Related papers: A novel scalable high performance diffusion solver…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Computational biology has increasingly turned to agent-based modeling to explore complex biological systems. Biological diffusion (diffusion, decay, secretion, and uptake) is a key driver of biological tissues. GPU computing can vastly…
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and…
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low…
In advancing discrete-based computational cancer models towards clinical applications, one faces the dilemma of how to deal with an ever growing amount of biomedical data that ought to be incorporated eventually in one form or another.…
Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multi-scale nature of cancer pose significant computational challenges. Coupling discrete cell-based models…
The finite cell method is a highly flexible discretization technique for numerical analysis on domains with complex geometries. By using a non-boundary conforming computational domain that can be easily meshed, automatized computations on a…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
The Cellular Potts Model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or…
This paper presents a finite volume method for simulating two-phase flows using a level set approach coupled with volume of fluid method capable of simulating sharp fluid interfaces. The efficiency of the method is a result of the fact that…
Purpose: This study aims to assess the robustness and accuracy of the face-centred finite volume (FCFV) method for the simulation of compressible laminar flows in different regimes, using numerical benchmarks. Design/methodology/approach:…
There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…
In this paper, we argue that iterative computation with diffusion models offers a powerful paradigm for not only generation but also visual perception tasks. We unify tasks such as depth estimation, optical flow, and amodal segmentation…
Hyperdimensional Computing (HDC) is a brain-inspired computing paradigm that represents and manipulates information using high-dimensional vectors, called hypervectors (HV). Traditional HDC methods, while robust to noise and inherently…
Diffusion models have demonstrated remarkable performance in image and video synthesis. However, scaling them to high-resolution inputs is challenging and requires restructuring the diffusion pipeline into multiple independent components,…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Computational fluid dynamics (CFD) is a branch of fluid mechanics that uses numerical methods to solve fluid flows. The finite volume method (FVM) is an important one. In FVM, space is discretized to many grid cells. When the number of grid…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
This work presents the face-centred finite volume (FCFV) paradigm for the simulation of compressible flows. The FCFV method defines the unknowns at the face barycentre and uses a hybridisation procedure to eliminate all the degrees of…
Large-scale classical simulation of quantum computers is crucial for benchmarking quantum algorithms, establishing boundaries of quantum advantage and exploring heuristic quantum algorithms. We present a full-state vector simulation…