Related papers: Calculating free energy profiles in biomolecular s…
Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…
Evidence suggests that the transport rate of a passive particle at long timescales is enhanced due to interactions with the surrounding active ones in a size- and composition-dependent manner. Using a system of particles with different…
Turbulent, relativistic nonthermal plasmas are ubiquitous in high-energy astrophysical systems, as inferred from broadband nonthermal emission spectra. The underlying turbulent nonthermal particle acceleration (NTPA) processes have…
Density functional theory (DFT) is an efficient instrument for describing a wide range of nanoscale phenomena: wetting transition, capillary condensation, adsorption, etc. In this paper, we suggest a method for obtaining the equilibrium…
Ions with similar charge-to-mass ratios cannot be separated from existing beam profile monitors (BPMs) in nuclear facilities in which low-energy radioactive ions are produced due to nuclear fusion reactions. In this study, we developed a…
We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments,…
We present an efficient method for propagating the time-dependent Kohn-Sham equations in free space, based on the recently introduced Fourier contour deformation (FCD) approach. For potentials which are constant outside a bounded domain,…
We show that, in strongly chaotic dynamical systems, the average particle velocity can be calculated analytically by consideration of Brownian dynamics in phase space, the method of images and use of the classical diffusion equation. The…
An improved one-dimensional mathematical model based on Pulsed Flow Equations (PFE) is derived by integrating the axial component of the momentum equation over the transient Womersley velocity profile, providing a dynamic momentum equation…
The diffusion equation is the primary tool to study the movement dynamics of a free Brownian particle, but when spatial heterogeneities in the form of permeable interfaces are present, no fundamental equation has been derived. Here we…
Quite recently I have proposed a nonperturbative dynamical effective field model (DEFM) to quantitatively describe the dynamics of interacting ferrofluids. Its predictions compare very well with the results from simulations. In this paper I…
A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…
We consider the overdamped Brownian dynamics of a particle starting inside a square potential well which, upon exiting the well, experiences a flat potential where it is free to diffuse. We calculate the particle's probability distribution…
We employ renewal processes to characterize the spatiotemporal dynamics of an active Brownian particle under stochastic orientational resetting. By computing the experimentally accessible intermediate scattering function (ISF) and…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…
Biological systems are non-linear, include unobserved variables and the physical principles that govern their dynamics are partly unknown. This makes the characterization of their behavior very challenging. Notably, their activity occurs on…
The electric microfield distribution (MFD) at an impurity ion is studied for two-component (TCP) electron-ion plasmas using molecular dynamics simulation and theoretical models. The particles are treated within classical statistical…
In contrast to normal diffusion, there is no canonical model for reactions between chemical species which move by anomalous subdiffusion. Indeed, the type of mesoscopic equation describing reaction-subdiffusion depends on subtle assumptions…
We introduce an algorithm based on Generalized Dual Method (GDM) to efficiently study the dynamics of a particle in quasiperiodic environments without the need to use periodic approximations or to save the information of the vertices that…