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The particle-scale dynamics of granular materials have commonly been characterized by the self-diffusion coefficient $D$. However, this measure discards the collective and topological information known to be an important characteristic of…
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are…
Systems of self-propelled particles are known for their tendency to aggregate and to display swarm behavior. We investigate two model systems, self-propelled rods interacting via volume exclusion, and sinusoidally-beating flagella embedded…
We investigate the wrinkling dynamics of an elastic filament immersed in a viscous fluid submitted to compression at a finite rate with experiments and by combining geometric nonlinearities, elasticity, and slender body theory. The drag…
The diffusion type is determined not only by microscopic dynamics but also by the environment properties. For example, the environment's fractal structure is responsible for the emergence of subdiffusive scaling of the mean square…
Inspired by motile cells in tissue formation, we find that active systems of self-aligning adhesive particles undergo ballistic aggregation through a flocking transition. This kinetic regime emerges when the cluster persistence length grows…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
The dynamics of a flexible filament sedimenting in a viscous fluid are explored analytically and numerically. Compared to the well-studied case of sedimenting rigid rods, the introduction of filament compliance is shown to cause a…
A recent study in turbulent flow simulation demonstrated the potential of generative diffusion models for fast 3D surrogate modeling. This approach eliminates the need for specifying initial states or performing lengthy simulations,…
The flapping states of a flexible fiber fully coupled to a three-dimensional turbulent flow are investigated via state-of-the-art numerical methods. Two distinct flapping regimes are predicted by the phenomenological theory recently…
Active and diffusive motion in Brownian particles are regularly observed in fluidic environments, albeit at different time scales. Here, we experimentally study the dynamics of highly asymmetric microclusters trapped in air employing…
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…
Aggregation-diffusion equations are foundational tools for modelling biological aggregations. Their principal use is to link the collective movement mechanisms of organisms to their emergent space use patterns in a concrete mathematical…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
Diffusion models have emerged as powerful generative frameworks by progressively adding noise to data through a forward process and then reversing this process to generate realistic samples. While these models have achieved strong…
Despite extensive progress in characterizing the emergent behavior of active matter, the microscopic origins of self-diffusion in interacting active systems remain poorly understood. Here, we develop a framework that quantitatively links…
The steady-state behavior of a dilute suspension of self-propelled filaments confined between planar walls subjected to the Couette-flow is reported herein. The effect of hydrodynamics has been taken into account using a mesoscale…
Turbulent mixing and entrainment at the boundary of a cloud is studied by means of direct numerical simulations that couple the Eulerian description of the turbulent velocity and water vapor fields with a Lagrangian ensemble of cloud water…