Related papers: Controlling reaction dynamics in chemical model sy…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
The bimodal behavior of the order parameter is studied in the framework of Boltzmann-Uehling-Uhlenbeck (BUU) transport model. In order to do that, simplified yet accurate method of BUU model is used which allow calculation of fluctuations…
Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor.…
At stationary environmental conditions, a catalyst's reaction rates may be restricted by thermodynamic laws, and certain performances can never be achieved (e.g., catalysts can not change the free energy difference between reactants and…
Recently the phase space structures governing reaction dynamics in Hamiltonian systems have been identified and algorithms for their explicit construction have been developed. These phase space structures are induced by saddle type…
We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
Pattern formation exhibited by a two-dimensional reaction-diffusion system in the fast inhibitor limit is considered from the point of view of interface motion. A dissipative nonlocal equation of motion for the boundary between high and low…
In a dynamical system, the transition between reactants and products is typically mediated by an energy barrier whose properties determine the corresponding pathways and rates. The latter is the flux through a dividing surface (DS) between…
In this paper, we develop the extremum-seeking approach to generate admissible trajectories in a neighborhood of a given reference curve in the state space. The cost function of the problem represents the distance between the current system…
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process with a tridiagonal transition matrix is applied to the analysis…
The pace and unpredictability of evolution are critically relevant in a variety of modern challenges: combating drug resistance in pathogens and cancer, understanding how species respond to environmental perturbations like climate change,…
We show that ultracold chemical reactions can be manipulated and controlled by using Rydberg-dressed interactions. Scattering in the ultracold regime is sensitive to long-range interactions, especially when weakly bound (or quasi-bound)…
By separating the effect of substituents from chemical process variables, such as reaction mechanism, solvent, or temperature, the Hammett equation enables control of chemical reactivity throughout chemical space. We used global regression…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
Driven particles in presence of crowded environment, obstacles or kinetic constraints often exhibit negative differential mobility (NDM) due to their decreased dynamical activity. We propose a new mechanism for complex many-particle systems…
The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…