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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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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Efficient DNA sequence compression with neural networks

Abstract Background The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models. Findings We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7–3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art. Conclusions GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.

Silva, Milton↗
DOE OSTI2020

Automatic microseismic event picking via unsupervised machine learning

SUMMARY Effective and efficient arrival picking plays an important role in microseismic and earthquake data processing and imaging. Widely used short-term-average long-term-average ratio (STA/LTA) based arrival picking algorithms suffer from the sensitivity to moderate-to-strong random ambient noise. To make the state-of-the-art arrival picking approaches effective, microseismic data need to be first pre-processed, for example, removing sufficient amount of noise, and second analysed by arrival pickers. To conquer the noise issue in arrival picking for weak microseismic or earthquake event, I leverage the machine learning techniques to help recognizing seismic waveforms in microseismic or earthquake data. Because of the dependency of supervised machine learning algorithm on large volume of well-designed training data, I utilize an unsupervised machine learning algorithm to help cluster the time samples into two groups, that is, waveform points and non-waveform points. The fuzzy clustering algorithm has been demonstrated to be effective for such purpose. A group of synthetic, real microseismic and earthquake data sets with different levels of complexity show that the proposed method is much more robust than the state-of-the-art STA/LTA method in picking microseismic events, even in the case of moderately strong background noise.

Chen, Yangkang↗
DOE OSTI2022

The essential character of the neutrino mechanism of core-collapse supernova explosions

Abstract Calibrating with detailed 2D core-collapse supernova (CCSN) simulations, we derive a simple CCSN explosion condition based solely upon the terminal density profiles of state-of-the-art stellar evolution calculations of the progenitor massive stars. This condition captures the vast majority of the behaviour of the one hundred 2D state-of-the-art models we performed to gauge its usefulness. The goal is to predict, without resort to detailed simulation, the explodability of a given massive star. We find that the simple maximum fractional ram pressure jump discriminant we define works well ∼90 per cent of the time and we speculate on the origin of the few false positives and false negatives we witness. The maximum ram pressure jump generally occurs at the time of accretion of the silicon/oxygen interface, but not always. Our results depend upon the fidelity with which the current implementation of our code F ornax adheres to Nature and issues concerning the neutrino–matter interaction, the nuclear equation of state, the possible effects of neutrino oscillations, grid resolution, the possible role of rotation and magnetic fields, and the accuracy of the numerical algorithms employed remain to be resolved. Nevertheless, the explodability condition we obtain is simple to implement, shows promise that it might be further generalized while still employing data from only the unstable Chandrasekhar progenitors, and is a more credible and robust simple explosion predictor than can currently be found in the literature.

Astronomy & Astrophysics↗
DOE OSTI2021

Unified model of short- and long-term HIV viral rebound for clinical trial planning

Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. Typically suspension of therapy is rapidly followed by rebound of viral loads to high, pre-therapy levels. Indeed, a recent study showed that approximately 90% of treatment interruption study participants show viral rebound within at most a few months of therapy suspension, but the remaining 10%, showed viral rebound some months, or years, after ART suspension. Some may even never rebound. We investigate and compare branching process models aimed at gaining insight into these viral dynamics. Specifically, we provide a theory that explains both short- and long-term viral rebounds, and post-treatment control, via a multitype branching process with time-inhomogeneous rates, validated with data from Li et al. We discuss the associated biological interpretation and implications of our best-fit model. To test the effectiveness of an experimental intervention in delaying or preventing rebound, the standard practice is to suspend therapy and monitor the study participants for rebound. We close with a discussion of an important application of our modelling in the design of such clinical trials.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Clock Precision beyond the Standard Quantum Limit at 10 −18 Level

Optical atomic clocks with unrivaled precision and accuracy have advanced the frontier of precision measurement science and opened new avenues for exploring fundamental physics. A fundamental limitation on clock precision is the standard quantum limit (SQL), which stems from the uncorrelated projection noise of each atom. State-of-the-art optical lattice clocks interrogate large ensembles to minimize the SQL, but density-dependent frequency shifts pose challenges to scaling the atom number. The SQL can be surpassed, however, by leveraging entanglement, though it remains an open problem to achieve quantum advantage from spin squeezing at state-of-the-art stability levels. Here, we demonstrate clock performance beyond the SQL, achieving a fractional frequency precision of 1.1 × 10 −18 for a single spin-squeezed clock. With cavity-based quantum nondemolition measurements, we prepare two spin-squeezed ensembles of ∼30 000 strontium atoms confined in a two-dimensional optical lattice. A synchronous clock comparison with an interrogation time of 61 ms achieves a metrological improvement of 2.0(2) dB beyond the SQL, after correcting for state preparation and measurement errors. These results establish the most precise entanglement-enhanced clock to date and offer a powerful platform for exploring the interplay of gravity and quantum entanglement.

cavity quantum electrodynamics↗
DOE OSTI2025

Evidence for large baryonic feedback at low and intermediate redshifts from kinematic Sunyaev-Zel’dovich observations with ACT and DESI photometric galaxies

Recent advances in cosmological observations have provided an unprecedented opportunity to investigate the distribution of baryons relative to the underlying matter. In this work, we show that the gas is more extended than the dark matter, and the amount of baryonic feedback at $z \lesssim 1$ disfavors low-feedback models such as that of state-of-the-art hydrodynamical simulation IllustrisTNG compared with high-feedback models such as that of the original Illustris simulation. This has important implications for bridging the gap between theory and observations and understanding galaxy formation and evolution. Furthermore, a better grasp of the baryon-dark matter link is critical to future cosmological analyses, which are currently impeded by our limited knowledge of baryonic feedback. Here, we measure the kinematic Sunyaev-Zel'dovich (kSZ) effect from the Atacama Cosmology Telescope (ACT), stacked on the luminous red galaxy (LRG) sample of the Dark Energy Spectroscopic Instrument (DESI) imaging survey. This is the first analysis to use photometric redshifts for reconstructing galaxy velocities. Due to the large number of galaxies comprising the DESI imaging survey, this is the highest signal-to-noise stacked kSZ measurement to date: we detect the signal at 13$σ$, finding strong evidence that the gas is more spread out than the dark matter, as well as a preference for larger feedback compared to some commonly used state-of-the-art hydrodynamical simulations. Here, our work opens up the possibility of recalibrating large hydrodynamical simulations using the kSZ effect. In addition, our findings highlight the importance of properly accounting for baryonic feedback with future surveys such as LSST through direct probes such as the kSZ, and shed light on long-standing enigmas in astrophysics, such as the “missing baryon” problem.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Comparison of spontaneous emission in trapped-ion multiqubit gates at high magnetic fields

Penning traps have been used for performing quantum simulations and sensing with hundreds of ions and provide a promising route toward scaling up trapped ion quantum platforms because of the ability to trap and control hundreds or thousands of ions in two- and three-dimensional crystals. In both Penning traps and the more common RF Paul traps, lasers are often used to drive multi-qubit entangling operations. A leading source of decoherence in these operations is off resonant spontaneous emission. While many trapped ion quantum computers or simulators utilize clock qubits, other systems, especially those with high magnetic fields such as Penning traps, rely on Zeeman qubits, which require a more complex calculation of this decoherence. We therefore examine theoretically the impacts of spontaneous emission on quantum gates performed with trapped-ion ground state Zeeman qubits in a high magnetic field. In particular, we consider two types of gates—light-shift ($\hat{σ}^z_i$ $\hat{σ}^z_j$) gates and Mølmer-Sørensen ($\hat{σ}^x_i$ $\hat{σ}^x_j$) gates—obtained with laser beams directed approximately perpendicular to the magnetic field (the quantization axis) and compare the decoherence errors in each. Within each gate type, we also compare different operating points with regards to the detunings, polarizations, and required intensity of the laser beams used to drive the gates. Here, we show that both gates can have similar performance at their optimal operating conditions at high magnetic fields and examine the experimental feasibility of various operating points. By examining the magnetic field dependence of each gate, we demonstrate that, when the P state fine structure splitting is large compared to the Zeeman splittings, the theoretical performance of the Mølmer-Sørensen gate is significantly better than that of the light-shift gate. Additionally, for the light-shift gate, we make an approximate comparison between the fidelities that can be achieved at high fields with the fidelities of state-of-the-art two-qubit trapped ion quantum gates. We show that, with regards to spontaneous emission, the achievable fidelity of the current NIST configuration is about an order of magnitude below that of the best low-field gates, but we also discuss several alternative configurations with potential error rates that are comparable with those for state-of-the art trapped ion gates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Electronic structure and lattice dynamics of 1⁢𝑇−VSe 2 : Origin of the three-dimensional charge density wave

To characterize in detail the charge density wave (CDW) transition of 1⁢𝑇−VSe 2 , its electronic structure and lattice dynamics are comprehensively studied by means of x-ray diffraction, muon spectroscopy, angle resolved photoemission (ARPES), diffuse and inelastic x-ray scattering, and state-of-the-art first-principles density functional theory calculations. Resonant elastic x-ray scattering does not show any resonant enhancement at either V or Se, indicating that the CDW peak at the 𝐾 edges describes a purely structural modulation of the electronic ordering. ARPES experiments identify (i) a pseudogap at 𝑇 > 𝑇⁢ CDW , which leads to a depletion of the density of states in the ML-M'L' plane at 𝑇 < 𝑇⁢ CDW , and (ii) anomalies in the electronic dispersion reflecting a sizable impact of phonons on it. A diffuse scattering precursor, characteristic of soft phonons, is observed at room temperature (RT) and leads to the full collapse of the low-energy phonon (𝜔 1 ) with propagation vector (0.25 0 −0.3) r.l.u. Here, we show that the frequency and linewidth of this mode are anisotropic in momentum space, reflecting the momentum dependence of the electron-phonon interaction (EPI), hence demonstrating that the origin of the CDW is, to a much larger extent, due to the momentum dependent EPI with a small contribution from nesting. The pressure dependence of the 𝜔 1 soft mode remains nearly constant up to 13 GPa at RT, with only a modest softening before the transition to the high-pressure monoclinic C2/m phase. The wide set of experimental data is well captured by our state-of-the art first-principles anharmonic calculations with the inclusion of van der Waals corrections in the exchange-correlation functional. The comprehensive description of the electronic and dynamical properties of VSe 2 reported here adds important pieces of information to the understanding of the electronic modulations in the family of transition-metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Lifetime measurements of states of S 35 , S 36 , S 37 , and S 38 using the AGATA γ -ray tracking spectrometer

Lifetimes or lifetime limits of a small number of excited states of the sulfur isotopes with mass numbers A = 35 , 36, 37, and 38 have been measured using the differential recoil-distance method. The isotopes of sulfur were populated in binary grazing reactions initiated by a beam of 36 S ions of energy 225 MeV incident on a thin 208 Pb target which was mounted in the Cologne plunger apparatus. The combination of the PRISMA magnetic spectrometer and an early implementation of the AGATA γ-ray tracking array was used to detect γ rays in coincidence with projectile-like nuclear species. Lifetime measurements of populated states were measured within the range from about 1 to 100 ps. The number of states for which lifetime measurements or lifetime limits were possible was limited by statistics. For 35 S, the lifetime was determined for the first 1/2 + state at 1572 keV; the result is compared with a previous published lifetime value. The lifetime of the 3 - state of 36 S at 4193 keV was determined and compared with earlier measurements. No previous lifetime information exists for the (6 + ) state at 6690 keV; a lifetime measurement with large associated error was made in the present work. For 37 S, the states for which lifetime limits were established were those at 646 keV with J π = 3/2 - and at 2776 keV with J π = 11/2 - ; there are no previously published lifetime values for excited states of 37 S. Finally, a lifetime limit was established for the J π =(6 + ) state of 38 S at 3675 keV; no lifetime information exists for this state in the literature. Measured lifetime values were compared with the results of state-of-the-art shell-model calculations based on the PSDPF, SDPF-U, and FSU effective interactions. In addition, nuclear magnetic-dipole and electric-quadrupole moments, branching ratios, mixing ratios, and electromagnetic transition rates, where available, have been compared with shell-model values. The current work suffers from poor statistics; nevertheless, lifetime values and limits have been possible, allowing a useful discussion of the ability of state-of-the-art shell-model calculations to reproduce the experimental results.

electromagnetic transitions↗
DOE OSTI2023

Fast and accurate simulations of calorimeter showers with normalizing flows

In this study, we introduce caloflow, a fast detector simulation framework based on normalizing flows. For the first time, we demonstrate that normalizing flows can reproduce many-channel calorimeter showers with extremely high fidelity, providing a fresh alternative to computationally expensive geant4 simulations, as well as other state-of-the-art fast simulation frameworks based on generative adversarial networks (GANs) or variational autoencoders (VAEs). In addition to the usual histograms of physical features and images of calorimeter showers, we introduce a new metric for judging the quality of generative modeling: the performance of a classifier trained to differentiate real from generated images. We show that GAN-generated images can be identified by the classifier with nearly 100% accuracy, while images generated from caloflow are better able to fool the classifier. More broadly, normalizing flows offer several advantages compared to other state-of-the-art approaches (GANs and VAEs), including tractable likelihoods, stable and convergent training, and principled model selection. Normalizing flows also provide a bijective mapping between data and the latent space, which could have other applications beyond simulation, for example, to detector unfolding.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Accelerating accurate simulations of calorimeter showers with normalizing flows and probability density distillation

Recently, we introduced caloflow, a high-fidelity generative model for GEANT4 calorimeter shower emulation based on normalizing flows. Here, we present caloflow v2, an improvement on our original framework that speeds up shower generation by a further factor of 500 relative to the original. The improvement is based on a technique called probability density distillation, originally developed for speech synthesis in the machine learning literature, and which we develop further by introducing a set of powerful new loss terms. We demonstrate that caloflow v2 preserves the same high fidelity as the original using qualitative (average images, histograms of high-level features) and quantitative (classifier metric between geant4 and generated samples) measures. The result is a generative model for calorimeter showers that matches the state of the art in speed (a factor of 10 4 faster than GEANT4) and greatly surpasses the previous state of the art in fidelity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Investigation of fast and efficient lossless compression algorithms for macromolecular crystallography experiments

Structural biology experiments benefit significantly from state-of-the-art synchrotron data collection. One can acquire macromolecular crystallography (MX) diffraction data on large-area photon-counting pixel-array detectors at framing rates exceeding 1000 frames per second, using 200 Gbps network connectivity, or higher when available. In extreme cases this represents a raw data throughput of about 25 GB s −1 , which is nearly impossible to deliver at reasonable cost without compression. Our field has used lossless compression for decades to make such data collection manageable. Many MX beamlines are now fitted with DECTRIS Eiger detectors, all of which are delivered with optimized compression algorithms by default, and they perform well with current framing rates and typical diffraction data. However, better lossless compression algorithms have been developed and are now available to the research community. Here one of the latest and most promising lossless compression algorithms is investigated on a variety of diffraction data like those routinely acquired at state-of-the-art MX beamlines.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Sentiment Analysis based Error Detection for Large-Scale Systems

Today's large-scale systems such as High Performance Computing (HPC) Systems are designed/utilized towards exascale computing, inevitably decreasing its reliability due to the increasing design complexity. HPC systems conduct extensive logging of their execution behaviour. In this paper, we leverage the inherent meaning behind the log messages and propose a novel sentiment analysis-based approach for the error detection in large-scale systems, by automatically mining the sentiments in the log messages. Our contributions are four-fold. (1) We develop a machine learning (ML) based approach to automatically build a sentiment lexicon, based on the system log message templates. (2) Using the sentiment lexicon, we develop an algorithm to detect system errors. (3) We develop an algorithm to identify the nodes and components with erroneous behaviors, based on sentiment polarity scores. (4) We evaluate our solution vs. other state-of-the-art machine/deep learning algorithms based on three representative supercomputers' system logs. Experiments show that our error detection algorithm can identify error messages with an average MCC score and f -score of 91% and 96% respectively, while state of the art ML/deep learning model (LSTM) obtains only 67% and 84%. To the best of our knowledge, this is the first work leveraging the sentiments embedded in log entries of large-scale systems for system health analysis.

error detection↗
DOE OSTI2022

GCoD: Graph Convolutional Network Acceleration via Dedicated Algorithm and Accelerator Co-Design

Graph Convolutional Networks (GCNs) have emerged as the state-of-the-art graph learning model. However, it remains notoriously challenging to inference GCNs over large graph datasets, limiting their application to large real-world graphs and hindering the exploration of deeper and more sophisticated GCN graphs. This is because real-world graphs can be extremely large and sparse. Furthermore, the node degree of GCNs tends to follow the power-law distribution and therefore have highly irregular adjacency matrices, resulting in prohibitive inefficiencies in both data processing and movement and thus substantially limiting the achievable GCN acceleration efficiency. To this end, this paper proposes the first GCN algorithm and accelerator Co-Design framework dubbed GCoD which can largely alleviate the aforementioned GCN irregularity and boost GCNs' inference efficiency. Specifically, on the algorithm level, GCoD integrates a divide and conquer GCN training strategy that polarizes the graphs to be either denser or sparser in local neighborhoods without compromising the model accuracy, resulting in graph adjacency matrices that (mostly) have merely two levels of workload and enjoys largely enhanced regularity and thus ease of acceleration. On the hardware level, we further develop a dedicated two-pronged accelerator with a separated engine to process each of the aforementioned workloads, further boosting the overall utilization and acceleration efficiency. Extensive experiments and ablation studies validate that our GCoD consistently outperforms state-of-the-art designs in terms of accelerator efficiency while maintaining or even improving the task accuracy. Additionally, we visualize GCoD trained graph adjacency matrices to better understand its advantages. All codes and pre-trained models will be released upon acceptance.

You, Haoran↗
DOE OSTI2023

Towards Efficient Alternating Current Optimal Power Flow Analysis on Graphical Processing Units

We present a solution of sparse ACOPF analysis on GPU. In particular, we discuss the performance bottlenecks and detail our efforts to accelerate the linear solver, a core component of ACOPF that dominates the computational time. ACOPF solutions of two large-scale systems, synthetic Northeast (25,000 buses) and Eastern (70,000 buses) \cite{birchfield2017tamu-cases} on GPU show promising speed-up compared to CPU based solution using a state-of-the-art solver. To our knowledge, this is the first result demonstrating acceleration of sparse ACOPF on GPUs.

Power grid analysis, GPU↗
DOE OSTI2024

Demystifying Cyberattacks: Potential for Securing Energy Systems With Explainable AI : Preprint

Modernization of energy systems has led to in- creased interactions among multiple critical infrastructures and diverse stakeholders making the challenge of operational decision making more complex and at times beyond cognitive capabilities of human operators. The state-of-the-art machine learning and deep learning approaches show promise of supporting users with complex decision-making challenges, such as those occurring in our rapidly transforming cyber-physical energy systems. However, successful adoption of data-driven decision support technology for critical infrastructure will be dependent on the ability of these technologies to be trustworthy and contextually interpretable. In this paper, we investigate the feasibility of implementing XAI for interpretable detection of cyberattacks in the energy system. Leveraging a proof-of-concept simulation use case of detection of a data falsification attack on a photovoltaic system using XGBoost algorithm, we demonstrate how Local Interpretable Model-Agnostic Explanations (LIME), a flavor XAI approach, can help provide contextual and actionable interpretation of cyberattack detection.

artificial intelligence↗
DOE OSTI2020

Modeling Needs for Power Semiconductor Devices and Power Electronics Systems: Preprint

As energy systems move towards wide-spread electrification, penetration of power semiconductor devices and power electronics continues to grow at a rapid pace. This paper attempts to review the state of the art in power semiconductor modeling and the existing state of modeling in general when in it comes to design of devices and systems. The modeling needs for semiconductor devices vary depending on the end goal, and the level of abstraction needed towards model formulation also changes with the size and complexity of system to be designed. Finally, key aspects of thermal design and modeling for power electronics are also discussed.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗