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Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
The hematopoietic system has a highly regulated and complex structure in which cells are organized to successfully create and maintain new blood cells. Feedback regulation is crucial to tightly control this system, but the specific…
Simulation is a useful tool in situations where training data for machine learning models is costly to annotate or even hard to acquire. In this work, we propose a reinforcement learning-based method for automatically adjusting the…
We introduce and discuss shape based models for finding the best interpolation data in compression of images with noise. The aim is to reconstruct missing regions by means of minimizing data fitting term in the $L^2$-norm between the images…
Effective properties of materials with random heterogeneous structures are typically determined by homogenising the mechanical quantity of interest in a window of observation. The entire problem setting encompasses the solution of a local…
The morphometric approach is a powerful ansatz for decomposing the chemical potential for a complex solute into purely geometrical terms. This method has proven accuracy in hard spheres, presenting an alternative to comparatively expensive…
Numerical simulation serves as a cornerstone in scientific modeling, yet the process of fine-tuning simulation parameters poses significant challenges. Conventionally, parameter adjustment relies on extensive numerical simulations, data…
Simulations of complex physical systems are typically realized by discretizing partial differential equations (PDEs) on unstructured meshes. While neural networks have recently been explored for surrogate and reduced order modeling of PDE…
Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…
Meta-materials are an important emerging class of engineered materials in which complex macroscopic behaviour--whether electromagnetic, thermal, or mechanical--arises from modular substructure. Simulation and optimization of these materials…
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape…
Model-driven analysis of biophysical phenomena is gaining increased attention and utility for medical imaging applications. In magnetic resonance imaging (MRI), the availability of well-established models for describing the relations…
Statistical data simulation is essential in the development of statistical models and methods as well as in their performance evaluation. To capture complex data structures, in particular for high-dimensional data, a variety of simulation…
Implicit sampling is a weighted sampling method that is used in data assimilation, where one sequentially updates estimates of the state of a stochastic model based on a stream of noisy or incomplete data. Here we describe how to use…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…