Related papers: Stochastic Modeling of Single Molecule Michaelis M…
Stochastic features of decay of a metastable phase have been investigated with the help of a new monodisperse approximation. This approximation is more precise than the already used one and namely it allows to give a very simple but rather…
Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled…
The space-time dynamics of rigid inhomogeneities (inclusions) free to move in a randomly fluctuating fluid bio-membrane is derived and numerically simulated as a function of the membrane shape changes. Both vertically placed (embedded)…
Two-component submonolayer growth on triangular lattice is qualitatively studied by kinetic Monte Carlo techniques. The hopping barrier governing surface diffusion of the atoms is estimated with an improved formula and using realistic pair…
We consider a class of stochastic kinetic equations, depending on two time scale separation parameters $\epsilon$ and $\delta$: the evolution equation contains singular terms with respect to $\epsilon$, and is driven by a fast ergodic…
We studied the single dimer dynamics in a lattice diffusive model as a function of particle density in the high densification regime. The mean square displacement is found to be subdiffusive both in one and two dimensions. The spatial…
The stochastic dynamics of biochemical reaction networks can be accurately described by discrete-state Markov processes where each chemical reaction corresponds to a state transition of the process. Due to the largeness problem of the state…
The past decade has seen a revived interest in the unavoidable or intrinsic noise in biochemical and genetic networks arising from the finite copy number of the participating species. That is, rather than modeling regulatory networks in…
We present an experimental study of the kinetics of orbitally-shaken macroscopic particles confined to a two-dimensional bounded domain. Discounting the forcing action of the external periodic actuation, the particles show translational…
Enyzme kinetics are cyclic. We study a Markov renewal process model of single-enzyme turnover in nonequilibrium steady-state (NESS) with sustained concentrations for substrates and products. We show that the forward and backward cycle times…
The reduced density matrix that characterises the state of an open quantum system is a projection from the full density matrix of the quantum system and its environment, and there are many full density matrices consistent with a given…
We discuss a discrete-time model for motion of substance in a channel of a network. For the case of stationary motion of the substance and for the case of time-independent values of the parameters of the model we obtain a new class of…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but…
We introduce a rejection-free continuous-time kinetic Monte Carlo framework to study stochastic systems governed by multiple concurrent dynamical mechanisms. In this approach, the relative activity of each dynamical channel emerges…
The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here, we study a general model…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…