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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

SHARP Assembly-Scale Multiphysics Demonstration Simulations

The NEAMS Reactor Product Line effort aims to develop an integrated multiphysics simulation capability for the design and analysis of future generations of nuclear power plants. The Reactor Product Line code suite’s multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. In this report, we describe our efforts to integrate thermal/hydraulics, neutronics, and structural mechanics modeling codes to perform coupled analysis of a representative fast sodium-cooled reactor fuel assembly. Over the past five years, the Reactor Product Line effort has developed high-fidelity single-physics codes for neutron transport modeling, in the PROTEUS code, and Large Eddy Simulation-based thermal/fluid modeling in the Nek5000 code. Both these codes have been exercised on over 100,000 processors of the IBM Blue Gene/P. The Diablo code has been used to perform structural mechanics and thermo-mechanical modeling. MOAB, the Reactor Geometry Generator (RGG), and MeshKit have been developed to generate and manipulate mesh and mesh-based data, in both serial and parallel environments. These tools together form a strong basis on which to build a multi-physics modeling capability. The goal of developing such a tool is to perform multi-physics neutronics, thermal/fluid, and structural mechanics modeling of the components inside a reactor core. While the focus of this report is on modeling a fast sodium-cooled reactor, it is also the goal that this simulation tool be useful for most reactor types. Here we report on the integration of PROTEUS and Nek5000 into the NEAMS framework. Both codes have been modified to read and write data from and to the MOAB library, in both serial and parallel environments. We focused on broad support for as many original physics code options as possible, rather than focusing only on near-term needs. Both codes were demonstrated through this interface on a relatively simple, seven-pin hexagonal fuel assembly. To support coupled analysis, the new multi-physics driver library COUPE was developed; this library provides flexible support for both loose and tight coupling, and can interface flexibly with codes in multiple programming languages. To couple results between the separate meshes used in each physics, the driver, PROTEUS, and Nek5000 all interface with the MBCoupler solution transfer tool provided with MOAB. Together, these tools form the basis of a new, coupled neutronics and thermal/fluid modeling code, that works in both serial and parallel. In a related effort, a driver in the Diablo code was used to access Nek5000-computed results written to a MOAB database, as well as the temperature data used to drive structural mechanics computations.

Tautges, Timothy J.↗
DOE OSTI2013

Truchas Reference Manual (V.2.8)

Truchas is executed in serial using a command of the form truchas [-h] [-d[:n ]] [-t] [-o:outdir ] [-r:rstfile ] infile assuming truchas is the name of the executable. The brackets denote optional arguments that are described in Table 1.1. The only required argument is the path to the input file infile . This file name must end with the extension “.inp" (without the quotes). The general format of the input file is described in the next section, and the following chapters describe the various Fortran namelists that go into the input file to describe the problem to be simulated. All of the output files are written to directory whose name is generated from the base name of the input file. For example, if the input file is myprob.inp, the output directory will be named myprob_output. The name of the output directory can be overridden using the -o option. The directory will be created if necessary. The precise manner of executing Truchas in parallel depends on the MPI implementation being used. This may be as simple as prefixing the serial invocation above with “mpirun -np n”, where n is the number of processes. But this varies widely and providing specific instructions is beyond the scope of this document. There is no difference in the Truchas arguments between serial and parallel, however.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Fiber optic transceiver FPGA mezzanine card (FMC)

A fiber optic transceiver FPGA mezzanine card (FMC) is capable of operating in radiation environments. The fiber optic transceiver FMC may be used with radiation-hardened and non-hardened FPGAs. The FMC may enable high speed serial communications, such as gigabit Ethernet, PCI express, serial rapid IO, and/or other high speed serial protocols over the fiber.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Compact, low power, high resolution ADC per pixel for large area pixel detectors

A compact ADC circuit can include one or more comparators, and a serial DAC (Digital-to-Analog) circuit that provides a signal to the comparator (or comparators). In addition, the ADC circuit can include a serial DAC redistribution sequencer that can provide a plurality of signals as input to the serial DAC circuit and is subject to a redistribution cycle and which receives as input a signal from a data multiplexer whose input connects electronically to an output of the comparator. The circuit can further include an ADC code register that provides an ADC output that connects electronically to the output of the comparator and the input to the data multiplexer. Shared logic circuitry for sharing common logic between pixels can be included, wherein the shared logic circuitry connects electronically to the data multiplexer and the ADC code register, wherein the shared logic circuitry promotes area and power savings for the pixel detector circuit.

Zimmerman, Tom↗
DOE OSTI2020

A 20 Gbps Data Transmitting ASIC with PAM4 for Particle Physics Experiments

We present the design principle and test results of a data transmitting ASIC, GBS20, for particle physics experiments. The goal of GBS20 will be an ASIC that employs two serializers each from the 10.24 Gbps lpGBT SerDes, sharing the PLL also from lpGBT. A PAM4 encoder plus a VCSEL driver will be implemented in the same die to use the same clock system, eliminating the need of CDRs in the PAM4 encoder. This way the transmitter module, GBT20, developed using the GBS20 ASIC, will have the exact lpGBT data interface and transmission protocol, with an output up to 20.48 Gbps over one fiber. With PAM4 embedded FPGAs at the receiving end, GBT20 will halve the fibers needed in a system and better use the input bandwidth of the FPGA. A prototype, GBS20v0 is fabricated using a commercial 65 nm CMOS technology. This prototype has two serializers and a PAM4 encoder sharing the lpGBT PLL, but no user data input. An internal PRBS generator provides data to the serializers. GBS20v0 is tested barely up to 20.48 Gbps. With lessons learned from this prototype, we are designing the second prototype, GBS20v1, that will have 16 user data input channels each at 1.28 Gbps. We present the design concept of the GBS20 ASIC and the GBT20 module, the preliminary test results, and lessons learned from GBS20v0 and the design of GBS20v1 which will be not only a test chip but also a user chip with 16 input data channels.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Compact, low power, high resolution ADC per pixel for large area pixel detectors

A compact ADC circuit can include one or more comparators, and a serial DAC (Digital-to-Analog) circuit that provides a signal to the comparator (or comparators). In addition, the ADC circuit can include a serial DAC redistribution sequencer that can provide a plurality of signals as input to the serial DAC circuit and is subject to a redistribution cycle and which receives as input a signal from a data multiplexer whose input connects electronically to an output of the comparator. The circuit can further include an ADC code register that provides an ADC output that connects electronically to the output of the comparator and the input to the data multiplexer. Shared logic circuitry for sharing common logic between pixels can be included, wherein the shared logic circuitry connects electronically to the data multiplexer and the ADC code register, wherein the shared logic circuitry promotes area and power savings for the pixel detector circuit.

Fahim, Farah↗
DOE OSTI2022

A signal packet router for the upgrade of the Muon spectrometer at the ATLAS experiment

Here, we present the design, characterization, and production of a signal packet router for the upgrade of the ATLAS forward muon detector. The router serves as a packet switch in one of the primary trigger paths. It handles up to 12 serial inputs at 4.8 Gbps/input from on-detector electronics and outputs four 4.8 Gbps to the trigger processing circuits. In the 12-to-4 packet switching process, the input streams are decoded and synchronized to a common clock domain for data packets forwarding and NULL packets suppression. Challenges in the design include operations of multi-giga hertz serial links with low and constant latency (<100 ns) for packet routing, as well as mitigation of radiation-induced effects in the harsh radiation environment over 10 years of detector operation. The Router design has been fully characterized and demonstrated to meet all specifications. In total 256 Routers were installed in the detector. Its design concept can be used in other similar applications, particularly in a radiation environment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser

NendoU from SARS-CoV-2 is responsible for the virus’s ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Time-resolved β-lactam cleavage by L1 metallo-β-lactamase

Abstract Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia . Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn 2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn 2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Advanced Modeling and Simulation Methods for Evaluation of Thermal Neutron Scattering Materials

With the rise of interest in thermal neutron scattering data for advanced reactor, criticality safety, and shielding applications, new experimental data are required for evaluation of new materials or for re-evaluation (or validations) of previously evaluated materials. New experimental data are evaluated in a three-step process: (1) computing the phonon characteristics, (2) computing the dynamic structure factor (DSF) from the data, and (3) using the experimental setup to simulate the experimental data. All three steps have challenges, ranging from the need for a sufficiently general material simulation code—a processing code that can compute the corresponding DSF—to having a detailed layout of the instrument/beamline/facility where the data were measured. Whereas phonon characteristics of materials can be computed using various methods (molecular dynamics, density functional theory, etc.), a high-fidelity computation of the DSF and the simulation of the experiment based on the DSF is vital to the accuracy of the evaluation. The latter two steps can be achieved by using the two corresponding code systems developed by instrument scientists at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory: (1) OCLIMAX, a program that calculates the dynamic structure factor from DFT and MD simulation results, and (2) MCViNE, a Monte Carlo neutron ray-tracing program designed to simulate neutron scattering experiments. Recently, polyethylene and yttrium hydride were measured at the Wide Angular-Range Chopper (ARCS) and SEQUOIA instrument stations of the SNS. These experiments are simulated using the density functional theory code, the Cambridge Serial Total Energy Package (CASTEP), to compute its phonon characteristics (eigenvalues/vectors and PDOS), which is then processed using OCLIMAX to yield the DSF, and finally the data at each instrument station are simulated by the MCViNE for comparison to the measured data for evaluation. For comparison to conventional evaluation methods, the scattering data processed from OCLIMAX are compared against those processed from the LEAPR module of NJOY, and the results from MCViNE simulations are compared against previously used simplified beamline models implemented in the Monte Carlo N-Particle (MCNP) code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity

Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli ( Ec )-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec- dGTPase, including an X-ray free-electron laser structure of the free Ec- -dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec- dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec- dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.

Barnes, Christopher O.↗
DOE OSTI2026

Detector alignment for X-ray crystallography using Millepede-II

I describe a method for accurately refining the geometrical parameters of segmented X-ray area detectors on the basis of serial crystallography data, using 'Millepede' – an algorithm created for a very similar problem in high-energy physics. The Millepede method for serial crystallography builds on the approach of Brewster et al. [Acta Cryst. (2018), D74, 877–894], in which the detector parameters are refined simultaneously with the parameters for each individual crystal. This accounts for the mutual dependency between the parameters and thereby avoids the bias and slow convergence problems that have afflicted older approaches in which the deviations between observed and calculated Bragg peak positions were taken directly as the updates for the detector panel positions. The Millepede method uses the special structure of the least-squares normal equations to reduce them to a much smaller form that can be solved very quickly, even compared with the sparse matrix methods used previously. This makes it practical to refine the detector geometry frequently and thereby maintain accurate calibration without specialized alignment campaigns. Tilts of detector panels out of the plane can be reliably refined, as can the overall distance of the detector in the beam direction. With a simulated test case, the new method produced panel shifts within 7% of the correct values with only one iteration, and produced almost exactly correct shifts after a second iteration. A simulated out-of-plane panel rotation was correctly determined to within 0.001°. Applied to experimental data from an X-ray free-electron laser, the method increased the indexable fraction of frames from 30% to 91% in a single iteration, and to 96% after two further iterations. Computing the geometry updates on the basis of 2060 crystals took only 0.819 s on desktop computing hardware, including the time taken to read the required data from disk. The scaling was found to be very close to linear for up to 100 980 sets of crystal parameters, which took only 78.2 s to process under the same conditions. The method has been applied as part of a real-time feedback system at a synchrotron radiation beamline, in which an out-of-plane detector tilt of 0.04° was detected and corrected. Possible further applications are also described here.

Millepede-II↗
DOE OSTI2015

XFEL diffraction: Developing processing methods to optimize data quality

Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shots with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Protein crystal structure from non-oriented, single-axis sparse X-ray data

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

TakeTwo : an indexing algorithm suited to still images with known crystal parameters

The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

SAD phasing of XFEL data depends critically on the error model

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data collection from crystals grown in microfluidic droplets

Protein crystals grown in microfluidic droplets have been shown to be an effective and robust platform for storage, transport and serial crystallography data collection with a minimal impact on diffraction quality. Single macromolecular microcrystals grown in nanolitre-sized droplets allow the very efficient use of protein samples and can produce large quantities of high-quality samples for data collection. However, there are challenges not only in growing crystals in microfluidic droplets, but also in delivering the droplets into X-ray beams, including the physical arrangement, beamline and timing constraints and ease of use. Here, the crystallization of two human gut microbial hydrolases in microfluidic droplets is described: a sample-transport and data-collection approach that is inexpensive, is convenient, requires small amounts of protein and is forgiving. It is shown that crystals can be grown in 50–500 pl droplets when the crystallization conditions are compatible with the droplet environment. Local and remote data-collection methods are described and it is shown that crystals grown in microfluidics droplets and housed as an emulsion in an Eppendorf tube can be shipped from the US to the UK using a FedEx envelope, and data can be collected successfully. Details of how crystals were delivered to the X-ray beam by depositing an emulsion of droplets onto a silicon fixed-target serial device are provided. After three months of storage at 4°C, the crystals endured and diffracted well, showing only a slight decrease in diffracting power, demonstrating a suitable way to grow crystals, and to store and collect the droplets with crystals for data collection. This sample-delivery and data-collection strategy allows crystal droplets to be shipped and set aside until beamtime is available.

59 BASIC BIOLOGICAL SCIENCES↗