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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Generalized large optics fabrication multiplexing

High precision astronomical optics are manufactured through deterministic computer controlled optical surfacing processes, such as subaperture small tool polishing, magnetorheological finishing, bonnet tool polishing, and ion beam figuring. Due to the small tool size and the corresponding tool influence function, large optics fabrication is a highly time-consuming process. The framework of multiplexed figuring runs for the simultaneous use of two or more tools is presented. This multiplexing process increases the manufacturing efficiency and reduces the overall cost using parallelized subaperture tools.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Improved microwave SQUID multiplexer readout using a kinetic-inductance traveling-wave parametric amplifier

We report on the use of a kinetic-inductance traveling-wave parametric amplifier (KITWPA) as the first amplifier in the readout chain of a microwave superconducting quantum interference device (SQUID) multiplexer (μmux). This μmux is designed to multiplex signals from arrays of low temperature detectors, such as superconducting transition-edge sensor microcalorimeters. When modulated with a periodic flux-ramp to linearize the SQUID response, the flux noise improves, on average, from 1.6 μ $\Phi$ 0 /$\sqrt{Hz}$ with the KITWPA off to 0.77 μ $\Phi$ 0 /$\sqrt{Hz}$ with the KITWPA on. When statically biasing the μmux to the maximally flux-sensitive point, the flux noise drops from 0.45 μ $\Phi$ 0 /$\sqrt{Hz}$ to 0.2 μ $\Phi$ 0 /$\sqrt{Hz}$⁠. We validate this new readout scheme by coupling a transition-edge sensor microcalorimeter to the μmux and detecting background radiation. In conclusion, the combination of μmux and KITWPA provides a variety of new capabilities including improved detector sensitivity and more efficient bandwidth utilization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

CRISPR-GRIT: Guide RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans

Candida albicans, an opportunistic fungal pathogen, causes severe infections in immunocompromised individuals. Limited classes and overuse of current antifungals have led to the rapid emergence of antifungal resistance. Thus, there is an urgent need to understand fungal pathogen genetics to develop new antifungal strategies. Genetic manipulation of C. albicans is encumbered by its diploid chromosomes requiring editing both alleles to elucidate gene function. Although the recent development of CRISPR-Cas systems has facilitated genome editing in C. albicans, large-scale and multiplexed functional genomic studies are still hindered by the necessity of cotransforming repair templates for homozygous knockouts. Here, we present CRISPR-GRIT (Guide RNAs with Integrated Repair Templates), a repair template-integrated guide RNA design for expedited gene knockouts and multiplexed gene editing in C. albicans. Here, we envision that this method can be used for high-throughput library screens and identification of synthetic lethal pairs in both C. albicans and other diploid organisms with strong homologous recombination machinery.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Heralded Multiplexed High-Efficiency Cascaded Source of Dual-Rail Entangled Photon Pairs Using Spontaneous Parametric Down-Conversion

Deterministic sources of high-fidelity entangled qubit pairs encoded in the dual-rail photonic basis, i.e., presence of a single photon in one of two orthogonal modes, are a key enabling technology of many applications of quantum information processing, including high-rate, high-fidelity quantum communications over long distances. The most popular and mature sources of such photonic entanglement, e.g., those that leverage spontaneous parametric down-conversion (SPDC) or spontaneous four-wave mixing, generate an entangled (so-called continuous-variable) quantum state that contains contributions from high-order photon terms that lie outside the span of the dual-rail basis, which is detrimental to most applications. One often uses low pump power to mitigate the effects of those high-order terms. However, that reduces the pair generation rate, and the source becomes inherently probabilistic. We investigate a cascaded source that performs a linear-optical entanglement swap between two SPDC sources, to generate a heralded photonic entangled state that has a higher fidelity (to the ideal Bell state) compared to a free-running SPDC source. Furthermore, with the Bell swap providing a heralding trigger, we show how to build a multiplexed source, which despite reasonable switching losses and detector loss and noise, yields a fidelity versus success probability trade-off of a high-efficiency source of high-fidelity dual-rail photonic entanglement. We find, however, that there is a threshold of 1.5 dB of loss per switch, beyond which multiplexing hurts the fidelity versus success probability trade-off.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Multiplexed CRISPR/Cas9 editing of the long-chain acyl-CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids

Long-chain acyl-CoA synthetases (LACS) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil-producing microalgae, including the diatom Phaeodactylum tricornutum , remain largely unknown. In P. tricornutum , a family of five genes ( ptACSL1 – ptACSL5 ) encodes LACS activities. For this work, we generated single lacs knockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localisations. ptACSL3 is localised in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. The ptACSL3 mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localised in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl-CoAs for lipid synthesis. Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A Multiplexed Hybrid Velocimeter

Optical velocimetry systems play a crucial role in studying the dynamic behavior of materials under extreme conditions. Two prominent systems used at the Nevada National Security Site are the velocity interferometer system for any reflector(VISAR) and the photon Doppler velocimeter (PDV) system. Their ability to accurately measure surface motion ranging from 0 to > 20km=s without interacting with material flow enables experimenters to construct thermodynamic equations of state for materials of interest. A number of modifications to VISAR and PDV have taken place over the past five decades, leading to improved performance, increased recording capacity, and a reduction in operational burden. Prior efforts to develop a hybrid velocimeter combining the advantages of both PDV and VISAR into a single diagnostic did not take into account progress in PDV technology or new optical components that had not been developed. This thesis describes the design and implementation of a multiplexed hybrid velocimeter (MHV) based on time-multiplexing techniques, an optical hybrid, and polarization-maintaining fiber and components. Data from experiments, compared with current velocity systems, serve to demonstrate the hybrid's performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Two-phase accurate multiplexed structured image capture (2pAc-MUSIC)

Multiplexed Structural Image Capture (MUSIC) technique uses modulation of light from a scene prior to imaging to encode the temporal evolution of target into spatial frequency shifts, with each shift corresponding to a unique time and resulting in individual distinct snapshots. Computational-processing of the multiplexed single-shot image can recover the nanosecond-resolution scene evolution. One of the limitations is the loss of spatial resolution of the recovered image due to limitations of the low-pass spatial frequency filtering depth. Here we demonstrated that two images with complementary spatial phases can be used to enhance the spatial resolutions. For this application, 2 Phase Accurate (2pAc)-MUSIC is implemented that a scene is encoded with two complementary phases. The increased spatial information captured reduces the lower frequency noise in the Fourier domain found in single-phase MUSIC. A recovery algorithm combines the 180-degree spatial frequency shifted images into a single scene and applies a spatial filter in the Fourier domain that has a larger depth than previously possible to achieve a scene with increased spatial resolution. The 2pAc-MUSIC can effectively enhance the spatial resolution by removing the overlapping zero-order spatial frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Additively manufactured multiplexed inertial coalescence filters

Multiphase flows often pose a significant challenge to the efficient and reliable design of thermofluidic systems. This paper describes multiplexed inertial coalescence filters composed of parallel helical pathways, designed to capture fine droplets (<40 µm) through inertial separation while maintaining a low pressure drop (<400 Pa). Filtration efficiencies for 7 µm and 30 µm droplets were characterized for varying flow conditions, with complete capture observed above a threshold flow rate. Models for filtration efficiency and pressure drop were developed and validated against experimental results to allow system design and optimization, enabled by the tunable additive manufacturing approach used to fabricate the filters. Filter quality factor was computed for varying droplet sizes, showcasing exceptional quality factor when compared to state-of-the-art filters documented in the literature. In conclusion, this multiplexed inertial coalescence filtration approach could find use in dehumidification systems, fog harvesting, chemical reactors, and microgravity droplet capture.

3D Printing↗

DOE OSTI2023

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Here, in this paper, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Multiplex Detection of Multiple-Quantum/Single-Quantum NMR Correlation Spectra

High-ordered multiple-quantum coherences have been used to gauge the size of coupled networks of nuclear spins but are seldom used in modern high-resolution solid-state NMR spectroscopy due to the low resolution of earlier techniques. Herein, we extend this work to the third dimension by designing an MQ spin counting experiment with full chemical resolution of the nuclei involved in the coherences. The technique uses multiplex processing to simultaneously acquire MQ/1Q correlation 2D spectra, with all even-ordered values of M, in the same amount of time it would take to acquire the 2Q/1Q spectrum alone. Further, we apply this multiplexed MQ/1Q correlation method to probe site clustering on functionalized silica surfaces and find the first evidence of clusters involving three or more functionalities. When applied to a supported zirconium metallocene, the observation of a 6Q coherence between six cyclopentadienyl proton nuclei confirms the colocation of two cyclopentadienyl ligands on a single metal center.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Extending the Near-Infrared Emission Range of Indium Phosphide Quantum Dots for Multiplexed In Vivo Imaging

This report of the reddest emitting indium phosphide quantum dots (InP QDs) to date demonstrates tunable, near-infrared (NIR) photoluminescence (PL) as well as PL multiplexing in the first optical tissue window while avoiding toxic constituents. This synthesis overcomes the InP “growth bottleneck” and extends the emission peak of InP QDs deeper into the first optical tissue window using an inverted QD heterostructure, specifically ZnSe/InP/ZnS core/shell/shell nanoparticles. The QDs exhibit InP shell thickness-dependent tunable emission with peaks ranging from 515–845 nm. The high absorptivity of InP yields effective photoexcitation of the QDs with UV, visible, and NIR wavelengths. These nanoparticles extend the range of tunable direct-bandgap emission from InP-based nanostructures, effectively overcoming a synthetic barrier that has prevented InPbased QDs from reaching their full potential as NIR imaging agents. Further, multiplexed lymph node imaging in a mouse model demonstrates the potential of the NIR-emitting InP particles for in vivo imaging.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro

The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Flexible organic integrated electronics for self-powered multiplexed ocular monitoring

Smart contact lens has drawn extensive research interests due to the noninvasive real-time detection of the human body to provide biomedical information for health management. However, it has been difficult to accurately measure the physiological signals in tears, and the use of external power source has also hindered the future applications. Here, we demonstrated an organic electrochemical transistor based multiplexed sensors self-powered by the organic solar cells (OSCs). The integrated device was fabricated via simple process including solution blade-coating and thermal evaporation. OSCs were optimized to provide optimal operation voltage for the sensors that exhibit semilog-linear response to the glucose and calcium ions in tear fluids without any peripheral circuits. The sensing signals can be transmitted to the laptop wirelessly through a near filed communication unit. This integrated self-powered multiplexed sensing device will provide real-time monitoring of the biomarkers in tears, prospected to be installed on the smart contact lens for the early detection and diagnosis of diabetes.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Alamos, Simon↗

DOE OSTI2024

A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging

Abstract Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca 2+ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca 2+ concentration using fluorescence lifetime imaging microscopy (FLIM).

Biochemistry & Molecular Biology↗

DOE OSTI2021

A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities

Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Analytical tools capable of quickly detecting both glycan and lignin deconstruction are needed to support the development and characterization of efficient enzymes/enzyme cocktails. Previously we have described nanostructure-initiator mass spectrometry-based assays for the analysis of glycosyl hydrolase and most recently an assay for lignin modifying enzymes. Here we integrate these two assays into a single multiplexed assay against both classes of enzymes and use it to characterize crude commercial enzyme mixtures. Application of our multiplexed platform based on nanostructure-initiator mass spectrometry enabled us to characterize crude mixtures of laccase enzymes from fungi Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity on both carbohydrate and aromatic substrates. Using time-series analysis we determined that crude laccase from Ab has the higher GH activity and that laccase from Mt has the higher activity against our lignin model compound. Inhibitor studies showed a significant reduction in Mt GH activity under low oxygen conditions and increased activities in the presence of vanillin (common GH inhibitor). Ultimately, this assay can help to discover mixtures of enzymes that could be incorporated into biomass pretreatments to deconstruct diverse components of lignocellulosic biomass.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Multiplexed structured imaging of laser induced fluorescence at 10 GHz rate

The frame rate of conventional high-speed imaging devices is limited by exposure time and signal read-out time. Structured imaging is able to push the frame rate beyond the limit of the imaging device. This work demonstrates the feasibility of potential TeraHz rate structured imaging with a multiplexed structured imaging setup. In this work, a multiplexed structured image capture system was employed to image UV laser induced krypton-II emission lines at 10 GHz. The measured emission intensity of the 764 nm line over time suggests a temporal resolution of 97 ps. The temporal resolution is adjustable, and the frame rate can be further increased to the TeraHz level.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Optically multiplexed neutron time-of-flight technique for inertial confinement fusion

Neutron time-of-flight (nTOF) detectors are crucial in diagnosing the performance of inertial confinement fusion (ICF) experiments, which implode targets of deuterium–tritium fuel to achieve thermonuclear conditions. These detectors utilize the fusion neutron energy spectrum to extract key measurements, including the hotspot ion temperature and fuel areal density. Previous work [Danly et al., Rev. Sci. Instrum. 94, 043502 (2023)] has demonstrated adding 1D spatial resolution to an nTOF-like detector using a neutron aperture and streak camera to measure the ion temperature profile of an ICF implosion. By contrast, the study presented herein explores modifying the 1D detector to use a fast photomultiplier tube (PMT) to validate the design of a 2D spatially resolved instrument based on reconstruction from 1D profiles. The modification would collect time-of-flight traces from separate scintillators in an imaging array with one PMT using optical fibers of varying lengths to time-multiplex the signals. This technique has been demonstrated in ride-along experiments on the OMEGA laser with 20 fiber-coupled scintillator channels connected to a Photek PMT210. Results provide constraints on the fiber lengths and PMT gating requirements to promote pulse fidelity throughout all channels. Calibration of the detector to fixed nTOFs can provide a preliminary estimate of the instrument response function (IRF), although measurement of the IRF is currently under way. These results suggest that nTOF signals can potentially be time-multiplexed with fibers so long as the design is strategic to mitigate signal-to-noise reduction, modal dispersion, and charge build-up in the PMT, which has implications beyond ion temperature imaging.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗