Related papers: TopoSPAM: Topology grounded Simulation Platform fo…
Recent advances in topological mechanics have revealed unusual phenomena such as topologically protected floppy modes and states of self-stress that are exponentially localized at boundaries and interfaces of mechanical networks. In this…
Metasurfaces are subwavelength structured thin films consisting of arrays of units that allow the controls of polarization, phase and amplitude of light over a subwavelength thickness. The recent developments in topological photonics have…
Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy…
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…
In this paper, we present a framework for multiscale topology optimization of fluid-flow devices. The objective is to minimize dissipated power, subject to a desired contact-area. The proposed strategy is to design optimal microstructures…
The rapid advances in 3D scanning and acquisition techniques have given rise to the explosive increase of volumetric digital models in recent years. This dissertation systematically trailblazes a novel volumetric modeling framework to…
Topological invariants have proved useful for analyzing emergent function as they characterize a property of the entire system, and are insensitive to local details, disorder, and noise. They support boundary states, which reduce the system…
This paper reports on technical aspects of Plasma Operational Simulation (POPSIM), a research framework for data-driven simulation and control built in the machine learning framework JAX. The objective of the project is to address the…
Computational modelling is helpful for elucidating the cellular mechanisms driving biological morphogenesis. Previous simulation studies of blood vessel growth based on the Cellular Potts model (CPM) proposed that elongated, adhesive or…
We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type and amount that is required for a…
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…
Understanding how living organisms spontaneously develop complex functional structures inspires innovative approaches in engineering design. Here, we introduce a decentralized generative model based on morphogenesis to autonomously grow…
Recent advances in cellular research demonstrate that scRNA-seq characterizes cellular heterogeneity, while spatial transcriptomics reveals the spatial distribution of gene expression. Cell representation is the fundamental issue in the two…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
When considering flows in biological membranes, they are usually treated as flat, though more often than not, they are curved surfaces, even extremely curved, as in the case of the endoplasmic reticulum. Here, we study the topological…
Cells and tissues change shape both to carry out their function and during pathology. In most cases, these deformations are driven from within the systems themselves. This is permitted by a range of molecular actors, such as active…
Tomography is a widely used tool for analyzing microstructures in three dimensions (3D). The analysis, however, faces difficulty because the constituent materials produce similar grey-scale values. Sometimes, this prompts the image…
The dynamics of active smectic liquid crystals confined on a spherical surface is explored through an active phase field crystal model. Starting from an initially randomly perturbed isotropic phase, several types of topological defects are…