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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

First on-line detection of radioactive fission isotopes produced by laser-accelerated protons

Abstract The on-going developments in laser acceleration of protons and light ions, as well as the production of strong bursts of neutrons and multi- $$\hbox {MeV}$$ MeV photons by secondary processes now provide a basis for novel high-flux nuclear physics experiments. While the maximum energy of protons resulting from Target Normal Sheath Acceleration is presently still limited to around $$100 \, \hbox {MeV}$$ 100 MeV , the generated proton peak flux within the short laser-accelerated bunches can already today exceed the values achievable at the most advanced conventional accelerators by orders of magnitude. This paper consists of two parts covering the scientific motivation and relevance of such experiments and a first proof-of-principle demonstration. In the presented experiment pulses of $$200 \, \hbox {J}$$ 200 J at $$\approx \, 500 \, \hbox {fs}$$ ≈ 500 fs duration from the PHELIX laser produced more than $$10^{12}$$ 10 12 protons with energies above $$15 \, \hbox {MeV}$$ 15 MeV in a bunch of sub-nanosecond duration. They were used to induce fission in foil targets made of natural uranium. To make use of the nonpareil flux, these targets have to be very close to the laser acceleration source, since the particle density within the bunch is strongly affected by Coulomb explosion and the velocity differences between ions of different energy. The main challenge for nuclear detection with high-purity germanium detectors is given by the strong electromagnetic pulse caused by the laser-matter interaction close to the laser acceleration source. This was mitigated by utilizing fast transport of the fission products by a gas flow to a carbon filter, where the $$\upgamma$$ γ -rays were registered. The identified nuclides include those that have half-lives down to $$39 \, \hbox {s}$$ 39 s . These results demonstrate the capability to produce, extract, and detect short-lived reaction products under the demanding experimental condition imposed by the high-power laser interaction. The approach promotes research towards relevant nuclear astrophysical studies at conditions currently only accessible at nuclear high energy density laser facilities.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

The role of ambient gas confinement, plasma chemistry, and focusing conditions on emission features of femtosecond laser-produced plasmas

Ultrafast laser ablation coupled with optical emission spectroscopy is currently under development for standoff detection of elements and their isotopes for a wide range of application areas. In this work, we explore the role of ambient air pressure during the interaction of an ultrafast laser beam with two metallic targets (brass and uranium) with significantly different oxygen gas-phase reactivity. Plasma plumes were generated by focusing ~800 nm, ~35 fs pulses from an ultrafast laser system using a long focal length lens with f = 1 m. Two-dimensional spectral imaging was performed over the pressure range of 30 mTorr-700 Torr air to evaluate emission dynamics, plasma chemistry, signal-to-background ratio, and characteristic parameters (i.e. excitation temperature, electron density). An increase in ambient air pressure during ultrafast laser ablation leads to plume confinement and subsequent changes in the emission dynamics due to plasma chemistry as well as changes in plasma generation conditions (i.e. focused fs laser ablation versus filament ablation). Ablation crater morphologies were also investigated via scanning electron microscopy. Results indicate atomic emission intensity and signal-to-background ratios peak at moderate pressure levels (~50-100 Torr air) for both targets studied, although plasma chemistry influences uranium emission signatures. The emission features of the uranium plasma at pressures = 10 Torr showed the presence of atoms and oxide molecules which are co-located within the plume. We also find filament ablation leads to wider, more shallow craters compared to focused laser ablation. Our study provides unique insight into the interplay between plume dynamics, confinement, and oxygen chemistry of fs laser-produced plasmas and how these phenomena evolve with changing ambient air pressure.

Laser-produced plasma↗
DOE OSTI2023

The TRAPUM L -band survey for pulsars in Fermi -LAT gamma-ray sources

ABSTRACT More than 100 millisecond pulsars (MSPs) have been discovered in radio observations of gamma-ray sources detected by the Fermi Large Area Telescope (LAT), but hundreds of pulsar-like sources remain unidentified. Here, we present the first results from the targeted survey of Fermi-LAT sources being performed by the Transients and Pulsars with MeerKAT (TRAPUM) Large Survey Project. We observed 79 sources identified as possible gamma-ray pulsar candidates by a Random Forest classification of unassociated sources from the 4FGL catalogue. Each source was observed for 10 min on two separate epochs using MeerKAT’s L-band receiver (856–1712 MHz), with typical pulsed flux density sensitivities of $\sim 100\, \mu$Jy. Nine new MSPs were discovered, eight of which are in binary systems, including two eclipsing redbacks and one system, PSR J1526−2744, that appears to have a white dwarf companion in an unusually compact 5 h orbit. We obtained phase-connected timing solutions for two of these MSPs, enabling the detection of gamma-ray pulsations in the Fermi-LAT data. A follow-up search for continuous gravitational waves from PSR J1526−2744 in Advanced LIGO data using the resulting Fermi-LAT timing ephemeris yielded no detection, but sets an upper limit on the neutron star ellipticity of 2.45 × 10−8. We also detected X-ray emission from the redback PSR J1803−6707 in data from the first eROSITA all-sky survey, likely due to emission from an intrabinary shock.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Inferring adversarial behaviour in cyber‐physical power systems using a Bayesian attack graph approach

Abstract Highly connected smart power systems are subject to increasing vulnerabilities and adversarial threats. Defenders need to proactively identify and defend new high‐risk access paths of cyber intruders that target grid resilience. However, cyber‐physical risk analysis and defense in power systems often requires making assumptions on adversary behaviour, and these assumptions can be wrong. Thus, this work examines the problem of inferring adversary behaviour in power systems to improve risk‐based defense and detection. To achieve this, a Bayesian approach for inference of the Cyber‐Adversarial Power System (Bayes‐CAPS) is proposed that uses Bayesian networks (BNs) to define and solve the inference problem of adversarial movement in the grid infrastructure towards targets of physical impact. Specifically, BNs are used to compute conditional probabilities to queries, such as the probability of observing an event given a set of alerts. Bayes‐CAPS builds initial Bayesian attack graphs for realistic power system cyber‐physical models. These models are adaptable using collected data from the system under study. Then, Bayes‐CAPS computes the posterior probabilities of the occurrence of a security breach event in power systems. Experiments are conducted that evaluate algorithms based on time complexity, accuracy and impact of evidence for different scales and densities of network. The performance is evaluated and compared for five realistic cyber‐physical power system models of increasing size and complexities ranging from 8 to 300 substations based on computation and accuracy impacts.

Sahu, Abhijeet↗
DOE OSTI2023

Development of a field-deployable qPCR assay for real-time pest monitoring in algal cultivation systems

Outdoor cultivation is commonly used to produce algal biomass for a variety of bioproducts including food, feed, fuel, pharmaceuticals, and nutraceuticals. Outdoor cultivation ponds are highly susceptible to pest pressures that may lead to periods of low productivity or even entire loss of the algal crop. Consequently, there is a need for rapid, real-time tracking of pests for early intervention to mitigate crop loss. In this work, we describe the development of a field deployable, low-cost qPCR assay for detecting both known and novel pests of a farmed eukaryotic alga species, Nannochloropsis sp. We performed a proximity guided metagenome deconvolution approach (ProxiMeta™) to discover novel pests that temporally correspond to periods of reduced pond productivity. This approach provided high-quality metagenome assemblies that were used to design qPCR probes to detect specific pests of interest. The portable qPCR assay, designed to be deployed at remote field locations, enables low-cost surveillance with a rapid (2 h) turn-around time. Frequent sampling allows for early detection and prompts intervention strategies to remedy infected ponds to minimize crop loss. The qPCR assay was used to successfully detect a known predatory bacterium within the order Bdellovibrionales both in the lab and at a remote field location. Furthermore, we assembled the genome of two novel, site-specific pests in the Saprospiraceae family and successfully designed qPCR probes that differentially detected their presence in two different pond locations. Ultimately, this assay has the potential to monitor multiple pests simultaneously and tailor targets to match likely pest infections that differ across geographical locations, helping to mitigate crop loss on a large scale.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Development of a wide bandwidth heterodyne dispersion interferometer for electron density measurement of atmospheric pressure plasmas

One of the challenges of electron density measurements of an atmospheric pressure plasma (APP) with a laser interferometer is the significant and unwanted phase shift caused by changes in the neutral gas density. These unwanted phase shifts can be mitigated and plasma density measured using an interferometer architecture called a dispersion interferometer (DI). A DI is composed of two nonlinear orientation patterned GaAs crystals for frequency doubling and measures the phase shift induced by a plasma in the interference signal between two second-harmonic beams. Measurement of plasma dynamics or a short plasma pulse in less than a millisecond is enabled with heterodyne detection in a DI using an acousto-optic cell with a frequency of 40 MHz. This heterodyne DI (HDI) is targeted to measure APPs in an electron density range of 10 20 –10 24 m −3 . Finally, the HDI achieves a line-integrated density resolution of 2 × 10 15 m −2 (a phase resolution of 0.005°) with a time constant of 1 μs using ensemble averaging techniques.

atmospheric pressure plasma↗
DOE OSTI2026

SENSEI: A Search for Diurnal Modulation in Sub-GeV Dark Matter Scattering

Dark matter particles with sufficiently large interactions with ordinary matter can scatter in the Earth’s atmosphere and crust before reaching an underground detector. This Earth-shielding effect can induce a directional dependence in the dark matter flux, leading to a sidereal daily modulation in the signal rate. We perform a search for such a modulation using data from the SENSEI experiment, targeting MeV-scale dark matter. We achieve nearly an order-of-magnitude improvement in sensitivity over previous direct-detection bounds for dark-matter masses below ∼ 1 MeV , assuming the standard halo model with a Maxwell-Boltzmann velocity distribution, and restrict the amplitude of a general daily modulation signal to be below 6.8 e / g / d .

Bloch, Itay M. [UC, Berkeley; LBL, Berkeley]↗
DOE OSTI2023

The 先生 (SENSEI†) Experiment: sub-GeV dark matter searches with skipper-CCD

Skipper-CCDs are pixeled Silicon-based detectors that can perform multiple non-disruptive measurements of the same charge package. Their sub-electron resolution allows the detection of eV energy transfers, such as that expected from ultra-light dark matter interacting with electrons in a Silicon target. SENSEI (Sub-Electron Noise Skipper Experimental Instrument) is the first experiment to use Skipper-CCD for this purpose and to publish world-leading results using this technology. In this talk, we present an overview of the SENSEI experiment and the current status after the successful commissioning of the second batch of science-grade sensors at SNOLAB. We will also discuss the prospects in rare-events searches with skipper-CCDs: from SENSEI’s 100 g detector to OSCURA’s 10 kg array, and more.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

The DUNE Near Detector

DUNE is a next-generation experiment aiming to provide precision measurements of neutrino oscillation parameters. It will detect neutrinos produced in the Long-Baseline Neutrino Facility beamline at Fermilab, using a Near Detector situated near the beam target where the neutrinos originate and a Far Detector located 1300 km away in South Dakota. A comparison of the spectra of neutrinos measured at the Far and the Near Detector will allow for the extraction of oscillation probabilities from which the oscillation parameters can be inferred. The specific role of the Near Detector is to serve as the experiment’s control: it will establish the no oscillation null hypothesis, measure and monitor the beam, constrain systematic uncertainties, and provide essential measurements of the neutrino interactions to improve models. The Near Detector complex will include three primary detector components: a liquid argon time projection chamber, a high-pressure gas time projection chamber and an on-axis beam monitor. The three detectors will serve important individual and overlapping functions, with two of them being also able to move transverse to the beam’s axis via the DUNE-PRISM program. The overall mission of the Near Detector, as well as the three sub-detectors’ unique capabilities and physics programs will be discussed in these proceedings.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

The SENSEI Experiment: sub-GeV dark matter searches with skipper-CCDs

Skipper-CCDs are pixeled Silicon-based detectors that can perform multiple non-disruptive measurements of the same charge package. Their sub-electron resolution allows the detection of eV energy transfers, such as that expected from ultra-light dark matter interacting with electrons in a Silicon target. SENSEI (Sub-Electron Noise Skipper Experimental Instrument) is the first experiment to use Skipper-CCD for this purpose and to publish world-leading results using this technology. In this talk, we present an overview of the SENSEI experiment and the current status after the successful commissioning of the second batch of science-grade sensors at SNOLAB. We will also discuss the prospects in rare-events searches with skipper-CCDs: from SENSEI’s 100 g detector to OSCURA’s 10 kg array, and more.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, a-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.

Arabidopsis, arogenate dehydratases, lignin, multi↗
DOE OSTI2021

New Orthophoto Generation Strategies from UAV and Ground Remote Sensing Platforms for High-Throughput Phenotyping

Remote sensing platforms have become an effective data acquisition tool for digital agriculture. Imaging sensors onboard unmanned aerial vehicles (UAVs) and tractors are providing unprecedented high-geometric-resolution data for several crop phenotyping activities (e.g., canopy cover estimation, plant localization, and flowering date identification). Among potential products, orthophotos play an important role in agricultural management. Traditional orthophoto generation strategies suffer from several artifacts (e.g., double mapping, excessive pixilation, and seamline distortions). The above problems are more pronounced when dealing with mid- to late-season imagery, which is often used for establishing flowering date (e.g., tassel and panicle detection for maize and sorghum crops, respectively). In response to these challenges, this paper introduces new strategies for generating orthophotos that are conducive to the straightforward detection of tassels and panicles. The orthophoto generation strategies are valid for both frame and push-broom imaging systems. The target function of these strategies is striking a balance between the improved visual appearance of tassels/panicles and their geolocation accuracy. The new strategies are based on generating a smooth digital surface model (DSM) that maintains the geolocation quality along the plant rows while reducing double mapping and pixilation artifacts. Moreover, seamline control strategies are applied to avoid having seamline distortions at locations where the tassels and panicles are expected. The quality of generated orthophotos is evaluated through visual inspection as well as quantitative assessment of the degree of similarity between the generated orthophotos and original images. Several experimental results from both UAV and ground platforms show that the proposed strategies do improve the visual quality of derived orthophotos while maintaining the geolocation accuracy at tassel/panicle locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Searching for Interstellar Quantum Communications

The modern search for extraterrestrial intelligence began with the seminal publications of Cocconi & Morrison and Schwartz & Townes, who proposed searching for narrowband signals in the radio spectrum and optical laser pulses. Over the last six decades, more than 100 dedicated search programs have targeted these wavelengths, all with null results. All of these campaigns searched for classical communications, that is, for a significant number of photons above a noise threshold, with the assumption of a pattern encoded in time and/or frequency space. I argue that future searches should also target quantum communications. They are preferred over classical communications with regard to security and information efficiency, and they would have escaped detection in all previous searches. The measurement of Fock state photons or squeezed light would indicate the artificiality of a signal. I show that quantum coherence is feasible over interstellar distances and explain for the first time how astronomers can search for quantum transmissions sent by ETI to Earth using commercially available telescopes and receiver equipment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Conceptual Design Report -- eSPS

The design of a primary electron beam facility at CERN is described. It re-enables the SPS as an electron accelerator, and leverages the development invested in CLIC technology for its injector and as accelerator R&D infrastructure. The facility would be relevant for several of the key priorities in the 2020 update of the European Strategy for Particle Physics, such as an electron-positron(e-p) Higgs factory, accelerator R&D, dark sector physics, and neutrino physics. In addition, it could serve experiments in nuclear physics. The electron beam delivered by this facility would provide access to light dark matter production significantly beyond the targets predicted by a thermal dark matter origin, and for natures of dark matter particles that are not accessible by direct detection experiments. It would also enable electro-nuclear measurements crucial for precise modelling the energy dependence of neutrino-nucleus interactions, which is needed to precisely measure neutrino oscillations as a function of energy. The implementation of the facility is the natural next step in the development of X-band high-gradient acceleration technology, a key technology for compact and cost-effective electron/positron linacs. It would also become the only facility with multi-GeV drive bunches and truly independent electron witness bunches for plasma wakefield acceleration. The facility would be used for the development and studies of a large number of components and phenomena for a future e-p Higgs and electroweak factory as the first stage of a next circular collider at CERN, and its cavities in the SPS would be the same type as foreseen for such a future collider. The operation of the SPS with electrons would train a new generation of scientists. The facility could be made operational in about five years and would operate in parallel and without interference with Run 4 at the LHC.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Studies on the scintillation light detection in the ProtoDUNE Dual Phase liquid-argon TPC and its capability for the supernova trigger in DUNE

The Deep Underground Neutrino Experiment (DUNE) is a long-baseline neutrino oscillation experiment that aims at addressing key questions in neutrino physics in the next decades. Its scientific program includes the detection of the neutrino flux from a core-collapse supernova. The DUNE far detector will have four 17-kt mass liquid-argon (LAr) time-projection chamber (TPC) modules. ProtoDUNE Dual Phase (DP), a dual-phase LAr TPC with 300 t of active mass and 6 m of drift distance, was operated with cosmic muons in 2019-2020 as part of an R&D program at the CERN Neutrino Platform to demonstrate the feasibility of the technology at such a large scale. In a LAr TPC, the photon detection system (PDS) provides fundamental timing information and trigger capabilities. The PDS of ProtoDUNE-DP, which consisted of 36 photomultiplier tubes (PMTs), counted on a dedicated light calibration system (LCS) to monitor the PMT response. In this dissertation, the characterization and validation of the ProtoDUNE-DP PDS and LCS components before their installation will be reviewed, highlighting the results of general interest for experiments that use liquid noble gasses as target medium. The results from the stable performance of both systems in the detector during 15 months will be presented next as well as the studies on the scintillation light detection in ProtoDUNE-DP, where the collection of light produced in LAr at 7 m from the photosensors has been achieved for the first time. It is worth pointing out that the excellent LAr purity and the large size of the detector have enabled to develop a unique data-driven investigation on aspects that are critical for LAr-based experiments but that are not completely understood. The analyses cover the characterization of the low-energy background detected by the PDS, the quantification of the electric field impact on the light yield, the evaluation of the Rayleigh scattering affecting the light propagation, and the analysis of the PMT detection efficiency. The effect of the VUV reflectivity of the detector materials will be also discussed. In addition, the estimation of the cosmic muon flux crossing the TPC and the study of the observed light yield by the PDS will be reported. Finally, the results from the simulation-based study of the supernova burst trigger capability with the PDS of a 12.1-kt active mass dual-phase LAr TPC as the one proposed for DUNE will be summarized. Several configurations of reflective foils installed in the TPC to enhance the light collection will be compared.

Gallego Ros, Ana↗
DOE OSTI2021

Studies on the scintillation light detection in the ProtoDUNE Dual Phase liquid-argon TPC and its capability for the supernova trigger in DUNE

The Deep Underground Neutrino Experiment (DUNE) is a long-baseline neutrino oscillation experiment that aims at addressing key questions in neutrino physics in the next decades. Its scientific program includes the detection of the neutrino flux from a core-collapse supernova. The DUNE far detector will have four 17-kt mass liquid-argon (LAr) time-projection chamber (TPC) modules. ProtoDUNE Dual Phase (DP), a dual-phase LAr TPC with 300 t of active mass and 6 m of drift distance, was operated with cosmic muons in 2019-2020 as part of an R&D program at the CERN Neutrino Platform to demonstrate the feasibility of the technology at such a large scale. In a LAr TPC, the photon detection system (PDS) provides fun- damental timing information and trigger capabilities. The PDS of ProtoDUNE-DP, which consisted of 36 photomultiplier tubes (PMTs), counted on a dedicated light calibration system (LCS) to monitor the PMT response. In this dissertation, the characterization and validation of the ProtoDUNE-DP PDS and LCS components before their installation will be reviewed, highlighting the results of general interest for experiments that use liquid noble gasses as target medium. The results from the stable performance of both systems in the detector during 15 months will be presented next as well as the studies on the scintillation light detection in ProtoDUNE-DP, where the collection of light produced in LAr at 7 m from the photosensors has been achieved for the first time. It is worth pointing out that the excellent LAr purity and the large size of the detector have enabled to develop a unique data-driven investigation on aspects that are critical for LAr- based experiments but that are not completely understood. The analyses cover the characterization of the low-energy background detected by the PDS, the quantification of the electric field impact on the light yield, the evaluation of the Rayleigh scattering affecting the light propagation, and the analysis of the PMT detection efficiency. The effect of the VUV reflectivity of the detector materials will be also discussed. In addition, the estimation of the cosmic muon flux crossing the TPC and the study of the observed light yield by the PDS will be reported. Finally, the results from the simulation-based study of the supernova burst trigger capability with the PDS of a 12.1-kt active mass dual-phase LAr TPC as the one proposed for DUNE will be summarized. Several configurations of reflective foils installed in the TPC to enhance the light collection will be compared

Gallego-Ros, Ana↗