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DOE OSTI2025

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H 2 ), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H 2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Human-automated vehicle interactions

This dissertation is proposed to answer the question: how can the interactions between human and automated vehicles be used to improve the overall performance of automated driving technology? Multiple different modules in automated vehicles such as the perception, motion plan and motion control modules can potentially be benefitted from human-automated vehicle interactions. For perception module, the self-correction of faulty sensors can be achieved using human demonstration data. For motion plan and motion control modules, the performance of the low-level motion controller can be improved with the help of human demonstration, and the behavior of the motion planner can be improved using human intervention data during automated driving. Moreover, a better model for a human driver could improve the overall efficiency and comfort of vehicles in connected mixed traffic. In this dissertation, the technical research toward these goals has been completed and has resulted in several peer-reviewed publications. Optimization methods and model predictive control are used extensively to improve energy efficiency while maintaining safe and comfort driving. An inverse model predictive control (IMPC) method has been developed and it has been proven to be effective in modeling the motion of human driven vehicles. The proposed method has demonstrated its benefits in both connected automated highway driving and the bilateral adaptation of human driver and automated driving controller in human-in-the loop simulations. The proposed future research seeks to broaden the application of IMPC by considering a more comprehensive cost function design and applying it to more complex driving situations.

Guo, Longxiang↗

DOE OSTI2021

HUMAN-AUTOMATED VEHICLE INTERACTIONS

Guo, Longxiang↗

DOE OSTI2016

Measurement of fiducial differential cross sections of gluon-fusion production of Higgs bosons decaying to WW *→eνμν with the ATLAS detector at s = 8 $$ \sqrt{s}=8 $$ TeV

This paper describes a measurement of fiducial and differential cross sections of gluon-fusion Higgs boson production in the H → W W*→ eνμν channel, using 20.3 fb -1 of proton-proton collision data. The data were produced at a centre-of-mass energy of √=8 TeV at the CERN Large Hadron Collider and recorded by the ATLAS detector in 2012. Cross sections are measured from the observed H→ W W*→ eνμν signal yield in categories distinguished by the number of associated jets. The total cross section is measured in a fiducial region defined by the kinematic properties of the charged leptons and neutrinos. Differential cross sections are reported as a function of the number of jets, the Higgs boson transverse momentum, the dilepton rapidity, and the transverse momentum of the leading jet. The jet-veto efficiency, or fraction of events with no jets above a given transverse momentum threshold, is also reported. All measurements are compared to QCD predictions from Monte Carlo generators and fixed-order calculations, and are in agreement with the Standard Model predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Physics-informed graph neural networks for predicting cetane number with systematic data quality analysis

Designing alternative fuels for advanced compression ignition engines necessitates a predictive model for cetane number (CN). In this study, the physics-informed graph neural networks are introduced for a reliable CN prediction by considering molecular features pertinent to the physical properties of molecules that affect CN. The reliability of measured data is another key factor to consider for improving the predictive model. Various experimental instruments for measuring CN exist, including standard and non-standard methods. In this regard, a systematic data quality analysis was carried out for the total 630 CNs collected from literature and new measurements in this study using Advanced Fuel Ignition Delay Analyzer (AFIDA). The results from this data curation process were reflected in the model by imposing lower sample weights on the data coming from less reliable measurement techniques. This approach effectively maximized the prediction accuracy while incorporating data from all available sources. Using the sample weights decreased the mean absolute error (MAE) up to 0.8 CN units. The accuracy was also improved by introducing the CN-related physical properties (the number of hydrogen bond donors and acceptors); the test set MAE is 5.74 and 7.01 for the model with and without such properties, respectively. Investigating molecular structural effects on CN was also carried out to gain chemical insights into factors used to design new fuel candidates. The dimensionality reduction analysis of feature vectors showed a clear clustering in terms of functional groups and CN and the structural effect derived from the model was consistent with the physicochemical insights. Finally, this physics-informed model and data curation would be helpful for accurate CN prediction and inform rational fuel design.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

IRNet: A General Purpose Deep Risidual Regression Framework for Materials Discovery

Materials discovery is crucial for making scientific advances in many domains. Collections of data from experiments and first-principle computations have spurred interest in applying machine learning methods to create predictive models capable of mapping from composition and crystal structures to materials properties. Generally, these are regression problems with the input being a 1D vector composed of numerical attributes representing the material composition and/or crystal structure. While neural networks consisting of fully connected layers have been applied to such problems, their performance often suffers from the vanishing gradient problem when network depth is increased. Hence, predictive modeling for such tasks has been mainly limited to traditional machine learning techniques such as Random Forest. In this paper, we study and propose design principles for building deep regression networks composed of fully connected layers with numerical vectors as input. We introduce a novel deep regression network with individual residual learning, IRNet, that places shortcut connections after each layer so that each layer learns the residual mapping between its output and input. We use the problem of learning properties of inorganic materials from numerical attributes derived from material composition and/or crystal structure to compare IRNet’s performance against that of other machine learning techniques. Using multiple datasets from the Open Quantum Materials Database (OQMD) and Materials Project for training and evaluation, we show that IRNet provides significantly better prediction performance than the state-of-the-art machine learning approaches currently used by domain scientists. We also show that IRNet’s use of individual residual learning leads to better convergence during the training phase than when shortcut connections are between multi-layer stacks while maintaining the same number of parameters.

deep learning↗

DOE OSTI2016

Advanced Controls for the Multi-pod Centipod WEC device

Dehlsen Associates, LLC (DA) has developed a Wave Energy Converter (WEC), Centipod, which is a multiple point absorber, extracting wave energy primarily in the heave direction through a plurality of point absorber floats sharing a common stable reference structure. The objective of this project was to develop advanced control algorithms that will be used to reduce Levelized Cost of Energy (LCOE). This project investigated the use of Model Predictive Control (MPC) to improve the power capture of the WEC. The MPC controller developed in this work is a state-space, “look ahead” controller approach using knowledge of past and current states to predict future states to take action with the PTO to maximize power capture while still respecting system constraints. In order to maximize power, which is the product of force and velocity, the controller must aim to create phase alignment between excitation force and velocity. This project showed a 161% improvement in the Annual Energy Production (AEP) for the Centipod WEC when utilizing MPC, compared to a baseline, fixed passive damping control strategy. This improvement in AEP was shown to provide a substantial benefit to the WEC’s overall Cost of Energy, reducing LCOE by 50% from baseline. The results of this work proved great potential for the adoption of Model Predictive Controls in Wave Energy Converters.

16 TIDAL AND WAVE POWER↗

DOE OSTI2014

The influence of disease categories on gene candidate predictions from model organism phenotypes

The molecular etiology is still to be identified for about half of the currently described Mendelian diseases in humans, thereby hindering efforts to find treatments or preventive measures. Advances, such as new sequencing technologies, have led to increasing amounts of data becoming available with which to address the problem of identifying disease genes. Therefore, automated methods are needed that reliably predict disease gene candidates based on available data. We have recently developed Exomiser as a tool for identifying causative variants from exome analysis results by filtering and prioritising using a number of criteria including the phenotype similarity between the disease and mouse mutants involving the gene candidates. Initial investigations revealed a variation in performance for different medical categories of disease, due in part to a varying contribution of the phenotype scoring component. In this study, we further analyse the performance of our cross-species phenotype matching algorithm, and examine in more detail the reasons why disease gene filtering based on phenotype data works better for certain disease categories than others. We found that in addition to misleading phenotype alignments between species, some disease categories are still more amenable to automated predictions than others, and that this often ties in with community perceptions on how well the organism works as model. In conclusion, our automated disease gene candidate predictions are highly dependent on the organism used for the predictions and the disease category being studied. Future work on computational disease gene prediction using phenotype data would benefit from methods that take into account the disease category and the source of model organism data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Comprehensive End-to-End Design of Novel High Energy Density Materials: II. Computational Modeling and Predictions

In this work, we have proposed a holistic approach to design novel energetic materials by bridging synthesis, experimental characterization, computational modeling, and validation. Multiscale computational modeling that combines first-principles calculations, analytical theory, and empirical statistical analysis served to further advance the proposed methodology. The established materials design guiding principles led to development of a set of new energetic molecules, PHE-1, PHE-2, and PHE-3, that represent improved variations of the heterocyclic energetics and are predicted to be superior to the existing conventional energetic materials. Molecular mechanisms of the enhanced performance and sensitivity of the proposed energetic materials as a function of their chemical composition and structure are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Molecular Simulation of Lithium Carbonate Reactive Vapor–Liquid Equilibria Using a Deep Potential Model

We developed a first-principles machine learning model for the reactive vapor–liquid phase behavior of molten Li 2 CO 3 . The model was trained on ab initio electronic density functional theory data using the Deep Potential (DP) methodology, and its accuracy was evaluated by comparing model predictions of density and viscosity to experimental measurements. Direct coexistence simulations with the DP model over time scales of tens of nanoseconds were used to observe equilibrium dissociation of Li 2 CO 3 into CO 2 residing primarily in the vapor phase and Li 2 O which remains dissolved in the liquid. The simulations covered a range of temperatures, overall system sizes, and vapor-to-liquid volume ratios. Results were analyzed in terms of the observed chemical composition of the liquid and vapor phases, product structure, and CO 2 partial pressures. In addition, we calculated equilibrium constants for the dissociation reaction by assuming ideal-solution behavior for the liquid. As expected on the basis of thermodynamic arguments and prior experiments for this system, the observed partial pressure of CO 2 in the gas phase depends on both the temperature and the ratio of vapor to liquid volumes, while the calculated equilibrium constants only depend on temperature. DP model predictions for the equilibrium constant of the reaction are generally consistent with the available experimental measurements. Furthermore, the present study establishes the validity of the DP methodology for the description of reactive, multiphase equilibria from first principles, with possible applications to many other systems of scientific and technological interest even in the absence of relevant experimental measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Automotive Silicon Carbide Power Module Cooling With A Novel Modular Manifold And Embedded Heat Sink

The next generation of integrated power electronics packages will implement wide-bandgap devices with ultrahigh device heat fluxes. Although jet impingement has received attention for power electronics thermal management, it is not used in commercial electric vehicles (EVs) because of the associated pressure drop and reliability concerns. Here, in this paper, we present a modular thermal management system designed for automotive power electronics. The system achieves superior thermal performance to benchmarked EVs, while adhering to reliability standards and with low pumping power. The system utilizes a low-cost and lightweight plastic manifold to generate jets over an optimized heat sink, which is embedded in the direct-bonded-copper (DBC) substrate. The embedded heat sink concept leverages additive manufacturing to add elliptical pin fins to the DBC substrate. The heat sink geometry is optimized for submerged jet impingement using a unit-cell model and an exhaustive search algorithm. The model predictions are validated using unit-cell experiments. A full-scale power module model is then used to compare the DBC-embedded heat sink against direct DBC cooling and baseplate-integrated heat sinks for single-sided (SS) and double-sided (DS) cooling concepts. Using the SS and DS DBC-embedded cooling concepts, the models predict a thermal resistance that represents a reduction of 75% and 85% compared to the 2015 BMW i3, respectively, for the same water-ethylene glycol inverter flow rate. We have shown that an inverter with a 100-kilo-Watt-per-liter power density is achievable with the proposed design.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Structural stability of thin overhanging walls during material extrusion additive manufacturing of thermoset-based ink

Recent developments have enabled material extrusion additive manufacturing of thermoset-based composite inks on the large scale. In addition, printing out-of-plane components is of broad interest to the polymer material extrusion community. Here, we address some of the challenges associated with both large-scale and out-of-plane thermoset material extrusion additive manufacturing by studying the height at which thin overhanging walls collapse. Walls at a range of overhang angles were printed until they collapsed. An optical camera captured the profile of each wall throughout the print, allowing the collapse height to be identified and the geometric fidelity to the programmed angle to be evaluated. Using previously measured rheological properties, predictive models were generated to approximate the collapse height and profile of the deflected walls. First, an analytical model was created to predict the height at which the walls would yield. The analytical model assumes the walls exhibit a perfectly linear profile; however, experiments proved this assumption to be false. Therefore, a finite element simulation was developed to account for the elastic deflection that occurs during printing. The finite element simulation predicts both the yield height and the deflected profile after the deposition of each layer. For the properties of the thermoset ink used here, the yield height predicted by the analytical model and finite element simulation are virtually identical. These predictions match experimental data reasonably well, but minor errors are observed. Accounting for the fully plastic moment appears to explain the small mismatch between experimental data and predictions. Additionally, the finite element simulation provides an excellent prediction of the deflected profile before the wall begins to collapse. Finally, by demonstrating that the collapse height and deflected profile of thin overhanging walls can be predicted, this work illustrates how the soft viscoelastic properties of thermoset-based composite inks limit the scale of a key feature required to print some nonplanar components. It also provides a basis to tailor in-process curing systems to suppress deflection and collapse of thin overhanging walls.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A Scoping Study to Develop a Computational Fluid Dynamics Based Model to Predict Radiological Materials Packaging Temperatures within a Generic Staging Building

The objective of this work is to perform computational fluid dynamics simulations of a ventilated radiological-material-package staging building to determine the effect of including or excluding a variety of physical effects and computational methods on both the predicted package temperatures and required computational resources. The generic building contains 640 drum-packages containing heat-generating, radiological material supported on four racks that are eight levels tall. Additionally, there is a forced ventilation system, lighting, and insulated walls. Computational models were constructed that included or excluded (a) shelving, (b) effects of unsteadiness, and (c) radiation heat transfer. Simulations with each drum modeled separately were compared to simpler simulations with sets of four drums represented by an equivalent box-package. These models employed between 106 to 107 elements. Steady state simulations predicted package temperatures that were within 0.1°C of simulations that included transient effects and required only one-eighth the computational resources. Calculations that excluded shelving predicted temperatures within 0.6°C of simulations that included shelving and required one-fourth the computational resources. Excluding radiation heat transfer systematically increased temperatures by around 1.5°C but reduced computational resources by a factor of four. The box-package model reduced the computational resources by a factor of 3, but systematically predicted higher temperatures by around 1.1°C. These results will be used to develop an efficient computational fluid dynamics model to assess the ability of different staging building designs to prevent the temperature of package components from exceeding specified limits.

42 ENGINEERING↗

DOE OSTI2021

Interpreting Write Performance of Supercomputer I/O Systems with Regression Models

This work seeks to advance the state of the art in HPC I/O performance analysis and interpretation. In particular, we demonstrate effective techniques to: (1) model output performance in the presence of I/O interference from production loads; (2) build features from write patterns and key parameters of the system architecture and configurations; (3) employ suitable machine learning algorithms to improve model accuracy. We train models with five popular regression algorithms and conduct experiments on two distinct production HPC platforms. We find that the lasso and random forest models predict output performance with high accuracy on both of the target systems. We also explore use of the models to guide adaptation in I/O middleware systems, and show potential for improvements of at least 15% from model-guided adaptation on 70% of samples, and improvements up to 10× on some samples for both of the target systems.

Xie, Bing↗

DOE OSTI2013

Multivariate Normal Tissue Complication Probability Modeling of Heart Valve Dysfunction in Hodgkin Lymphoma Survivors

Purpose: To establish a multivariate normal tissue complication probability (NTCP) model for radiation-induced asymptomatic heart valvular defects (RVD). Methods and Materials: Fifty-six patients treated with sequential chemoradiation therapy for Hodgkin lymphoma (HL) were retrospectively reviewed for RVD events. Clinical information along with whole heart, cardiac chambers, and lung dose distribution parameters was collected, and the correlations to RVD were analyzed by means of Spearman's rank correlation coefficient (Rs). For the selection of the model order and parameters for NTCP modeling, a multivariate logistic regression method using resampling techniques (bootstrapping) was applied. Model performance was evaluated using the area under the receiver operating characteristic curve (AUC). Results: When we analyzed the whole heart, a 3-variable NTCP model including the maximum dose, whole heart volume, and lung volume was shown to be the optimal predictive model for RVD (Rs = 0.573, P<.001, AUC = 0.83). When we analyzed the cardiac chambers individually, for the left atrium and for the left ventricle, an NTCP model based on 3 variables including the percentage volume exceeding 30 Gy (V30), cardiac chamber volume, and lung volume was selected as the most predictive model (Rs = 0.539, P<.001, AUC = 0.83; and Rs = 0.557, P<.001, AUC = 0.82, respectively). The NTCP values increase as heart maximum dose or cardiac chambers V30 increase. They also increase with larger volumes of the heart or cardiac chambers and decrease when lung volume is larger. Conclusions: We propose logistic NTCP models for RVD considering not only heart irradiation dose but also the combined effects of lung and heart volumes. Our study establishes the statistical evidence of the indirect effect of lung size on radio-induced heart toxicity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2017

Adsorption Equilibrium and Kinetics at Goethite-Water and Related Interfaces

This research study is an important component of a broader comprehensive project, “Geochemistry of Interfaces: From Surfaces to Interlayers to Clusters,” which sought to identify and evaluate the critical molecular phenomena at metal-oxide interfaces that control many geochemical and environmental processes. The primary goal of this research study was to better understand and predict adsorption of metal ions at mineral/water surfaces. Macroscopic data in traditional batch experiments was used to develop predictive models that characterize sorption in complex systems containing a wide range of background solution compositions. Our studies focused on systems involving alkaline earth metal (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ) and heavy metal (Hg 2+ , Co 2+ , Cd 2+ , Cu 2+ , Zn 2+ , Pb 2+ ) cations. The anions we selected for study included Cl - , NO 3 - , ClO 4 - , SO 4 2- , CO 3 2- and SeO 3 2- and the background electrolyte cations we examined included (Na + , K + , Rb + and Cs + ) because these represent a range of ion sizes and have varying potentials for forming ion-pairs or ternary complexes with the metal ions studied. The research led to the development of a modified titration congruency approach for estimating site densities for mineral oxides such as goethite. The CD-MUSIC version of the surface complexation modeling approach was applied to potentiometric titration data and macroscopic adsorption data for single-solute heavy metals, oxyanions, alkaline earth metals and background electrolytes over a range of pH and ionic strength. The model was capable of predicting sorption in bi-solute systems containing multiple cations, cations and oxyanions, and transition metal cations and alkaline earth metal ions. Incorporation of ternary complexes was required for modeling Pb(II)-Se(IV) and Cd(II)-Se(IV) systems. -Both crystal face contributions and capacitance values were shown to be sensitive to varying specific surface area but were successfully accounted for in the modeling strategy. The insights gained from the macroscopic, spectroscopic and CD-MUSIC modeling developed in this study can be used to guide the implementation of less complex models which may be more applicable to field conditions. The findings of this research suggest that surface complexation models can be used as a predictive tool for fate and transport modeling of metal ions and oxyanions in fresh and saline systems typical of energy production waters and wastewaters.

42 ENGINEERING↗

DOE OSTI2017

Measurement of inclusive and differential cross sections in the H → ZZ * → 4ℓ decay channel in pp collisions at $ \sqrt{s}=13 $ TeV with the ATLAS detector

Inclusive and differential fiducial cross sections of Higgs boson production in proton-proton collisions are measured in the H → ZZ * → 4ℓ decay channel. The proton-proton collision data were produced at the Large Hadron Collider at a centre-of-mass energy of 13 TeV and recorded by the ATLAS detector in 2015 and 2016, corresponding to an integrated luminosity of 36.1 fb –1 . The inclusive fiducial cross section in the H → ZZ * → 4ℓ decay channel is measured to be 3.62±0.50(stat) –0.20 +0.25 (sys) fb, in agreement with the Standard Model prediction of 2.91 ± 0.13 fb. The cross section is also extrapolated to the total phase space including all Standard Model Higgs boson decays. Several differential fiducial cross sections are measured for observables sensitive to the Higgs boson production and decay, including kinematic distributions of jets produced in association with the Higgs boson. Good agreement is found between data and Standard Model predictions. Here, the results are used to put constraints on anomalous Higgs boson interactions with Standard Model particles, using the pseudo-observable extension to the kappa-framework.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗