Related papers: BioVEC: A program for Biomolecule Visualization wi…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells…
The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the…
Vision-language models (VLMs) have demonstrated strong capabilities in multimodal perception and reasoning. However, deploying large VLMs on mobile devices remains challenging due to their substantial computational and memory demands. A…
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…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
We present the Virtual Beamline (VBL) application, an interactive web-based platform for visualizing high-intensity laser-matter interactions using particle-in-cell (PIC) simulations, with future potential for experimental data…
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…
Biogenic Volatile Organic Compounds (BVOCs) play a critical role in biosphere-atmosphere interactions, being a key factor in the physical and chemical properties of the atmosphere and climate. Acquiring large and fine-grained BVOC emission…
The study of animal behavior increasingly relies on (semi-) automatic methods for the extraction of relevant behavioral features from video or picture data. To date, several specialized software products exist to detect and track animals'…
We present a data-driven generative framework for synthesizing blood vessel 3D geometry. This is a challenging task due to the complexity of vascular systems, which are highly variating in shape, size, and structure. Existing model-based…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
In recent years, deep generative models for graphs have been used to generate new molecules. These models have produced good results, leading to several proposals in the literature. However, these models may have troubles learning some of…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for biomolecular normal mode analysis. The multiscale virtual particle model is proposed for the discretization of biomolecular density data in…
The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Faithfully reconstructing textured shapes and physical properties from videos presents an intriguing yet challenging problem. Significant efforts have been dedicated to advancing such a system identification problem in this area. Previous…