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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…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
"Self-organization" has become a watchword in developmental biology, characterizing observations in which embryonic or induced stem cells of animals replicate morphological steps and outcomes seen in intact embryos. While the term was…
Contemporary sensorimotor learning approaches typically start with an existing complex agent (e.g., a robotic arm), which they learn to control. In contrast, this paper investigates a modular co-evolution strategy: a collection of primitive…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
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…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…
We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using…
The maintenance of tissue and organ structures during dynamic homeostasis is often not well understood. In order for a system to be stable, cell renewal, cell migration and cell death must be finely balanced. Moreover, a tissue's shape must…
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.…
Biological cells sense and respond to mechanical forces, but how such a mechanosensing proccess takes place in a nonlinear inhomogeneous fibrous matrix remains unknown. We show that cells in a fibrous matrix induce deformation fields that…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…
Solvent-based techniques usually involve preparing dilute blends of electron-donor and electron-acceptor materials dissolved in a volatile solvent. After some form of coating onto a substrate, the solvent evaporates. An initially…
Multiscale problems are widely observed across diverse domains in physics and engineering. Translating these problems into numerical simulations and solving them using numerical schemes, e.g. the finite element method, is costly due to the…
Sound modelling is the process of developing algorithms that generate sound under parametric control. There are a few distinct approaches that have been developed historically including modelling the physics of sound production and…
Computational phantoms are widely used in medical imaging research, yet current systems to generate controlled, clinically meaningful anatomical variations remain limited. We present AbdomenGen, a sequential volume-conditioned diffusion…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
In active matter systems, deformable boundaries provide a mechanism to organize internal active stresses and perform work on the external environment. To study a minimal model of such a system, we perform particle-based simulations of an…
The goal of this work is to investigate the capability of a neural operator (DeepONet) to accurately capture the complex deformation of a platelet's membrane under shear flow. The surrogate model approximated by the neural operator predicts…