Related papers: ATP Synthase: A Moonlighting Enzyme with Unprecede…
Living systems efficiently use chemical fuel to do work, process information, and assemble patterns despite thermal noise. Whether high efficiency arises from general principles or specific fine-tuning is unknown. Here, applying a recent…
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
We develop meanfield approximation and numerical quadrature schemes for the evaluation of Angular-Dependent interatomic Potentials (ADPs) for magnesium and magnesium hydrides at finite temperature (thermalization) and arbitrary atomic molar…
Mitochondria are critical organelles in eukaryotes that produce the energy currency ATP. In nerve axons, mitochondria are known to align at almost regular intervals to maintain a constant ATP concentration, but little is known about the…
Artificial molecular machines are often driven by the periodic variation of an external parameter. This external control exerts work on the system of which a part can be extracted as output if the system runs against an applied load.…
Enhanced enzyme diffusion (EED), in which the diffusion coefficient of an enzyme transiently increases during catalysis, has been extensively reported experimentally. We numerically and analytically demonstrate that such enzymes can act as…
The maximum entropy principle (MEP) apparently allows us to derive, or justify, fundamental results of equilibrium statistical mechanics. Because of this, a school of thought considers the MEP as a powerful and elegant way to make…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of F1-ATP synthase and the bacterial flagellum, we present a minimal model of an externally…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B connected via a linker C. The existing ISAPT algorithm displays…
One of the main issues that real energy converters present, when they produce effective work, is the inevitable entropy production. Within the context of Non-equilibrium Thermodynamics, entropy production tends to energetically degrade…
We show that a reversible pumping mechanism operating between two states of a kinetic network can give rise to Poisson transitions between these two states. An external observer, for whom the pumping mechanism is not accessible, will…
Metadamping is the phenomenon of either enhanced or diminished intrinsic dissipation in a material stemming from the material's internal structural dynamics. It has been previously shown that a locally resonant elastic metamaterial may be…
Machine learning interatomic potentials (MLIPs) offer near-ab initio accuracy with the efficiency of classical force fields, making them attractive for modeling electrolytes. Collecting a diverse training set is essential for their accuracy…
We propose a novel mechanism for dark energy, based on an extended seesaw for scalar fields, which does not require any new physics at energies below the TeV scale. A very light quintessence mass is usually considered to be technically…
It is well known in enzyme kinetics that the Michaelis-Menten (MM) equation is applicable only to enzymes in the steady state. We show that the result obtained in the previous work [Phys. Rev. Lett. 107, 218301 (2011)] is inconsistent with…
We introduce and analyze the notion of mutual entropy-production (MEP) in autonomous systems. Evaluating MEP rates is in general a difficult task due to non-Markovian effects. For bipartite systems, we provide closed expressions in various…