Endocytosis of viruses and nanoparticles. We study cellular uptake of viruses and nanoparticles via clathrin-mediated endocytosis focusing on how the kinetics of this process depends on the virus/nanoparticle size. Rate of bimolecular reactions in crowded cytoplasm. We developed a theory of bimolecular reactions in crowded cytoplasm, which explains how the presence of crowders modifies the reaction rate compared to that in the absence of crowding agents. Stochastic gating in insect respiration. We proposed a model that accounts for the effect of stochastic gating on transport of oxygen molecules in insect respiration. Our analysis explains how the rates of closing and opening of the stochastic gate affect the diffusive flux of oxygen molecules. Transport in channels of varying width. Our analysis of transport in channels with corrugated walls focuses on the slowdown of diffusion in such channels, compared to that in channels with flat walls, due to entropy wells and barriers. Trapping by striped channel walls. The major finding of our analysis of trapping of diffusing particles by striped channel walls is that the effective trapping rate of the wall is independent of the wall curvature. This rate is determined only by the stripe surface fraction.
| 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 |
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