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Dynamic trajectories can be modeled with a Markov State Model (MSM). The reduction of continuous space coordinates to discretized coordinates can be done by statistical binning process. In addition to that, the transition probabilities can…
Dusty plasma medium turns out to be an ideal system for studying the strongly coupled behavior of matter. The large size and slow response make their dynamics suitable to be captured through simple diagnostic tools. Furthermore, as the…
Particle transport in random media obeying a given mixing statistics is key in several applications in nuclear reactor physics and more generally in diffusion phenomena emerging in optics and life sciences. Exact solutions for the…
Diffusion of self-propelled particles in the presence of randomly distributed obstacles in three dimensions is studied using molecular dynamics simulations. It is found that depending on the magnitude of the propelling force and the…
Self-diffusion coefficients, $D^*$, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean-squared displacements (MSDs) of mobile species. MSDs derived from simulation exhibit statistical…
The macroscopic transport properties in a disordered potential, namely diffusion and weak/strong localization, closely depend on the microscopic and statistical properties of the disorder itself. This dependence is rich of counter-intuitive…
We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013)]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their…
Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…
In the present paper we give a brief summary of some recent theoretical advances in the treatment of inhomogeneous fluids and methods which have applications in the study of dynamical properties of liquids in situations of extreme…
Processes of mixing and segregation in a packed bed of granular material stirred by a periodically moving rectangular bar are simulated by the discrete element method (DEM). Influence of mechanical properties of the particle material…
Tracer diffusion in crowded environments is central to many biological and soft matter systems, but quantitative frameworks for linking tracer motion to environmental structure remain limited. Here, we study the transport of rigid tracers…
We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion of…
This work presents a data-driven framework for multi-scale parametrization of velocity-dependent dispersive transport in porous media. Pore-scale flow and transport simulations are conducted on periodic pore geometries, and volume-averaging…
There is an increasing interest in the study of metamaterials and periodic materials across disciplines. These are anisotropic and their properties present directionality. For example, the wave speed depends on the propagation direction.…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
The dynamics of a tracer particle in a glassy matrix of obstacles displays slow complex transport as the free volume approaches a critical value and the void space falls apart. We investigate the emerging subdiffusive motion of the test…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
Mathematically modelling diffusive and advective transport of particles in heterogeneous layered media is important to many applications in computational, biological and medical physics. While deterministic continuum models of such…