Related papers: Maxent-Stress Optimization of 3D Biomolecular Mode…
Creating machines capable of understanding the world in 3D is essential in assisting designers that build and edit 3D environments and robots navigating and interacting within a three-dimensional space. Inspired by advances in language and…
Crystal structure optimization is fundamental to materials modeling but remains computationally expensive when performed with density-functional theory (DFT). Machine-learning (ML) approaches offer substantial acceleration, yet existing…
We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…
Generative AI has made rapid progress in text, image, and video synthesis, yet text-to-3D modeling for scientific design remains particularly challenging due to limited controllability and high computational cost. Most existing 3D…
For 3D medical image (e.g. CT and MRI) segmentation, the difficulty of segmenting each slice in a clinical case varies greatly. Previous research on volumetric medical image segmentation in a slice-by-slice manner conventionally use the…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
Biomedical imaging is unequivocally dependent on the ability to reconstruct interpretable and high-quality images from acquired sensor data. This reconstruction process is pivotal across many applications, spanning from magnetic resonance…
We propose a method that efficiently learns distributions over articulation model parameters directly from depth images without the need to know articulation model categories a priori. By contrast, existing methods that learn articulation…
FRET experiments can yield state-specific structural information on complex dynamic biomolecular assemblies. However, FRET experiments need to be combined with computer simulations to overcome their sparsity. We introduce (i) an automated…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
This paper presents a light-weight, high-quality texture synthesis algorithm that easily generalizes to other applications such as style transfer and texture mixing. We represent texture features through the deep neural activation vectors…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Cellular Electron Cryo-Tomography (CECT) is a powerful 3D imaging tool for studying the native structure and organization of macromolecules inside single cells. For systematic recognition and recovery of macromolecular structures captured…
In this work, we introduce an algorithmic approach to generate microvascular networks starting from larger vessels that can be reconstructed without noticeable segmentation errors. Contrary to larger vessels, the reconstruction of…
Microstructure--property relationships are key to effective design of structural materials for advanced applications. Advances in computational methods enabled modeling microstructure-sensitive properties using 3D models (e.g., finite…
Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…
A single-particle cryo-electron microscopy (cryo-EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional (3-D) molecular structure at unknown locations, taken under unknown…
Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the…
The structural design process for buildings is time-consuming and laborious. To automate this process, structural engineers combine optimization methods with simulation tools to find an optimal design with minimal building mass subject to…
We have developed a novel scanning probe-based methodology to study cell biomechanics. The time dependence of the force exerted by the cell surface on a scanning probe at constant local deformation has been used to extract local…