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Simulation is an important step in robotics for creating control policies and testing various physical parameters. Soft robotics is a field that presents unique physical challenges for simulating its subjects due to the nonlinearity of…
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
A universal framework for modeling composites and fabrics of micro- and nanofibers, such as carbon nanotubes, carbon fibers and amyloid fibrils, is presented. Within this framework, fibers are represented with chains of rigid bodies, linked…
Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid…
The fragmentation of small, brittle, flexible, inextensible fibers is investigated in a fully-developed, homogeneous, isotropic turbulent flow. Such small fibers spend most of their time fully stretched and their dynamics follows that of…
We propose a numerical method for fluid deformable surfaces governed by surface Stokes flow and Helfrich bending energy under active growth, aiming to model shape evolution of the epithelium in developmental processes. To prevent…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
We develop a unified continuum modeling framework for viscous fluids and hyperelastic solids using the Gibbs free energy as the thermodynamic potential. This framework naturally leads to a pressure primitive variable formulation for the…
Self-organized dynamic patterns in dense active matter are striking manifestations of non-equilibrium physics. A prominent example is the macroscopic elliptical motion observed in quasi-2D bacterial suspensions, which has lacked a physical…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
Classically, the constitutive behavior of materials is described either phenomenologically, or by homogenization approaches. Phenomenological approaches are computationally very efficient, but are limited for complex non-linear and…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
Cellular biology abound with filaments interacting through fluids, from intracellular microtubules, to rotating flagella and beating cilia. While previous work has demonstrated the complexity of capturing nonlocal hydrodynamic interactions…
To capture specific characteristics of non-Newtonian fluids, during the past years fractional constitutive models have become increasingly popular. These models are able to capture in a simple and compact way the complex behaviour of…
In this paper homogenization of a mathematical model for biomechanics of a plant tissue with randomly distributed cells is considered. Mechanical properties of a plant tissue are modelled by a strongly coupled system of…
In this paper, we study a hydrodynamic phase-field system modeling the deformation of functionalized membranes in incompressible viscous fluids. The governing PDE system consists of the Navier-Stokes equations coupled with a convective…
The structure, thermodynamics and slow activated dynamics of the equilibrated metastable regime of glass-forming fluids remains a poorly understood problem of high theoretical and experimental interest. We apply a highly accurate…
In this paper, we first develop a mathematical model for long-range, hydrophobic attraction between amphiphilic particles. The non-pairwise interactions follow from the first variation of a hydrophobic attraction domain functional. The…
In this work it is shown how the immersed boundary method of (Peskin2002) for modeling flexible structures immersed in a fluid can be extended to include thermal fluctuations. A stochastic numerical method is proposed which deals with…