Related papers: Statistical spatial analysis for cryo-electron tom…
Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic…
The field of cryo-electron microscopy has made astounding advancements in the past few years, mainly due to advancements in electron detectors' technology. Yet, one of the key open challenges of the field remains the processing of…
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 electroencephalography (EEG) signal is a non-stationary, stochastic, and highly non-linear bioelectric signal for which achieving high classification accuracy is challenging, especially when the number of subjects is limited. As…
Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of bio-molecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
Accurately determining resonance frequencies and quality factors (Q) is crucial in accelerator physics and radiofrequency engineering, as these factors have direct impacts on system design, operational stability, and research results. The…
Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\"odinger or Dirac equation for the appropriate collision problem using the…
Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a new dataset…
We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…
Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…
We target the problem of estimating the center of mass of noisy 2-D images. We assume that the noise dominates the image, and thus many standard approaches are vulnerable to estimation errors. Our approach uses a surrogate function to the…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
We study the distributed computing setting in which there are multiple servers, each holding a set of points, who wish to compute functions on the union of their point sets. A key task in this setting is Principal Component Analysis (PCA),…
Atomic probe tomography (APT), based on the work of Erwin Mueller, is able to generate three-dimensional chemical maps in atomic resolution. The required instruments for APT have evolved over the last 20 years from an experimental to an…
Particle-in-Cell (PIC) simulations are widely used for modeling plasma kinetics by tracking discrete particle dynamics. However, their computational cost remains prohibitively high, due to the need to simulate large numbers of particles to…
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances…
The Exascale Computing Project (ECP) is invested in co-design to assure that key applications are ready for exascale computing. Within ECP, the Co-design Center for Particle Applications (CoPA) is addressing challenges faced by…
PyEOC is an open-source Python code for determining electro-optic (EO) coefficients of thin-film materials from the static and dynamic reflectivity measurements. It uses the experimental results, the transfer-matrix method and implements a…
Cryo-electron microscopy (cryoEM) is an increasingly popular method for protein structure determination. However, identifying a sufficient number of particles for analysis (often >100,000) can take months of manual effort. Current…