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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A hidden Markov model for population-level cervical cancer screening data

The Cancer Registry of Norway has been administrating a national cervical cancer screening program since 1992 by coordinating triennial cytology exam screenings for the female population between 25 and 69 years of age. Up to 80% of cancers are prevented through mass screening, but this comes at the expense of considerable screening activity and leads to overtreatment of clinically asymptomatic precancers. Here, we present a continuous-time, time-inhomogeneous hidden Markov model which was developed to understand the screening process and cervical cancer carcinogenesis in detail. By leveraging 1.7 million individual's multivariate time-series of medical exams performed over a 25-year period, we simultaneously estimate all model parameters. We show that an age-dependent model reflects the Norwegian screening program by comparing empirical survival curves from observed registry data and data simulated from the proposed model. The model can be generalized to include more detailed individual-level covariates as well as new types of screening exams. By utilizing individual screening histories and covariate data, the proposed model shows potential for improving strategies for cancer screening programs by personalizing recommended screening intervals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models

Abstract Background Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER. Results The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a $$\sim$$ ∼ $3000 Xilinx Alveo U50 FPGA accelerator card, $$\sim$$ ∼ 227× faster than the optimized SSV implementation in nhmmer . Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer’s SSV with one thread and 35× faster than nhmmer with four threads, and uses $$\sim$$ ∼ 31% the energy of a traditional high end Intel CPU. Conclusions HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes

Objective: Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. Results: In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Classification of Photovoltaic Failures with Hidden Markov Modeling, an Unsupervised Statistical Approach

Failure detection methods are of significant interest for photovoltaic (PV) site operators to help reduce gaps between expected and observed energy generation. Current approaches for field-based fault detection, however, rely on multiple data inputs and can suffer from interpretability issues. In contrast, this work offers an unsupervised statistical approach that leverages hidden Markov models (HMM) to identify failures occurring at PV sites. Using performance index data from 104 sites across the United States, individual PV-HMM models are trained and evaluated for failure detection and transition probabilities. This analysis indicates that the trained PV-HMM models have the highest probability of remaining in their current state (87.1% to 93.5%), whereas the transition probability from normal to failure (6.5%) is lower than the transition from failure to normal (12.9%) states. A comparison of these patterns using both threshold levels and operations and maintenance (O&M) tickets indicate high precision rates of PV-HMMs (median = 82.4%) across all of the sites. Although additional work is needed to assess sensitivities, the PV-HMM methodology demonstrates significant potential for real-time failure detection as well as extensions into predictive maintenance capabilities for PV.

classification↗
NASA NTRS1994

(abstract) Modeling Protein Families and Human Genes: Hidden Markov Models and a Little Beyond

We will first give a brief overview of Hidden Markov Models (HMMs) and their use in Computational Molecular Biology. In particular, we will describe a detailed application of HMMs to the G-Protein-Coupled-Receptor Superfamily. We will also describe a number of analytical results on HMMs that can be used in discrimination tests and database mining. We will then discuss the limitations of HMMs and some new directions of research. We will conclude with some recent results on the application of HMMs to human gene modeling and parsing.

Hidden Markov Models HMMs proteins computational m↗
DOE OSTI2022

Finding Hidden Patterns in High Resolution Wind Flow Model Simulations

Wind flow data is critical in terms of investment decisions and policy making. High resolution data from wind flow model simulations serve as a supplement to the limited resource of original wind flow data collection. Given the large size of data, finding hidden patterns in wind flow model simulations are critical for reducing the dimensionality of the analysis. In this work, we first perform dimension reduction with two autoencoder models: the CNN-based autoencoder (CNN-AE) [1], and hierarchical autoencoder (HIER-AE) [2], and compare their performance with the Principal Component Analysis (PCA). We then investigate the super-resolution of the wind flow data. By training a Generative Adversarial Network (GAN) with 300 epochs, we obtained a trained model with 2× resolution enhancement. We compare the results of GAN with Convolutional Neural Network (CNN), and GAN results show finer structure as expected in the data field images. Also, the kinetic energy spectra comparisons show that GAN outperforms CNN in terms of reproducing the physical properties for high wavenumbers and is critical for analysis where high-wavenumber kinetics play an important role.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A Right-handed neutrino portal to the hidden sector: active neutrinos and their twins in an F-theory model

We analyze the neutrino phenomenology in an SU(5) F-theory model with both a visible sector and a twin hidden sector. At low energies, the strong and weak scales of the two sectors may differ but the spectrum of states is described by the MSSM (MSSM') in the visible (twin) sectors. What is special about the model is that there are right-handed neutrinos which couple to both sectors via Yukawa couplings. As a result, assuming 3 right-handed neutrinos with a large mass much greater than the weak scale, at tree-level the seesaw mechanism results in 3 massive Majorana neutrinos and 3 massless ones. The massless neutrinos acquire mass via radiative corrections. In our analysis, the massless neutrinos are predominantly active neutrinos, while the massive neutrinos are predominantly sterile neutrinos. We fit the active neutrino masses and mixing angles and discuss the phenomenology of the lightest sterile neutrino. Finally we consider some possible scenarios for cosmology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Spinning black hole scattering at $ \mathcal{O} $(G 3 S 2 )(G 3 S 2 ): Casimir terms, radial action and hidden symmetry

We resolve subtleties in calculating the post-Minksowskian dynamics of binary systems, as a spin expansion, from massive scattering amplitudes of fixed finite spin. In particular, the apparently ambiguous spin Casimir terms can be fully determined from the gradient of the spin-diagonal part of the amplitudes with respect to S 2 = −s(s+1)ħ 2 , using an interpolation between massive amplitudes with different spin representations. From two-loop amplitudes of spin-0 and spin-1 particles minimally coupled to gravity, we extract the spin Casimir terms in the conservative scattering angle between a spinless and a spinning black hole at $ \mathcal{O} $(G 3 S 2 ), finding agreement with known results in the literature. This completes an earlier study [Phys. Rev. Lett. 130 (2023), 021601] that calculated the non-Casimir terms from amplitudes. We also illustrate our methods using a model of spinning bodies in electrodynamics, finding agreement between scattering amplitude predictions and classical predictions in a root-Kerr electromagnetic background up to $ \mathcal{O} $(α 3 S 2 ). For both gravity and electrodynamics, the finite part of the amplitude coincides with the two-body radial action in the aligned spin limit, generalizing the amplitude-action relation beyond the spinless case. Surprisingly, the two-loop amplitude displays a hidden spin-shift symmetry in the probe limit, which was previously observed at one loop. We conjecture that the symmetry holds to all orders in the coupling constant and is a consequence of integrability of Kerr orbits in the probe limit at the first few orders in spin.

Classical Theories of Gravity↗
DOE OSTI2023

Hidden symmetry in the double copy

We show that the Killing tensor of the Kerr spacetime has an analogue in the $\sqrt{Kerr}$ gauge theory solution related to it by the classical double copy. This hidden symmetry of $\sqrt{Kerr}$ leads to an additional constant of motion for color-charged point particles moving in it, implying integrability of the equation of motion. These are the gauge theory counterparts to the Carter constant and the integrability of the geodesic equation in a Kerr background.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Observation of muonic Dalitz decays of chib mesons and precise spectroscopy of hidden-beauty states

The decays of the χb1 (1P), χb2 (1P), χb1 (2P) and χb2 (2P) mesons into the Υ(1S)μ + μ − final state are observed with a high significance using proton-proton collision data collected with the LHCb detector and corresponding to an integrated luminosity of 9 fb −1 . The newly observed decays together with the Υ(2S) → Υ(1S)π + π − and Υ(3S) → Υ(2S)π+π− decay modes are used for precision measurements of the mass and mass splittings for the hidden-beauty states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Hidden symmetries, spin and charge of artificial magnetic monopoles

Here, we discuss the non-Abelian artificial magnetic monopoles associated with n-level energy crossing in quantum systems. We found that hidden symmetries reveal themselves as observables such as spin, hypercharge, and other physical degrees of freedom. We illustrated our results on concrete examples of two and three energy-level crossings. Our findings can be helpful for modeling various phenomena in physical systems such as SU(N) topological insulators and spintronic devices based on topological insulators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Hidden Killing fields, geometric symmetries and black hole mergers

Highlights: • Construction of geometric models with a variable degree of symmetry. • Formulation of Energy and Momentum Balance Laws. • Description of backreactions on spacetime geometries caused by dissipative effects. • Analytic description of accretion and/or merger processes in GR. • Exact model for the merger of two extremal Reissner–Nordström black holes. In the present work, using the recently introduced framework of local geometric deformations, special types of vector fields – so-called hidden Killing vector fields – are constructed, which solve the Killing equation not globally, but only locally, i.e. in local subregions of spacetime. Taking advantage of the fact that the vector fields coincide locally with Killing fields and therefore allow the consideration of integral laws that convert into exact physical conservation laws on local scales, balance laws in dynamical systems without global Killing symmetries are derived that mimic as closely as possible the conservation laws for energy and angular momentum of highly symmetric models. The utility of said balance laws is demonstrated by a concrete geometric example, namely a toy model for the binary merger of two extremal Reissner–Nordström black holes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Plant synthetic biology as a tool to help eliminate hidden hunger

Agricultural systems are under increasing pressure from declining environmental conditions, a growing population, and changes in consumer preferences, resulting in widespread malnutrition-related illnesses. Improving plant nutritional content through biotechnology techniques such as synthetic biology is a promising strategy to help combat hidden hunger caused by the lack of affordable and healthy foods in human diets. Production of compounds usually found in animal-rich diets, such as vitamin D or omega-3 fatty acids, has been recently demonstrated in planta. Here, we review recent biotechnological approaches to biofortifying plants with vitamins, minerals, and other metabolites, and summarise synthetic biology advances that offer the opportunity to build on these early biofortification efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

QCD hidden-color hexadiquark in the core of nuclei

Hidden-color configurations are a key prediction of QCD with important physical consequences. In this work we examine a QCD color-singlet configuration in nuclei formed by combining six scalar [ud] diquarks in a strongly bound SU (3) C channel. The resulting hexadiquark state is a charge-2, spin-0, baryon number-4, isospin-0, color-singlet state. It contributes to alpha clustering in light nuclei and to the additional binding energy not saturated by ordinary nuclear forces in as well as the alpha-nuclei sequence of interest for nuclear astrophysics. We show that the strongly bound combination of six scalar isospin-0 [ud] diquarks within the nuclear wave function - relative to free nucleons - provides a natural explanation of the EMC effect measured by the CLAS collaboration's comparison of nuclear parton distribution function ratios for a large range of nuclei. Overall, these experiments confirmed that the EMC effect; i.e., the distortion of quark distributions within nuclei, is dominantly identified with the dynamics of neutron-proton (“isophobic”) short-range correlations within the nuclear wave function rather than proton-proton or neutron-neutron correlations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

The hidden structure of hydrodynamic transport in random fracture networks

We study the large-scale dynamics and prediction of hydrodynamic transport in random fracture networks. The flow and transport behaviour is characterized by first passage times and displacement statistics, which show heavy tails and anomalous dispersion with a strong dependence on the injection condition. The origin of these behaviours is investigated in terms of Lagrangian velocities sampled equidistantly along particle trajectories, unlike classical sampling strategies at a constant rate. The velocity series are analysed by their copula density, the joint distribution of the velocity unit scores, which reveals a simple, albeit hidden, correlation structure that can be described by a Gaussian copula. Based on this insight, we derive a Langevin equation for the evolution of equidistant particle speeds. In this framework, particle motion is quantified by a stochastic time-domain random walk, the joint density of particle position, and speed satisfies a Klein–Kramers equation. The upscaled theory quantifies particle motion in terms of the characteristic fracture length scale and the distribution of Eulerian flow velocities. That is, it is predictive in the sense that it does not require the a priori knowledge of transport attributes. The upscaled model captures non-Fickian transport features, and their dependence on the injection conditions in terms of the velocity point statistics and average fracture length. It shows that the first passage times and displacement moments are dominated by extremes occurring at the first step. The presented approach integrates the interaction of flow and structure into a predictive model for large-scale transport in random fracture networks.

42 ENGINEERING↗
DOE OSTI2026

Prelithiated SiO x /Graphite-NMC811 Cells: Capacity Loss, Impedance Rise and Hidden Degradation Pathways Revealed Using Three-Electrode Diagnostics

Electrodes containing SiO x /graphite (Gr) materials are attractive as anodes for high-energy lithium-ion batteries. However, their mechanical deformation, electrochemical response, and impedance evolution during long-term cycling are strongly coupled, complicating accurate diagnosis of performance fade mechanisms. In this work, the behavior of electrochemically prelithiated SiO x /Gr anodes paired with NMC811 cathodes is systematically investigated using techniques that include in-situ dilatometry, three-electrode electrochemistry, and multiscale post-cycling microscopy. The SiO x /Gr electrode exhibits a maximum expansion of 49% upon lithiation to 10 mV vs Li + /Li, with 84% of the expansion and 91% of the capacity being reversible. In full cells, relatively stable cycling with only 12% capacity fade over 500 cycles is observed. Three-electrode experiments reveal cell-level impedance growth, which is dominated by the NMC811 cathode: the SiO x /Gr anode exhibits minimal net impedance rise and an initial impedance decrease at low potentials. Despite this apparent electrochemical stability, cross-sectional SEM, PFIB tomography, and cryo-STEM reveal irreversible anode thickening caused by the accumulation of an inorganic-rich solid electrolyte interphase (SEI) permeating the anode bulk. Electrode potential-shift analysis further demonstrates that Li + ions released from lithium reservoirs in the prelithiated anode mask true lithium inventory loss during aging. These results demonstrate that low-expansion SiO x /Gr anodes can simultaneously exhibit favorable cycling and impedance metrics while undergoing substantial, hidden degradation, underscoring the importance of electrode-resolved diagnostics for evaluating prelithiated silicon-based anodes.

25 ENERGY STORAGE↗
DOE OSTI2022

As–Se Pentagonal Linkers to Induce Chirality and Polarity in Mixed-Valent Fe–Se Tetrahedral Chains Resulting in Hidden Magnetic Ordering

A novel mixed-valent hybrid chiral and polar compound, Fe 7 As 3 Se 12 (en) 6 (H 2 O), has been synthesized by a single-step solvothermal method. The crystal structure consists of 1D [Fe 5 Se 9 ] chains connected via [As 3 Se 2 ]–Se pentagonal linkers and charge-balancing interstitial [Fe(en) 3 ] 2+ complexes (en = ethylenediamine). Neutron powder diffraction verified that interstitial water molecules participate in the crystal packing. Magnetic polarizability of the produced compound was confirmed by X-ray magnetic circular dichroism (XMCD) spectroscopy. X-ray absorption spectroscopy (XAS) and 57 Fe Mössbauer spectroscopy showed the presence of mixed-valent Fe 2+ /Fe 3+ in the Fe–Se chains. Magnetic susceptibility measurements reveal strong antiferromagnetic nearest neighbor interactions within the chains with no apparent magnetic ordering down to 2 K. Hidden short-range magnetic ordering below 70 K was found by 57 Fe Mössbauer spectroscopy, showing that a fraction of the Fe 3+ /Fe 2+ in the chains are magnetically ordered. Nevertheless, complete magnetic ordering is not achieved even at 6 K. Analysis of XAS spectra demonstrates that the fraction of Fe 3+ in the chain increases with decreasing temperature. Computational analysis points out several competing ferrimagnetic ordered models within a single chain. Here, this competition, together with variation in the Fe oxidation state and additional weak intrachain interactions, is hypothesized to prevent long-range magnetic ordering.

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

New Trick for an Old Dog: From Prediction to Properties of “Hidden Clathrates” Ba 2 Zn 5 As 6 and Ba 2 Zn 5 Sb 6

The zinc–antimony phase space has been heavily investigated due to the structural complexity and abundance of high-performing thermoelectric materials. Consequentially, the desire to use zinc and antimony as framework elements to encage rattling cations and achieve phonon-glass-electron-crystal-type properties has remained an enticing goal with only two alkali metal clathrates to date, Cs 8 Zn 18 Sb 28 and K 58 Zn 122 Sb 207 . Guided by Zintl electron-counting predictions, here we explored the Ba–Zn–Pn (Pn = As, Sb) phase space proximal to the expected composition of the type-I clathrate. In situ powder X-ray diffraction studies revealed two “hidden” compounds which can only be synthesized in a narrow temperature range. The ex situ synthesis and crystal growth unveiled that instead of type-I clathrates, compositionally close but structurally different new clathrate-like compounds formed, Ba 2 Zn 5 As 6 and Ba 2 Zn 5 Sb 6 . These materials crystallize in a unique structure, in the orthorhombic space group Pmna with the Wyckoff sequence i 2 h 6 gfe. Single-phase synthesis enabled the exploration of their transport properties. Rattling of the Ba cations in oversized cages manifested low thermal conductivity, which, coupled with the high Seebeck coefficients observed, are prerequisites for a promising thermoelectric material. Potential for further optimization of the thermoelectric performance by aliovalent doping was computationally analyzed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗