Related papers: TopoSPAM: Topology grounded Simulation Platform fo…
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…
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive…
Understanding how cells respond to external stimuli is a central challenge in biomedical research and drug development. Current computational frameworks for modelling cellular responses remain restricted to two-dimensional representations,…
For the shape control of deformable free-form surfaces, simulation plays a crucial role in establishing the mapping between the actuation parameters and the deformed shapes. The differentiation of this forward kinematic mapping is usually…
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…
One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching…
Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex $3D$ shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well…
Shape analysis and classification are popular methods for biologists, biophysicists and mathematicians investigating relationships between object function and form. Classic shape descriptors, such as sphericity, can be powerful but may be…
Morphogenesis of living systems involves topological shape transformations which are highly unusual in the inanimate world. Here we demonstrate that a droplet of a nematic liquid crystal changes its equilibrium shape from a simply-connected…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
We present a novel, physically-based morphing technique for elastic shapes, leveraging the differentiable material point method (MPM) with space-time control through per-particle deformation gradients to accommodate complex topology…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Visual robot navigation within large-scale, semi-structured environments deals with various challenges such as computation intensive path planning algorithms or insufficient knowledge about traversable spaces. Moreover, many…
Growing experimental evidence indicates that topological defects could serve as organizing centers in the morphogenesis of tissues. Here, we provide a quantitative explanation for this phenomenon, rooted in the buckling theory of deformable…