Related papers: Coarse-graining dense, deformable active particles
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Aggregation processes in systems of planar macromolecules and colloids drive a broad range of phenomena in natural systems and soft materials. Depending on chemical architecture, intermolecular interactions in these systems may favor…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Active Brownian particles (ABPs), when subject to purely repulsive interactions, are known to undergo activity-induced phase separation broadly resembling an equilibrium (attraction-induced) gas-liquid coexistence. Here we present an…
The rheology of dense granular shear flows is influenced by friction and particle shape. We investigate numerically the impact of non-spherical particle geometries under shear on packing fraction, stress ratios, velocity fluctuations, force…
Mechanochemical processes on surfaces such as the cellular cortex or epithelial sheets, play a key role in determining patterns and shape changes of biological systems. To understand the complex interplay of hydrodynamics and material flows…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the…
Two very basic constructions involving experimental procedures are the formation of coarse-grained versions of experiments, and the formation of branching sequential experiments. The latter allow for the conditioning of states on the…
The hydrodynamic theory of active nematics has been often used to describe the spatio-temporal dynamics of cell flows and motile topological defects within soft confluent tissues. Those theories, however, often rely on the assumption that…
Curved particles have been shown to stabilize a range of states with unique order in dense suspensions of colloidal bent core liquid crystals. The shape of the colloidal rods encourages the formation of curved director fields. However,…
We review recent progress in the theoretical description of anisotropic hard colloidal particles. The shapes considered range from rods and dumbbells to rounded cubes, polyhedra and to biaxial particles with arbitrary shape. Our focus is on…
Colloidal gels are prime examples of functional materials exhibiting disordered, amorphous, yet meta-stable forms. They maintain stability through short-range attractive forces and their material properties are tunable by external forces.…
The theory of elastic interaction of micron size axially symmetric colloidal particles immersed into confined nematic liquid crystal has been proposed. General formulas are obtained for the self energy of one colloidal particle and…
Biological membranes often exhibit heterogeneous protein patterns, which cells control. Strong patterns, like the polarity spot in budding yeast, can be described as surface condensates, formed by physical interactions between constituents.…
The emergence of macroscopic variables can be effected through {\it coarse graining}. Despite practical and fundamental benefits conveyed by this partitioning of state space, the apparently subjective nature of the selection of coarse…
We report, for the first time, some experimental observations regarding a new type of long range interaction between rigid particles that prevails when they are suspended in an soft elastic gel. A denser particle submerges itself to a…
Glasses behave as solids on experimental time scales due to their slow relaxation. Growing dynamic length scales due to cooperative motion of particles are believed to be central to this slow response. For quiescent glasses, however, the…
Living materials such as membranes, cytoskeletal assemblies, cell collectives and tissues can often be described as active solids -- materials that are energized from within, with elastic response about a well defined reference…