Related papers: Resolving structural dynamics in situ through cryo…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Crystal surfaces are sensitive to the surrounding environment, where atoms left with broken bonds reconstruct to minimize surface energy. In many cases, the surface can exhibit chemical properties unique from the bulk. These differences are…
Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal…
A novel and highly efficient computational framework for reconstructing binary-type images suitable for models of various complexity seen in diverse biomedical applications is developed and validated. Efficiency in computational speed and…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
Single-particle reconstruction in cryo-electron microscopy (cryo-EM) is an increasingly popular technique for determining the 3-D structure of a molecule from several noisy 2-D projections images taken at unknown viewing angles. Most…
Synthetic generation of three-dimensional cell models from histopathological images aims to enhance understanding of cell mutation, and progression of cancer, necessary for clinical assessment and optimal treatment. Classical reconstruction…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Cryo-ET allows to generate tomograms of biological samples in situ, capturing complex structures in their native context. Despite low signal-to-noise ratio in reconstructed volumes, the large number of copies of the same macromolecules…
Modern electron tomography has progressed to higher resolution at lower doses by leveraging compressed sensing methods that minimize total variation (TV). However, these sparsity-emphasized reconstruction algorithms introduce tunable…
Open-set 3D macromolecule detection in cryogenic electron tomography eliminates the need for target-specific model retraining. However, strict VRAM constraints prohibit processing an entire 3D tomogram, forcing current methods to rely on…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
Accurate pose estimation and shift correction are key challenges in cryo-EM due to the very low SNR, which directly impacts the fidelity of 3D reconstructions. We present an approach for pose estimation in cryo-EM that leverages…
Technological developments in high resolution time-of-flight neutron detectors have raised the prospect of tomographic reconstruction of elastic strain fields from Bragg-edge strain images. This approach holds the potential to provide a…
We present a novel method for characterizing the microstructure of a material from volumetric datasets such as 3D image data from computed tomography (CT). The method is based on a new statistical model for the distribution of voxel…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
Realistic microscale domains are an essential step towards making modern multiscale simulations more applicable to computational materials engineering. For this purpose, 3D computed tomography scans can be very expensive or technically…
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. Here we explore methods to generate template libraries and algorithms to query…