Alexander M. Berezhkovskii

Tel: (301) 451-7244

General Approach

To develop theoretical methods to analyze kinetic and transport processes in biological systems.

Current Research Interests

Facilitated membrane transport; receptor, transporter and channel clustering; blockage of membrane channels; clathrin-mediated endocytosis.

Chemical reaction dynamics in solution; protein folding; single-molecule optical spectroscopy and pulling experiments.

Morphogen gradient dynamics; cell-to-cell communication; fluctuating occupancy of cell-surface receptors. 

Diffusion, reactions, and transport in complex geometries.

Selected Recent Publications (DCB Publications List)

1. A.M. Berezhkovskii and A.V. Barzykin. Search for a Small Hole in a Cavity Wall by Intermittent Bulk and Surface Diffusion. J. Chem. Phys. 136, 054115 (2012).

2. A.M. Berezhkovskii and L. Dagdug. Effect of Binding on Escape from Cavity through Narrow Tunnel. J. Chem. Phys. 136, 124110 (2012).

3. A.M. Berezhkovskii, L. Dagdug,  V.A. Lizunov, J. Zimmerberg, and S.M. Bezrukov. Clusters of Absorbing Disks on a Reflecting Wall: Competition for Diffusing Particles. J. Chem. Phys. 136, 211102 (2012).

4. A. Banerjee, A.M. Berezhkovskii and R. Nossal. Stochastic Model of Clathrin-Coated Pit Assembly. Biophys. J. 102, 2725 (2012).

5. L. Dagdug,  M.-V. Vazquez, A.M. Berezhkovskii, V.Yu. Zitserman, and S.M. Bezrukov. Diffusion in the Presence of Cylindrical Obstacles Arranged in a Square Lattice Analyzed with Generalized Fick-Jacobs Equation. J. Chem. Phys. 136, 204106 (2012).

6. L. Dagdug,  A.M. Berezhkovskii, Yu.A. Makhnovskii, V.Yu. Zitserman, and S.M. Bezrukov. Force-Dependent Mobility and Entropic Rectification in Tubes of Periodically Varying Diameter. J. Chem. Phys. 136, 214110, 6 pp. (2012).

7. A.M. Berezhkovskii. Aris-Taylor Dispersion from Single-Particle Point of View. J. Chem. Phys. 137, 066101 (2012).

8. A. Banerjee, A. Berezhkovskii and R. Nossal. Distribution of Lifetime and Maximum Size of Abortive Clathrin-Coated Pits. Phys. Rev. E 86, 031907 (2012).

9. E.M. Nestorovich, V. A. Karginov, A.M. Berezhkovskii, A. V. Parsegian, and S.M. Bezrukov. Kinetics and Thermodynamics of Binding Reactions as Exemplified Anthrax Toxin Channel Blockage with a Cataionic Cyclodextrin Derivative. PNAS 109, 18453 (2012).

10. L. Dagdug, A.M. Berezhkovskii, and S.M. Bezrukov. Particle Lifetime in Cylindrical Cavity with Absorbing Spot on the Wall. Going beyond the Narrow Escape Problem. J. Chem. Phys. 137, 234108 (2012).

11. A.M. Berezhkovskii, L. Dagdug, M.-V. Vazquez, V.A. Lizunov, J. Zimmerberg, and S.M. Bezrukov. Trappin of  Diffusing Particles by Clusters of Absorbing Disks on a Reflecting Wall with Disk Centers on Sites of a Square Lattice. J. Chem. Phys. 138, 064105 (2013).

12. A.M. Berezhkovskii, R.D. Murphy, and N.-V. Buchete. Network Random Walk Model of Two-State Protein Folding: Test of the Theory. J. Chem. Phys. 138, 036101 (2013).

13. S.M. Rappaport, A.M. Berezhkovskii, J. Zimmerberg, and S.M. Bezrukov. Thermodynamics of Inter-Leaflet Cavitation in Lipid Bilayer Membranes. Phys. Rev. E 87, 022715 (2013).

14. A.M. Berezhkovskii and S.Y. Shvartsaman. Kinetics of Receptor Occupancy during Morphogen Gradient Formation. J. Chem. Phys. 138, 244105 (2013).

15. A.M. Berezhkovskii and A. Szabo. Effect of Ligand Diffusion on Occupancy Fluctuations of Cell-Surface Receptors. J. Chem. Phys. 139, 121910 (2013).

16. A.M. Berezhkovskii and A.T. Skvortsov. Aris-Taylor Dispersion with Drift and Diffusion of Particles on the Tube Wall.  J. Chem. Phys. 139, 084101 (2013).

17. A.E. Antipov, A.V. Barzykin, A.M. Berezhkovskii, Yu.A. Makhnovskii, V.Yu. Zitserman, and S.M. Aldoshin. Effective Diffusion Coefficient of a Brownian Particle in a Periodically Expanded Conical Tube. Phys. Rev. E 88, 054101 (2013).

18. J. R. Kalnin and A.M. Berezhkovskii. On the Relation between Lifson-Jackson and Derrida Formulas for Effective Diffusion Coefficient. J. Chem. Phys. 139, 196101 (2013).

19. A.M. Berezhkovskii and A. Szabo. Diffusion along the Splitting/Commitment Probability Reaction Coordinate. J. Phys. Chem. B 117, 13115 (2013).

20. A.M. Berezhkovskii and S.Y. Shvartsaman. On the GFP-based Analysis of Morphogen Gradients. Biophys. J. 106, L13 (2014).

21. A.M. Berezhkovskii, L. Dagdug, V.A. Lizunov, J. Zimmerberg, and S.M. Bezrukov. Trappin by Clusters of Channels, Receptors, and Transporters: Quantitative Description.  Biophys. J. 106, 500 (2014).

22. A.M. Berezhkovskii, L. Dagdug, and S.M. Bezrukov. Discriminating between Anomalous Diffusion and Transient Behavior in Micro-heterogeneous environment. Biophys. J. 106, L09 (2014).

23. P.A. Gurnev, T.L. Yap, C.M. Pfefferkorn, T.K. Rostovtseva, A.M. Berezhkovskii, J.C. Lee, V.A. Parsegian, and S.M. Bezrukov. Alpha-Synuclein Binding and Translocation by Alpha-Hemolysin Channel. Biophys. J. 106, 556 (2014).


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Last updated: March 2014

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