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Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
Many processes in chemistry, physics, and biology depend on thermally activated events in which the system changes its state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation…
A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion)…
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…
The long-time behavior of a reaction-diffusion front between one static (e.g. porous solid) reactant A and one initially separated diffusing reactant B is analyzed for the mean-field reaction-rate density R(\rho_A,\rho_B) =…
The research is important for a molecular theory of liquid and has a wide interest as an example solving the problem when dynamic parameters of systems can be indirectly connected with their equilibrium properties. In frameworks of the…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
Catalytically active enzymes have recently been observed to exhibit enhanced diffusion. In a recent work [C. Riedel et al., Nature 517, 227 (2015)], it has been suggested that this phenomenon is correlated with the degree of exothermicity…
Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
The reactive process of barrier escaping from the metastable potential well is studied together with the extension of Kramers' rate formula to the fractional case. Characteristic quantities are computed for an thimbleful of insight into the…
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction…
The Kramers' survival probability has been generalized by using nonextensive formalism. This nonextensive survival probability is studied in detail and associated Kramers' rate has been calculated in the high and low viscosity limit. It has…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
In this work we compare previously measured energy barriers over the course of temperature with the results of simulations of the behaviour of the energy barriers. For the measurements the temperature dependent magnetorelaxation method…
The prevalent scheme of a diffusion-mediated bimolecular reaction $A+B\rightarrow P$ is an adaptation of that proposed by Briggs and Haldane for enzyme action [{\em Biochem J.\/}, 19:338--339, 1925]. The purpose of this Note is to explain,…
Based on a true phase space probability distribution function and an ensemble averaging procedure we have recently developed [Phys. Rev. E 65, 021109 (2002)] a non-Markovian quantum Kramers' equation to derive the quantum rate coefficient…
We expand on a previous study of fronts in finite particle number reaction-diffusion systems in the presence of a reaction rate gradient in the direction of the front motion. We study the system via reaction-diffusion equations, using the…