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At least 1,333 records · Page 74

All sources NASA NTRS DOE OSTI

DOE OSTI2019

High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA

Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Meta-optic accelerators for object classifiers

Rapid advances in deep learning have led to paradigm shifts in a number of fields, from medical image analysis to autonomous systems. These advances, however, have resulted in digital neural networks with large computational requirements, resulting in high energy consumption and limitations in real-time decision-making when computation resources are limited. Here, we demonstrate a meta-optic–based neural network accelerator that can off-load computationally expensive convolution operations into high-speed and low-power optics. In this architecture, metasurfaces enable both spatial multiplexing and additional information channels, such as polarization, in object classification. End-to-end design is used to co-optimize the optical and digital systems, resulting in a robust classifier that achieves 93.1% accurate classification of handwriting digits and 93.8% accuracy in classifying both the digit and its polarization state. This approach could enable compact, high-speed, and low-power image and information processing systems for a wide range of applications in machine vision and artificial intelligence.

42 ENGINEERING↗

DOE OSTI2023

Highly multicolored light-emitting arrays for compressive spectroscopy

Miniaturized, multicolored light-emitting device arrays are promising for applications in sensing, imaging, computing, and more, but the range of emission colors achievable by a conventional light-emitting diode is limited by material or device constraints. In this work, we demonstrate a highly multicolored light-emitting array with 49 different, individually addressable colors on a single chip. The array consists of pulsed-driven metal-oxide-semiconductor capacitors, which generate electroluminescence from microdispensed materials spanning a diverse range of colors and spectral shapes, enabling facile generation of arbitrary light spectra across a broad wavelength range (400 to 1400 nm). When combined with compressive reconstruction algorithms, these arrays can be used to perform spectroscopic measurements in a compact manner without diffractive optics. As an example, we demonstrate microscale spectral imaging of samples using a multiplexed electroluminescent array in conjunction with a monochrome camera.

42 ENGINEERING↗

DOE OSTI2020

Light-powered CO 2 fixation in a chloroplast mimic with natural and synthetic parts

Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl–coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.

Miller, Tarryn E.↗

DOE OSTI2018

A Novel Approach to Realize of All Optical Frequency Encoded Dibit Based XOR and XNOR Logic Gates Using Optical Switches with Simulated Verification

Since last few decades optics has already proved its strong potentiality for conducting parallel logic, arithmetic and algebraic operations due to its super-fast speed in communication and computation. So many different logical and sequential operations using all optical frequency encoding technique have been proposed by several authors. Here, we have keened out all optical dibit representation technique, which has the advantages of high speed operation as well as reducing the bit error problem. Exploiting this phenomenon, we have proposed all optical frequency encoded dibit based XOR and XNOR logic gates using the optical switches like add/drop multiplexer (ADM) and reflected semiconductor optical amplifier (RSOA). Also the operations of these gates have been verified through proper simulation using MATLAB (R2008a).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Analysis of Errors in Recording and Reading of a Holographic Prism on Photothermorefractive Glass

The influence of deviation of recording and reading conditions of multiplex Bragg gratings from calculated values on the parameters of restorable fan of beams of a holographic prism (HP) formed by Bragg gratings in photothermorefractive glass is analyzed. Deviations are specified either as a rotation of the sample around one of three orthogonal axes Oxyz or as simultaneous rotation of the sample around two axes. It is shown that errors in the sample installation do not affect quality of the HP in recording if all gratings are recorded with the same deviation from an ideal position. However, difference in errors at the recording of each grating results is a reduction of flatness of fan of the HP and a loss of its working capacity. Ultimate values of errors of rotation around the Ox and Oy axes allowing one to maintain HP functionality, i.e., simultaneous reconstruction of all its beams, are calculated. It is established that, in the case of an ideally recorded HP, errors in the stage of reading may result in twisting the fan and disrupting its flatness.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Acousto-Optic Commutation of Fiber-Optic Channels

An acousto-optic commutator of fiber-optic channels based on a ТеО{sub 2} two-coordinate deflector has been proposed and realized. The commutator yields switching of optical radiation from a single output waveguide into a two-dimensional input matrix of waveguides, or vice versa, switching from any matrix waveguide into a single output one. The main interrelated parameters have been obtained. It has been established that the commutator has a short response time of 2–10 μs, yields up to several hundreds of switching channels, low insertion losses of 2–5 dB, and a considerable inter-channel isolation from –35 to –60 dB. Experiments were performed for the output matrix containing 19 waveguides. The channel multiplexing operating mode of this commutator has been demonstrated, which is simultaneous transmission of a signal from the output waveguide into a given number of waveguides of the input matrix.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Investigation of the Static and Dynamic Characteristics for a Wafer-Fused C-band VCSEL in the Mode of the Optical-Electric Converter

The results of an experimental study for a long wavelength vertical cavity surface-emitting laser of a wafer-fused construction as an effective resonant cavity enhanced photodetector of analog optical signals are described. The device is of interest for a number of promising microwave photonics applications and for creation of a low-cost photoreceiver in a high-speed fiber optics telecommunication system with dense wavelength division multiplexing. The schematic of the testbed, the original technique allowing to calculate the passband of the built-in optical cavity, and the results of measuring dark current, current responsivity, amplitude- and phase-frequency characteristics during the process of photo-detection are demonstrated.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

A Superconducting Resonator with a Hafnium Microbridge at Temperatures of 50–350 mK

A high-quality superconducting resonator with a microbridge of hafnium film for use in a circuit for readout a terahertz-band imaging array with frequency division multiplexing is demonstrated experimentally. The variability of the impedance of the bridge at a frequency of 1.5 GHz, which is a key factor in the control of the quality of the resonator, is studied. The bridge, having a thickness of about 50 nm, a critical temperature T{sub C} ≈ 380 mK, and a plan size of 2.5 × 2.5 μm, was connected as a load of a resonator made of niobium film with a thickness of about 100 nm (T{sub C} ~ 9 K). It is shown that the bridge smoothly changes its impedance proportionally to the bias power in the entire temperature range. The effective thermal insulation of the bridge was measured in a dilution cryostat at temperatures of 50–300 mK. Thermal conductivity G of the bridge was calculated and found to be ~4 × 10{sup –13} W/K, which gives an estimate of the sensitivity of the structure in the bolometric mode NEP ≈ 8 × 10{sup –19} W/Hz{sup 1/2} at a temperature of 150 mK.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

First demonstration of a TES based cryogenic Li 2 MoO 4 detector for neutrinoless double beta decay search

Cryogenic calorimetric experiments to search for neutrinoless double-beta decay (0vββ) are highly competitive, scalable and versatile in isotope. The largest planned detector array, CUPID, is comprised of about 1500 individual Li 2 100 MoO 4 detector modules with a further scale up envisioned for a follow up experiment (CUPID-1T). In this article, we present a novel detector concept targeting this second stage with a low impedance TES based readout for the Li 2 MoO 4 absorber that is easily mass-produced and lends itself to a multiplexed readout. We present the detector design and results from a first prototype detector operated at the NEXUS shallow underground facility at Fermilab. The detector is a 2-cm-side cube with 21 g mass that is strongly thermally coupled to its readout chip to allow rise-times of ~0.5 ms. This design is more than one order of magnitude faster than present NTD based detectors and is hence expected to effectively mitigate backgrounds generated through the pile-up of two independent two neutrino decay events coinciding close in time. Together with a baseline resolution of 1.95 keV (FWHM) these performance parameters extrapolate to a background index from pile-up as low as 5 • 10 –6 counts/keV/kg/yr in CUPID size crystals. The detector was calibrated up to the MeV region showing sufficient dynamic range for 0vββ searches. In combination with a SuperCDMS HVeV detector this setup also allowed us to perform a precision measurement of the scintillation time constants of Li 2 MoO 4 , which showed a primary component with a fast O(20 μs) time scale. Similar content being viewe

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

Efficient Parallel Discrete Event Simulation on Cloud/Virtual Machine Platforms

Cloud and Virtual machine (VM) technologies present new challenges with respect to performance and monetary cost in executing parallel discrete event simulation (PDES) applications. Due to the introduction of overall cost as a metric, the traditional use of the highest-end computing configuration is no longer the most obvious choice. Moreover, the unique runtime dynamics and configuration choices of Cloud and VM platforms introduce new design considerations and runtime characteristics specific to PDES over Cloud/VMs. Here, an empirical study is presented to guide an understanding of the dynamics, trends, and trade-offs in executing PDES on Cloud/VM platforms. Performance and cost measures obtained from multiple PDES applications executed on the Amazon EC2 Cloud and on a high-end VM host machine reveal new, counterintuitive VM--PDES dynamics and guidelines. One of the critical aspects uncovered is the fundamental mismatch in hypervisor scheduler policies designed for general cloud workloads versus the virtual time ordering needed for PDES workloads. This insight is supported by experimental data revealing the gross deterioration in PDES performance traceable to VM scheduling policy. To overcome this fundamental problem, the design and implementation of a new deadlock-free scheduler algorithm are presented, optimized specifically for PDES applications on VMs. The scalability of our scheduler has been tested up to 128 VMs multiplexed on 32 cores, showing significant improvement in the runtime relative to the default Cloud/VM scheduler. The observations, algorithmic design, and results are timely for emerging cloud/VM-based installations, highlighting the need for PDES-specific support in high performance discrete event simulations on Cloud/VM platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

A Programming Framework for Neuromorphic Systems with Emerging Technologies

Neuromorphic computing is a promising post-Moore's law era technology. A wide variety of neuromorphic computer (NC) architectures have emerged in recent years, ranging from traditional fully digital CMOS to nanoscale implementations with novel, beyond CMOS components. There are already major questions associated with how we are going to program and use NCs simply because of how radically different their architecture is as compared with the von Neumann architecture. When coupled with the implementations using emerging device technologies, which add additional issues associated with programming devices, it is clear that we must define a new way to program and develop for NC devices. In this work, we discuss a programming framework for NC devices implemented with emerging technologies. We discuss how we have applied this framework to program a NC system implemented with metal oxide memristors. We utilize the framework to develop two applications for the memristive NC device: a simple multiplexer and a simple control task (the cart-pole problem). Finally, we discuss how this framework can be extended to NC systems implemented with a variety of novel device components and materials.

Schuman, Catherine↗

DOE OSTI2024

Compiler-Driven FPGA Virtualization with SYNERGY

FPGAs are increasingly common in modern applications, and cloud providers now support on-demand FPGA acceleration in datacenters. Applications in datacenters run on virtual infrastructure, where consolidation, multi-tenancy, and workload migration enable economies of scale that are fundamental to the provider's business. However, a general strategy for virtualizing FPGAs has yet to emerge. While manufacturers struggle with hardware-based approaches, we propose a compiler/runtime-based solution called Synergy. We show a compiler transformation for Verilog programs that produces code able to yield control to software atsub-clock-tickgranularity according to the semantics of the original program. Synergy uses this property to efficiently support core virtualization primitives: suspend and resume, program migration, and spatial/temporal multiplexing, on hardware which is availabletoday.We use Synergy to virtualize FPGA workloads across a cluster of Intel SoCs and Xilinx FPGAs on Amazon F1. The workloads require no modification, run within 3--4x of unvirtualized performance, and incur a modest increase in FPGA fabric usage.

Computer Science↗

DOE OSTI2014

ADARA

The ADARA software is a collection of programs which gather neutron scattering data from multiple detector banks, multiplex the data into a single stream and distribute that stream to analysis, reduction and translation utilities in real-time.

Miller, Ross↗

DOE OSTI2022

dkainer/RWRtoolkit

a set of command-line and R tools for performing Random-walk with Restart analyses on multiplex networks in any species

Kainer, David↗

DOE OSTI2019

wuhrlab/BACIQ

Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signals generated by isobaric tags, which encode the samples’ origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein’s peptides and the signal-strength of these measurements. However, typically the average peptide ratio is reported as the estimate of relative protein abundance, which is only the most likely ratio with a very naive model. Moreover, there is no sense on the confidence in these measurements. Here, we present a mathematically rigorous approach that integrates peptide signal strengths and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: It removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; Confidence can be assigned without replicates; For repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; and For repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ, we reanalyzed previously published data on subcellular protein movement upon treatment with an Exportin-1 inhibiting drug. We detect ~2x more highly significant movers, down to subcellular localization changes of ~1% . Thus, our method drastically increases the value obtainable from quantitative proteomics experiments helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.

Peshkin, Leonid↗

DOE OSTI2021

wuhrlab/TMTProC

The TMTProC module is the group of Matlab scripts associated with our paper "TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level".

Johnson, Alex↗

DOE OSTI2020

Detection of Head and Neck Cancer Based on Longitudinal Changes in Serum Protein Abundance

Head and Neck Squamous Cell Carcinoma (HNSCC) is significantly represented in the military population with substantial impact on military operations. Two-thirds of new HNSCC cases are first diagnosed at advanced stage III or IV with lymph node metastases. Thus, there is an urgent need of biomarkers for early detection and risk stratification. Archived serum samples from the Department of Defense Serum Repository provide a unique resource for longitudinal studies of HNSCC in the military and the identification of early detection biomarkers. Methods: We identified 175 patients diagnosed with HNSCC with 175 matched healthy controls and retrieved a total of 978 serum samples drawn at the time of diagnosis, 2 and 4 years prior to diagnosis, and 2 years after diagnosis. Following immunoaffinity depletion, serum samples were analyzed by targeted proteomics assays for multiplexed quantification of a panel of 146 candidate protein biomarkers from the curated literature. Results: We derived a 13-protein signature that distinguishes case versus controls based on longitudinal changes in serum protein concentration. The abundances of each of the 13 proteins remain constant over time in control subjects. The area under the curve for the derived random forest classifier was 0.90. Conclusions: This 13-protein classifier is highly promising for detection of HNSCC prior to overt symptoms. Impact: Use of longitudinal samples has significant potential to identify biomarkers for detection and risk stratification.

59 BASIC BIOLOGICAL SCIENCES↗