Assembly of clathrin coated vesicles. We studied the dynamics of the clathrin coated pit formation with the goal to rationalize the role of cargo in the vesicle formation. Channel-facilitated membrane transport. We worked on the theory that would allow one to analyze the data on blockage of Anthrax channel by multi-charged high-affinity toxin inhibitor, and extract the information about the blocker interaction with the channel. Ligand concentration measurements by cell surface receptors. We developed a general theory of the measurement process, which showed how the accuracy of the cell concentration measurements depends on the averaging time and the number of receptors on the cell surface. Morphogen gradient formation in the Drosophila Embryo. We generalized our theory of local accumulation time to the case of nonlinear kinetics of morphogen degradation, and established the relation between local accumulation time and the first-passage time of the morphogen molecules from the source to the observation point. Protein folding. We developed a theory that showed how the character of folding kinetics depends on the chain length of the protein. Transport in complex environment. Brownian dynamics simulations were used to study the dependence of the effective mobility and diffusion coefficient of a particle on the driving force in tubes of varying shape. Our results show that the dependence may be qualitatively different depending on the shapes of the tube and the entropic traps. Trapping by clusters of absorbing disks. We suggested a general approach to trapping by clusters of absorbing disks, which took into account completion of the disks for diffusing particles. Using the approach we obtained a general formula for the rate constant characterizing trapping by a cluster formed by identical disks, centers of which occupied neighboring sites of a triangular lattice.

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Berezhkovskii, Alexander M; Dagdug, Leonardo; Lizunov, Vladimir A et al. (2014) Trapping by clusters of channels, receptors, and transporters: quantitative description. Biophys J 106:500-9
Berezhkovskii, Alexander M; Shvartsman, Stanislav Y (2014) On the GFP-based analysis of dynamic concentration profiles. Biophys J 106:L13-5
Berezhkovskii, Alexander M; Dagdug, Leonardo; Bezrukov, Sergey M (2014) From normal to anomalous diffusion in comb-like structures in three dimensions. J Chem Phys 141:054907
Dagdug, Leonardo; Berezhkovskii, Alexander M; Skvortsov, Alexei T (2014) Aris-Taylor dispersion in tubes with dead ends. J Chem Phys 141:024705
Gurnev, Philip A; Yap, Thai Leong; Pfefferkorn, Candace M et al. (2014) Alpha-synuclein lipid-dependent membrane binding and translocation through the *-hemolysin channel. Biophys J 106:556-65
Berezhkovskii, Alexander M; Dagdug, Leonardo; Bezrukov, Sergey M (2014) Discriminating between anomalous diffusion and transient behavior in microheterogeneous environments. Biophys J 106:L09-11
Berezhkovskii, Alexander M; Murphy, Ronan D; Buchete, Nicolae-Viorel (2013) Note: network random walk model of two-state protein folding: test of the theory. J Chem Phys 138:036101
Berezhkovskii, Alexander M; Shvartsman, Stanislav Y (2013) Kinetics of receptor occupancy during morphogen gradient formation. J Chem Phys 138:244105
Berezhkovskii, Alexander M; Szabo, Attila (2013) Diffusion along the Splitting/Commitment Probability Reaction Coordinate. J Phys Chem B :
Berezhkovskii, Alexander M; Dagdug, Leonardo; Vazquez, Marco-Vinicio et al. (2013) Trapping 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

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