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Same-sex sexual behavior is ubiquitous in the animal kingdom, but its adaptive origins remain a prominent puzzle. Here I suggest the possibility that same-sex sexual behavior arises as a consequence of the competition between an…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
The article sets forth comprehensive basics of thermodynamics of chemical equilibrium as balance of the thermodynamic forces. Based on the linear equations of irreversible thermodynamics, De Donder definition of the thermodynamic force, and…
The question of deriving general force/flux relationships that apply out of the linear response regime is a central topic of theories for nonequilibrium statistical mechanics. This work applies an information theory perspective to compute…
Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross.…
We study the formation of coherent structures in a system with long-range interactions where particles moving on a circle interact through a repulsive cosine potential. Non equilibrium structures are shown to correspond to statistical…
The behaviour of a di-nuclear system in the regime of strong pairing correlations is studied with the methods of statistical mechanics. It is shown that the thermal averaging is strong enough to assure the application of thermodynamical…
Adaptation is used by biological sensory systems to respond to a wide range of environmental signals, by adapting their response properties to the statistics of the stimulus in order to maximize information transmission. We derive rules of…
We derive a model for the non-isothermal reaction-diffusion equation. Combining ideas from non-equilibrium thermodynamics with the energetic variational approach we obtain a general system modeling the evolution of a non-isothermal chemical…
A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and…
On the basis of information theory, a new formalism of classical non-relativistic mechanics of a mass point is proposed. The particle trajectories of a general dynamical system defined on an (1+n)-dimensional smooth manifold are treated…
When modelling driven steady states of matter, it is common practice either to choose transition rates arbitrarily, or to assume that the principle of detailed balance remains valid away from equilibrium. Neither of those practices is…
The physics of walking is explored, using a toy as a concrete example and a 'toy' model applied to it. Besides the Newton's second law, the problem is also discussed from the thermodynamical perspective. Once the steady state (constant…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
It is shown that statistical mechanics is applicable to isolated quantum systems with finite numbers of particles, such as complex atoms, atomic clusters, or quantum dots in solids, where the residual two-body interaction is sufficiently…
Thermodynamic uncertainty relations elucidate the intricate balance between the precision of current and the thermodynamic costs or dissipation, marking a recent and enthralling advancement at the confluence of statistical mechanics,…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
The nonequilibrium thermodynamics of interacting quantum many-body systems is investigated within the framework of thermal time-dependent density functional theory using a generalized linear-response formulation for the full quantum work…
Deriving macroscopic phenomenological laws of irreversible thermodynamics from simple microscopic models is one of the tasks of non-equilibrium statistical mechanics. We consider stationary energy transport in crystals with reference to…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…