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 one can describe protein folding using the splitting/commitment probability as a one-dimensional reaction coordinate. 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.
| Berezhkovskii, Alexander M; Makarov, Dmitrii E (2018) Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics. J Chem Phys 148:201102 |
| Berezhkovskii, Alexander M; Bezrukov, Sergey M (2018) Stochastic Gating as a Novel Mechanism for Channel Selectivity. Biophys J 114:1026-1029 |
| Berezhkovskii, Alexander M; Makarov, Dmitrii E (2018) Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate. J Phys Chem Lett 9:2190-2195 |
| Skvortsov, Alexei T; Berezhkovskii, Alexander M; Dagdug, Leonardo (2018) Trapping of diffusing particles by short absorbing spikes periodically protruding from reflecting base. J Chem Phys 149:044106 |
| Berezhkovskii, Alexander M; Bezrukov, Sergey M (2018) Effect of stochastic gating on the flux through a membrane channel: a steady-state approach. J Phys Condens Matter 30:254006 |
| Dagdug, Leonardo; Berezhkovskii, Alexander M; Zitserman, Vladimir Yu (2018) Note: Diffusion-limited annihilation in cavities. J Chem Phys 148:246101 |
| Berezhkovskii, Alexander M; Bezrukov, Sergey M (2018) Mapping Intrachannel Diffusive Dynamics of Interacting Molecules onto a Two-Site Model: Crossover in Flux Concentration Dependence. J Phys Chem B : |
| Skvortsov, Alexei T; Berezhkovskii, Alexander M; Dagdug, Leonardo (2018) Trapping of diffusing particles by spiky absorbers. J Chem Phys 148:084103 |
| Berezhkovskii, Alexander M; Dagdug, Leonardo; Bezrukov, Sergey M (2017) Mean Direct-Transit and Looping Times as Functions of the Potential Shape. J Phys Chem B 121:5455-5460 |
| Berezhkovskii, Alexander M; Dagdug, Leonardo; Bezrukov, Sergey M (2017) First passage, looping, and direct transition in expanding and narrowing tubes: Effects of the entropy potential. J Chem Phys 147:134104 |
Showing the most recent 10 out of 83 publications
