Related papers: PolyMorph: Extension of PolyHoop for tissue morpho…
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable…
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modelling this process can provide novel insights into development and the principles that orchestrate the…
Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins,…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Biological systems can form complex three-dimensional structures through the collective behavior of agents that share a common update rule and operate without central control. How such distributed control gives rise to precise global…
This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support…
We present NeuroMorph, a new neural network architecture that takes as input two 3D shapes and produces in one go, i.e. in a single feed forward pass, a smooth interpolation and point-to-point correspondences between them. The…
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surrounding microenvironment. An important challenge in the field is…
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…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
This paper presents a new C++ framework, DELPHES, performing a fast multipurpose detector response simulation. The simulation includes a tracking system, embedded into a magnetic field, calorimeters and a muon system, and possible very…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
This paper introduces Polyphorm, an interactive visualization and model fitting tool that provides a novel approach for investigating cosmological datasets. Through a fast computational simulation method inspired by the behavior of Physarum…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from…
We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
An emerging theme across many domains of science and engineering is materials that change shape, often dramatically. Determining their structure involves solving a shape optimization problem where a given energy functional is minimized with…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…