scholarly journals NE-CAT Crystallography Beamlines for Challenging Structural Biology Research

2014 ◽  
Vol 70 (a1) ◽  
pp. C335-C335
Author(s):  
Igor Kourinov ◽  
Malcolm Capel ◽  
Surajit Banerjee ◽  
Frank Murphy ◽  
David Neau ◽  
...  
Keyword(s):  
Structural Biology ◽  
State Of The Art ◽  
Time Data ◽  
Large Area ◽  
Software Suite ◽  
X Ray ◽  
Unit Cells ◽  
Experienced Resident ◽  
Collection Strategies ◽  
Biology Research

The NorthEastern Collaborative Access Team (NE-CAT) focuses on the design and operation of synchrotron X-ray beamlines for the solution of technically challenging structural biology problems and provides an important resource for the national and international research community. Currently NE-CAT operates two undulator beamlines: 24ID-C - tunable in the energy range from 6 to 22keV and 24ID-E - not-tunable, but optimized for Se SAD experiments. Both beamlines are equipped with state-of-the-art instrumentation. MD2 microdiffractometers installed at both beamlines provide very clean beams down to 5 microns in diameter and are capable of visualizing micron-sized crystals. Large area detectors (ADSC Quantum 315 at 24ID-E beamline and Pilatus-6MF at 24ID-C beamline), not only provide the best diffraction data, but also make possible to resolve large unit cells. Both beamlines are equipped with ALS style automatic sample mounters. Locally developed software suite RAPD provides data collection strategies, quasi-real time data integration and scaling and simple automated MR/SAD pipeline through 384 core computing cluster. Users of the beamlines are supported by experienced resident crystallographers. To meet the needs of technically challenging crystallographic projects, cutting-edge hardware and software ideas are implemented. A summary of beamline capabilities, technology, scientific highlights and details of availability will be presented. Funding for NE-CAT is provided through P41 grant from the NIGMS and from the NE-CAT member institutions.

Online data analysis at the ESRF bioSAXS beamline, BM29

2016 ◽  
Vol 49 (1) ◽  
pp. 203-212 ◽  
Author(s):  
Martha Elisabeth Brennich ◽  
Jérôme Kieffer ◽  
Guillaume Bonamis ◽  
Alejandro De Maria Antolinos ◽  
Stephanie Hutin ◽  
...  
Keyword(s):  
Structural Biology ◽  
Primary Analysis ◽  
Online Data ◽  
X Ray ◽  
Processing Pipeline ◽  
X Ray Scattering ◽  
Automated Processing ◽  
Automated Data Acquisition ◽  
Collection Strategies

High-throughput small-angle X-ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using theEDNAframework.

scholarly journals New opportunities in structural biology with XFEL: from sources to structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C19-C19
Author(s):  
Soichi Wakatsuki
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Structural Biology ◽  
Single Particle ◽  
De Novo ◽  
Reconstruction Algorithm ◽  
Simultaneous Recording ◽  
Atomic Resolution ◽  
X Ray ◽  
Biology Research

X-ray free electron lasers (XFEL) have shown the promise of providing new opportunities in structural biology research with their extremely high peak brilliance and short pulses. It is reaching the stage where biologically important questions can be tackled using XFEL based on the "diffract-before-destroy" concept. The first part of this presentation will focus on macromolecular crystallography using XFEL with results obtained at LCLS so far and future scope. R&D efforts being pursued at SLAC/LCLS include new beam modes, (two-color beam for de novo phasing, wider bandwidth for SAXS/WAXS and spectroscopy), beam multiplexing, a dedicated new station for in-air data collection, next generation detectors, data analysis incorporating pulse-by-pulse spectrometer measurements and post refinement. These projects are being pursued in collaboration with many groups locally and globally with a goal to provide integrated facilities for cutting edge structural biology research. For example, two-color self-seeded XFEL mode is being developed for simultaneous recording of diffraction data at two energies in order to optimize the dispersive difference between the two wavelengths for phasing. Another area of collaborative effort is a development of dedicated station for in-air data collection with a variety of sample delivery schemes. The second part will discuss a possible roadmap towards atomic resolution single particle imaging using XFEL. Here, key questions are ·Can XFEL single particle 3D structural analysis at atomic resolution be done? ·What is the pulse characteristics required? ·Can we overcome the radiation damage at soft X-ray regime? ·What is the highest resolution attainable in comparison with cryoEM? A workshop at LCLS is being organized to discuss these questions in 4 areas: radiation damage, image reconstruction algorithm, beam modes and instrumentation, sample delivery and heterogeneity. The outcome of the workshop and follow-up discussions will be presented.

scholarly journals Two-dimensional imaging detectors for structural biology with X-ray lasers

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130334 ◽  
Author(s):  
Peter Denes
Keyword(s):  
Structural Biology ◽  
Peak Power ◽  
State Of The Art ◽  
High Peak Power ◽  
Free Electron Lasers ◽  
X Ray ◽  
The Past ◽  
Current State ◽  
Pixel Detectors ◽  
Imaging Detectors

Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors—monolithic or hybrid—are the standard for XFELs today. For structural biology, improvements are needed for today's 10–100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art.

Reflections on the Many Facets of Protein Microcrystallography

2014 ◽  
Vol 67 (12) ◽  
pp. 1793 ◽  
Author(s):  
Marion Boudes ◽  
Damià Garriga ◽  
Fasséli Coulibaly
Keyword(s):  
Structural Biology ◽  
State Of The Art ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Many ◽  
The Impact

The use of X-ray crystallography for the structure determination of biological macromolecules has experienced a steady expansion over the last 20 years with the Protein Data Bank growing from <1000 deposited structures in 1992 to >100 000 in 2014. The large number of structures determined each year not only reflects the impact of X-ray crystallography on many disciplines in the biological and medical fields but also its accessibility to non-expert laboratories. Thus protein crystallography is now largely a mainstream research technique and is routinely integrated in high-throughput pipelines such as structural genomics projects and structure-based drug design. Yet, significant frontiers remain that continuously require methodological developments. In particular, membrane proteins, large assemblies, and proteins from scarce natural sources still represent challenging targets for which obtaining the large diffracting crystals required for classical crystallography is often difficult. These limitations have fostered the emergence of microcrystallography, novel approaches in structural biology that collectively aim at determining structures from the smallest crystals. Here, we review the state of the art of macromolecular microcrystallography and recent progress achieved in this field.

scholarly journals 2D perovskite-based high spatial resolution X-ray detectors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amlan Datta ◽  
John Fiala ◽  
Shariar Motakef
Keyword(s):  
Spatial Resolution ◽  
High Spatial Resolution ◽  
State Of The Art ◽  
Frame Rate ◽  
Modulation Transfer ◽  
Large Area ◽  
X Ray ◽  
Current State ◽  
X Ray Imaging ◽  
Imaging Results

AbstractX-ray radiography is the most widely used imaging technique with applications encompassing medical and industrial imaging, homeland security, and materials research. Although a significant amount of research and development has gone into improving the spatial resolution of the current state-of-the-art indirect X-ray detectors, it is still limited by the detector thickness and microcolumnar structure quality. This paper demonstrates high spatial resolution X-ray imaging with solution-processable two-dimensional hybrid perovskite single-crystal scintillators grown inside microcapillary channels as small as 20 µm. These highly scalable non-hygroscopic detectors demonstrate excellent spatial resolution similar to the direct X-ray detectors. X-ray imaging results of a camera constructed using this scintillator show Modulation Transfer Function values significantly better than the current state-of-the-art X-ray detectors. These structured detectors open up a new era of low-cost large-area ultrahigh spatial resolution high frame rate X-ray imaging with numerous applications.

scholarly journals Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 496 ◽  
Author(s):  
Michelle Miller ◽  
Sweta Maheshwari ◽  
Wuxian Shi ◽  
Yuan Gao ◽  
Nam Chu ◽  
...  
Keyword(s):  
Data Collection ◽  
State Of The Art ◽  
Crystallographic Data ◽  
High Flux ◽  
Macromolecular Crystallography ◽  
Vector Data ◽  
Linear Trajectory ◽  
X Ray ◽  
Single Loop ◽  
Collection Strategies

Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II—AMX and FMX—deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins—Akt1, PI3Kα, and CDP-Chase—to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or “raster-collect”, a more automated approach for a larger number of crystals (using CDP-Chase as an example).

Revisiting the High-Pressure Properties of the Metal-Organic Frameworks ZIF-8 and ZIF-67

2020 ◽  
Author(s):  
Pia Vervoorts ◽  
Stefan Burger ◽  
Karina Hemmer ◽  
Gregor Kieslich
Keyword(s):  
High Pressure ◽  
State Of The Art ◽  
Energy Landscape ◽  
Structural Flexibility ◽  
Zeolitic Imidazolate Frameworks ◽  
Stimuli Responsive ◽  
X Ray Diffraction ◽  
X Ray ◽  
Open Questions ◽  
Metal Organic

The zeolitic imidazolate frameworks ZIF-8 and ZIF-67 harbour a series of fascinating stimuli responsive properties. Looking at their responsitivity to hydrostatic pressure as stimulus, open questions exist regarding the isotropic compression with non-penetrating pressure transmitting media. By applying a state-of-the-art high-pressure powder X-ray diffraction setup, we revisit the high-pressure behaviour of ZIF-8 and ZIF-67 up to <i>p</i> = 0.4 GPa in small pressure increments. We observe a drastic, reversible change of high-pressure powder X-ray diffraction data at <i>p</i> = 0.3 GPa, discovering large volume structural flexibility in ZIF-8 and ZIF-67. Our results imply a shallow underlying energy landscape in ZIF-8 and ZIF-67, an observation that might point at rich polymorphism of ZIF-8 and ZIF-67, similar to ZIF-4(Zn).<br>

Revisiting the High-Pressure Properties of the Metal-Organic Frameworks ZIF-8 and ZIF-67

2020 ◽  
Author(s):  
Pia Vervoorts ◽  
Stefan Burger ◽  
Karina Hemmer ◽  
Gregor Kieslich
Keyword(s):  
High Pressure ◽  
State Of The Art ◽  
Energy Landscape ◽  
Structural Flexibility ◽  
Zeolitic Imidazolate Frameworks ◽  
Stimuli Responsive ◽  
X Ray Diffraction ◽  
X Ray ◽  
Open Questions ◽  
Metal Organic

The zeolitic imidazolate frameworks ZIF-8 and ZIF-67 harbour a series of fascinating stimuli responsive properties. Looking at their responsitivity to hydrostatic pressure as stimulus, open questions exist regarding the isotropic compression with non-penetrating pressure transmitting media. By applying a state-of-the-art high-pressure powder X-ray diffraction setup, we revisit the high-pressure behaviour of ZIF-8 and ZIF-67 up to <i>p</i> = 0.4 GPa in small pressure increments. We observe a drastic, reversible change of high-pressure powder X-ray diffraction data at <i>p</i> = 0.3 GPa, discovering large volume structural flexibility in ZIF-8 and ZIF-67. Our results imply a shallow underlying energy landscape in ZIF-8 and ZIF-67, an observation that might point at rich polymorphism of ZIF-8 and ZIF-67, similar to ZIF-4(Zn).<br>

Infra-Red Reflectance Microscopy (IRRM) for Daisy Chain Flip Chip Device Failure Analysis

2004 ◽  
Author(s):  
Carlo Grilletto ◽  
Steve Hsiung ◽  
Andrew Komrowski ◽  
John Soopikian ◽  
Daniel J.D. Sullivan ◽  
...  
Keyword(s):  
Failure Analysis ◽  
Flip Chip ◽  
State Of The Art ◽  
Failure Mechanisms ◽  
Simple Metal ◽  
X Ray ◽  
Infra Red ◽  
Cause Of Failure ◽  
Reflectance Microscopy ◽  
Ir Emission

Abstract This paper describes a method to "non-destructively" inspect the bump side of an assembled flip-chip test die. The method is used in conjunction with a simple metal-connecting "modified daisy chain" die and makes use of the fact that polished silicon is transparent to infra-red (IR) light. The paper describes the technique, scope of detection and examples of failure mechanisms successfully identified. It includes an example of a shorting anomaly that was not detectable with the state of the art X-ray equipment, but was detected by an IR emission microscope. The anomalies, in many cases, have shown to be the cause of failure. Once this has been accomplished, then a reasonable deprocessing plan can be instituted to proceed with the failure analysis.

scholarly journals COVID-19 infection map generation and detection from chest X-ray images

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Aysen Degerli ◽  
Mete Ahishali ◽  
Mehmet Yamac ◽  
Serkan Kiranyaz ◽  
Muhammad E. H. Chowdhury ◽  
...  
Keyword(s):  
State Of The Art ◽  
Ground Truth ◽  
Clinical Use ◽  
X Ray ◽  
Learning Techniques ◽  
Map Generation ◽  
Severity Grading ◽  
Chest X Ray ◽  
Novel Method ◽  
Aided Diagnosis

AbstractComputer-aided diagnosis has become a necessity for accurate and immediate coronavirus disease 2019 (COVID-19) detection to aid treatment and prevent the spread of the virus. Numerous studies have proposed to use Deep Learning techniques for COVID-19 diagnosis. However, they have used very limited chest X-ray (CXR) image repositories for evaluation with a small number, a few hundreds, of COVID-19 samples. Moreover, these methods can neither localize nor grade the severity of COVID-19 infection. For this purpose, recent studies proposed to explore the activation maps of deep networks. However, they remain inaccurate for localizing the actual infestation making them unreliable for clinical use. This study proposes a novel method for the joint localization, severity grading, and detection of COVID-19 from CXR images by generating the so-called infection maps. To accomplish this, we have compiled the largest dataset with 119,316 CXR images including 2951 COVID-19 samples, where the annotation of the ground-truth segmentation masks is performed on CXRs by a novel collaborative human–machine approach. Furthermore, we publicly release the first CXR dataset with the ground-truth segmentation masks of the COVID-19 infected regions. A detailed set of experiments show that state-of-the-art segmentation networks can learn to localize COVID-19 infection with an F1-score of 83.20%, which is significantly superior to the activation maps created by the previous methods. Finally, the proposed approach achieved a COVID-19 detection performance with 94.96% sensitivity and 99.88% specificity.

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