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Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the…
The effect of multiplicative stochastic perturbations on Hamiltonian systems on the plane is investigated. It is assumed that perturbations fade with time and preserve a stable equilibrium of the limiting system. The paper investigates…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
Are spinodal instabilities the leading mechanism in the fragmentation of a fermionic system? Numerous experimental indications suggest such a scenario and stimulated much effort in giving a suitable description, without being finalised in a…
We present our study on the emergent states of two interacting nonlinear systems with differing dynamical time scales. We find that the inability of the interacting systems to fall in step leads to difference in phase as well as change in…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
We explore the dynamics of active elements performing persistent random motion with fluctuating active speed and in the presence of translational noise in a $d$-dimensional harmonic trap, modeling active speed generation through an…
Dynamic simulation plays a crucial role in power system transient stability analysis, but traditional numerical integration-based methods are time-consuming due to the small time step sizes. Other semi-analytical solution methods, such as…
Using experiments on a colloidal particle trapped in an optical tweezer, we confirm a recent proposal to increase the effective mobility or clock rate of systems described by Langevin dynamics, by simultaneously scaling deterministic forces…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
One of the general mechanisms that give rise to the slow cooperative relaxation characteristic of classical glasses is the presence of kinetic constraints in the dynamics. Here we show that dynamical constraints can similarly lead to slow…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
The equations for the sliding of a single block driven by an elastic force show numerically a fast and a slow step in their dynamics when a dimensionless parameter is very large, a limit pertinent for many applications. An asymptotic…
Identification of the parameters of stable linear dynamical systems is a well-studied problem in the literature, both in the low and high-dimensional settings. However, there are hardly any results for the unstable case, especially…
The assumption that quantum systems relax to a stationary state in the long-time limit underpins statistical physics and much of our intuitive understanding of scientific phenomena. For isolated systems this follows from the eigenstate…
The ability to describe strongly interacting matter at finite temperature and baryon density provides the means to determine, for instance, the equation of state of QCD at non-zero baryon chemical potential. From a theoretical point of…
A central task in the analysis of human movement behavior is to determine systematic patterns and differences across experimental conditions, participants and repetitions. This is possible because human movement is highly regular, being…
Multistability of mesoscopic, driven biochemical reaction systems has implications to a wide range of cellular processes. Using several simple models, we show that one class of bistable chemical systems has a deterministic counterpart in…
We study a class of elastic systems described by a (hyperbolic) partial differential equation. Our working example is the equation of a vibrating string subject to linear disturbance. The main goal is to establish conditions for…