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NASA NTRS2015

Fast Grasp Contact Computation for a Serial Robot

A system includes a controller and a serial robot having links that are interconnected by a joint, wherein the robot can grasp a three-dimensional (3D) object in response to a commanded grasp pose. The controller receives input information, including the commanded grasp pose, a first set of information describing the kinematics of the robot, and a second set of information describing the position of the object to be grasped. The controller also calculates, in a two-dimensional (2D) plane, a set of contact points between the serial robot and a surface of the 3D object needed for the serial robot to achieve the commanded grasp pose. A required joint angle is then calculated in the 2D plane between the pair of links using the set of contact points. A control action is then executed with respect to the motion of the serial robot using the required joint angle.

Shi, Jianying↗

DOE OSTI2021

Serial communication tapping and transmission to routable networks

Apparatuses and methods for tapping serial communications and transforming the serial data into a format appropriate for routable networks are significant for purposes of security and troubleshooting, especially in critical infrastructure networks. Communication taps should be completely passive such that any failure would not interrupt the serial communications. Furthermore, automatic determination of unspecified serial protocol frames allow general implementation across various networks, or across devices within a single network, without the need to customize for each implementation.

Edgar, Thomas W.↗

DOE OSTI2024

Serial communication tapping and transmission to routable networks

Edgar, Thomas W.↗

DOE OSTI2021

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography

Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

All polymer microfluidic chips—A fixed target sample delivery workhorse for serial crystallography

The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around “workhorse” for serial crystallography measurements. In conclusion, this Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Serial-Refine Method for Fast Wake-Steering Yaw Optimization

In this paper we present the Serial-Refine method for quickly finding the optimal yaw angles in wake steering. The method optimizes turbine angles serially from upstream to downstream using a small number of candidate angles. The presented results show that Serial-Refine finds solutions that are at least as good as former conventional optimization approaches but that require much less computation time.

17 WIND ENERGY↗

NASA NTRS1989

A unifying framework for rigid multibody dynamics and serial and parallel computational issues

A unifying framework for various formulations of the dynamics of open-chain rigid multibody systems is discussed. Their suitability for serial and parallel processing is assessed. The framework is based on the derivation of intrinsic, i.e., coordinate-free, equations of the algorithms which provides a suitable abstraction and permits a distinction to be made between the computational redundancy in the intrinsic and extrinsic equations. A set of spatial notation is used which allows the derivation of the various algorithms in a common setting and thus clarifies the relationships among them. The three classes of algorithms viz., O(n), O(n exp 2) and O(n exp 3) or the solution of the dynamics problem are investigated. Researchers begin with the derivation of O(n exp 3) algorithms based on the explicit computation of the mass matrix and it provides insight into the underlying basis of the O(n) algorithms. From a computational perspective, the optimal choice of a coordinate frame for the projection of the intrinsic equations is discussed and the serial computational complexity of the different algorithms is evaluated. The three classes of algorithms are also analyzed for suitability for parallel processing. It is shown that the problem belongs to the class of N C and the time and processor bounds are of O(log2/2(n)) and O(n exp 4), respectively. However, the algorithm that achieves the above bounds is not stable. Researchers show that the fastest stable parallel algorithm achieves a computational complexity of O(n) with O(n exp 4), respectively. However, the algorithm that achieves the above bounds is not stable. Researchers show that the fastest stable parallel algorithm achieves a computational complexity of O(n) with O(n exp 2) processors, and results from the parallelization of the O(n exp 3) serial algorithm.

Fijany, Amir↗

NASA NTRS1987

Charge-coupled-device parallel-to-serial converter

A CCD parallel-to-serial converter comprising two successions of charge transfer stages, recurrently side-loaded with respective ones of parallelly supplied charge packets, then serially unloaded by time-interleaved respective shift register operations. The charge packets converted to time-division-multiplexed serial form are supplied to a shared electrometer, and the electrometer response is de-multiplexed. Preferably, shift register operations are carried forward concurrently at the same rate, but with the final charge transfer stages clocked in phases staggered in time.

Tower, John R.↗

NASA NTRSDate not supplied

Spectrally Dependent Radiometric Measurement Errors Due to Ccd Serial Pixel-to-Pixel Readout Interference in the Ocean Color Instrument of the NASA PACE Mission

The Ocean Color Instrument on NASA’s PACE mission is a 322 887 nm hyperspectral imager with 1 km x 1 km nadir spatial resolution and 5 nm spectral resolution utilizing charge-coupled devices (CCDs) operating in Time Delay Integration (TDI) mode where each TDI column represents a different wavelength in 0.625 nm increments. After TDI, the charge is moved into serial output pixels and read out. The spatial resolution requires an 8.5 MHz readout rate. This only allows 59 ns for the CCD reset and video to be asserted and settled before sampling. The response exhibits serial pixel-to-pixel readout interference due to the lack of full settling. Each serial pixel value has a dependence on the value of the preceding pixel value. This leads to a spectrally dependent radiometric measurement error of up to 0.3 %. We explain the operation of the detection system, the behavior of the interference, and show the resulting measurement error based on data from both ground testing and on-orbit characterization.

Remote Sensing↗

NASA NTRS2024

Spectrally Dependent Radiometric Measurement Errors Due to CCD Serial Pixel-to-Pixel Readout Interference in the Ocean Color Instrument of the NASA PACE Mission

Remote Sensing↗

DOE OSTI2020

RD53A: A large-scale prototype chip for the phase II upgrade in the serially powered HL-LHC pixel detectors

The phase II upgrade of the HL-LHC experiments within the LHC intends to deepen the studies of the Higgs boson and to allow the discovery of further particles by adding an integrated luminosity of about 4000 fb -1 over 10 years of operation. This upgrade would overwhelm the installed pixel detector readout chips with higher hit rates and radiation levels than ever before. To match these extreme requirements the RD53 collaboration, a joint effort between ATLAS and CMS, developed RD53A, a new generation pixel detector readout chip prototype manufactured in a 65 nm CMOS technology. It is half the size of the final pixel chips and designed to meet requirements in the face of 3 GHz/cm 2 hit rate after irradiation to 500 Mrad. The detector is able to use 50×50 μm 2 or 25×100 μm 2 pixels with high readout speed of up to 4 links per chip with 1.28 Gbit/s each. Shunt–LDO regulators integrated on the bottom of the chip provide the required voltages to the two power domains, analog and digital. These regulators enable serial powering of the pixel modules, which is the only feasible, radiation hard scheme to ensure acceptable power cable losses and to stay within the material budget for the future pixel detectors. Finally, an overview of the status and challenges of serial powering and the Shunt–LDO regulator development will be given.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses ( D 1/2 ) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography

Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip , 21 , 4831–4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

Serial Propellant Tank Pressure Behavior in Artemis 1 Orion-ESM Propulsion System

An oscillatory pressure behavior was observed throughout the Orion-ESM propulsion system during the Artemis I mission. This behavior was attributed to propellant oscillations within the serial line connecting the two propellant tanks for each commodity. A linearized dynamic model of the serial propellant tank system was derived to explain this behavior. The model showed excellent agreement with the flight data, with the predicted system natural frequencies matching the flight data within 1%.

Liquid propulsion systems↗

NASA NTRSDate not supplied

Three-Dimensional Reconstruction of Defects and Structures in Additively Manufactured Parts with Automated Serial Sectioning

Metal additive manufacturing (AM) processes have been demonstrated to be effective at reducing costs and lead times associated with complex components for space flight applications. Laser powderbed fusion (L-PBF) is a commonly used AM technology due to the ability to produce complex parts with fine feature resolution in a wide variety of alloys and applications. L-PBF, like many other manufacturing processes, can produce minor flaws in parts when in nominal operation as well as process-escape defects when process abnormalities occur. The effects of the flaws and methods of detecting the flaws are a subject of interest to understand the difficulties in detecting these flaws with current technology and how much risk the flaws or defects pose to potential flight parts. Using a RoboMet.3D automated serial sectioning system, seeded defects as well as minor process flaws can be imaged and reconstructed in three dimensions to compare to non-destructive evaluation (NDE) techniques, such as x-ray computed tomography (CT), neutron CT, and in-situ monitoring. The RoboMet automates the metallography process by automatically grinding, polishing, and imaging samples in a single system and providing the control data for NDE comparisons to know the real size of defects built into coupons. These comparisons provide an understanding behind the technological limitations of the NDE techniques for different alloys. The same serial sectioning methods have also been utilized to characterize the surfaces of parts to reconstruct the surfaces and take measurements of internal features not easily examined with non-destructive methods. Using the RoboMet, fine lattice structures built with L-PBF have been characterized to determine the actual thicknesses of struts and density of the lattice structures. These structures have been used as finer build supports for the L-PBF process, designs for fine catalysts, and other design considerations for small components. The RoboMet data helps to inform the modeling and design efforts around these fine components.

additive manufacturing↗

DOE OSTI2022

Chemical crystallography by serial femtosecond X-ray diffraction

Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2,3 and electron microdiffraction 4–11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15–17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18–20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT 1 R and CysLT 2 R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w

97 MATHEMATICS AND COMPUTING↗