Related papers: Microscopic Reversibility or Detailed Balance in I…
Voltage-activated ion channels vary randomly between open and closed states, influenced by the membrane potential and other factors. Signal transduction is enhanced by noise in a simple ion channel model. The enhancement occurs in a finite…
The impossibility of attaining equilibrium for cyclic chemical reaction networks with irreversible steps is apparently due to a divergent entropy production rate. A deeper reason seems to be the violation of the detailed balance condition.…
The aim of this article is to build on the use of tools from computational algebra initiated in Craciun, Dickenstein, Shiu, Sturmfels (JSC, 2009), for the study of general kinetic systems, which have a wide range of applications in…
Irreversibility, crucial in both thermodynamics and information theory, is naturally studied by comparing the evolution -- the (forward) channel -- with an associated reverse -- the reverse channel. There are two natural ways to define this…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
We discuss various models of ion transport through cell membrane channels. Recent experimental data shows that sizes of ion channels are compared to those of ions and that only few ions may be simultaneously in any single channel.…
The behavior of lattice models in which time reversibility is enforced at the level of trajectories (microscopic reversibility) is studied analytically. Conditions for ergodicity breaking are explored, and a few examples of systems…
Thermal contact is the archetype of non-equilibrium processes driven by constant non-equilibrium constraints when the latter are enforced by reservoirs exchanging conserved microscopic quantities. At a mesoscopic scale only the energies of…
We study ion pair dissociation in water at ambient conditions using a combination of classical and ab initio approaches. The goal of this study is to disentangle the sources of discrepancy observed in computed potentials of mean force. In…
Aggregated Markov models provide a flexible framework for stochastic dynamics that develops on multiple timescales. For example, Markov models for ion channels often consist of multiple open and closed state to account for "slow" and "fast"…
We investigate nonequilibrium critical properties of $O(n)$-symmetric models with reversible mode-coupling terms. Specifically, a variant of the model of Sasv\'ari, Schwabl, and Sz\'epfalusy is studied, where violation of detailed balance…
Janus motors with chemically active and inactive hemispheres can operate only under nonequilibrium conditions where detailed balance is broken by fluxes of chemical species that establish a nonequilibrium state. A microscopic model for…
In light of the dynamical-systems approach to entropy production in repeated quantum measurements, proposed and illustrated in Commun. Math. Phys. 357, 77-123 (2018) [arXiv:1607.00162] and J. Stat. Phys. 182, 44 (2021) [arXiv:2012.03885],…
For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them is essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
Coupling hadronic kinetic theory models to fluid dynamics in phenomenological studies of heavy ion collisions requires a prescription for ``particlization''. Existing particlization models are based on implicit or explicit assumptions about…
The method of complementary channel for analysis of reversibility (sufficiency) of a quantum channel with respect to families of input states (pure states for the most part) are considered and applied to Bosonic linear (quasi-free)…
We consider stochastically modeled chemical reaction systems with mass-action kinetics and prove that a product-form stationary distribution exists for each closed, irreducible subset of the state space if an analogous deterministically…