Related papers: Manipulating single enzymes by an external harmoni…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
The control of chemical reactions is a recurring theme in physics and chemistry. Traditionally, chemical reactions have been investigated by tuning thermodynamic parameters, such as temperature or pressure. More recently, physical methods…
We study spin-rotation effects in a magnetic molecule bridged between two conducting leads. Dynamics of the total angular momentum couples spin tunneling to the mechanical rotations. Landau-Zener spin transition produced by the…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
There is a vast amount of literature concerning the appropriateness of various perturbation parameters for the standard quasi-steady state approximation in the Michaelis-Menten reaction mechanism, and also concerning the relevance of these…
We study the stationary dynamics of energy exchange in an ensemble of phase oscillators, coupled through a mean-field mechanical interaction and added with friction and an external periodic excitation. The degree of entrainment between…
We have proposed the neck linker swing model to investigate the mechanism of mechanochemical coupling of kinesin. The Michaelis-Menten-like curve for velocity vs ATP concentration at different loads has been obtained, which is in agreement…
The transformation of a system from one state to another is often mediated by a bottleneck in the system's phase space. In chemistry these bottlenecks are known as \emph{transition states} through which the system has to pass in order to…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase…
We consider a stochastic model of the Michaelis-Menten (MM) enzyme kinetic reactions in terms of Stochastic Differential Equations (SDEs) driven by Poisson Random Measures (PRMs). It has been argued that among various Quasi-Steady State…
Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic electrodes is investigated theoretically. Magnetic moments of the electrodes are assumed to be collinear and parallel…
The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At non-dilute conditions, interactions among the components can give rise to coexisting…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Single magnetic molecules may be the smallest functional magnets. An electric-field controllable spin state of magnetic molecules is of fundamental importance for applications while its realization remains challenging. To date the observed…
The magnetization switching dynamics of biaxial single-domain homogeneous ferromagnetic particles, in which the two easy axes are perpendicular to each other, is simulated using a 4-state clock model. A zero-field mapping of the statics…
We present a proposal for controlling the conversion of ultracold atoms into molecules by fixing the phase difference between two oscillating magnetic fields. The scheme is based on the use of a magnetic Feshbach resonance with a field…
We observe asymmetric transition rates between Zeeman levels (spin-flips) of magnetically trapped atoms. The asymmetry strongly depends on the spectral shape of an applied noise. This effect follows from the interplay between the internal…