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Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…
Periodic driving is used to steer physical systems to unique stationary states or nonequilibrium steady states (NESS), producing enhanced properties inaccessible to non-driven systems. For open quantum systems, characterizing the NESS is…
"Pedagogical derivations for Nos\'e's dynamics can be developed in two different ways, (i) by starting with a temperature-dependent Hamiltonian in which the variable $s$ scales the time or the mass, or (ii) by requiring that the equations…
We present a novel mechanism for thermalizing a system of particles in equilibrium and nonequilibrium situations, based on specifically modeling energy transfer at the boundaries via a microscopic collision process. We apply our method to…
A collisional model of a confined quasi-two-dimensional granular mixture is considered to analyze homogeneous steady states. The model includes an effective mechanism to transfer the kinetic energy injected by vibration in the vertical…
We study the relaxation dynamics of a run and tumble particle in a one-dimensional piecewise linear potential $U(x)=b|x|$, from delta-function initial conditions at $x=0$ to steady state. In addition to experiencing active telegraphic…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
The dynamics of a system composed of elastic hard particles confined by an isotropic harmonic potential are studied. In the low-density limit, the Boltzmann equation provides an excellent description, and the system does not reach…
We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…
We study the dynamic properties of a thermal autonomous machine made up of two quantum Brownian particles, each of which is in contact with an environment at different temperature and moves on a periodic sinusoidal track. When such tracks…
In this study, we examine the dynamics of a one-dimensional Frenkel-Kontorova chain consisting of nanosize clusters (the ''particles'') and photochromic molecules (the ''bonds''), and being subjected to a periodic substrate potential.…
This work concerns the theoretical description of the quantum dynamics of molecular junctions with thermal fluctuations and probability losses To this end, we propose a theory for describing non-Hermitian quantum systems embedded in…
We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
Recently it was demonstrated theoretically and experimentally that the presence of a moving conductor can break the reciprocity in the interactions between magnetic dipoles. In this article we investigate the influence of nonreciprocity on…
A model of homogeneously driven dissipative system, consisting of a collection of $N$ particles that are characterized by only their velocities, is considered. Adopting a discrete time dynamics, at each time step, a pair of velocities is…
A stochastic differential equation that describes the dynamics of single-domain magnetic particles at any temperature is derived using a classical formalism. The deterministic terms recover existing theory and the stochastic process takes…
The linear stability of a magnetized plasma accompanying temperature gradient was reexamined by using plasma kinetic theory. The anisotropic velocity distribution function was decomposed into two components. One is proportional to the…