Related papers: MorphoSim: An efficient and scalable phase-field f…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
Phase-field modeling is an effective but computationally expensive method for capturing the mesoscale morphological and microstructure evolution in materials. Hence, fast and generalizable surrogate models are needed to alleviate the cost…
The Syncytial Mesh Model introduces a three-layered framework for large-scale brain dynamics integrating local neural circuitry, macrostructural connectivity, and a slow mesoscale control-field substrate associated with astrocytic syncytial…
Phase field method has been widely used because of its excellent ability to simulate fracture problems. At present, the implementation process is mainly based on commercial software, and the operation process is relatively complex. In this…
We develop a stochastic whole-brain and body simulator of the nematode roundworm Caenorhabditis elegans (C. elegans) and show that it is sufficiently regularizing to allow imputation of latent membrane potentials from partial calcium…
Phase field crystals (PFC) are a tool for simulating materials at the atomic level. They combine the small length-scale resolution of molecular dynamics (MD) with the ability to simulate dynamics on mesoscopic time scales. We show how PFC…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo…
Cellular morphodynamics requires solving systems of coupled partial differential equations on moving bulk and surface domains, where advection-dominant transport, structure preservation, and severe mesh distortions make robust simulation…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
Scientists and engineers often create accurate, trustworthy, computational simulation schemes - but all too often these are too computationally expensive to execute over the time or spatial domain of interest. The equation-free approach is…
Organogenesis has been studied for decades, but fundamental questions regarding the control of growth and shape remain unsolved. We have recently shown that of all proposed mathematical models only ligand-receptor based Turing models…
High-throughput imaging workflows, such as Parallel Rapid Imaging with Spectroscopic Mapping (PRISM), generate data at rates that exceed conventional real-time processing capabilities. We present a scalable FPGA-based preprocessing pipeline…
The motion of microstructural interfaces is important in modeling materials that undergo twinning and structural phase transformations. Continuum models fall into two classes: sharp-interface models, where interfaces are singular surfaces;…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
We developed a novel reduced-order multi-scale method for solving large time-domain wavefield simulation problems. Our algorithm consists of two main stages. During the first "off-line" stage the fine-grid operator (of the graph Laplacian…
Validity of fluid models breaks down for non-thermal or weakly collisional plasmas which often occur e.g. in the solar wind. In these regimes one has to resort to modelling through the first-principle Vlasov-Maxwell system, but its…
In this article, a new generic higher-order finite-element framework for massively parallel simulations is presented. The modular software architecture is carefully designed to exploit the resources of modern and future supercomputers.…
The Single Chain Mean Field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double…
T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralise infected and cancerous cells. However, there is limited quantitative understanding of the migration process in 3D extracellular matrices (ECMs) and…