Related papers: TopoSPAM: Topology grounded Simulation Platform fo…
Morphological instabilities of growing tissues that impinge on passive materials are typical of invasive cancers. To explain these instabilities in experiments on breast epithelial spheroids in an extracellular matrix, we develop a…
Humans build 3D understandings of the world through active object exploration, using jointly their senses of vision and touch. However, in 3D shape reconstruction, most recent progress has relied on static datasets of limited sensory data…
Topological phases of matter are ubiquitous in crystals, but less is known about their existence in amorphous systems, that lack long-range order. In this perspective, we review the recent progress made on theoretically defining amorphous…
Connecting cell behavior to tissue shape and mechanics is a key challenge in the physics of morphogenesis. Cytoskeletal turnover precludes a fixed reference state, and tensions are actively generated independently of strain; so conventional…
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…
Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here we showcase…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
This work introduces a new theoretical model for active matter ("complementary-spins" or c-spins), exploring the interplay of positional and orientational order in mobile agents with rotational freedom, divided into two populations with…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…
Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell…
Research in manipulation of deformable objects is typically conducted on a limited range of scenarios, because handling each scenario on hardware takes significant effort. Realistic simulators with support for various types of deformations…
To create heterogeneous, multiscale structures with unprecedented functionalities, recent topology optimization approaches design either fully aperiodic systems or functionally graded structures, which compete in terms of design freedom and…
The global topology of the Universe can affect long-range gravitational forces via boundary conditions. Detailed studies of non-trivial topologies require simulations that natively adopt such geometries. Cosmological $N$-body simulations…
We introduce a novel model, comprising self-avoiding surfaces and incorporating edges and tubules, that is designed to characterize the structural morphologies and transitions observed within the endoplasmic reticulum (ER). By employing…
Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be…
Liquid shells, such as lipid vesicles and soap bubbles, are ubiquitous throughout biology, engineered matter, and everyday life. Their creation and disintegration are defined by a singularity that separates a topologically distinct extended…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
There is now growing evidence of the emergence and biological functionality of liquid crystal features, including nematic order and topological defects, in cellular tissues. However, how such features that intrinsically rely on particle…
Collective guidance of out-of-equilibrium systems without using external fields is a challenge of paramount importance in active matter, ranging from bacterial colonies to swarms of self-propelled particles. Designing strategies to guide…
Topological correctness is critical for segmentation of tubular structures, which pervade in biomedical images. Existing topological segmentation loss functions are primarily based on the persistent homology of the image. They match the…