Related papers: Mem3DG: Modeling Membrane Mechanochemical Dynamics…
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…
Flexible elastic structures, such as beams, rods, ribbons, plates, and shells, exhibit complex nonlinear dynamical behaviors that are central to a wide range of engineering and scientific applications, including soft robotics, deployable…
Flexible slender structures such as rods, ribbons, plates, and shells exhibit extreme nonlinear responses bending, twisting, buckling, wrinkling, and self contact, that defy conventional simulation frameworks. Discrete Differential Geometry…
Motivation: Despite its great success in various physical modeling, differential geometry (DG) has rarely been devised as a versatile tool for analyzing large, diverse and complex molecular and biomolecular datasets due to the limited…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
We present a differentiable representation, DMesh, for general 3D triangular meshes. DMesh considers both the geometry and connectivity information of a mesh. In our design, we first get a set of convex tetrahedra that compactly tessellates…
The purpose of this paper is to study the shapes and stabilities of bio-membranes within the framework of exterior differential forms. After a brief review of the current status in theoretical and experimental studies on the shapes of…
Mesh generation is a crucial step in numerical simulations, significantly impacting simulation accuracy and efficiency. However, generating meshes remains time-consuming and requires expensive computational resources. In this paper, we…
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…
Qualifying the discrepancy between 3D geometric models, which could be represented with either point clouds or triangle meshes, is a pivotal issue with board applications. Existing methods mainly focus on directly establishing the…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
Soft robots utilizing inflatable dielectric membranes can realize intricate functionalities through the application of non-mechanical fields. However, given the current limitations in simulations, including low computational efficiency and…
Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Traditional methods for biological shape inference, such as deep learning (DL) and active contour models, face important limitations in 3D. DL approaches require large annotated datasets, which are often impractical to obtain, while active…
Recent probabilistic methods for 3D triangular meshes capture diverse shapes by differentiable mesh connectivity, but face high computational costs with increased shape details. We introduce a new differentiable mesh processing method that…
This article presents the development and validation of a hybrid multi-sphere discrete element framework - Rigid3D, for the simulation of granular systems with arbitrarily shaped particles in 3D space. In this DEM framework, a non-spherical…
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…
Modern 3D engines and graphics pipelines require mesh as a memory-efficient representation, which allows efficient rendering, geometry processing, texture editing, and many other downstream operations. However, it is still highly difficult…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…