Related papers: Conformational Nonequilibrium Enzyme Kinetics: Gen…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe". It remains a question what the minimally required description for the…
Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…
The conceptual difference between equilibrium and non-equilibrium steady state (NESS) is well established in physics and chemistry. This distinction, however, is not widely appreciated in dynamical descriptions of biological populations in…
A number of properties of systems in a nonequilibrium steady state (NESS) are investigated by a generalization of the Onsager-Machlup (OM) path integral approach for systems in an equilibrium state (ES). A thermodynamics formally identical…
Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…
A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and…
Accurate predictions of reactive mixing are critical for many Earth and environmental science problems. To investigate mixing dynamics over time under different scenarios, a high-fidelity, finite-element-based numerical model is built to…
Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
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…
Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and…
Mass action systems capture chemical reaction networks in homogeneous and dilute solutions. We suggest a notion of generalized mass action systems that admits arbitrary nonnegative power-law rate functions and serves as a more realistic…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…
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…
In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
A link between memory effects in quantum kinetic equations and nonequilibrium correlations associated with the energy conservation is investigated. In order that the energy be conserved by an approximate collision integral, the one-particle…