Related papers: The 3D coarse-graining formulation of interacting …

The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…

We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where…

We present an elastic simulator for domains defined as evolving implicit functions, which is efficient, robust, and differentiable with respect to both shape and material. This simulator is motivated by applications in 3D reconstruction: it…

Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…

We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…

We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…

Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…

Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…

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…

We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…

Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating and responsive media, e.g., polymeric materials such…

This paper is focused on the question of simulation and visualiza- tion of 3D gel and paste dynamic effects. In a first part, we introduce a 3D physically based particle (or mass-interaction) model, with a small number of masses and few…

The dynamics of flexible filaments entrained in flow, important for understanding many biological and industrial processes, are computationally expensive to model with full-physics simulations. This work describes a data-driven technique to…

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints.…

This work presents the development, analysis and numerical simulations of a biophysical model for 3D cell deformation and movement, which couples biochemical reactions and biomechanical forces. We propose a mechanobiochemical model which…

We propose a method to non-rigidly align a three-dimensional (3D) volumetric image with a two-dimensional (2D) planar image representing a projection of the deformed volume. The application in mind comes from biological studies in which 2D…

Marine ecosystems are in the spotlight, because environmental changes are threatening biodiversity and ecological functions. In this context, microalgae play key ecological roles both in planktonic and benthic ecosystems. Consequently, they…

We devise a soft, solvent-free, coarse-grained model for lipid bilayer membranes. The non-bonded interactions take the form of a weighted-density functional which allows us to describe the thermodynamics of self-assembly and packing effects…

We present a simple set of data structures, and a collection of methods for constructing and updating the structures, designed to support the use of cohesive elements in simulations of fracture and fragmentation. Initially all interior…

This paper is concerned with the partitioned iterative formulation to simulate the fluid-structure interaction of a nonlinear multibody system in an incompressible turbulent flow. The proposed formulation relies on a three-dimensional (3D)…