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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Experience with the alpaka performance portability library in the CMS software

ion Library for Parallel Kernel Acceleration) is a header-only C++ library that provides performance portability across different back-ends, abstracting the underlying levels of parallelism. It supports serial and parallel execution on CPUs, and extremely parallel execution on NVIDIA, AMD and Intel GPUs.This contribution will show how alpaka is used in the CMS software to develop and maintain a single code base; to use different toolchains to build the code for each supported back-end, and link them into a single application; to seamlessly select the best backend at runtime, and implement portable reconstruction algorithms that run efficiently on CPUs and GPUs from different vendors. It will describe the validation and deployment of the alpaka-based implementation in the CMS High Level Trigger, and highlight how it achieves near-native performance.

Alawieh, Jaafar [CERN]↗
DOE OSTI2023

Data Reliability in BIM and Performance Analytics: A Survey of Contemporary AECO Practice

As awareness around building energy consumption increases, practitioners are encouraged to consider performance aspects regarding the built environment more closely and find ways to improve its efficiency. Improvements in building information modeling (BIM) and building performance simulation (BPS) tools present opportunities to facilitate information communication with a wider range of stakeholders. The building sector can benefit from the integration of performance informatics; however, there has been limited success in utilizing available technologies that promote data integration and management in favor of enriching our knowledge and understanding of buildings as artifacts of information. This phenomenon was investigated by conducting a survey, together with a review of relevant literature, to depict the relevant challenges and opportunities for the architecture, engineering, construction, and owner-operated (AECO) industry, as it undergoes digital transformation, as well as the working practices that have formed around them. It is argued that the current tools available to practitioners do not support effective data serialization between design and analytics processes, affecting the collaboration between team members. Lastly, a series of functional goals are proposed to support a higher level of reliability in the ways information is mobilized, by rethinking the technologies and methods for organizing information systems.

42 ENGINEERING↗
DOE OSTI2020

A microchip microcontroller-based transducer controller for non-contact scanning probe microscopy with phase-locked loop, amplitude, and Q control

An inexpensive yet versatile transducer controller for non-contact scanning probe microscopy (SPM) based on a PIC32 microcontroller from Microchip Technology, Inc is described. In addition to feedback control using the amplitude or phase of the signal from the non-contact transducer, the controller includes a phase-locked loop for frequency-shift feedback, as well as fixed-amplitude, quality factor (Q) control, and self-excitation modes. Apart from the input amplifiers, output buffers, and the Q-control circuit, all other functions of the controller are instantiated in software on the microchip, enabling rapid changes in operating parameters if needed. The controller communicates with a host personal computer via a simple serial connection. The controller has been tested with a quartz tuning-fork transducer but can be used with any oscillating non-contact transducer.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis

Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted intensities are affected by partiality. To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of equivalent reflections within each bin. This binning and averaging often involve a loss of information. Here, we propose an alternative approach, which we call low-pass spectral analysis (LPSA). In this method, the data are projected onto the subspace defined by a set of trigonometric functions, with frequencies up to a certain cutoff. This approach attenuates undesirable high-frequency features and facilitates retrieving the underlying dynamics. A time-lagged embedding step can be included prior to subspace projection to improve the stability of the results with respect to the parameters involved. Subsequent modal decomposition allows to produce a low-rank description of the system's evolution. Using a synthetic time-evolving model with incomplete and partial observations, we analyze the LPSA results in terms of quality of the retrieved signal, as a function of the parameters involved. We compare the performance of LPSA to that of a range of other sophisticated data analysis techniques. We show that LPSA allows to achieve excellent dynamics reconstruction at modest computational cost. Finally, we demonstrate the superiority of dynamics retrieval by LPSA compared to time binning and merging, which is, to date, the most commonly used method to extract dynamical information from TR-SFX data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Filling data analysis gaps in time-resolved crystallography by machine learning

There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.

Trujillo, Justin (ORCID:0000000285505360)↗
DOE OSTI2021

Simplified feedback control system for scanning tunneling microscopy

A Scanning Tunneling Microscope (STM) is one of the most important scanning probe tools available to study and manipulate matter at the nanoscale. In a STM, a tip is scanned on top of a surface with a separation of a few Å. Often, the tunneling current between the tip and the sample is maintained constant by modifying the distance between the tip apex and the surface through a feedback mechanism acting on a piezoelectric transducer. This produces very detailed images of the electronic properties of the surface. The feedback mechanism is nearly always made using a digital processing circuit separate from the user computer. Here, we discuss another approach using a computer and data acquisition through the universal serial bus port. We find that it allows successful ultralow noise studies of surfaces at cryogenic temperatures. We show results on different compounds including a type II Weyl semimetal (WTe2), a quasi-two-dimensional dichalcogenide superconductor (2H–NbSe2), a magnetic Weyl semimetal (Co3Sn2S2), and an iron pnictide superconductor (FeSe).

Martín-Vega, Francisco (ORCID:0000000333177833)↗
DOE OSTI2022

Structured illumination with thermal imaging (SI-TI): A dynamically reconfigurable metrology for parallelized thermal transport characterization

The recent push for the “materials by design” paradigm requires synergistic integration of scalable computation, synthesis, and characterization. Among these, techniques for efficient measurement of thermal transport can be a bottleneck limiting the experimental database size, especially for diverse materials with a range of roughness, porosity, and anisotropy. Traditional contact thermal measurements have challenges with throughput and the lack of spatially resolvable property mapping, while non-contact pump-probe laser methods generally need mirror smooth sample surfaces and also require serial raster scanning to achieve property mapping. Here, we present structured illumination with thermal imaging (SI-TI), a new thermal characterization tool based on parallelized all-optical heating and thermometry. Experiments on representative dense and porous bulk materials as well as a 3D printed thermoelectric thick film (~50 μm) demonstrate that SI-TI (1) enables paralleled measurement of multiple regions and samples without raster scanning; (2) can dynamically adjust the heating pattern purely in software, to optimize the measurement sensitivity in different directions for anisotropic materials; and (3) can tolerate rough (~3 μm) and scratched sample surfaces. Here, this work highlights a new avenue in adaptivity and throughput for thermal characterization of diverse materials.

42 ENGINEERING↗
DOE OSTI2022

The ultrafast pixel array camera system and its applications in high energy density physics

Diagnostics in high energy density physics, shock physics, and related fields are primarily driven by a need to record rapidly time-evolving signals in single-shot events. These measurements are often limited by channel count and signal degradation issues on cable links between the detector and digitizer. Here we present the Ultrafast Pixel Array Camera (UPAC), a compact and flexible detector readout system with 32 waveform-recording channels at up to 10 Gsample/s and 1.8 GHz analog bandwidth. The compact footprint allows the UPAC to be directly embedded in the detector environment. A key enabling technology is the PSEC4A chip, an eight-channel switch-capacitor array sampling device with up to 1056 samples/channel. The UPAC system includes a high-density input connector that can plug directly into an application-specific detector board, programmable control, and serial readout, with less than 5 W of power consumption in full operation. We present the UPAC design and characterization, including a measured timing resolution of ~20 ps or better on acquisitions of sub-nanosecond pulses with minimal system calibrations. Example applications of the UPAC are also shown to demonstrate operation of a solid-state streak camera, an ultrafast imaging array, and a neutron time-of-flight spectrometer.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Anomalous Hall effect in nanoscale structures of the antiferromagnetic Weyl semimetal Mn 3 Sn at room temperature

The magnetic Weyl semimetallic state in the chiral antiferromagnet Mn 3 Sn has attracted interest for its potential in memory technology. Despite vanishingly small magnetization, the material exhibits large transverse responses that can be electrically manipulated, similar to ferromagnets. Through deposition on heated Si/SiO 2 substrates, we have fabricated polycrystalline Mn 3 Sn films that have coarse surfaces, the thinner of which have a discontinuous structure comprised of grains with diameters of the order of 100 nm. Here we confirm that these grains retain the anomalous Hall effect arising in the time reversal symmetry broken chiral antiferromagnetic phase of Mn 3 Sn at room temperature by serially connecting the grains with an additional conducting layer. These results pave the path for the potential applications of nanoscale Mn 3 Sn systems, which could be useful in the development of energy efficient memory devices.

36 MATERIALS SCIENCE↗
DOE OSTI2023

TeraChem protocol buffers ( TCPB ): Accelerating QM and QM/MM simulations with a client–server model

The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. Here, we describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI - )—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A superconducting nanowire binary shift register

We present a design for a superconducting nanowire binary shift register, which stores digital states in the form of circulating supercurrents in high-kinetic-inductance loops. Adjacent superconducting loops are connected with nanocryotrons, three-terminal electrothermal switches, and fed with an alternating two-phase clock to synchronously transfer the digital state between the loops. A two-loop serial-input shift register was fabricated with thin-film NbN and a bit error rate of less than 10 –4 was achieved, when operated at a maximum clock frequency of 83 MHz and in an out-of-plane magnetic field of up to 6 mT. A shift register based on this technology offers an integrated solution for low-power readout of superconducting nanowire single photon detector arrays and is capable of interfacing directly with room-temperature electronics and operating unshielded in high magnetic field environments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A fast, dense Chebyshev solver for electronic structure on GPUs

Matrix diagonalization is almost always involved in computing the density matrix needed in quantum chemistry calculations. In the case of modest matrix sizes (≲4000), performance of traditional dense diagonalization algorithms on modern GPUs is underwhelming compared to the peak performance of these devices. This motivates the exploration of alternative algorithms better suited to these types of architectures. We newly derive, and present in detail, an existing Chebyshev expansion algorithm whose number of required matrix multiplications scales with the square root of the number of terms in the expansion. Focusing on dense matrices of modest size, our implementation on GPUs results in large speed ups when compared to diagonalization. Additionally, we improve upon this existing method by capitalizing on the inherent task parallelism and concurrency in the algorithm. Furthermore, this improvement is implemented on GPUs by using CUDA and HIP streams via the MAGMA library and leads to a significant speed up over the serial-only approach for smaller (≲1000) matrix sizes. Finally, we apply our technique to a model system with a high density of states around the Fermi level, which typically presents significant challenges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A six degrees of freedom femtosecond laser system for fabrication of small-scale mechanical property specimens

Here, we present the details of a novel ultra-short pulsed laser machining workstation that has been employed for high-throughput laser machining of small-scale mechanical property specimens. This system employs a six degrees of freedom hexapod positioning stage capable of macroscopic movements at high positional accuracy. We developed a methodology that uses quantitative image analysis to measure key parameters required to minimize the hexapod positioning and rotational error. Application of this system to laser machining of small-scale 316L stainless steel tensile specimens and ultra-high molecular weight polyethylene compressive specimens using eucentric tilt and rotation about the specimen axis will be shown, where serial laser milling at a specimen tilt angle of 10° was used to effectively eliminate any taper in the sample cross section that is typically found in laser machining.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Nm-scale electrical resistance imaging on CdTe by scanning spreading resistance microscopy

Local resistance imaging can provide information on nm-scale carrier distribution in semiconductor devices. Scanning spreading resistance microscopy (SSRM), an atomic force microscopy-based nm-scale resistance mapping technique, has been developed for carrier delineation in Si microdevices. We report on the development and validation of SSRM on CdTe materials, by testing on molecular beam epitaxy (MBE) grown CdTe films. The probe/CdTe contact resistance was suppressed sufficiently below sample's spreading resistance by pressing the probe into the sample with ∼mN contact force and applying a large sample/probe forward bias voltage (V s ), which was understood by analyzing current-voltage (I-V) involving a serially connected insulating top layer with underlying spreading resistance. The carrier concentration as deduced from the resistance measurement, using a single mobility value, is consistent with Hall measurement with a standard deviation of 14% based on a set of MBE films with carrier concentrations in the range of 10 15 –10 16 /cm 3 . The doping polarity was readily identified by flipping V s polarity, where the resistance with reverse V s is orders of magnitude larger than forward V s . While focusing on the SSRM technique validation, we also show an example on an As-doped Cd(Se,Te) polycrystalline thin film of a high-performance CdTe solar cell, which illustrates the local resistance nonuniformity with up to two orders of magnitude differences, indicating if local mobility is roughly constant, local carrier concentration can have significant nonuniformity.

14 SOLAR ENERGY↗
DOE OSTI2026

Metrology for femtosecond pulsed x-ray heating in diamond anvil cell experiments at the European XFEL: Revisiting the iron phase diagram up to 150 GPa

The development of pulsed intense x-ray sources, such as free electron laser, offers new avenues for high pressure experiments. Here, we study the feasibility and metrology of x-ray heating in diamond anvil cells at the European x-ray free electron laser. This method enables one to volumetrically heat the sample while inhibiting chemical migration and probing the crystallographic structure of the sample throughout the heating with a high repetition rate. We focus our study on iron, whose phase diagram is well established up to 100 GPa, to explore the possibilities and limitations of this technique. We volumetrically heat iron samples at starting pressures ranging from 10 to 138 GPa, using the x-ray beam pulsed at 4.5 MHz in a serial pump-and-probe experimental design. Experimental challenges arise from temperature gradients within the sample, changes in temperature at the 100 ns timescale, the difficulty of direct temperature estimates, the effect of thermal pressure, and the presence of metastable crystallites due to rapid cycles of heating and cooling. Hence, we develop a multi-crystal-like data processing method that allows us to account for sample heterogeneity in probed conditions. We then calibrate our measurements using known physical properties of iron under pressure. Thermal pressure in our experiments increases from 4% of the isochoric prediction at 10 GPa to 23% at 138 GPa, and we show that our data are in agreement with most previous observations of iron in this pressure range. The method can now be implemented at higher pressures and temperatures and on materials with unknown phase diagrams.

Materials science↗
DOE OSTI2020

Improved bacterial recombineering by parallelized protein discovery

Exploiting bacteriophage-derived homologous recombination processes has offered precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we present a high-throughput method for SSAP discovery that we call “serial enrichment for efficient recombineering” (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli , while PapRecT enables efficient recombineering in Pseudomonas aeruginosa , a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM

Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.

Saha, Ambarneil↗
DOE OSTI2026

Cryogenic electron tomography by the numbers: Charting underexplored lineages in structural cell biology

Imaging cells and their interactions across the whole biosphere with molecular-scale resolution is key for understanding structure–function relations. Cryogenic electron tomography (cryo-ET) is a powerful method for obtaining this critical information. However, cryo-ET studies are challenging and often limited to a small number of cell types per study. Here, we collate cryo-ET data from hundreds of cells and tissues across the biosphere to i) identify emerging methodological trends, ii) pinpoint strategies to reduce imaging time and costs, iii) quantitatively compare methods for cell freezing and sectioning, and iv) census cryo-ET species coverage across all domains of life. Comparing the fraction of cellular material within a single lamella across all domains of life reveals an order of magnitude difference between eukaryotes (1%) compared to bacteria (9%) and archaea (14%). We calculate the fraction of cellular material which can be imaged using distinct sectioning methods on multicellular communities and tissues—identifying serial lift-out as a powerful approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2 to 3 orders of magnitude lower than in sequence libraries and 4 to 5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and highlight where future cryo-ET research would be most impactful.

HPF↗