Related papers: Mechanics, Energetics, Entropy and Kinetics of a B…
We investigate a kinetic model for interacting particles whose masses are integer multiples of an elementary mass. These particles undergo binary collisions which preserve momentum and energy but during which some number of elementary…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
Two species of particles in a binary granular system typically do not have the same mean kinetic energy, in contrast to the equipartition of energy required in equilibrium. We investigate the role of the heating mechanism in determining the…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
Entropy in nonequilibrium statistical mechanics is investigated theoretically so as to extend the well-established equilibrium framework to open nonequilibrium systems. We first derive a microscopic expression of nonequilibrium entropy for…
The influence of the heating mechanism on the kinetic energy densities of the components of a vibrated granular mixture is investigated. Collisions of the particles with the vibrating wall are inelastic and characterized by two coefficients…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
The mechanism of irreversible dynamics in the systems with mixing is analyzed. The procedure of splitting of system on equilibrium subsystems and studying of dynamics of one of them under condition of its interaction with other subsystems…
We derive a formulation of the First Law of nonequilibrium thermodynamics for biological information-processing systems by partitioning entropy in the Second Law into microscopic and mesoscopic components and by assuming that natural…
The Boltzmann and Gibbs approaches to statistical mechanics have very different definitions of equilibrium and entropy. The problems associated with this are discussed and it is suggested that they can be resolved, to produce a version of…
Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable non-racemic steady states of nonequilibrium chemical systems have been discussed as…
Active systems evade the rules of equilibrium thermodynamics by constantly dissipating energy at the level of their microscopic components. This energy flux stems from the conversion of a fuel, present in the environment, into sustained…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
A classical particle system coupled with a thermostat driven by an external constant force reaches its steady state when the ensemble-averaged drift velocity does not vary with time. The statistical mechanics of such a system is derived…
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…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…