Related papers: MorphoSim: An efficient and scalable phase-field f…
We develop a special phase field/diffusive interface method to model the nuclear architecture reorganization process. In particular, we use a Lagrange multiplier approach in the phase field model to preserve the specific physical and…
Morphogenesis is a tightly regulated process that has been studied for decades. We are developing data-based and image-basd mechanistic models for a range of developmental processes with a view to integrate the available knowledge and to…
The development of novel materials in recent years has been accelerated greatly by the use of computational modelling techniques aimed at elucidating the complex physics controlling microstructure formation in materials, the properties of…
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith…
A new approach is developed for computational modelling of microstructure evolution problems. The approach combines the phase-field method with the recently-developed laminated element technique (LET) which is a simple and efficient method…
Numerical investigation of the interaction of electromagnetic fields with eukaryotic cells requires specifically adapted computer models. Virtual microdosimetry, used to investigate exposure, requires volumetric cell models, which are…
Systematic validation is an essential part of algorithm development. The enormous dataset sizes and the complexity observed in many recent time-resolved 3D fluorescence microscopy imaging experiments, however, prohibit a comprehensive…
With the aim of efficiently simulating three-dimensional multiphase turbulent flows with a phase-field method, we propose a new discretization scheme for the biharmonic term (the 4th-order derivative term) of the Cahn-Hilliard equation.…
We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and…
Automated cell segmentation in microscopy images is essential for biomedical research, yet conventional methods are labor-intensive and prone to error. While deep learning-based approaches have proven effective, they often require large…
Animal morphogenesis often involves significant shape changes of epithelial tissue sheets. Great progress has been made in understanding the underlying cellular driving forces and their coordination through biomechanical feedback loops.…
Deep learning has revolutionized medical and biological imaging, particularly in segmentation tasks. However, segmenting biological cells remains challenging due to the high variability and complexity of cell shapes. Addressing this…
A new type of microfluidic system for biological cell manipulation, a CMOS/microfluidic hybrid, is demonstrated. The hybrid system starts with a custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated in a…
In this article, we discuss the stability of soft quasicrystalline phases in a coupled-mode Swift-Hohenberg model for three-component systems, where the characteristic length scales are governed by the positive-definite gradient terms.…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
Rigorous computer simulations of propagating electromagnetic fields have become an important tool for optical metrology and optics design of nanostructured components. As has been shown in previous benchmarks some of the presently used…
Stacked intelligent metasurfaces (SIMs) extend the concept of reconfigurable intelligent surfaces by cascading multiple programmable layers, enabling advanced electromagnetic wave transformations for communication and sensing applications.…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
The difficulties in dealing with discontinuities related to a sharp crack are overcome in the phase-field approach for fracture by modeling the crack as a diffusive object being described by a continuous field having high gradients. The…