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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…
High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta…
In this report we study the problem of determining three-dimensional orientations for noisy projections of randomly oriented identical particles. The problem is of central importance in the tomographic reconstruction of the density map of…
In this paper, we outline the use of Mixture Models in density estimation of large astronomical databases. This method of density estimation has been known in Statistics for some time but has not been implemented because of the large…
Realizing high-throughput aberration-corrected Scanning Transmission Electron Microscopy (STEM) exploration of atomic structures requires rapid tuning of multipole probe correctors while compensating for the inevitable drift of the optical…
The scanning electron microscopy (SEM) is probably one the most fascinating examination approach that has been used since more than two decades to detailed inspection of micro scale objects. Most of the scanning electron microscopes could…
We present a novel approach for extracting 3D atomic-level information from transmission electron microscopy (TEM) images affected by significant noise. The approach is based on formulating depth estimation as a semantic segmentation…
Cryo-electron microscopy is a technique in structural biology for discovering/determining the 3D structure of small molecules. A key step in this process is detecting common lines of intersection between unknown embedded image planes. We…
Dynamic Bayesian networks provide a compact and natural representation for complex dynamic systems. However, in many cases, there is no expert available from whom a model can be elicited. Learning provides an alternative approach for…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from large-scale datasets through self-supervised pre-training methods. However, these…
Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic or near-atomic resolution. However, applications are so far mainly limited to radiation-hard samples because the required doses are too high for…
The 3D microstructure of solid oxide fuel cell anodes significantly influences their electrochemical performance, but conventional methods for acquiring high-resolution microstructural 3D data such as focused ion beam scanning electron…
Electron tomography (ET) has become a standard technique for 3D characterization of materials at the nano-scale. Traditional reconstruction algorithms such as weighted back projection suffer from disruptive artifacts with insufficient…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Finding an optimal match between two different crystal structures underpins many important materials science problems, including describing solid-solid phase transitions, developing models for interface and grain boundary structures. In…
Over the last two decades, scanning tunnelling microscopy (STM) has become one of the most important ways to investigate the structure of crystal surfaces. STM has helped achieve remarkable successes in surface science such as finding the…
Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimensional atomic scale structure of samples in structural biology and materials science. In structural biology, three-dimensional structures of…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…
We consider the multi-target detection problem of recovering a set of signals that appear multiple times at unknown locations in a noisy measurement. In the low noise regime, one can estimate the signals by first detecting occurrences, then…