相关论文: Sensitivity Amplification in the Phosphorylation-D…

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…

It is well known since the pioneering work of Goldbeter and Koshland [Proc. Natl. Acad. Sci. USA, vol. 78, pp. 6840-6844 (1981)] that cellular phosphorylation- dephosphorylation cycle (PdPC), catalyzed by kinase and phosphatase under…

Phase field crystal (PFC) models constitute a field theoretical approach to solidification, melting and related phenomena at atomic length and diffusive time scales. One of the advantages of these models is that they naturally contain…

Phase separation routinely occurs in both living and synthetic systems. These phases are often complex and distinguished by features including crystallinity, nematic order, and a host of other nonconserved order parameters. For systems at…

Multicomponent phase separation is a routine occurrence in both living and synthetic systems. Thermodynamics provides a straightforward path to determine the phase boundaries that characterize these transitions for systems at equilibrium.…

Fragility index and cooperativity length characterizing the molecular mobility in the amorphous phase are for the first time calculated in drawn polylactide (PLA). The microstructure of the samples is investigated from wide-angle X-ray…

The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…

A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…

We propose a thermodynamically consistent minimal model to study synchronization which is made of driven and interacting three-state units. This system exhibits at the mean-field level two bifurcations separating three dynamical phases: a…

For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The…

Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…

Nonequilibrium phase transitions are routinely observed in both natural and synthetic systems. The ubiquity of these transitions highlights the conspicuous absence of a general theory of phase coexistence that is broadly applicable to both…

Collective temporal organization in complex systems is commonly attributed to synchronization, resonance, or proximity to dynamical instabilities. Here we identify a distinct mechanism by which coherent, synchronization-like behavior can…

We study the decoherence dynamics of dipole-coupled two-level quantum systems in Ramsey-type experiments. We focus on large networks of two-level systems, confined to two spatial dimensions and with positional disorder giving rise to…

The recently developed Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and…

A discrete time crystal (DTC) is the paradigmatic example of a phase of matter that occurs exclusively in systems out of equilibrium. This phenomenon is characterized by the spontaneous symmetry breaking of discrete time-translation and…

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…

We consider the dynamics of a periodic chain of N coupled overdamped particles under the influence of noise. Each particle is subjected to a bistable local potential, to a linear coupling with its nearest neighbours, and to an independent…

The Escherichia coli chemoreceptors form an extensive array that achieves cooperative and adaptive sensing of extracellular signals. The receptors control the activity of histidine kinase CheA, which drives a nonequilibrium…

In the presence of a (time-dependent) macroscopic electric field the electron dynamics of dielectrics cannot be described by the time-dependent density only. We present a real-time formalism that has the density and the macroscopic…