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At least 1,027 records · Page 57

HUNTRESS: a fast heuristic for reconstructing phylogenetic trees of tumor evolution (HUNTRESS) v0.1

We introduce HUNTRESS (Histogrammed UNion Tree REconStruction heuriStic), a computational method for tumor phylogeny reconstruction from noisy genotype matrices derived from single-cell sequencing data, whose running time is linear with the number of cells and quadratic with the number of mutations. Provided that the input genotype matrix includes no false positives, each cellular subpopulation is at least a user defined fraction of the total number of cells, and the number of cells are much bigger than the number of mutations considered, HUNTRESS computes the ground truth tumor phylogeny with high probability. On simulated data HUNTRESS is faster than available alternatives with comparable or better accuracy. Additionally, the phylogenies reconstructed by HUNTRESS on two single-cell sequencing data sets agree with the best known evolutionary scenarios for the associated tumors.

Buluc, Aydin↗

LANDSAT 4 investigations of thematic mapper and multispectral scanner applications

The utility of TM data natural resource assessment was evaluated with emphasis on manual interpretation and digital classification. The improved spatial resolution of TM data, as compared with MSS data, aided in the location of roads, small stock ponds, and many other land features, permitting positive identification of landmarks. With the TM, there was more efficient manual interpretation of land use, better identification of resource types, and improved assessment of the ecological status of natural vegetation. Band 5 and band 7 aided in defining water resources, wetland vegetation resources, and other terrain features. Results from TM and TM simulator data suggest that the coefficient of variation for major land cover types is less for TM data than for equivalent MSS data. Although the amount of information in bands 5 and 7 is small, it is unique since the same information cannot be derived from the MSS four-band spectral region.

Lauer, D. T.↗

Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces

Here, this paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems and then deployed for potential energy prediction for C 5 H 5 using B2PLYP-D3/6-311++G(d,p) for high-fidelity simulation data and Hartree–Fock 6-31G for low-fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subsurface Characterization and Machine Learning Predictions at Brady Hot Springs Results

Geothermal power plants typically show decreasing heat and power production rates over time. Mitigation strategies include optimizing the management of existing wells - increasing or decreasing the fluid flow rates across the wells - and drilling new wells at appropriate locations. The latter is expensive, time-consuming, and subject to many engineering constraints, but the former is a viable mechanism for periodic adjustment of the available fluid allocations. Data and supporting literature from a study describing a new approach combining reservoir modeling and machine learning to produce models that enable strategies for the mitigation of decreased heat and power production rates over time for geothermal power plants. The computational approach used enables translation of sets of potential flow rates for the active wells into reservoir-wide estimates of produced energy and discovery of optimal flow allocations among the studied sets. In our computational experiments, we utilize collections of simulations for a specific reservoir (which capture subsurface characterization and realize history matching) along with machine learning models that predict temperature and pressure timeseries for production wells. We evaluate this approach using an "open-source" reservoir we have constructed that captures many of the characteristics of Brady Hot Springs, a commercially operational geothermal field in Nevada, USA. Selected results from a reservoir model of Brady Hot Springs itself are presented to show successful application to an existing system. In both cases, energy predictions prove to be highly accurate: all observed prediction errors do not exceed 3.68% for temperatures and 4.75% for pressures. In a cumulative energy estimation, we observe prediction errors that are less than 4.04%. A typical reservoir simulation for Brady Hot Springs completes in approximately 4 hours, whereas our machine learning models yield accurate 20-year predictions for temperatures, pressures, and produced energy in 0.9 seconds. This paper aims to demonstrate how the models and techniques from our study can be applied to achieve rapid exploration of controlled parameters and optimization of other geothermal reservoirs. Includes a synthetic, yet realistic, model of a geothermal reservoir, referred to as open-source reservoir (OSR). OSR is a 10-well (4 injection wells and 6 production wells) system that resembles Brady Hot Springs (a commercially operational geothermal field in Nevada, USA) at a high level but has a number of sufficiently modified characteristics (which renders any possible similarity between specific characteristics like temperatures and pressures as purely random). We study OSR through CMG simulations with a wide range of flow allocation scenarios. Includes a dataset with 101 simulated scenarios that cover the period of time between 2020 and 2040 and a link to the published paper about this project, where we focus on the Machine Learning work for predicting OSR's energy production based on the simulation data, as well as a link to the GitHub repository where we have published the code we have developed (please refer to the repository's readme file to see instructions on how to run the code). Additional links are included to associated work led by the USGS to identify geologic factors associated with well productivity in geothermal fields. Below are the high-level steps for applying the same modeling + ML process to other geothermal reservoirs: 1. Develop a geologic model of the geothermal field. The location of faults, upflow zones, aquifers, etc. need to be accounted for as accurately as possible 2. The geologic model needs to be converted to a reservoir model that can be used in a reservoir simulator, such as, for instance, CMG STARS, TETRAD, or FALCON 3. Using native state modeling, the initial temperature and pressure distributions are evaluated, and they become the initial conditions for dynamic reservoir simulations 4....

15 GEOTHERMAL ENERGY↗

Development of a Data Overflow Protection System for Super-Kamiokande to Maximize Data from Nearby Supernovae

Neutrinos from very nearby supernovae, such as Betelgeuse, are expected to generate more than ten million events over 10 s in Super-Kamokande (SK). At such large event rates, the buffers of the SK analog-to-digital conversion board (QBEE) will overflow, causing random loss of data that are critical for understanding the dynamics of the supernova explosion mechanism. In order to solve this problem, two new data-acquisition (DAQ) modules were developed to aid in the observation of very nearby supernovae. The first of these, the SN module, is designed to save only the number of hit photomultiplier tubes during a supernova burst and the second, the Veto module, prescales the high-rate neutrino events to prevent the QBEE from overflowing based on information from the SN module. In the event of a very nearby supernova, these modules allow SK to reconstruct the time evolution of the neutrino event rate from beginning to end using both QBEE and SN module data. This paper presents the development and testing of these modules together with an analysis of supernova-like data generated with a flashing laser diode. We demonstrate that the Veto module successfully prevents DAQ overflows for Betelgeuse-like supernovae as well as the long-term stability of the new modules. During normal running the Veto module is found to issue DAQ vetos a few times per month resulting in a total dead-time less than 1 ms, and does not influence ordinary operations. Additionally, using simulation data we find that supernovae closer than 800 pc will trigger the Veto module, resulting in a prescaling of the observed neutrino data.

F20 Instrumentation and technique↗

An Eigensystem Realization Algorithm (ERA) for modal parameter identification and model reduction

A method, called the Eigensystem Realization Algorithm (ERA), is developed for modal parameter identification and model reduction of dynamic systems from test data. A new approach is introduced in conjunction with the singular value decomposition technique to derive the basic formulation of minimum order realization which is an extended version of the Ho-Kalman algorithm. The basic formulation is then transformed into modal space for modal parameter identification. Two accuracy indicators are developed to quantitatively identify the system modes and noise modes. For illustration of the algorithm, examples are shown using simulation data and experimental data for a rectangular grid structure.

Juang, J. N.↗

Near-wall modelling of compressible turbulent flows

Work was carried out to extend the near-wall models formulated for the incompressible Reynolds stress equations to compressible flows. The idea of splitting the compressible dissipation function into a solenoidal part that is not sensitive to changes of compressibility indicators and a compressible part that is directly affected by these changes is adopted. This means that all models involving the dissipation rate could be expressed in terms of the solenoidal dissipation rate and an equation governing its transport could be formulated to close the set of compressible Reynolds stress equations. The near-wall modelling of the dissipation rate equation is investigated and its behavior near a wall is studied in detail using k-epsilon closure. It is found that all existing modelled equations give the wrong behavior for the dissipation rate near a wall. Improvements are suggested and the resultant behavior is found to be in good agreement with near-wall data. Furthermore, the present modified k-epsilon closure is used too calculate a flat plate boundary layer and the results are compared with four existing k-epsilon closures. These comparisons show that all closures tested give essentially the same flow properties, except in a region very close to the wall. In this region, the present k-epsilon closure calculations are in better agreement with measurements and direct simulation data; in particular, the behavior of the dissipation rate.

So, Ronald M. C.↗

Quantifying Epistemic Uncertainty in Binary Classification via Accuracy Gain

ABSTRACT Recently, a surge of interest has been given to quantifying epistemic uncertainty (EU), the reducible portion of uncertainty due to lack of data. We propose a novel EU estimator in the binary classification setting, as the posterior expected value of the empirical gain in accuracy between the current prediction and the optimal prediction. In order to validate the performance of our EU estimator, we introduce an experimental procedure where we take an existing dataset, remove a set of points, and compare the estimated EU with the observed change in accuracy. Through real and simulated data experiments, we demonstrate the effectiveness of our proposed EU estimator.

97 MATHEMATICS AND COMPUTING↗

Temperature Effects on Interdiffusion of Al and U-Mo under Irradiation

A high-energy Xe ion irradiation experiment was conducted to investigate the temperature dependence of interdiffusion in bilayer Al-UMo samples under irradiation. The amount of interdiffusion achieved at a fixed dose with the increase of temperature showed a clear transition at 175 degrees C (with an estimated error in the range of ± 10 degrees C) from temperature-independent to temperature-dependent behavior. The activation energy derived from the curve of interdiffusion quantity vs. irradiation temperature is 0.77 ± 0.16 eV. This information has been utilized to understand the temperature effect on the interdiffusion process that occurred at the interfaces of U-Mo particles and the Al matrix in U-Mo/Al dispersion fuels, whose magnitude significantly impacts the fuel's performance. Although this temperature effect was deemed important, it cannot be examined directly using in-pile irradiation data, as fuel temperatures cannot be measured in reactor irradiation and are highly correlated with fission rate and thermal conductivity evolution. To connect the knowledge accumulated from ion irradiation with in-pile irradiation data, simulation of a full-sized U-Mo/Al dispersion fuel plate irradiated in the FUTURE test in the BR2 reactor was performed with the Dispersion Analysis Research Tool (DART), a dispersion fuel performance code. DART is equipped with an interaction or interdiffusion layer (IL) growth correlation formulated to describe the temperature dependence of ion mixing results. The agreement between calculated and measured fuel meat constituent volume fractions and swelling data demonstrated that the temperature effect on in-pile Al-UMo interdiffusion is well captured with the correlation. In this case, the fitted activation energy is 0.70 eV. Considering the uncertainties associated with the ion irradiation data, the activation energy obtained from in-pile data fitting is in accord with that from ion irradiation results.

36 MATERIALS SCIENCE↗

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

Prong Segmentation using Point Set Transformers in Multiple View Neutrino Detectors

NOvA is a long-baseline neutrino experiment studying neutrino oscillations by detecting neutrinos from the NuMI beam at Fermilab. Its physics analysis relies on accurate prong segmentation, which involves matching each hit to its source particle and identifying the particle type. This task has commonly been addressed using a combination of traditional clustering algorithms and convolutional neural networks (CNNs). However, NOvA’s detector design presents data as two sparse and decoupled 2D images (XZ and YZ views) rather than a native 3D representation, posing a significant challenge for traditional CNN-based models. In this talk, we propose a novel neural network based on the Point Set Transformer. By treating detector hits as sparse point clouds and implementing a cross-view attention mechanism, our model enables efficient information mixing between both views. Evaluated on NOvA simulated data, our model achieves superior accuracy while requiring significantly fewer computational resources compared to other models. Furthermore, the model demonstrates great performance when applied to Liquid Argon Time Projection Chamber (LArTPC) data, which shows its potential as a universal prong segmentation algorithm for multiple view neutrino detectors.

Liu, Jiaxi [UC, Irvine]↗

Remote Sensing of Coastal Wetlands Biomass Using Thematic Mapper Wavebands

Spectral data, simulating thematic mapper bands 3, 4 and 5 were gathered in salt and brackish marshes using a hand-held radiometer. Simple regression models were developed equating spectral radiance indicies with total live biomass for S. alterniflora in a salt marsh and for a variety of plant species in a brackish marsh. Models were then tested and compared to harvest estimates of biomass. In the salt marsh, biomass estimates from spectral data were similar to harvest biomass estimates during most of the growing season. Estimates of annual net aerial primary productivity calculated from spectral data were within 21% of production estimated from harvest data. During August, biomass estimates from spectral data in the brackish marsh were similar to biomass estimated by harvesting techniques but not always comparable at other times in the growing season.

Hardisky, M. A.↗

Tracking Blade Tip Vortices for Numerical Flow Simulations of Hovering Rotorcraft

Blade tip vortices generated by a helicopter rotor blade are a major source of rotor noise and airframe vibration. This occurs when a vortex passes closely by, and interacts with, a rotor blade. The accurate prediction of Blade Vortex Interaction (BVI) continues to be a challenge for Computational Fluid Dynamics (CFD). Though considerable research has been devoted to BVI noise reduction and experimental techniques for measuring the blade tip vortices in a wind tunnel, there are only a handful of post-processing tools available for extracting vortex core lines from CFD simulation data. In order to calculate the vortex core radius, most of these tools require the user to manually select a vortex core to perform the calculation. Furthermore, none of them provide the capability to track the growth of a vortex core, which is a measure of how quickly the vortex diffuses over time. This paper introduces an automated approach for tracking the core growth of a blade tip vortex from CFD simulations of rotorcraft in hover. The proposed approach offers an effective method for the quantification and visualization of blade tip vortices in helicopter rotor wakes. Keywords: vortex core, feature extraction, CFD, numerical flow visualization

Numerical↗

Utilizing remote sensing of thematic mapper data to improve our understanding of estuarine processes and their influence on the productivity of estuarine-dependent fisheries

The land-water interface of coastal marshes may influence the production of estuarine-dependent fisheries more than the area of these marshes. To test this hypothesis, a spatial model was created to explore the dynamic relationship between marshland-water interface and level of disintegration in the decaying coastal marshes of Louisiana's Barataria, Terrebonne, and Timbalier basins. Calibrating the model with Landsat Thematic Mapper satellite imagery, a parabolic relationship was found between land-water interface and marsh disintegration. Aggregated simulation data suggest that interface in the study area will soon reach its maximum and then decline. A statistically significant positive linear relationship was found between brown shrimp catch and total interface length over the past 28 years. This relationship suggests that shrimp yields will decline when interface declines, possibly beginning about 1995.

Browder, Joan A.↗

Development of Efficient Process for Manufacturing of Thermoplastic Composites with Tailored Properties (CRADA 511)

This is a collaborative effort between Battelle Memorial Institute as manager and operator of Pacific Northwest National Laboratory (PNNL) and ESI North America Inc. (“ESI” or “Participant”) to apply computation and data analytics to the challenge of light weighting with a focus on the battery enclosures of electric vehicles (EVs). EVs use heavy batteries to increase range and power. A complex-shaped battery enclosure is required to meet a host of challenging performance requirements. The ability to virtually develop composite parts such as battery enclosure with tailored properties to meet required performance will be highly valuable to the automotive industry. However, efficient simulation of composite-manufacturing processes remains a challenging issue since simulation involves multiscale models in space and time, highly non-linear and anisotropic behavior, strongly coupled multi-physics, and complex geometries. This work will advance the state of the art by reducing the computational burden of composite optimization by using simulation data from a limited number of configurations off-line and then developing a reduced order model (ROM) using data analytics and machine learning (ML). Develop a data driven approach to link features of the material and manufacturing processes to the mechanical properties of thermoplastic composite parts.

42 ENGINEERING↗

Improved visualization of flow field measurements

A capability is proposed that makes it feasible to apply to measured flow field data the visualization tools developed to display numerical solutions for computational fluid dynamic problems. The measurement monitor surface (MMS) methodology was used for the analysis of flow field measurements within a low-aspect-ratio transonic axial-flow fan rotor acquired with two-dimensional laser anemometry. It is shown that the MMS method may be utilized to generate input for the multidimensional processing and analytical tools developed for numerical flow field simulation data. Thus an experimenter utilizing an interactive graphics program could illustrate scalar quantities such as Mach number by profiles, contour lines, carpet plots, and surfaces employing various color intensities. Also, flow directionality can be shown by the display of vector fields and particle traces.

Miles, Jeffrey Hilton↗

Real-Time Radiological Source Term Estimation for Multiple Sources in Cluttered Environments

A particle filter algorithm is presented to estimate the position, strength, and cardinality of an unknown number of radioactive point sources in an obstacle-rich environment using count measurements. The algorithm addresses gaps in the prior literature by incorporating two novel elements. The first is a precomputation step in which local terrain and obstacle data is processed to compute attenuation kernels throughout the search area. This enables rapid estimation performance in obstacle-rich environments as measurements are gathered. The second novel feature is a dynamic particle allocation technique in which the number of particles is adjusted in real time to meet convergence goals. This feature allows the algorithm to scale more efficiently to scenarios with a larger number of sources. A series of computational experiments using simulated data demonstrates the algorithm’s performance in a cluttered environment with up to eight sources.

Kemp, Samuel↗

Using Distributed Fiber-optic Strain Sensing to Estimate Generalized Modal Coordinates from Flight-test Data

A method for estimating the generalized modal coordinates of an aircraft during flight has been developed. The Fiber-optic Sensing System (FOSS) offers an efficient and cost-effective method of measuring the strain at thousands of points along the wings. The estimation of modal coordinates was implemented as a two-step process. First, a maximum likelihood method is used to estimate the statistical properties of the sensors and generalized modal coordinates. Second, the strain mode shapes from the finite element model are used along with the statistical properties from the first step to estimate the generalized modal coordinates over time. Using simulated data from the X-56A Multi-Utility Technology Testbed (MUTT), different methods of modal coordinate estimation were compared to demonstrate the benefits and weaknesses of each. These were compared against the exact solution and an ordinary least squares (a more traditional method) estimate. Modal coordinate estimation methods were then applied to flight-test data from the X-56A aircraft to show that the method continues to work well with actual test data. The new estimation method provides insights unavailable from more classical approaches.

Jeffrey Ouellette↗