Related papers: MorphoSim: An efficient and scalable phase-field f…
In this work, we apply phase field simulations to examine the coarsening behavior of morphologically complex two-phase microstructures in which the phases have highly dissimilar mobilities, a condition approaching that found in experimental…
Homogenisation empowers the efficient macroscale system level prediction of physical scenarios with intricate microscale structures. Here we develop an innovative powerful, rigorous and flexible framework for asymptotic homogenisation of…
Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving,…
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…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
We simulate the electrical response of multiple disjoint biological 3D cells undergoing an electropermeabilization process. Instead of solving the boundary value problem in the unbounded volume, we reduce it to a system of boundary…
Recent advances in deep learning-based image reconstruction techniques have led to significant progress in phase retrieval using digital in-line holographic microscopy (DIHM). However, existing deep learning-based phase retrieval methods…
A phase field approach is proposed to model the chemotaxis of Dictyostelium discoideum. In this framework, motion is controlled by active forces as determined by the Meinhardt model of chemical dynamics which is used to simulate directional…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
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…
Automatic analysis of spatio-temporal microscopy images is inevitable for state-of-the-art research in the life sciences. Recent developments in deep learning provide powerful tools for automatic analyses of such image data, but heavily…
The detection of cell shape changes in 3D time-lapse images of complex tissues is an important task. However, it is a challenging and tedious task to establish a comprehensive dataset to improve the performance of deep learning models. In…
We develop and analyse the first second-order phase-field model to combine melting and dissolution in multi-component flows. This provides a simple and accurate way to simulate challenging phase-change problems in existing codes.…
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…
A symmetric phase field model is used to study wavelength selection in two dimensions. We study the problem in a finite system using a two-pronged approach. First we construct an action and, minimizing this, we obtain the most probable…
Xenium, a new spatial transcriptomics platform, enables subcellular-resolution profiling of complex tumor tissues. Despite the rich morphological information in histology images, extracting robust cell-level features and integrating them…
Multiscale simulations facilitate the efficient exploration of large spatiotemporal scales in chemical and physical systems, yet particle-based simulations become prohibitively expensive at time and length scales beyond the molecular level.…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Accurate performance estimation of future many-node machines is challenging because it requires detailed simulation models of both node and network. However, simulating the full system in detail is unfeasible in terms of compute and memory…