Related papers: Coarse-graining bistability with the Martini force…
In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
In this work, we study lattice structures that exhibit a bistable behavior, i. e., they can snap from one stable state to another, and are also completely reversible, capable of reverting back to its original state through a heat treatment.…
The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
We study an experimental system of hard granular squares in two dimensions, energized by vibration. The interplay of order in the orientations and positions of anisotropic particles allows for a rich set of phases. We measure the structure…
This work presents a rigorous framework based on coarse-graining to analyze highly compressible turbulence. We show how the requirement that viscous effects on the dynamics of large-scale momentum and kinetic energy be negligible ---an…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
How chirality propagates across scales remains an open question in many biological and synthetic systems. An especially clear manifestation of this propagation is found in in vitro gliding assays of cytoskeletal filaments on surfaces,…
Multiscale phenomena which include several processes occuring simultaneously at different length scales and exchanging energy with each other, are widespread in magnetism. These phenomena often govern the magnetization reversal dynamics,…
Phase separation in a low-density gas-like phase and a high-density liquid-like one is a common trait of biological and synthetic self-propelling particles' systems. The competition between motility and stochastic forces is assumed to fix…
The effect of oscillatory shear strain on nonaffine rearrangements of individual particles in a three-dimensional binary glass is investigated using molecular dynamics simulations. The amorphous material is represented by the Kob-Andersen…
In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed,…
The propagation of a probe field in an N-type four level cold atomic system is investigated under the influence of multiple coherent fields. Coherent control of quantum interference enables switching of the probe field between transparency…
The evolution of the microstructure due to spinodal decomposition in phase separated mixtures has a strong impact on the final material properties. In the late stage of coarsening, the system is characterized by the growth of a single…
Based on Brownian dynamics simulations, we investigate the thermodynamic signatures of non-equilibrium steady states in a confined colloidal suspensions under shear flow. Specifically, we consider a thin film consisting of charged particles…
The paper uses the spring potential to present interaction between the coarse-grained interfacial particles of the $\alpha$-Al2O3/$\alpha$-Al2O3 and $\alpha$-Fe2O3/$\alpha$-Fe2O3 contacts in the sliding friction study of these micron-scale…
In bistable systems, the stability of front structures often influences the dynamics of extended patterns. We show how the combined effect of an instability to curvature modulations and proximity to a pitchfork front bifurcation leads to…
In this paper we study noise-induced bistability in a specific circuit with many biological implications, namely a single-step enzymatic cycle described by Michaelis Menten equations with quasi-steady state assumption. We study the system…