Dynamics of multisite phosphorylation. Multi-site phosphorylation dynamics is usually interpreted in terms of the processive and distributive mechanisms, which, in fact, are special limiting cases of the general phosphorylation dynamics. We study the phosphorylation dynamics in general, focusing on how these limiting cases arise for the special choice of the parameters Diffusion-limited trapping by patchy surfaces. In biological systems, diffusing solutes are typically trapped by active sites on the otherwise reflecting surfaces. We study trapping by patchy surfaces focusing on how the trapping rate depends on the patch surface fraction. Collective growth in simple cell networks. We study collective growth in a simple cell network with the goal to rationalize why different cells of the network grow with different rates. Non-trivial effects of the substrate dissociation rate on the enzymatic velocity. Based on general arguments, it was recently proposed that the enzymatic velocity can be increased by increasing the substrate dissociation rate. We study a general model of the multistate enzyme dynamics with the goal to specify the conditions under which such acceleration of the enzymatic reaction can occur. Bulk-mediated surface transport. We study surface transport of solute molecules which are allowed to dissociate from the surface and then come back. Our goal was to understand the origin of the anomalous subdiffusion of the molecules in such systems reported by different groups. Effect of stochastic gating on channel-facilitated membrane transport. Although stochastic gating in channel-facilitated membrane transport has been studied for many decades, there is no theory that explains how the solute flux through the channel depends on that gating rate and the solute dynamics in the channel. We developed such a theory which shows that significant deviations from the common sense expectation may occur at fast gating if the gating rate becomes comparable with the rate of the solute passage through the channel.
| 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; Makarov, Dmitrii E (2017) Communication: Coordinate-dependent diffusivity from single molecule trajectories. J Chem Phys 147:201102 |
| 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 |
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