys. 115 7253-7259 (2001). PDF-download

15. 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

14. Force-Velocity Relation for Growing Microtubules (A.B.K. and M.E.Fisher) Biophys. J. 80, 149-154 (2001). PDF-download

2000

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

12. 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

11. 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

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

9. 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

8. Asymmetric Simple Exclusion Model with Local Inhomogeneity (A.B.K.), J. Phys. A: Math. Gen., 31, 1153-1164 (1998). PDF-download

7. 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

6. A Simplified “Ratchet” Model of Molecular Motors (A.B.K. and B.Widom ), J. Stat. Phys., 93, 633-645 (1998)

1997

5. 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

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

1996

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

1995

2. 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

1. 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

Continue reading “Publications” →

Members

 

Current Members

Principal Investigator
Visiting Scholars
Postdocs
Graduate Students
Undergraduate Students
Anatoly B. Kolomeisky
  • Sophia Lyu

Former Members

Postdocs
Graduate Students
Undergraduate Students
Visiting Scholars
Summer Students

 

 

Research

 

Research overview

Our research group is working in the area of statistical mechanics of complex systems and theoretical biophysics. We are using analytical and computational tools.

Dynamics of Cancer Development

Cancer starts after initially healthy tissue cells accumulate several specific mutations or other genetic alterations. The dynamics of cancer development is a very complex phenomenon due to multiple involved biochemical and biophysical processes. In our approach, the cancer initiation process is viewed as a set of stochastic transitions between discrete states defined by the different numbers of mutated cells. We evaluate the dynamic processes associated with the cancer initiation using a discrete-state stochastic description of the formation of tumors as a fixation of cancerous mutations in tissues.

Unlocking the Therapeutic Potential of Peptides: A Machine Learning Approach

Harnessing the power of machine learning to uncover the therapeutic potential of antimicrobial peptides (AMPs) offers an exciting avenue in the fight against a spectrum of threats, from antibiotic-resistant bacteria to fungi and antimalarial parasites. By leveraging bioinformatic tools, we’ve extracted an extensive set of physicochemical descriptors of peptides. Our sophisticated approach employs both supervised and unsupervised machine learning methods to manage this high-dimensional data, pinpointing the pivotal physicochemical features that empower peptides to combat bacteria, fungi, and malaria parasites effectively.

Theoretical Description of the Action of Antimicrobial Peptides on Bacteria

The emergence of multidrug-resistant bacteria and limitations in the number of bacterial targets remain among the main challenges in discovering new antibacterial therapies. Antimicrobial peptides (AMPs) are compounds naturally produced during immune responses of living organisms against bacterial infections, making them a strong alternative to conventional antibiotics. We study the activity of antimicrobial peptides, both in combination and alone, against bacteria using first-passage stochastic methods, Monte-Carlo simulations as well as mean-field descriptions.

Development of Morphogen Gradient Formation

The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen gradients is a result of complex processes that involve diffusion and degradation of locally produced signaling molecules. We are developing discrete-state stochastic models for investigating the corresponding reaction-diffusion models.

 

Mechanisms of Motor Protein Transport

A group of catalytic proteins, known as motor proteins, such as kinesins, dyneins, myosins, DNA and RNA polymerases operate in biological cells by consuming energy provided by ATP hydrolysis. They play crucial roles in cell division, cellular transport, muscle contraction and genetic transcription. Current experimental techniques allow measurements of biochemical and mechanical  properties of motor proteins with single-molecule precision. However, the main fundamental question related to motor proteins – how the chemical energy is transformed into mechanical motion – is still unanswered. We are developing stochastic models of the motion of motor proteins which take into consideration the  biochemical complexity of these processes. Our theoretical methods will be used to describe existing and future experiments on motor protein transport.

Dynamics of Surface-mounted Thioethers

Recent single-molecule experiments indicated that thioethers (dialkylsulphides) deposited on the gold surface may act as thermally or mechanically activated molecular motors, although the factors affecting the properties of such surface-mounted rotors are not yet clearly understood. In particular, it was found that for the thioethers containing up to six carbon atoms in each chain the rotational energy barriers are almost independent on the alkyl chain length with the only exception of the dimethylsulphide for which the rotation is almost barierless. This observation contradicts the naive assumption that the rotation activation energies should increase with the increase of the molecule size. We use molecular dynamics simulations to study the dynamics of thioethers and other surface-mounted rotors.

Dynamics of Polymer Translocation across Nanopores

The transfer of DNA, RNA and proteins through cell membranes is fundamental to the understanding of multiple biological processes. The transport of linear polymer molecules across the nanopores is also important in many chemical and industrial processes. However, our theoretical understanding of these complex phenomena is still very limited. Experiments suggest that the dynamics of translocation strongly depends on the size, flexibility, and chemical and electrostatic interactions between the polymers and the pores. We are developing theoretical models which explicitly take into account these properties.

Polymerization/Depolymerization Processes in Microtubule and Actin Filaments

Microtubules and actin filaments are rigid cylindrical biopolymers which are important in cell division, in internal organization of cells and in cell motility. It is known that the growth of microtubules and actin filaments generate forces which determine the biological functioning of these biopolymers. We are developing detailed models of microtubule and actin filaments growth which take into account the complex structure and the lateral interactions of monomers in these biopolymers. We are also interested in explaining the dynamic instability phenomena in microtubules and the coupling between actin filaments growth and cell membrane tension. Our theoretical work is done in collaboration with experimental group of Prof. W. Brownell from Baylor College of Medicine.

Thermodynamics of Electrolytes

Electrolytes play important roles in science and industry. However, the complete thermodynamic description of these systems is still an open question. Current experimental and theoretical studies are focused on critical properties of ionic fluids where controversial results exist. We are developing Debye-Huckel-based theories for lattice models of electrolytes. Our theories are focusing on the effects of size- and charge asymmetry of charged particles on macroscopic thermodynamic properties. We are checking our theoretical predictions with extensive computer simulations. In this area our collaborator is Prof. Panagiotopoulos from Princeton University.

1D Nonequilibrium Multi-Particle Transport

Multi-particle transport phenomena are important for understanding the mechanisms of nonequilirbrium processes in chemistry, physics and biology (such as gel electrophoresis, kinetics of biopolymerization, ion channels, traffic problems, polymer dynamics, surface growth, anomalous conductivity). The complexity of these problems arises from the nonequilibrium nature of these phenomena. We are investigating the effects of detachments/attachments, inhomogeneity, chemical processes and particles size on transport properties of interacting particles. These problems are studied by the means of exact analysis, mean-field theories and Monte Carlo simulations.

Theory of Biocrystallization Processes

Recently, we started a new project on theoretical modeling of biocrystallization processes, mainly protein crystallization. The range of molecule-molecule interactions in proteins, (in contrast to simple compounds like water, nitrogen, etc.) is much smaller than the size of the molecules. This leads to a complex dynamics of crystallization, which is not well understood theoretically. We are developing simple models of protein crystallization which take into account the intermediate states and phase transitions. Our theoretical efforts are accompanied by experimental work with Prof. P. Vekilov from University of Houston.

Protein-DNA Interaction

Protein searching and recognizing the targets on DNA was the subject of many experimental and theoretical studies. It is often argued that some proteins are capable of finding their targets 10-100 times faster than predicted by the three-dimensional diffusion rate. However, recent single-molecule experiments showed that the diffusion constants of the protein motion along DNA are usually small. This controversy pushed us to revisit this problem. We are investigating this problem both analytically and computationally to throw some light into the physical-chemical aspects of the target search and recognition. Currently we are performing extensive Monte Carlo simulations.

 

 

Prof. Anatoly B. Kolomeisky

Anatoly B. Kolomeisky

Professor, Department of Chemistry, Rice University

Department of Chemical and Biomolecular Engineering, Rice University

Center for Theoretical Biological Physics, Rice University

Phone:713-348-5672
Email:tolya@rice.edu
Fax:(713) 348-5155
Curriculum Vitae in PDF format
List of publications in PDF format

Scientific interests:

Scientific interests: statistical mechanics of complex systems, theoretical physical chemistry and biophysics, non-equilibrium statistical physics, random walks, thermodynamics of electrolytes, asymmetric exclusion processes, protein nucleation and crystallization, polymer translocation, biopolymer growth, protein-DNA interactions, molecular dynamics of artificial molecular motors, rotors and nanocars.

INVITED TALKS

  1. Cooperativity in Bacterial Membrane Association Controls the Synergistic Activities of Antimicrobial Peptides, McGill Molecular Science Mini-Meeting: Machine Learning and Statistical Mechanics, McGill University, Montreal, Canada, July 2024.
  2. Symmetry Breaking of Forward/Backward Transition Times of Single Particles is Determined by Crowding, Deviations from Equilibrium and Method of Measurements Wilhelm and Else Heraeus Seminar ”Nonequilibrium Dynamics of Colloidal Micro- and Nanoparticles” Bad Honnef, Germany, June 2024.
  3. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, Workshop ”Nonequilibrium Dynamics, Information, Processing, and Aging of Living Cells – Initiative for the Theoretical Sciences.” City University of New York, Graduate Center, New York, May 2024.
  4. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, University of Oregon, Department of Chemistry,
    Eugene, Oregon, April 2024.
  5. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, Free University Berlin, Department of Physics, Berlin, Germany, November 2023.
  6. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, Max Planck Institute, Goettingen, Germany, November 2023.
  7. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, Purdue University, Department of Physics, West Lafayette, Indiana, Septmeber 2023.

  8. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, International Conference on Biological Physics, Seoul, South Korea, August 2023.

  9. Microscopic Mechanisms of Cooperative Communications within Single Nanocataysts, Abo Academy, Turku, Finland, July 2023.

  10. How to Find Targets That Are Always Hidden: The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors, Workshop “Signatures of Nonequilibrium Fluctuations in Life”, International Center for Theoretical Physics, Trieste, Italy, May 2023.

  11. When Will the Cancer Start?, Colloquium, University of Florence, Department of Physics, Florence, Italy, March 2023.

  12. Cooperativity in Bacterial Membrane Association Controls the Synergistic Activities of Antimicrobial Peptides, CECAM Workshop, Lausanne, Switzerland, November 2022.

  13. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, Technion University, Haifa, Israel, October 2022.

  14. When Will the Cancer Start?, Seminar, Department of Physics of Living Systems, EPL Lausanne, Switzerland, October 2022.

  15. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, Department of Biomedical Engineering, Technion, Haifa, Israel, October 2022.

  16. How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA, International Conference, “Protein-DNA Interactions: from Biophysics to Cell Biology”, Weizmann Institute, Rehovot, Israel, October 2022.

  17. Microscopic Mechanisms of Cooperative Communications within Single Nanocataysts, American Chemical Society Fall 2022 Meeting, Chicago, August 2022.

  18. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, 6-th Midwest Single Molecule Workshop, University of Nebraska Medical Center, Omaha, Nebraska, August 2022.

  19. Understanding the Molecular Mechanisms of Transcriptional Bursting, 17-th Theoretical Chemistry Symposium (TCS-2021), online presentation, December 2021.

  20. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, Department of Chemistry, Texas Lutheran University, Seguin, Texas, November 2021.

  21. How to Understand Mechanisms of Protein Search for Targets on DNA, University of Buffalo, Department of Chemistry, Buffalo, NY, October 2021.

  22. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, Department of Chemistry, Cornell University, Ithaca, New York, September 2021.

  23. When Will the Cancer Start?, University of Texas, Department of Chemistry, Austin, TX, September 2021.

  24. Determining Mechanisms of Complex Chemical and Biological Processes Using Network Analysis, online presentation, ACS Spring 2021 Virtual Meeting, April 2021.

  25. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, online presentation, Colloquium, Department of Physics, Ben-Gurion University, April 2021.

  26. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, online presentation, 2nd Texas Biophysics Workshop, Midwest State University, February 2021.

  27. Stochastic Mechanisms of Cell-Size Regulation in Bacteria, online presentation, International Conference on Statistical Biological Physics, ICTS, Bangalore, India, December 2020.

  28. When Will the Cancer Start?, online presentation, Department of Chemistry, University of Calcutta, India, September 2020.

  29. Understanding Molecular Mechanisms of Biological Error Correction, online presentation, Florida State University, Institute of Molecular Biophysics, September 2020.

  30. Understanding Molecular Mechanisms of Biological Error Correction, Korean Institute for Advanced Studies, Seoul, South Korea, January 2020.

  31. When Will the Cancer Start?, International Biophysical Conference, Asian-Pacific Center for Theoretical Physics, POSTECH, Pohang, South Korea, January 2020.

  32. When Will the Cancer Start?, Department of Chemistry, University of Southern California, November 2019.

  33. Understanding Molecular Mechanisms of Biological Error Correction, Department of Chemistry, University of California Irvine, November 2019.

  34. Understanding Molecular Mechanisms of Biological Error Correction, Department of Chemistry, University of Illinois Chicago, September 2019.

  35. When Will the Cancer Start?, Department of Chemistry, University of Chicago, September 2019.

  36. How to Understand Mechanisms of Protein Search for Targets on DNA, Laboratory of Statistical Physics, Ecole Normale Superior, Paris, May 2019.

  37. When Will the Cancer Start?, Laboratory of Statistical Physics, Ecole Normale Superior, Paris, May 2019.

  38. Understanding Molecular Mechanisms of Biological Error Correction, Sorbonne University, Jean Perrin Laboratory, Paris, May 2019.

  39. Motor Proteins and Molecular Motors, Indian Institute of Technology at Ropar, Department of Mathematics, February 2019.

  40. How to Understand the Formation of Signaling Profiles in Biological Development, International Conference “Multiscale Simulation Mathematical Modeling

  41. Understanding Molecular Mechanisms of Biological Error Correction, University of Goettingen, Department of Physics, Goettingen, Germany, December 2018.

  42. How to Understand Mechanisms of Protein Search for Targets on DNA, Ludwig Maximilian University, Department of Physics, Munich, Germany, December 2018.

  43. How to Understand the Formation of Signaling Profiles in Biological Development, Free University, Department of Mathematics, Berlin, Germany, November 2018.

  44. Theoretical Investigations of Chemical and Biological Processes with Alternating Dynamics, Telluride Workshop on Biophysics, Telluride, Colorado, July 2018.
  45. Understanding Molecular Mechanisms of Biological Error Correction, Massachusetts Institute of Technology, Boston, March 2018.
  46. Protein Search for Targets on DNA: the Role of DNA Sequence Symmetry and Heterogeneity, International Workshop “Protein-DNA Interactions: From Biophysics to Cancer Biology”, Rice University, Houston, TX, December 2017.
  47. How to Understand the Formation of Signaling Profiles in Biological Development, Department of Chemical Engineering, Indian Institute of Technology Mumbai, India, November 2017.
  48. Understanding Molecular Mechanisms of Biological Error Correction, Indian Institute of Science Education and Research, Department of Chemistry, Pune, India, November 2017.
  49. Collective Dynamics of Interacting Molecular Motors, International Center for Theoretical Sciences, Tata Institute of Fundamental Research, Program “Collective Dynamics of-, on- and around Filaments in Living Cells: Motors, MAPs, TIPs and Tracks,” Bangalore, India, October 2017.
  50. Understanding Molecular Mechanisms of Biological Error Correction, University of Houston at Clear Lake, October 2017.
  51. Understanding Molecular Mechanisms of Biological Error Correction, Department of Physics, Arizona State University, October 2017.
  52. Understanding Molecular Mechanisms of Biological Error Correction, Department of Chemistry, MIT, Boston, September 2017.
  53. Current-Generating “Double Layer Shoe” with a Porous Sole, Symposium on Liquid Theory in honor of Ben Widom’s 90-th birthday, ACS National Meeting, Washington DC, August 2017.
  54. How to Understand the Formation of Signaling Profiles in Biological Development, Department of Physics, Ludwig Maximilian University, Munich, Germany, May 2017.
  55. Understanding Molecular Mechanisms of Biological Error Correction, International Conference on Physics of Living Systems, Paris, France, June 2017.
  56. Collective Dynamics of Interacting Molecular Motors, Beijing Jiaotong University, Beijing, China, May 2017.
  57. How to Understand the Formation of Signaling Profiles in Biological Development, Shanghai Jiaotong University, China, May 2017.
  58. Understanding Molecular Mechanisms of Biological Error Correction, Department of Chemistry, Beijing University (PKU), China, May 2017.
  59. Understanding Mechanisms of Complex Chemical and Biological Processes Using Network Analysis, Humboldt Colloquium, Washington, DC, March 2017.
  60. Determining Mechanisms of Complex Chemical and Biological Processes Using Network Analysis, Workshop on Fluctuations in Nonequilibrium Systems, Pohang, POSTECH, Korea, December 2016.
  61. How to Understand the Formation of Signaling Profiles in Biological Development, Southwestern Regional Meeting, American Chemical Society, Galveston, Texas, November 2016.
  62. Protein Search for Targets on DNA: The Role of DNA Sequence Symmetry and Heterogeneity, Venice Meeting on Fluctuations in Small Complex Systems III, Venice, Italy, October 2016.
  63. How to Understand the Formation of Signaling profiles in Biological Development, Department of Chemistry, Tel Aviv University, Israel, May 2016.
  64. How to Understand the Formation of Signaling profiles in Biological Development, Lokey Distinguished Lecture, Technion, Haifa, Israel, May 2016.
  65. How to Understand Molecular Transport Throug Channels: The Role of Interactions, Department of Physics, Bar Ilan University, Ramat Gan, Israel, May 2016.
  66. How to Understand the Formation of Signaling profiles in Biological Development, Soft Matter and Biophysics Seminar, Weizmann Institute of Science, Rehovot, Israel, May 2016.
  67. Collective Dynamics of Interacting Molecular Motors, Statistical Mechanics Seminar, Weizmann Institute of Science, Rehovot, Israel, May 2016.
  68. Protein Search for Targets on DNA: The Role of Sequence Heterogeneity, Multiple Targets and Traps, Department of Chemistry, Ben-Gurion University, Beersheva, Israel, May 2016.
  69. How to Understand Molecular Transport Throug Channels: The Role of Interactions, Department of Physics, Ben-Gurion University, Beersheva, Israel, May, 2016.
  70. How to Understand Molecular Transport Throug Channels: The Role of Interactions, Department of Physics, University of Virginia, Charlottsville, VA, April 2016.
  71. How to Understand the Formation of Signaling profiles in Biological Development, Statistical Physocs Seminar, University of Maryland, College Park, MD, February 2016.
  72. How to Unerstand Mechanism of protein Search for Targets on DNA, Biochemistry and Biophysics Seminar, NIH, Bethesda, MD, February 2016.
  73. How to Understand Signalling Mechanisms in Biological Development , Department of Chemistry, Imperial Colledge, London, UK, November 2015.
  74. How to Understand Molecular Transport through Channels: The Role of Interactions, Department of Physics, Cambridge University, Cambridge, UK, October 2015.
  75. How to Understand Signaling Mechanisms in Biological Development, Physics Colloquium, Oxford University, Oxford, UK, October 2015.
  76. How to Understand Mechanism of Protein Search for Targets on DNA, Biophysics Seminar, Princeton University, Princeton, New Jersey, September 2015.
  77. Dynamics of Assembly and Disassembly of Microtubule Protein Filaments: Theoretical Analysis, Telluride Workshop on Biophysical Dynamics, Telluride, Colorado, July 2015.
  78. Dynamics of Assembly and Disassembly of Microtubule Protein Filaments: Theoretical Analysis, Francqui Symposium on Aggregation of Biological Molecules, Brussels, Belgium, June 2015.
  79. How to Understand Mechanism of Protein Search for Targets on DNA, Free University of Brussels, Departmen of Physics, Brussels, Belgium, June 2015.
  80. How to Understand Molecular Transport through Channels: The Role of Interactions Leiden Workshop on Nanothermodynamics and Stochastic Thermodynamics, Leiden, Netherlands, December 2014.
  81. Dynamics of the Singlet Fission Process, Workshop “Biologically Inspired Light-Driven Processes,” Rice University, Houston, TX, December 2014.
  82. How to Understand Signaling Mechanisms in Biological Development, Center for Fundamental Studies in Physics, Rio de Janeiro, Brazil, October 2014.
  83. How to Understand Mechanism of Protein Search for Targets on DNA, Department of Physics, University of Rio Grande du Sul, Porto Alegre, Brazil, October 2014.
  84. How to Understand Mechanism of Protein Search for Targets on DNA, Department of Physics, University of Sao Paulo, Brazil, october 2014.
  85. How to Understand Signaling Mechanisms in Biological Development, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, September 2014.
  86. How to Understand the Formation of Morphogen Gradients during Biological Development, Mini-Symposium “Application of Statistical Physics in Quantitative Biology, 9-th European Conference on Mathematical and Theoretical Biology, Goteborg, Sweden, June 2014.
  87. Speed-Selectivity Paradox in the Protein Search for Targets on DNA, Is It Real or Not? Biomedical Center, Uppsala University, Sweden, June 2014.
  88. How to Understand Signaling Mechanisms in Biological Development, Department of Chemistry, University of Southern California, Los Angeles, CA, April 2014.
  89. Mechanisms and Topology Determination of Complex Networks from First-Passage Theoretical Approach, South-West Regional Meeting of American Chemical Society, Waco, TX, November 2013.
  90. How to Understand Complex Processes in Chemistry, Physics and Biology Using Simple Models, Norway-Texas Collaborative Research Seminar, Trondheim, Norway, October 2013.
  91. How to Understand Signaling Mechanisms in Biological Development, Department of Chemical Engineering, Stanford University, Stanford, CA, September 2013.
  92. Mechanisms and Topology Determination of Complex Networks from First-Passage Theoretical Approach, International Conference on Multiscale Motility of Molecular Motors, Potsdam, Germany, September 2013.
  93. Mechanisms and Topology Determination of Complex Networks from First-Passage Theoretical Approach, Kavli Institute of Theoretical Physics in China, Statphys Satellite Conference, Beijing, China, July 2013.
  94. How Interactions Control Transport through Channels, Telluride Workshop on Nonequilibrium Phenomena, Nonadiabatic Dynamics and Spectroscopy, Telluride, Colorado, July 2013.
  95. Speed-Selectivity Paradox in the Protein Search for Targets on DNA, Is It Real or Not? Telluride Workshop on Biophysical Dynamics, Telluride, Colorado, July 2013.
  96. Random Hydrolysis Controls the Dynamic Instability in Microtubules, SIAM Conference on Applications of Dynamic Systems, Snowbird, Utah, May 2013.
  97. How Interactions Affect Multiple Kinesin Dynamics, American Physical Society Meeting, Baltimore, March 2013.
  98. Mechanism of Fast Protein Search for Targets on DNA: Strong Coupling between 1D and 3D Motions, Michael E. Fisher’s Symposium, University of Maryland, College Park, October 2012.
  99. How Interactions Control Transport through Channels, Department of Chemistry, University of Utah, Salt Lake City, October 2012.
  100. How Interactions Control Transport through Channels, CECAM Workshop, “Polymer Translocation through Nanopores,” Mainz, Germany, September 2012.
  101. Mechanism of Fast Protein Search for Targets on DNA: Strong Coupling between 1D and 3D Motions, International Workshop “Search and Stochastic Phenomena in Complex Physical and Biological Systems, Palma de Mallorca, Spain, June 2012.
  102. Formation of a Morphogen Gradient: Acceleration by Dissociation, Department of Physics, University of Barcelona, Spain, May 2012.
  103. How to Understand Signaling Mechanisms in Biological Development, Department of Chemistry, University of California at Irvine, Irvine, April 2012.
  104. Formation of a Morphogen Gradient: Acceleration by Dissociation, Department of Chemistry, Cornell University, Ithaca, New York, March 2012.
  105. Formation of Signaling Molecules Concentration Profiles, Department of Physics, Syracuse University, Syracuse, New York, March 2012.
  106. How Proteins Find and Recognize Their Targets on DNA, Department of Chemistry, University of Rochester, Rochester, New York, March 2012.
  107. Can We Understand Complex Dynamics of Motor Proteins Using Simple Models? Conference “Multiscale Methods and Validation in Medicine and Biology,” San Francisco, California, February 2012.
  108. How Proteins Find and Recognize Their Targets on DNA, Department of Chemistry, Nanjing University, Nanjing, China, December 2011.
  109. Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms?Zhejiang Gongshang University, Hangzhou, China, December 2011.
  110. How Proteins Find and Recognize Their Targets on DNA, Zhejang University, Hangzhou, China, December 2011.
  111. Formation of Signaling Molecules Concentration Profiles, Department of Chemistry, Peking University, beijing, China, December 2011.
  112. Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms? Institute of Chemical Physics, Dalian, China, December 2011.
  113. How Proteins Find and Recognize Their Targets on DNA, University of Science and Technology of China, Hefei, China, November 2011.
  114. Formation of a Morphogen Gradient, NORDITA, Stockholm, Sweden, October 2011.
  115. Physical-Chemical Aspects of Protein-DNA Interactions: Mechanisms of Facilitated Target Search, CECAM Workshop “Dynamics of Protein-Nucleic Acid Interactions: Integrating Simulations with Experiments,” Zurich, Switzerland, September 2011.
  116. How to Accelerate Protein Search for Targets on DNA: Location and Dissociation, Conference “DNA Search: From Biophysics to Cell Biology,” Safed, Israel, September 2011.
  117. Dynamics of Nanocars and Molecular Rotors on Surfaces: What Are Fundamental Mechanisms? Conference on Functional and Nanostructured Materials FNMA-11, Szczecin, Poland, September 2011.
  118. What Are Fundamental Mechanisms for the Motion of Nanocars and Molecular Rotors on Surfaces? 43-rd IUPAC World Chemistry Congress, San Juan, Puerto Rico, August 2011.
  119. Nanocars and Molecular Rotors: What are Fundamental Mechanisms of Motion? Department of Chemistry and Biochemistry, University of California Los Angeles, May 2011.
  120. How Proteins Find and Recognize Their Targets on DNA, University of Illinois, Urbana-Champaign, Department of Material Sciences, November 2010.
  121. Dynamic Properties of Motor Proteins in the Divided-Pathway Model, SIAM Conference on Life Sciences, Pittsburgh, Pennsylvania, July 2010.
  122. Channel-Facilitated Molecular Transport Across Cellular Membranes, ESPCI, Paris, France, June 2010.
  123. How Proteins Find and Recognize Their Targets on DNA, Joseph Fourier University, Grenoble, France, June 2010.
  124. Can We Understand the Complex Dynamics of Molecular Motors Using Simple Models? Conference “Thermodynamics and Kinetics of Molecular Motors,” Santa Fe, New Mexico, May 2010.
  125. Channel-Facilitated Molecular Transport Across Cellular Membranes, The Ohio State University, Mathematical Biosciences Institute, Workshop “Transport in Cells,” Columbus, Ohio, April 2010.
  126. How Proteins Find and Recognize Their Targets on DNA, Arizona State University, Center for Biological Physics, Tempe, Arizona, March 2010.
  127. Interactions between Motor Proteins can Explain Collective Transport of Kinesins, Biophysical Society Meeting, Mini-Symposium “Tug of War – Molecular Motors Interact,” San Francisco, February 2010.
  128. How Proteins Find and Recognize Their Targets on DNA, Tata Institute for Fundamental Research, Mumbai, India, February 2010.
  129. How Proteins Find and Recognize Their Targets on DNA, Indian Institute of Science, Bangalore, India, January 2010.
  130. Spatial Fluctuations Affect Dynamics of Motor Proteins, Indian Institute of Technology, Golden Jubilee Conference on Interaction, Stability, Transport and Kinetics, Kanpur, India, February 2010.
  131. Theoretical Studies of Coupled Parallel Exclusion Processes, Indian Institute of Technology, Golden Jubilee Conference on Non-Equilibrium Statistical Physics, Kanpur, India, January 2010.
  132. Complex Dynamics of Motor Proteins: A Theorist’s View, University of Texas, Center for Nonlinear Dynamics, Austin, November 2009.
  133. How Proteins Find and Recognize Their Targets on DNA, University of Chicago, Department of Chemistry, September 2009.
  134. Complex Dynamics of Motor Proteins: A Theorist’s View, University of Illinois, Department of Physics, Chicago, September 2009.
  135. Complex Dynamics of Motor Proteins: A Theorist’s View, Laboratory of Statistical Physics, Ecole Normale Superieure, Paris, France, July 2009.
  136. Thermally-Driven Nanocars and Molecular Rotors: What Can We Learn from Molecular Dynamics Simulations, Telluride Research Workshop on Single Molecules, Telluride, Colorado, June 2009.
  137. Thermally-Driven Nanocars and Molecular Rotors: What Can We Learn from Molecular Dynamics Simulations, University of Zelena Gura, Department of Physics, Poland, June 2009.
  138. How Proteins Find and Recognize Their Targets on DNA, XIV Statistical Physics Minisymposium, Institute of Mathematics, Czestochowa University of Technology, Poland, June 2009.
  139. How Proteins Find Targets on DNA, International Conference “From DNA-inspired Physics to Physics-Inspired DNA,” ICTP, Trieste, Italy, June 2009.
  140. How Proteins Find and Recognize Their Targets on DNA, Laboratory of Statistical Physics, Ecole Normale Superieure, Paris, France, May 2009.
  141. Spatial Fluctuations Affect Dynamics of Motor Proteins, Max-Planck Institute for Physics of Complex Systems, Dresden, Germany, May 2009.
  142. Thermally-Driven Nanocars and Molecular Rotors: What Can We Learn from Molecular Dynamics Simulations, 237 ACS National Meeting, Salt Lake City, March 2009.
  143. Can We Understand the Complex Dynamics of Polymer Translocation Using Simple Models? Mesilla Workshop on Multi-Scale Modeling of Biological Systems, Las Cruces, New Mexico, February 2009.
  144. Motor Proteins: A Theorist’s View, Ludwig-Maximilian University, Munich, Center fro Nanosciences, Germany, December 2008.
  145. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Technical University of Munich, Department of Physics, Germany, December 2008.
  146. Can We Understand the Complex Dynamics of Polymer Translocation Using Simple Models? Research Center Juelich, Germany, December 2008.
  147. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Max-Planck Institute of Colloidal Sciences, Potsdam, Germany, December 2008.
  148. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, University of Stuttgart, Department of Physics, Germany, November 2008.
  149. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Max-Planck Institute of Polymer Sciences, Mainz, Germany, November 2008.
  150. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Harvard University, Department of Chemistry, Boston, September 2008.
  151. Can We Understand the Complex Dynamics of Polymer Translocation Using Simple Models? Massachusetts Institute of Technology, Department of Chemistry, Boston, September 2008.
  152. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Syracuse University, Department of Physics Colloquium, September 2008.
  153. Molecular Motors Interacting with Their Own tracks , International Conference on Statistical Physics SIGMAPHI2008, Crete, Greece, July 2008.
  154. Molecular Motors Interacting with Their Own Tracks , Annual SIAM Conference, San Diego, California, July 2008.
  155. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Weizmann Research Institute, Rehovot, Israel, December 2007.
  156. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, University of Tel Aviv, Department of Chemistry, Tel-Aviv, Israel, December 2007.
  157. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Technion, Department of Physics, Haifa, Israel, December 2007.
  158. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion, Bar-Ilan University, Department of Physics Colloquium, Ramat-Gan, Israel, November 2007.
  159. Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models? University of Texas Medical Branch, Galveston, Texas, September 2007.
  160. How Proteins Find Its Targets on DNA: Mechanism of Facilitated Diffusion , University of Texas, Austin, September 2007.
  161. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry, 234-th American Chemical Society Annual Meeting, Boston, August 2007.
  162. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry, Telluride Research Workshop: “Nonequilibrium Phenomena, Nonadiabatic Dynamics and Spectroscopy.” Telluride, Colorado, July 2007.
  163. Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach, Gordon Research Conference on “Thin Films and Growth Mechanisms,” Mount Holyoke College, South Hadley, Massachusetts, June 2007.
  164. Burnt-Bridge Model of Molecular Motor Transport, SIAM Conference on Applications of Dynamical Systems, Snowbird, Utah, May 2007.
  165. Discrete Stochastic Models of Single-Molecule Motor Protein Dynamics, Workshop Theory, Modeling and Evaluation of Single-Molecule Measurements, Lorentz Center, University of Leiden, Netherlands, April 2007.
  166. Coupling of Two Motor Proteins: a New Motor Can Move Faster, Department of Chemistry, University of Nevada, Reno, February 2007.
  167. Channel-Facilitated Molecular Transport Across Membranes: Attraction, Repulsion and Asymmetry, Statistical Mechanics Meeting, Rutgers University, New Jersey, December 2006.
  168. Growth Dynamics of Cytoskeleton Proteins: Multiscale Theoretical Analysis, International Workshop on Multiscale Modeling of Complex Fluids, Prato, Italy, July 2006.
  169. Can We Understand the Complex Dynamics of Motor Proteins Using Simple Stochastic Models? International Workshop on Stochastic Models in Biological Sciences, Warsaw, Poland, May 2006.
  170. Coupling of Two Motor Proteins: a New Motor Can Move Faster, University of California Santa Barbara, Kavli Institute of Theoretical Physics, May 2006.
  171. Coupling of Two Motor Proteins: a New Motor Can Move Faster, Department of Chemistry, University of Wisconsin, Madison, March 2006.
  172. Asymmetric Exclusion Processes on Parallel Channels, Indian Institute of Technology, Kanpur, India, February 2006.
  173. Coupling of Two Motor Proteins: a New Motor Can Move Faster, Institute for Physical Science and Technology, University of Maryland, College Park, December 2005.
  174. Coupling of Two Motor Proteins: a New Motor Can Move Faster, Department of Chemistry, University of Montreal, Canada, November 2005.
  175. Growth Dynamics of Cytoskeleton Proteins: Multiscale Theoretical Analysis, Workshop I: Multiscale Modeling in Soft Matter and Biophysics, Institute for Pure and Applied Mathematics, University of California Los Angeles, September 2005.
  176. Coupling of Two Motor Proteins: a New Motor Can Move Faster, McGovern Lecture in Biomedical Computing and Imaging, Texas Medical Center, September 2005.
  177. Coupling of Two Motor Proteins: a New Motor Can Move Faster , The Telluride Scientific Research Workshop “Single-Molecule Measurements: Kinetics, Fluctuations, and Non-Equilibrium Thermodynamics,” Telluride, Colorado, August 2005.
  178. Coupling of Two Motor Proteins: a New Motor Can Move Faster , 6-th SIAM Conference on Control and its Applicability, Symposium on Brownian Motors and Protein Dynamics, New Orleans, July 2005.
  179. Coupling of Two Motor Proteins: a New Motor Can Move Faster , Department of Chemistry, Cornell University, Ithaca, New York, May 2005.
  180. Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments, Department of Chemistry, University of Pennsylvania, Philadelphia, December 2004.
  181. Simple Models of Rigid Multifilament Biopolymer’s Growth Dynamics, Department of Chemical Engineering, University of California, Los Angeles, October 2004.
  182. Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments, Materials Research Laboratory, University of California, Santa Barbara, October 2004.
  183. Can We Understand the Complex Dynamics of Motor Protein Using Simple Stochastic Models?, BU-Harvard-MIT Theoretical Chemistry Lecture Series, Boston, October 2004.
  184. Simple Models of Rigid Multifilament Biopolymers’s Growth Dynamics, Department of Physics, Brandeis University, Waltham, Massachussetts, October 2004.
  185. Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments, Department of Chemistry, Iowa State University, Ames, Iowa, September 2004.
  186. Dynamics of Polymer Translocation Through a Nanopore: Theory Meets Experiments, International Conference on Biological Physics, Goteborg, Sweden, August 2004.
  187. Simple Stochastic Models of Motor Protein Dynamics, SIAM Conference on Mathematical Aspects of Material Science, Los Angeles, May 2004.
  188. Physical-Chemical Analysis of the Factors Influencing the Behavior of Flasks During the Heating in Jewelry Casting Process: Development of the Optimal Model of Burnout Furnace , Santa Fe Symposium, Albuquerque, New Mexico, May 2004.
  189. Understanding Mechanochemical Coupling in Kinesins Using First-Passage Times, Proteomics Workshop IV: Molecular Machines, Institute for Pure and Applied Mathematics, University of California, Los Angeles, May 2004.
  190. Lattice Models of Electrolytes, Institute of Condensed Matter Physics, Ukrainian Academy of Science, Lviv, Ukraine, May 2004.
  191. Effect of Detachments in Asymmetric Simple Exlusion Processes, Fock School on Quantum and Computational Chemistry, Novgorod, Russia, April 2004.
  192. Nucleation of Ordered Solid Phases of Proteins via Unstable and Metastable High-Density States: Phenomenological Approach, Spring 2004 Materials Research Society, San Francisco, April 2004.
  193. Dynamics of Polymer Translocation Through a Long Nanopore, Department of Chemical Engineering, Princeton University, December 2003.
  194. Phenomenological Theory of Protein Nucleation Phenomena, Institute for Physical Science and Technology, University of Maryland, College Park, November 2003.
  195. Lattice Models of Electrolytes, Department of Physics, University of Washington, Seattle, October 2003.
  196. Dynamics of Polymer Translocation Through a Long Nanopore, Department of Chemistry, University of Washington, Seattle, October 2003.
  197. Simple Models of Electrolytes, 15-h American Conference on Crystal Growth and Epitaxy, Keystone, Colorado, July 2003.
  198. Physical-Chemical Analysis of the Factors Influencing the Behavior of Flasks During the Heating in Jewelry Casting Process. Development of the Optimal Model of Burnout Furnace 2-nd International Jewelry Symposium JEWELRY MANUFACTURING: TECHNOLOGIES, MAIN PROBLEMS AND PROSPECTS, Saint Petersburg, Russia, July 2003.
  199. Effect of Detachments in Asymmetric Simple Exclusion Processes European Research Council Chemistry Committees Workshop on Computer Modeling of Chemical and Biological Systems, Porto, Portugal, May 2003.
  200. Dynamics of Polymer Translocation Through a Long Nanopore, Department of Chemical Engineering, University of Houston, April, 2003.
  201. Stochastic Models with Waiting-Time Distributions for Translocatory Motor Proteins 225-th American Chemical Society National Meeting, New Orleans, March 2003.
  202. Polymer Translocation Through a Long Nanopore,Department of Chemistry, Moscow State University, Moscow, Russia, December, 2002.
  203. Polymer Translocation Through a Long Nanopore,19-th Southwestern Theoretical Chemistry Conference, University of Houston,November, 2002.
  204. Simple Stochastic Models Can Explain the Dynamics of Motor Proteins, Symposium COOPERATIVITY IN BIOPHYSICAL SYSTEMS, Institute fur Festkoerperforschung at Forschungcentrum Juelich, Germany, October, 2002.
  205. Lattice Models of Electrolytes, Department of Mathematics, Rice University, Houston,September, 2002.
  206. Polymer Translocation Through a Long Nanopore, Institute for Physical Science and Technology, University of Maryland, August, 2002.
  207. Stochastic Models of Biological Transport, Department of Chemistry, Moscow State University, Moscow, Russia, May, 2002.
  208. Polymer Translocation Through a Long Nanopore, Department of Chemistry, University of Southern California, March, 2002.
  209. Polymer Translocation Through a Long Nanopore, Department of Chemistry, University of California at Los Angeles, March, 2002.
  210. Polymer Translocation Through a Long Nanopore, Department of Chemistry, University of California at Berkeley, February, 2002.
  211. Stochastic Models of Biological Transport, Department of Biology, Moscow State University, Moscow, Russia, December, 2001.
  212. Stochastic Models of Biological Transport, Department of Chemistry, University of Houston, Houston, Texas, October, 2001.
  213. Stochastic Models of Biological Transport, Department of Physics, Sam Houston State University, Huntsville, Texas, September, 2001.
  214. Nanotechnology: What Can We Learn from Biology, The International Conference NANOSPACE 2001, Galveston, Texas, March, 2001.
  215. Motor Proteins and the Forces They Exert, Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, January, 2000.
  216. Motor Proteins and the Forces They Exert, Department of Chemistry, Rice University, Houston, January, 2000.
  217. Motor Proteins and the Forces They Exert, Department of Chemistry, Duke University, Durham, NC January, 2000.
  218. Motor Proteins and the Forces They Exert, Department of Chemistry, University of Nevada, Reno, December, 1999.
  219. Motor Proteins and the Forces They Exert, Department of Chemistry, Washington University, St. Louis, December, 1999.
  220. Domain-Wall Picture of Asymmetric Simple Exclusion Processes, Department of Chemistry, University of California, San Diego, January 1998.