相关论文: Sensitivity Amplification in the Phosphorylation-D…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
Entropy production plays a fundamental role in the study of non-equilibrium systems by offering a quantitative handle on the degree of time-reversal symmetry breaking. It depends crucially on the degree of freedom considered as well as on…
We show that the exact exchange-correlation potential of time-dependent density-functional theory displays dynamical step structures that have a spatially non-local and time non-local dependence on the density. Using one-dimensional…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Dissipation is commonly regarded as an obstacle to quantum control, as it induces decoherence and irreversibility. Here we demonstrate that dissipation can instead be exploited as a resource to reshape the dynamics of interacting quantum…
Dynamic fragmentation simulations are essential for predicting material response at high strain rates, yet explicit dynamic simulations that combine an extrinsic cohesive-zone model (CZM) with penalty-based contact often exhibit severe…
Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements,…
The oscillatory dynamics of natural and man-made systems can be disrupted by their time-varying interactions, leading to oscillation quenching phenomena in which the oscillations are suppressed. We introduce a framework for analyzing,…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
By using the holographic approach, we investigate the interplay between the order parameter and Goldstone modes in the real-time dynamics of the chiral phase transition. By quenching the system to a different thermal bath and obtaining…
The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…
We show the emergence of Floquet time crystal (FTC) phases in the Floquet dynamics of periodically driven $p$-spin models, which describe a collection of spin-1/2 particles with all-to-all $p$-body interactions. Given the mean-field nature…
Using a controlled analytic non-perturbative treatment, that accounts for the quantum nature of the phonons, we derive a model that generically describes cooperative breathing-mode at strong electron-phonon interaction in one-band…
Motility and nonreciprocity are two primary mechanisms for self-organization in active matter. In a recent study [Phys. Rev. Lett. 131, 148301 (2023)], we explored their joint influence in a minimal model of two-species quorum-sensing…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
We study both theoretically and experimentally switching dynamics in surface stabilized ferroelectric liquid crystal cells with asymmetric boundary conditions. In these cells the bounding surfaces are treated differently to produce…
Development of thermodynamic induction up to second order gives a dynamical bifurcation for thermodynamic variables and allows for the prediction and detailed explanation of nonequilibrium phase transitions with associated spontaneous…
The temporal behaviour of segmentation clock oscillations show phase synchrony via mean field like coupling of delta protein restricting to nearest neighbours only, in a configuration of cells arranged in a regular three dimensional array.…
A class of coupled cell-bulk ODE-PDE models is formulated and analyzed in a two-dimensional domain, which is relevant to studying quorum sensing behavior on thin substrates. In this model, spatially segregated dynamically active signaling…