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It has been well established that particulate systems show the jamming transition and critical scaling behaviors associated with it. However, our knowledge is limited to (nearly) monodisperse systems. Recently, a binary mixture of jammed…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Diffusion dynamics in multiplex networks can model a diverse number of real-world processes. In some specific configurations of these systems, the super-diffusion phenomenon arises, in which the diffusion is faster in the multiplex network…
Heterogeneous diffusion processes occur in many different fields such as transport in living cells or diffusion in porous media. A characterization of the transport parameters of such processes can be achieved by ensemble-based methods,…
In this paper crack initiation, propagation and branching phenomena are simulated using the Pseudo-Spring Smooth Particle Hydrodynamics (SPH) in two and three-dimensional domains. The pseudo-spring analogy is used to model material damage.…
A recent study has demonstrated that phase separation in binary liquid mixtures is arrested in the presence of elastic networks and can lead to a nearly uniformly-sized distribution of the dilute-phase droplets. At longer timescales, these…
Gradient-driven diffusion in crowded, multicomponent mixtures is a topic of high interest because of its role in biological processes such as transport in cell membranes. In partially phase-separated solutions, gradient-driven diffusion…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
Superdiffusion is an anomalous transport behavior. Recently, a new mechanism, termed the ``nodal mechanism," has been proposed to induce superdiffusion in quantum models. However, existing realizations of the nodal mechanism have so far…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
This work extends the classical dumbbell (two-bead) model of polymer chains to a more detailed multi-bead representation, where each polymer chain consists of $N$ beads connected by $N-1$ springs. We develop a thermodynamically consistent…
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…
Artificial neural network potentials (NNPs) have emerged as effective tools for understanding atomic interactions at the atomic scale in various phenomena. Recently, we developed highly transferable NNPs for {\alpha}-iron and…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…
Dynamic rupture propagation along an interface between two different elastic solids under shear dominated loading is studied numerically by a 2-D lattice particle model (LPM). The configuration of the lattice particle model consists of two…
The biotransport of the intravascular nanoparticle (NP) is influenced by both the complex cellular flow environment and the NP characteristics. Being able to computationally simulate such intricate transport phenomenon with high efficiency…
Driven particles in presence of crowded environment, obstacles or kinetic constraints often exhibit negative differential mobility (NDM) due to their decreased dynamical activity. We propose a new mechanism for complex many-particle systems…
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a…