Related papers: Multicellular simulations with shape and volume co…
We show how the nonlinear interaction effects `volume filling' and `adhesion' can be incorporated into the fractional subdiffusive transport of cells and individual organisms. To this end, we use microscopic random walk models with…
This article provides numerical evidence that under volume constraint the ball is the set which maximizes the perimeter of the least-perimeter partition into cells with prescribed areas. We introduce a numerical maximization algorithm which…
We derive novel algorithms for optimization problems constrained by partial differential equations describing multiscale particle dynamics, including non-local integral terms representing interactions between particles. In particular, we…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…
We demonstrate how concepts of statistical mechanics of interacting particles can have important implications in the choice of interaction potentials to model qualitative properties of cell aggregates in theoretical biology. We illustrate…
We propose a space mapping-based optimization algorithm for microscopic interacting particle dynamics which are inappropriate for direct optimization. This is of relevance for example in applications with bounded domains such that the…
Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
On the basis of a model we capture the role of strong attractive interaction in suppressing the rotational degrees of freedom of the system and volume exclusion in keeping microscopic symmetry-breaking intact to result in super-diffusive…
The intracellular transport process plays an important role in delivering essential materials throughout branched geometries of neurons for their survival and function. Many neurodegenerative diseases have been associated with the…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Units of complex systems -- such as neurons in the brain or individuals in societies -- must communicate efficiently to function properly: e.g., allowing electrochemical signals to travel quickly among functionally connected neuronal areas…
The ability of many living systems to actively self-propel underlies critical biomedical, environmental, and industrial processes. While such active transport is well-studied in uniform settings, environmental complexities such as geometric…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
In this paper, we present a framework for multiscale topology optimization of fluid-flow devices. The objective is to minimize dissipated power, subject to a desired contact-area. The proposed strategy is to design optimal microstructures…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
In this paper, we generalize the chance optimization problems and introduce constrained volume optimization where enables us to obtain convex formulation for challenging problems in systems and control. We show that many different problems…
This article revolves around shape and topology optimization, in the applicative context where the objective and constraint functionals depend on the solution to a physical boundary value problem posed on the optimized domain. We introduce…