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At least 667 records · Page 37

Accurate Prediction of Algal Biomass Lipid, Protein, and Carbohydrate Composition with Machine Learning Regression Modelling of Near-IR Spectra

During large scale algal biomass cultivation, it is difficult to reliably control relative composition to target levels. Rapid determination of chemical composition is feasible by using near infrared (NIR) spectral data. We sought to build and improve on reliable high-throughput screening prediction method based on partial least squares regression (PLSR) by the application of artificial neural networks (ANN) and associated optimization strategies. The algal biomass sample set was designed and created in an iterative process of culturing in physiologically diverse conditions at the GAI field site, followed by compositional analyses at NREL. The workflow allowed us to identify gaps in compositional space for informing the subsequent cultivation and sampling efforts and generated a high quality set of 210 unique samples with chemical analysis results, spectral scanning data, and cultivation metadata. We observed a significant improvement in the performance of carbohydrate content predictions using an optimized ANN model compared to PLSR, with > 16% reduction in mean absolute percent error (MAPE) when tested on the same set of reserved data. The optimized ANN models for FAME and protein prediction performed exceptionally well with 5.99% and 5.09% MAPE, respectively. Application of these methods to detection and quantification of minor biomass constituents that are relevant to certain product streams has shown positive preliminary results, opening the possibility for extensions to the outputs of this powerful data type. All models are accompanied by prediction uncertainties and unsupervised spectral outlier detection to alert an operator to unreliable spectral data. These tools can be deployed for rapid determination of algal culture status, and cultivation and biomass quality improvement.

algal biofuels↗

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

A critical statistical task in the analysis of shotgun proteomics data involves controlling the false discovery rate (FDR) among the reported set of discoveries. This task is most commonly solved at the peptide-spectrum match (PSM) level by using target-decoy competition (TDC), in which a set of observed spectra are searched against a database containing a mixture of real (target) and decoy peptides. The PSM-level procedure can be adapted to the peptide level by selecting the top-scoring PSM per peptide prior to FDR estimation. Here, we investigate both PSM-level and peptide-level FDR control methods and come to two conclusions. First, although the TDC procedure is provably correct under certain assumptions, we observe that one of these assumptions - that incorrect PSMs are independent of one another - is frequently violated. Hence, we empirically demonstrate that TDC-based PSM-level FDR estimates can be liberally biased. Further, we propose that researchers avoid PSM-level results and instead focus on peptide-level analysis. Second, we investigate three ways to carry out peptide level TDC and show that the most common method ("PSM-only") offers the lowest statistical power in practice. The most powerful method, peptide-level FDR with PSM competition ("PSM-and-peptide"), carries out competition first at the PSM level and then again at the peptide level. In our experiments, this approach yields an average increase of 17% more discovered peptides at a1% FDR threshold relative to the PSM-only method.

59 BASIC BIOLOGICAL SCIENCES↗

Construction of linearly independent non-orthogonal AGP states

We show how to construct a linearly independent set of antisymmetrized geminal power (AGP) states, which allows us to rewrite our recently introduced geminal replacement models as linear combinations of non-orthogonal AGPs. Furthermore, this greatly simplifies the evaluation of matrix elements and permits us to introduce an AGP-based selective configuration interaction method, which can reach arbitrary excitation levels relative to a reference AGP, balancing accuracy and cost as we see fit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Using heterogeneous data to identify signatures of dengue outbreaks at fine spatio-temporal scales across Brazil

Dengue virus remains a significant public health challenge in Brazil, and seasonal preparation efforts are hindered by variable intra- and interseasonal dynamics. Here, we present a framework for characterizing weekly dengue activity at the Brazilian mesoregion level from 2010–2016 as time series properties that are relevant to forecasting efforts, focusing on outbreak shape, seasonal timing, and pairwise correlations in magnitude and onset. In addition, we use a combination of 18 satellite remote sensing imagery, weather, clinical, mobility, and census data streams and regression methods to identify a parsimonious set of covariates that explain each time series property. The models explained 54% of the variation in outbreak shape, 38% of seasonal onset, 34% of pairwise correlation in outbreak timing, and 11% of pairwise correlation in outbreak magnitude. Regions that have experienced longer periods of drought sensitivity, as captured by the “normalized burn ratio,” experienced less intense outbreaks, while regions with regular fluctuations in relative humidity had less regular seasonal outbreaks. Both the pairwise correlations in outbreak timing and outbreak trend between mesoresgions were best predicted by distance. Our analysis also revealed the presence of distinct geographic clusters where dengue properties tend to be spatially correlated. Forecasting models aimed at predicting the dynamics of dengue activity need to identify the most salient variables capable of contributing to accurate predictions. Our findings show that successful models may need to leverage distinct variables in different locations and be catered to a specific task, such as predicting outbreak magnitude or timing characteristics, to be useful. This advocates in favor of “adaptive models” rather than “one-size-fits-all” models. The results of this study can be applied to improving spatial hierarchical or target-focused forecasting models of dengue activity across Brazil.

59 BASIC BIOLOGICAL SCIENCES↗

VERA Enhancements for Cross Section Shielding and Geometry Capabilities

Two tasks were undertaken in FY22 that focus on VERA enhancements. The first task involved improvements to the new cross section shielding capability that was added to VERA in FY21. This cell-based capability solves the slowing down problem for each pin cell using Dancoff factors calculated from the whole-core problem. The Dancoff factors are determined for each subgroup level for important sets of materials such as fuel rods, control rods, fuel rods loaded with gad, etc. The cross-section shielding is then performed for each cell using a 1D cylindrical collision probabilities (CP) calculation to obtain the equivalence cross sections required for the core transport calculations. The advantage of this method over the whole-core subgroup calculations is efficiency, since far fewer sweeps of the entire core are required.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Measuring the Density Fields around Bright Quasars at z ~ 6 with XQR-30 Spectra

Measuring the density of the intergalactic medium using quasar sight lines in the epoch of reionization is challenging due to the saturation of Ly α absorption. Near a luminous quasar, however, the enhanced radiation creates a proximity zone observable in the quasar spectra where the Ly α absorption is not saturated. In this study, we use 10 high-resolution ( R ≳ 10,000) z ~ 6 quasar spectra from the extended XQR-30 sample to measure the density field in the quasar proximity zones. We find a variety of environments within 3 pMpc distance from the quasars. We compare the observed density cumulative distribution function (CDF) with models from the Cosmic Reionization on Computers simulation and find a good agreement between 1.5 and 3 pMpc from the quasar. This region is far away from the quasar hosts and hence approaching the mean density of the universe, which allows us to use the CDF to set constraints on the cosmological parameter σ 8 = 0.6 ± 0.3. The uncertainty is mainly due to the limited number of high-quality quasar sight lines currently available. Utilizing the more than 200 known quasars at z ≳ 6, this method will allow us to tighten the constraint on σ 8 to the percent level in the future. In the region closer to the quasar within 1.5 pMpc, we find that the density is higher than predicted in the simulation by 1.23 ± 0.17, suggesting that the typical host dark matter halo mass of a bright quasar ( M 1450 < -26.5) at z ~ 6 is .

79 ASTRONOMY AND ASTROPHYSICS↗

A Self-learning Neural Network Approach for Radio Frequency Interference Detection and Removal in Radio Astronomy

In this work, we present a novel neural network (NN) method for the detection and removal of radio frequency interference (RFI) from the raw digitized signal in the signal processing chain of a typical radio astronomy experiment. The main advantage of our method is that it does not require a training set. Instead, our method relies on the fact that the true signal of interest coming from astronomical sources is thermal and therefore described as a Gaussian random process, which cannot be compressed. We employ a variational encoder/decoder network to find the compressible information in the data stream that can explain the most variance with the fewest degrees of freedom. We demonstrate it on a set of toy problems and stored ring buffers from the Baryon Mapping eXperiment prototype. We find that the RFI subtraction is effective at cleaning simulated time streams: While we find that the power spectra of the RFI-cleaned time streams output by the NN suffer from extra signal consistent with additive noise, we find that it is generally around percent level across the band and sub 10% in contaminated spectral channels even when RFI power is an order of magnitude larger than the signal. We discuss the advantages and limitations of this method and possible implementation in the front end of future radio experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

SU-C-202-01: Incorporating Time-Dependent Hypoxia in IMRT Planning

Purpose: To incorporate uncertainties in oxygenation of tumor cells into radiation therapy planning via robust optimization. The model is demonstrated using a clinical prostate cancer case. Methods: The tumor oxygenation levels are determined based on pre- and mid-treatment PET scans. To account for oxygenation changes, we use a radio-sensitivity factor for the effective dose necessary to treat hypoxic cells. Due to the unpredictable nature of re-oxygenation of hypoxic cells, the radio-sensitivity factor and its change is modeled to reside in a time-dependent uncertainty set. This uncertainty can adapt to both pre- and mid-treatment scans, resulting in a two-stage robust treatment planning model. We develop a robust counterpart reformulation that transforms the original NP-hard problem into a linear program consisting of finitely many linear constraints, which can be solved efficiently. Results: The robust plan is compared to both the corresponding fractionated plan which ignores hypoxia, and to the commonly practiced dose-escalated plan that uniformly increases dose based on initial oxygen concentrations. For PTV, the robust plan improves D{sub 50}, D{sub 95}, and EUD by 4% on average compared to fractionated, and by 11% compared to the optimal escalated plan. Moreover, the robust plan spared organs at risk similar to the fractionated plan, while the escalated plan led to over 170% increase of Bladder D{sub 30}. Conclusion: The proposed robust adaptive model can improve tumor coverage by increasing dose to hypoxic tumor voxels that is overlooked by common fractionated treatments. In addition, the robust model anticipates the re-oxygenation process, thus reducing the excess dose at later fractions in comparison to uniform dose-escalation methods.

60 APPLIED LIFE SCIENCES↗

Sci-Sat AM: Radiation Dosimetry and Practical Therapy Solutions - 09: Stability of a water calorimetry system as a primary standard for absorbed dose to water

Purpose: To investigate the stability of a water calorimetry system as a primary standard for absorbed dose to water using measurements performed in cobalt-60 and high-energy linac photon beams over a span of more than a decade. Methods: Calorimetry measures adsorbed dose directly by recording the amount of heat created when ionizing radiation passes through matter. The radiation-induced temperature rise was measured using two thermistors calibrated against the NRC temperature primary standard, using an AC bridge with lock-in amplifier for precise measurement. The calorimeter system was operated under thermal equilibrium at 4 °C (to eliminate convection) with drifts in water temperature less than 0.1 mK/min. Seven water vessels of various designs were used to make repeated measurements over the course of 17 years. Results: The standard uncertainty achieved for a set of ten calorimeter measurements (4 Gy delivered) was generally well below 0.15 % while the variation between multiple sets for a given vessel was consistent with this value. The long-term stability of the system combined with inter-vessel variations indicated that there was good control of the radiochemistry (chemical heat defect). Conclusions: The measurements performed over a period of several years showed that the combined water calorimeters showed stability at +/− 0.25 % level. Thus, rather than relying on a particular vessel as an artifact one can realize the Gray through the more generalized method of combining a glass vessel, high-purity water and thermistor probes. This provides increased robustness in the dissemination of absorbed dose to Canadian users.

60 APPLIED LIFE SCIENCES↗

Real-space representation of the quasiparticle self-consistent GW self-energy and its application to defect calculations

The quasiparticle self-consistent (QS) GW (G for Green's function, W for screened Coulomb interaction) approach incorporates the corrections of the quasiparticle energies from their Kohn-Sham density functional theory (DFT) eigenvalues by means of an energy-independent and Hermitian self-energy matrix usually given in the basis set of the DFT eigenstates. By expanding these into an atom-centered basis set (specifically here the linearized muffin-tin orbitals) a real space representation of the self-energy corrections becomes possible. In this work, We show that this representation is relatively short-ranged. This offers opportunities to construct the self-energy of a complex system from parts of the system by a cut-and-paste method. Specifically for a point defect, represented in a large supercell, the self-energy can be constructed from those of the host and a smaller defect-containing cell. The self-energy of the periodic host can be constructed simply from a GW calculation for the primitive cell. We show for the case of the As Ga in GaAs that the defect part can already be well represented by a minimal eight-atom cell and allows us to construct the self-energy for a 64-atom cell in good agreement with direct QSGW calculations for the large cell. Using this approach to an even larger 216-atom cell shows the defect band approaches an isolated defect level. The calculations also allow us to identify a second defect band which appears as a resonance near the conduction band minimum. The results on the extracted defect levels agree well with Green's function calculations for an isolated defect and with experimental data.

36 MATERIALS SCIENCE↗

Methods to Evaluate Subcolumn Profiles Based on Two-Point Diagnostics

In atmospheric models, stochastic generation of subgrid-scale profiles or “subcolumns” has been used for a variety of purposes. Such subcolumns can be generated from subgrid probability density functions (PDFs) at different vertical levels, when such PDFs are available. To do so, the generator needs to decide how strongly points should be correlated in the vertical, that is, how much the values should be overlapped. This is sometimes called “PDF overlap.” To assess vertical correlation in a simplified, observable setting, here the vertical correlation of vertical velocity in subcloud layers is examined. Doppler lidar is used to evaluate the vertical profiles of vertical velocity produced by a large-eddy simulation (LES) model and the Subgrid Importance Latin Hypercube Sampler (SILHS) subcolumn generator. In order to diagnose unrealistic features in subcolumn profiles, various statistical diagnostics are examined here, including the bivariate PDF of vertical velocity at two separated points (i.e., altitudes), the two-point velocity correlation, the integral correlation length, the PDF of two-point velocity differences, and the skewness and kurtosis of two-point velocity differences. The profiles produced by LES match lidar well, except that they are too smooth at small scales. The profiles produced by SILHS exhibit sharp jumps from updraft to downdraft that are not observed in the lidar data. To reduce the generation of these unrealistically sharp jumps, the SILHS sampling method is revised. The diagnostics confirm that the revised sampling method reduces the overprediction of sharp jumps.

54 ENVIRONMENTAL SCIENCES↗

Shape-constrained Input Estimation for Efficient Multi-shaker Vibration Testing

Multi-shaker vibration testing is gaining interest from structural dynamics test engineers as it can provide a much more accurate match to complicated field vibration responses than traditional single-axis shaker tests. However, the force capabilities of the small modal shakers typically used in multi-shaker vibration tests has limited the achievable response levels. To date, most multi-shaker vibration tests have been performed using a variety of standard, commercially-available control systems. While these control systems are adequate for a wide range of multiple-input/multiple-output tests, their control algorithms have not been tailored for the specific problem of multi-shaker vibration tests: efficiently coordinating the various shakers to work together to achieve a desired response. Here, a new input estimation algorithm is developed and demonstrated using simulations and actual test data. This algorithm, dubbed shape-constrained input estimation, is shown to effectively coordinate multiple shakers using a set of constraint vectors based on the deflection shapes of the test structure. This is accomplished by using the singular vector shapes of the system frequency response matrix, which allows the constraint vectors to automatically change as a function of frequency. Simulation and test results indicate a significant reduction in the input forces required to achieve a desired response. Finally, the results indicate that shape-constrained input estimation is an effective method to achieve higher response levels from limited shaker forces which will enable higher level multi-shaker vibration tests to be performed.

42 ENGINEERING↗

Multitask methods for predicting molecular properties from heterogeneous data

Data generation remains a bottleneck in training surrogate models to predict molecular properties. We demonstrate that multitask Gaussian process regression overcomes this limitation by leveraging both expensive and cheap data sources. In particular, we consider training sets constructed from coupled-cluster (CC) and density functional theory (DFT) data. We report that multitask surrogates can predict at CC-level accuracy with a reduction in data generation cost by over an order of magnitude. Of note, our approach allows the training set to include DFT data generated by a heterogeneous mix of exchange–correlation functionals without imposing any artificial hierarchy on functional accuracy. More generally, the multitask framework can accommodate a wider range of training set structures—including the full disparity between the different levels of fidelity—than existing kernel approaches based on Δ-learning although we show that the accuracy of the two approaches can be similar. Consequently, multitask regression can be a tool for reducing data generation costs even further by opportunistically exploiting existing data sources.

Chemistry↗

Propagator quantum chemical study of S-cis-(Z)-2-(2-formylethenyl)pyrrole: electronic structure and aspects of intramolecular hydrogen bond manifestation in ionization spectra

For the purpose of investigation of the electronic structures of functionalized pyrroles with potential biological activity the electronic structures and ionization spectra of S-cis-(Z)-2-(2-formylethenyl)pyrrole (FP) were calculated by the propagator quantum chemical method. The calculations were performed using the third-order algebraic diagrammatic construction method (ADC(3)) for one-particle Green´s function (electronic propagator) and the 6–31G** basis set. Going from FP (possessing the intramolecular hydrogen bond H⋯O) to its conformation FPR (without H⋯O bonding), the O1s-ionization energy and the ionization energy of the σ-type lone electron pair orbital of the O atom decrease by ~0.2 eV, which is a consequence of stopping the electron density transfer from the O atom. A strong electron density transfer through the hydrogen bond from the O atom to the NH group occurs in the nitrogen core level ionization spectrum as evidenced by a lower N1s-ionization energy of FP (by ~0.7 eV ) compared to that of FPR. The valence shell ionization spectra of FP and FPR calculated using the ADC(3) method are characterized by a high density of the satellite states. The results obtained indicate that the electronic structures of the compounds of the considered class are characterized by pronounced effects of electron correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Silver clusters tune up electronic properties of graphene nanoflakes: A comprehensive theoretical study

Graphene-silver composites reflect a synergic effect of both components with enhanced electronic, adsorption and catalytic properties. We introduce here the detailed theoretical study on geometric, thermodynamic and electronic properties of silver clusters Ag n (n=2–10) adsorbed on graphene nanoflakes as a model for silver-graphene composites. First, a benchmark study is performed on Ag n …coronene complexes (n=2, 4) by evaluating various functional against reported high level ab-initio method for the selection of best functional for further calculations. Then, density functional theory study at the best chosen level is performed to inquire how clustering of adsorbate attached with carbon surface can impact geometric, electronic and thermodynamic properties of silver-graphene composites. Furthermore, the interaction energies are corrected for dispersion and basis set superposition error in order to get more realistic estimate of interaction energies. In progression, we investigated the dependence of interaction energy upon cluster size and dimensionality. For Ag n …coronene, the binding energies increase monotonically as the number of atoms in the cluster increases. However, for Ag n …dodecabenzocoronene, the interaction energies show a sudden drop at Ag 7 …dodecabenzocoronene. The difference in behavior between Ag n …dodecabenzocoronene and Ag n …coronene for interaction energy is attributed to edge effect present in coronene. Furthermore, coplanar orientations of the silver clusters on polyaromatic hydrocarbons have higher interaction energies. The 2D-3D transition of the silver cluster is observed for Ag 7 …coronene. CDA analysis reveals that backdonation from dodecabenzocoronene to silver clusters is more dominant in Ag 4 –Ag 7 whereas other clusters have dominant charge transfer to dodecabenzocoronene. Charge transfer analysis via constrained density functional theory (CDFT) reveals significant energy lowering from charge donor-acceptor interactions. Further energy decomposition analysis (EDA) using absolutely-localized molecular orbitals (ALMO) suggests that, while charge-transfer is important in these systems, the sum of electrostatics, Pauli repulsion, and London dispersion are far more significant as silver cluster size increases. NCI results also support the presence of van der Waals and electrostatic interactions. The hollow top is most favorite interaction sites compared to bridge top and head top binding sites over coronene lattice. The ionization potential, electron affinity, frontier molecular orbital analysis, chemical hardness, softness, chemical potential, and Fermi levels are deliberated to verify the stability and reactivity of most stable silver-graphene composites. The remarkable outcome of the current findings makes our silver-graphene composite as a potential applicant for high performance electronic and catalytic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fourth-order partial differential equation noise removal on welding images

Partial differential equation (PDE) has become one of the important topics in mathematics and is widely used in various fields. It can be used for image denoising in the image analysis field. In this paper, a fourth-order PDE is discussed and implemented as a denoising method on digital images. The fourth-order PDE is solved computationally using finite difference approach and then implemented on a set of digital radiographic images with welding defects. The performance of the discretized model is evaluated using Peak Signal to Noise Ratio (PSNR). Simulation is carried out on the discretized model on different level of Gaussian noise in order to get the maximum PSNR value. The convergence criteria chosen to determine the number of iterations required is measured based on the highest PSNR value. Results obtained show that the fourth-order PDE model produced promising results as an image denoising tool compared with median filter.

42 ENGINEERING↗

Resilience Design Patterns - A Structured Approach to Resilience at Extreme Scale (version 1.0)

Reliability is a serious concern for future extreme-scale high-performance computing (HPC) systems. Projections based on the current generation of HPC systems and technology roadmaps suggest that very high fault rates in future systems. The errors resulting from these faults will propagate and generate various kinds of failures, which may result in outcomes ranging from result corruptions to catastrophic application crashes. Practical limits on power consumption in HPC systems will require future systems to embrace innovative architectures, increasing the levels of hardware and software complexities. The resilience challenge for extreme-scale HPC systems requires management of various hardware and software technologies that are capable of handling a broad set of fault models at accelerated fault rates. These techniques must seek to improve resilience at reasonable overheads to power consumption and performance. While the HPC community has developed various solutions, application-level as well as system-based solutions, the solution space of HPC resilience techniques remains fragmented. There are no formal methods and metrics to investigate and evaluate resilience holistically in HPC systems that consider impact scope, handling coverage, and performance & power eciency across the system stack. Additionally, few of the current approaches are portable to newer architectures and software ecosystems, which are expected to be deployed on future systems. In this document, we develop a structured approach to the management of HPC resilience based on the concept of resilience-based design patterns. A design pattern is a general repeatable solution to a commonly occurring problem. We identify the commonly occurring problems and solutions used to deal with faults, errors and failures in HPC systems. The catalog of resilience design patterns provides designers with reusable design elements. We define a design framework that enhances our understanding of the important constraints and opportunities for solutions deployed at various layers of the system stack. The framework may be used to establish mechanisms and interfaces to coordinate flexible fault management across hardware and software components. The framework also enables optimization of the cost-benefit trade-os among performance, resilience, and power consumption. The overall goal of this work is to enable a systematic methodology for the design and evaluation of resilience technologies in extreme-scale HPC systems that keep scientific applications running to a correct solution in a timely and cost-ecient manner in spite of frequent faults, errors, and failures of various types.

97 MATHEMATICS AND COMPUTING↗

Process-based cost estimation framework for assessing economic viability of environmentally and socially sustainable rare earth element feedstocks

Rare Earth Elements (REEs) are critical raw material inputs that are required to enable the energy transition. Constraints on the U.S. supply of conventional REE feedstocks and the desire to diversify U.S. reliance on foreign supply chains have motivated the pursuit of REE recovery from unconventional feedstocks including waste products. Recovery of REEs from unconventional sources is also motivated by environmental and social considerations, including the potential to offset new mining activity and subsidize the remediation of REE-containing wastes from coal, natural gas, and other mineral extraction activities. Sourcing REEs from unconventional feedstocks would reduce supply chain constraints and minimize the environmental impacts of REE extraction, but current processes to exploit these feedstocks have uncertain technical and economic performance and the processes have not been demonstrated at scale. This work aims to reduce uncertainty in evaluating the performance of new REE production pathways. A database of operating and capital expenses for REE recovery and establish consistent process unit costs for common stages in the conventional supply chain are developed. Market prices are used to develop well-defined methods for determining product values for a diverse set of products that can be generated (e.g. oxalates, alloys, end-use products such as magnets) but are not typically considered in technoeconomic analyses. Finally, to provide insight on the effects of economies of scale and feedstock purity on capital and operating costs, process unit level cost functions relating total costs per kilogram of REE produced are reported. These tools can be applied to assess and facilitate scale-up of REE production from diverse sources of REEs.

Fritz, Alison↗