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A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…

The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…

Autocatalytic processes underlie diverse systems in which replication is triggered at interfaces, including heterogeneous catalysis on solid substrates, enzyme activity at membranes, viral infections, biofilm growth, and spatially…

We have a general knowledge of the principles by which catalysts accelerate the rate of chemical reactions but no precise understanding of the geometrical and physical constraints to which their design is subject. To analyze these…

This chapter presents, from a quantum-mechanical point of view, a tutorial discussion of elementary collision processes in the bulk of a gas discharge. Instead of merely listing kitchen-made cross section formulae and unrelated cross…

Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…

Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…

Kinetics of the first order phase transition has been investigated. The case when the droplets sizes have a limit value is considered. An analytical theory for such process has been constructed and all main characteristics of the process…

This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…

We investigate the catalytic reactions model used in cell modeling. The reaction kinetic is defined through the energies of different species of molecules following random independent distribution. The related statistical physics model has…

Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…

A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…

Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic…

Thermal operations are a generic description for allowed state transitions under thermodynamic restrictions. However, the quest for simpler methods to encompass all these processes remains unfulfilled. We resolve this challenge through the…

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…

Non-ideal deterministic system "tank with liquid-electric motor" is studied. Two delay-approximation models are considered. Impact of the delay on the emergence, evolution and disappearance of regular and chaotic limit sets (attractors) of…

Phase transitions, such as the freezing of water and the magnetisation of a ferromagnet upon lowering the ambient temperature, are familiar physical phenomena. Interestingly, such a collective change of behaviour at a phase transition is…

Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…

We introduce a simple model of heterogeneous catalysis on a disordered surface which consists of two types of randomly distributed sites with different adsorption rates. Disorder can create a reactive steady state in situations where the…

We demonstrate that autocatalytic reactions, where a product catalyzes its own formation, can be significantly accelerated when the product molecules are indistinguishable from each other. This ``combinatorial enhancement," analogous to the…