Related papers: Systematic time-scale-bridging molecular dynamics …
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…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
Knowledge of the underlying mechanisms of multiphase flow dynamics in porous media is crucial for optimizing subsurface engineering applications like geological carbon sequestration. However, studying the micro-mechanisms of multiphase…
In this paper, the inherent gradient flow structures of thermo-poro-visco-elastic processes in porous media are examined for the first time. In the first part, a modelling framework is introduced aiming for describing such processes as…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
We investigate both ensemble and time-averaged mean-squared displacements of particles in a polydisperse granular system in a homogeneous cooling state. The system contains an arbitrary number of species of different sizes and masses. The…
We apply a recently proposed novel thermostating mechanism to an interacting many-particle system where the bulk particles are moving according to Hamiltonian dynamics. At the boundaries the system is thermalized by deterministic and…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
Many features of granular media can be modelled as a fluid of hard spheres with {\em inelastic} collisions. Under rapid flow conditions, the macroscopic behavior of grains can be described through hydrodynamic equations. At low-density, a…
We present an extended investigation of a recently introduced model of gravitationally confined, collisionless plasma (Barbieri et al. 2024a), which showed that rapid temperature fluctuations at the base of the plasma, occurring on…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Aqueous two-phase systems (ATPSs), that is, phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a…
We develop a novel Monte Carlo strategy for the simulation of the Boltzmann-BGK model with both low-collisional and high-collisional regimes present. The presented solution to maintain accuracy in low-collisional regimes and remove…
Semi-analytical methods, based on Eulerian perturbation theory, are a promising tool to follow the time evolution of cosmological perturbations at small redshifts and at mildly nonlinear scales. All these schemes are based on two…
We have developed and implemented a numerical evolution scheme for a class of stochastic problems in which the temporal evolution occurs on widely-separated time scales, and for which the slow evolution can be described in terms of a small…