A5012768564- Advanced X-ray Imaging Techniques
- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- Image and Signal Denoising Methods
- Mathematical Analysis and Transform Methods
- Medical Imaging Techniques and Applications
- X-ray Spectroscopy and Fluorescence Analysis
- Digital Filter Design and Implementation
- Electron and X-Ray Spectroscopy Techniques
- Advanced MRI Techniques and Applications
- Distributed and Parallel Computing Systems
- Crystallography and Radiation Phenomena
- Advanced X-ray and CT Imaging
- Seismic Imaging and Inversion Techniques
- NMR spectroscopy and applications
- Advanced Wireless Communication Techniques
- Superconducting Materials and Applications
- Particle Accelerators and Free-Electron Lasers
- Advanced Neuroimaging Techniques and Applications
- Radar Systems and Signal Processing
- X-ray Diffraction in Crystallography
- Advanced Data Processing Techniques
- Ultra-Wideband Communications Technology
- Topic Modeling
- Experimental Learning in Engineering
Lawrence Berkeley National Laboratory
2015-2024
Research Applications (United States)
2017-2024
Arizona State University
2021
Applied Mathematics (United States)
2021
Alive Hospice
2020
University of Maryland, College Park
2006-2018
University of California, Berkeley
2013-2015
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered individual bioparticles. This allows us go beyond the traditional crystallography single-particle imaging approaches for structure investigations. employ angular recover three-dimensional (3D) of nanoscale viruses diffraction data measured at Linac Coherent Light Source. Correlations provide with a comprehensive structural fingerprint 3D virus, which we both...
Significance Fluctuation X-ray scattering is an emerging imaging technique that seeks to overcome the low data-to-parameter ratio encountered in traditional small- and wide-angle methods. By acquiring a large number of ultrashort exposures on ensemble molecules, this produces dataset contains structural information far beyond what obtainable from solution methods without requiring crystallization. However, reconstructing underlying molecular shape data challenging, as each image averaged...
Periodic constant-amplitude zero-autocorrelation (CAZAC) waveforms u are analyzed in terms of the discrete periodic ambiguity function A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</sub> . Elementary number-theoretic considerations illustrate that peaks not stable under small perturbations its domain. Further, it is proved analysis vector-valued CAZAC depends on methods from theory frames. Finally, techniques introduced to characterize...
Significance Fluctuation X-ray scattering is a biophysical structural characterization technique that overcomes low data-to-parameter ratios encountered in traditional methods used for studying noncrystalline samples. By collecting series of ultrashort exposures on an ensemble particles at free-electron laser, information-dense experimental data can be extracted ultimately result structures with greater level detail than obtained using methods. In this article we demonstrate the practical...
An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate artifacts electron diffraction data, solving the phase problem and increasing thicknesses of samples in materials science, solid-state chemistry, small molecule crystallography. For high-energy transmission diffraction, we show recovers accurate complex structure factors wide range thicknesses, orientations,...
Significance Single-particle diffraction is an emerging technique in which images are collected from individual particles, and used to study molecular structure multiple conformational states that may be inaccessible through other methods. However, determining these experiments challenging, since orientations of imaged particles unknown highly contaminated with noise. Furthermore, the number useful often limited by achievable single-particle hit rates, currently around 0.1%. We introduce...
The introduction of BERTopic marked a crucial advancement in topic modeling and presented model that outperformed both traditional modern models terms metrics on variety corpora. However, unique issues arise when is performed scientific articles. This paper introduces BERTeley, an innovative tool built upon BERTopic, designed to alleviate these shortcomings improve the usability conducting corpus consisting accomplished through BERTeley's three main features: article preprocessing, using...
Advanced experimental facilities worldwide are probing structure and chemistry, disorder, dynamics electronic properties, through time, over length scales spanning macroscopic to atomic resolution, in multiple dimensions (e.g., hyperspectral tomography, nano-spectroscopy), under extreme environmental conditions stimulated reactions. In order do so, they collecting more data at faster rates. One critical challenge is build algorithms that can analyze, interpret, understand the information...
X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to nanometer scale. The resolution and quality 3D reconstruction limited by availability alignment parameters that correct mechanical shifts sample or stage images constitute a scan. In this paper we describe an algorithm marker-free, fully automated accurately aligned reconstructed data. Our approach solves tomographic jointly with projection data based on rigid-body...
There are several natural constructions of constant amplitude zero autocorrelation (off the DC-component) waveforms. We adopt a construction for waveforms length K, where K is non-square-free integer. This property used in derivation frequency shifting (Doppler) detection algorithm which we derive. number theoretic properties account this algorithm, as well analogous but different square-free case. A variety relevant examples given along with technical rationale algorithm.
Significance X-ray photon correlation spectroscopy (XPCS) is a powerful technique that can probe broad range of space and time scales will become increasingly due to coming advancements in coherence. Assessing translational rotational diffusion key quantity analyzing material structures dynamics, with applications across molecular biology, drug discovery, materials science. While methods for estimating coefficients from XPCS data are well-developed, there no algorithms measuring the...
Grazing-incidence small-angle X-ray scattering (GISAXS) is an important technique in the characterization of samples at nanometre scale. A key aspect GISAXS data analysis accurate simulation to match measurement. The distorted-wave Born approximation (DWBA) a widely used model for patterns. For certain classes sample such as nanostructures embedded thin films, where electric field intensity variation significant relative size structures, multi-slice DWBA theory more than conventional method....
The setting is that of vector-valued codes length N. background for this our construction new complex valued constant amplitude zero autocorrelation (off dc) - CAZACs, which serve as coefficients phase coded waveforms with prescribed ambiguity function behavior. Vector-valued CAZACs are relevant in light vector sensor and MIMO technologies. goal to define the discrete function. Our notion frame multiplication allows us make definition. theory relevance such functions developed, including...
Abstract Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution data are collected using exposures below rotational diffusion times, resulting angularly anisotropic snapshots that provide several orders of magnitude more information than traditional data. Such experiments can be performed the ultrashort pulses provided by a free-electron laser source, allowing one to collect large number diffraction patterns relatively short time. Here, we describe test...
Significance X-ray nanocrystallography is a powerful imaging technique which able to determine the atomic structure of macromolecule from large ensemble nanocrystals. Determining this challenging because images are noisy, and individual crystal sizes, orientations, incident photon flux densities unknown. Additionally, lattice symmetries may lead orientation ambiguities. Here, we show how size, density, noisy data. We also demonstrate that these data can be used perform reconstruction without...
Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This `shape transform' signal introduces enough additional information to allow the molecular densities be determined diffracted intensities directly, without prior or resolution restrictions. However, various correlations amongst occupancies/vacancies at crystal surface result in a subtle yet critical problem shape transform phasing...
Constant amplitude zero autocorrelation (off the dc component) waveforms are constructed. These called CAZAC waveforms. In d-dimensional case they consist of N vectors, where is given, and generally greater than d. The constructions algebraic have been implemented in user friendly software. They added feature that a spanning set for all signals. As such, large, numerically stable presence machine imperfections give good signal reconstruction various noises. one dimensional provides effective...
ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) Los Alamos Laboratory. supports real-time via a cross-facility workflow spanning LCLS HPC centers such as NERSC OLCF. Our work therefore constitutes initial path-finding US Department of Energy's (DOE)...
X-ray photon correlation spectroscopy (XPCS) is a powerful technique for analyzing particle systems by investigating their dynamics in suspensions across broad range of temporal and spatial scales. This done illuminating samples with coherent x-ray beams calculating the function obtained scattering images. XPCS uniquely suited studying Brownian dynamics, consisting translational rotational diffusion. While traditional image analysis techniques can extract diffusion components, they are...
X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In past few decades, there have been significant advancements in brightness and detector technology instruments at synchrotron sources. These led to emergence new observations discoveries, with improved capabilities such as faster frame rates, larger fields view, higher resolution dimensionality. enabled material science community...
The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It an that reconstructs electron density sample by matching computed X-ray data external observations, and simultaneously enforcing constraints in real Fourier space. This paper presents first ever MTIP acceleration efforts on contemporary graphics processing units (GPUs). Compute Unified Device Architecture (CUDA) programming model accelerate...