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We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
This paper discusses the latest generation of the MONARC (MOdels of Networked Analysis at Regional Centers) simulation framework, as a design and modelling tool for large scale distributed systems applied to HEP experiments. A…
The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…
In this work, we introduce a novel computational framework that we developed to use numerical simulations to investigate the complexity of brain tissue at a microscopic level with a detail never realised before. Directly inspired by the…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
Advances in single-cell sequencing have enabled high-resolution profiling of diverse molecular modalities, while integrating unpaired multi-omics single-cell data remains challenging. Existing approaches either rely on pair information or…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
In this tutorial paper, we will firstly review some basic simulation concepts and then introduce the parallel and distributed simulation techniques in view of some new challenges of today and tomorrow. More in particular, in the last years…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified software interface. Our framework is intrinsically parallel, and conveniently separates all components in memory. It…
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
We present a hybrid vertex/cell-centred model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular nodal network, while the cell boundaries are formed by an…
In this article, we continue our mathematical study of organic solar cells (OSCs) and propose a two-scale (micro- and macro-scale) model of heterojunction OSCs with interface geometries characterized by an arbitrarily complex morphology.…