Related papers: TopoSPAM: Topology grounded Simulation Platform fo…

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.…

Living biological tissue is a complex system, constantly growing and changing in response to external and internal stimuli. These processes lead to remarkable and intricate changes in shape. Modeling and understanding both natural and…

Topological analysis of the magnetic field in simulated plasmas allows the study of various physical phenomena in a wide range of settings. One such application is magnetic reconnection, a phenomenon related to the dynamics of the magnetic…

Social simulation is essential for understanding collective human behavior by modeling how individual interactions give rise to large-scale social dynamics. Recent advances in large language models (LLMs) have enabled multi-agent frameworks…

We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…

Active matter encompasses different nonequilibrium systems in which individual constituents convert energy into non-conservative forces or motion at the microscale. This review provides an elementary introduction to the role of topology in…

We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems…

Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…

We present SoftSMPL, a learning-based method to model realistic soft-tissue dynamics as a function of body shape and motion. Datasets to learn such task are scarce and expensive to generate, which makes training models prone to overfitting.…

Medical tubular anatomical structures are inherently three-dimensional conduits with lumens, enclosing walls, and complex branching topologies. Accurate reconstruction of their geometry and topology is crucial for applications such as…

Topological materials occupy a frontier in condensed-matter physics thanks to their remarkable electronic and quantum properties, yet their cross-scale design remains bottlenecked by inefficient discovery workflows. Here, we introduce…

The fields of mechanobiology and biomechanics are expanding our understanding of the complex behavior of soft biological tissues across multiple scales. Given the intricate connection between tissue microstructure and its macroscale…

Motivation: Understanding the spatial architecture of tissues is essential for decoding the complex interactions within cellular ecosystems and their implications for disease pathology and clinical outcomes. Recent advances in multiplex…

Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides…

Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…

Navigating topological transitions in cellular mechanical systems is a significant challenge for existing simulation methods. While abstract models lack predictive capabilities at the cellular level, explicit network representations…

We present TopoGaussian, a holistic, particle-based pipeline for inferring the interior structure of an opaque object from easily accessible photos and videos as input. Traditional mesh-based approaches require tedious and error-prone mesh…

Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…

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 simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…