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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Predicting Compliance in an Epidemiological Model: Constructs from Psychological Theory and Research

Vaccination and the alternative behavior, vaccine refusal, are a classic example of manifesting behaviors driven by social norms and norm violations. Establishing how norms emerge, and under what circumstances people choose to violate them are key issues to understand in modeling epidemics. Interactions between individuals can lead to large-scale patterning of behavior (emergent phenomena). As norm violations are revealed through human behavior, drawing on psychological theory and principles to predict those violations is a viable approach for more human-constrained epidemiological models. As an example of the implications at scale, vaccine refusal is correlated with the spread of mis/disinformation about vaccine side-effects. Considering the complexities of network dynamics, the downstream effects means that if even a small group within a population are persuaded against vaccination, there is a reservoir from which disease and disease outbreaks can propagate. This work will attempt to identify those psychological indicators, to define circumstances that predict health behaviors, and identify potentially modifiable antecedents of health behavior, and factors that influence changes toward health protective behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Nuclear System-of-Systems Capabilities Analytic Process

This dissertation discusses the impetus for, development of, and initial demonstration of NuSCAPTM: the Nuclear System-of-Systems Capabilities Analytic Process TM . NuSCAP is an approach executed via a Python® application that enables capabilities-based vulnerability analyses of military systems of systems (SOS) exposed to prompt nuclear weapon effects. The NuSCAP application calls on industry-standard, fast-running nuclear weapon effects tools and the Monte Carlo N-Particle®1 (MCNP®) code to evaluate the impact of nuclear weapon environments on the military capabilities of a complex and networked SOS.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2023

Quantifying automated vehicle benefits in reducing driving stress: a simulation experiment approach

Driving is a stressful activity because of the mental workload required to maneuver a vehicle in certain travel contexts, such as congested traffic, multi-modal networks requiring complex interaction with surrounding vehicles, and aggressive driving. Autonomous vehicles (AVs), on the other hand, can reduce the mental workload by performing most of the driving tasks and providing users with a comfortable ride. This study develops a pathway model to relate different health determinants, including travel reliability, safety, driving comfort, and value of time, to Autonomous vehicles driving and studies their impact on the value of driving stress. A case study example of Autonomous vehicles simulation is used to determine the impact of these health determinants. The value of driving stress in Autonomous vehicles is estimated as a function of the value of these individual health determinants. The results show that the perception of safe or unsafe driving in Autonomous vehicles is the most important factor in changing the perception of driving stress in Autonomous vehicles. Similarly, perceptions of comfortable driving in Autonomous vehicles and reduced workload with a higher value of time also reduce driving stress in Autonomous vehicles. These results allow Autonomous vehicles adoption models to explicitly consider driving stress reduction as a benefit and can improve understanding of Autonomous vehicles adoption, which may require quantitative analysis of underlying motivating benefits, including driving stress reduction.

Khattak, Zulqarnain H.↗
DOE OSTI2021

A t FUT4 and A t FUT6 Are Arabinofuranose-Specific Fucosyltransferases

The bulk of plant biomass is comprised of plant cell walls, which are complex polymeric networks, composed of diverse polysaccharides, proteins, polyphenolics, and hydroxyproline-rich glycoproteins (HRGPs). Glycosyltransferases (GTs) work together to synthesize the saccharide components of the plant cell wall. The Arabidopsis thaliana fucosyltransferases (FUTs), At FUT4, and At FUT6, are members of the plant-specific GT family 37 (GT37). At FUT4 and At FUT6 transfer fucose (Fuc) onto arabinose (Ara) residues of arabinogalactan (AG) proteins (AGPs) and have been postulated to be non-redundant AGP-specific FUTs. At FUT4 and At FUT6 were recombinantly expressed in mammalian HEK293 cells and purified for biochemical analysis. We report an updated understanding on the specificities of At FUT4 and At FUT6 that are involved in the synthesis of wall localized AGPs. Our findings suggest that they are selective enzymes that can utilize various arabinogalactan (AG)-like and non-AG-like oligosaccharide acceptors, and only require a free, terminal arabinofuranose. We also report with GUS promoter-reporter gene studies that AtFUT4 and AtFUT6 gene expression is sub-localized in different parts of developing A. thaliana roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Neuroevolution Application to Collaborative and Heuristics-Based Connected and Autonomous Vehicle Cohort Simulation at Uncontrolled Intersection

Artificial intelligence is gaining tremendous attractiveness and showing great success in solving various problems, such as simplifying optimal control derivation. This work focuses on the application of Neuroevolution to the control of Connected and Autonomous Vehicle (CAV) cohorts operating at uncontrolled intersections. The proposed method implementation’s simplicity, thanks to the inclusion of heuristics and effective real-time performance are demonstrated. The resulting architecture achieves nearly ideal operating conditions in keeping the average speeds close to the speed limit. It achieves twice as high mean speed throughput as a controlled intersection, hence enabling lower travel time and mitigating energy inefficiencies from stop-and-go vehicle dynamics. Low deviation from the road speed limit is hence continuously sustained for cohorts of at most 50 m long. This limitation can be mitigated with additional lanes that the cohorts can split into. The concept also allows the testing and implementation of fast-turning lanes by simply replicating and reconnecting the control architecture at each new road crossing, enabling high scalability for complex road network analysis. The controller is also successfully validated within a high-fidelity vehicle dynamic environment, showing its potential for driverless vehicle control in addition to offering a new traffic control simulation model for future autonomous operation studies.

Jacquelin, Frederic (ORCID:0000000183154344)↗
DOE OSTI2022

Findings on Subtask 3.1 - Bakken Rich Gas Enhanced Oil Recovery Project

Total in-place oil for the Bakken petroleum system (BPS) (which includes the Bakken and Three Forks Formations) has been estimated to be 600 billion barrels (bbl). However, BPS wells have decline rates as high as 85% over the first 3 years of their lives, and primary recovery factors typically range from 3% to 10% of original oil in place. Given the low initial recovery rates, even small incremental productivity improvements could dramatically increase technically recoverable oil in the BPS. One potential solution is enhanced oil recovery (EOR) using gas injection, such as carbon dioxide (CO2) or hydrocarbon (HC) gases. While commonly used in conventional reservoirs, CO2 EOR in unconventional tight oil reservoirs has been limited to pilot tests. EOR using rich gas (mixture of methane, ethane, and propane) has also been employed in numerous pilots in several unconventional plays and has recently been successfully applied in the Eagle Ford play. If successful, large-scale gas-based EOR in the BPS could dramatically increase oil productivity and recovery factors and extend the life of the play for decades. While CO2 may be a technically suitable working fluid for EOR in the BPS, supplies are limited and costs for using CO2 in EOR pilots are prohibitively high. Meanwhile, produced gas flaring has presented challenges for BPS operators in North Dakota. Analysis conducted by the North Dakota Pipeline Authority indicates that the current gas-gathering infrastructure in North Dakota is insufficient to accommodate all of the associated gas that is produced from the BPS. The geographically isolated location of North Dakota relative to large natural gas markets, combined with suppressed natural gas prices, has made it economically challenging for industry to invest capital in expanding gas-gathering infrastructure in the state. These circumstances led to a research program conducted by the Energy & Environmental Research Center (EERC) in partnership with Liberty Resources Management Company LLC (LR) to examine the potential to use rich gas injection for EOR and mitigate flaring. A rich gas EOR pilot test was designed and executed by LR at its Stomping Horse development area in Williams County, North Dakota. From July 2018 through May 2019, a total of 160 million standard cubic feet (MMscf) of rich produced gas was injected into the BPS using five different wells in a sequential injection strategy. LR’s Leon–Gohrick drill spacing unit (DSU) was used as the test site. Regulatory oversight was provided by the North Dakota Industrial Commission (NDIC). Technical support was provided by the EERC through a series of laboratory, modeling, and field-based activities, and additional post-pilot research activities incorporated learnings from the test, developed new laboratory data, improved fracture modeling methods, and developed machine learning and big data analytics. The results from the Stomping Horse rich gas EOR pilot activities indicate that developing an effective, economical EOR approach for the BPS will require more field tests. Another key lesson learned from the Stomping Horse tests is that detailed pre- and posttest data on reservoir conditions and fluids production are essential. Robust reservoir characterization provides information that is crucial to creating realistic geomodels and conducting valid dynamic simulations of potential EOR scenarios. A detailed understanding of the completions and production history of offset wells is also necessary for valid test result interpretations. This knowledge is essential to designing the operational parameters of injectivity tests and interpreting the results. A conformance control strategy is also essential to success. Laboratory-based examinations of rich gas interactions with reservoir fluids and rocks were conducted, with an emphasis on determining the ability to mobilize oil in the tight reservoir rocks and shales of the BPS. Injection fluid composition was shown to have a positive impact on reducing reservoir oil minimum miscibility pressure (MMP), reducing interfacial tension (IFT), and altering wettability. IFT and contact angle measurements demonstrated that wettability can be altered in the presence of rich gas, suggesting the potential to improve oil recovery. Iterative modeling of surface infrastructure and reservoir performance using data generated by the various project activities was conducted. A geologic model of the Stomping Horse area was built; history-matched oil, gas, and water production was used in simulations of various EOR scenarios. Early programmatic modeling results were used to support LR’s design and operation of the EOR pilot and to provide insight regarding optimization of future commercial-scale BPS EOR design and operations. Post-pilot modeling focused on alternative methods of understanding complex fracture networks and accelerating simulation time. These led to improved simulation run times and provide excellent history-matching results. Several of these iterative models were used as the bases for developing algorithms into machine learning and big data analytics. History matching in reservoir simulation is time-consuming and computer processing-intensive. Machine learning algorithms were created, and an automated history-matching tool was developed. A large set of synthetic reservoir simulations were created to generate well responses (oil, gas, and water production, well bottomhole pressure [BHP], and tracer or propane breakthrough) for a set of EOR operating parameters that included offset well status (open or closed), injectate (rich gas or propane), injection rate, and injection well BHP. A user interface was developed to provide real-time visualization. Machine learning-based models were developed to provide rapid forecasting of well performance given a set of user-defined EOR operating parameters. These predictive models allow the user to modify the offset well status, injection rate, and injection well BHP and rapidly forecast future production performance. The combination of real-time visualization tools with real-time forecasting tools provides a framework for real-time control—operational changes that the EOR site operator can enact (e.g., changing gas injection rates) to affect the observed performance and potentially improve the EOR outcome. There is great reason to be optimistic about the future of EOR in the Bakken. The results of the laboratory studies suggest significant potential for high rates of oil mobilization using produced field gas injection under the right conditions. The results of the lab studies, combined with rigorous statistical analysis of well production data and associated modeling efforts, confirm the notion that fluid mobility within the reservoir is controlled by fractures. As more knowledge is gained about the nature and distribution of fracture networks in the Bakken, the industry will be in a better position to predict and, ultimately, influence fluid mobility. New field tests are necessary to develop a more complete understanding of those conditions. Thoughtful and creatively engineered field tests within a well-characterized geologic setting will yield the fundamental knowledge needed to take Bakken oil production to the next level. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission’s Oil and Gas Research Program and Computer Modelling Group.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2021

State changes: insights from the U.S. Long Term Ecological Research Network

Understanding the complex and unpredictable ways ecosystems are changing and predicting the state of ecosystems and the services they will provide in the future requires coordinated, long-term research. This paper is a product of a U.S. National Science Foundation funded Long Term Ecological Research (LTER)network synthesis effort that addressed anticipated changes in future populations and communities. Each LTER site described what their site would look like in50 or 100 yr based on long-term patterns and responses to global change drivers in each ecosystem. Common themes emerged and predictions were grouped into state change, connectivity, resilience, time lags, and cascading effects. Here, we report on the “state change” theme, which includes examples from the Georgia Coastal (coastal marsh), Konza Prairie (mesic grassland), Luquillo(tropical forest), Sevilleta (arid grassland), and Virginia Coastal (coastal grassland) sites. Ecological thresholds(the point at which small changes in an environmental driver can produce an abrupt and persistent state change in an ecosystem quality, property, or phenomenon) were most commonly predicted. For example, in coastal ecosystems, sea-level rise and climate change could convert salt marsh to mangroves and coastal barrier dunes to shrub thicket. Reduced fire frequency has converted grassland to shrubland in mesic prairie, whereas overgrazing combined with drought drive shrub encroachment in arid grasslands. Lastly, tropical cloud forests are susceptible to climate-induced changes in cloud base altitude leading to shifts in species distributions. Overall, these examples reveal that state change is a likely outcome of global environmental change across adverse range of ecosystems and highlight the need for long-term studies to sort out the causes and consequences of state change. The diversity of sites within the LTER network facilitates the emergence of overarching concepts about state changes as an important driver of ecosystem structure, function, services, and futures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

How Many Trip Requests Could We Support? An Activity-Travel Based Vehicle Scheduling Approach

In a world of ever-changing travel behavior and ever-increasing modal options, is vital to have integrated models that could capture the interactions between supply and demand layers of travel. Addressing this need, we propose three different versions of network representation and mathematical models for the activity-based vehicle routing problem to connect activity-travel graphs of passengers (demand layer) to spatio-temporal networks of vehicles (supply layer). Versions I and II are arc-based, while version III is path-based. In version I, we introduce the concept of activity-travel graphs for passengers. For vehicles, we construct space–time networks and add a new dimension, called “under-service state”, to track the execution status of trip requests at any location and time. In version II, we reduce the complexity of the network structure by eliminating the state dimension and some other modifications in the structure of the passengers’ and vehicles’ network. Although both versions can capture various behavioral constraints of the activity-based vehicle routing problem (e.g., mandatory and optimal activities, duration of activities, chain of activities, preferred starting and ending times of activities), due to the high level of complexity of the network structure, both versions can only solve small-sized problems. To tackle the computational complexity, we propose a path-based network representation in version III, and to make a balance between the disutility of passengers and vehicles, we present a tolled user equilibrium problem. Mathematical models are coded in C and GAMS and implemented on real-world Phoenix regional transportation network with more than 39 million trip requests, which demonstrate the effectiveness of the proposed solution for the original and restricted master problems.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2022

Conjugated Polyelectrolyte-Based Complex Fluids as Aqueous Exciton Transport Networks

The ability to assemble artificial systems that mimic aspects of natural light-harvesting functions is fascinating and attractive for materials design. Given the complexity of such a system, a simple design pathway is desirable. Here, we argue that associative phase separation of oppositely charged conjugated polyelectrolytes (CPEs) can provide such a path in an environmentally benign medium: water. We find that complexation between an exciton–donor and acceptor CPE leads to formation of a complex fluid. We interrogate exciton transfer from the donor to the acceptor CPE within the complex fluid and find that transfer is highly efficient. We also find that excess molecular ions can tune the modulus of the inter-CPE complex fluid. Even at high ion concentrations, CPEs remain complexed with significantly delocalized electronic wavefunctions. In conclusion, our work lays the rational foundation for complex, tunable aqueous light-harvesting systems via the intrinsic thermodynamics of associative phase separation.

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

Reducing uncertainty of high-latitude ecosystem models through identification of key parameters

Abstract Climate change is having significant impacts on Earth’s ecosystems and carbon budgets, and in the Arctic may drive a shift from an historic carbon sink to a source. Large uncertainties in terrestrial biosphere models (TBMs) used to forecast Arctic changes demonstrate the challenges of determining the timing and extent of this possible switch. This spread in model predictions can limit the ability of TBMs to guide management and policy decisions. One of the most influential sources of model uncertainty is model parameterization. Parameter uncertainty results in part from a mismatch between available data in databases and model needs. We identify that mismatch for three TBMs, DVM-DOS-TEM, SIPNET and ED2, and four databases with information on Arctic and boreal above- and belowground traits that may be applied to model parametrization. However, focusing solely on such data gaps can introduce biases towards simple models and ignores structural model uncertainty, another main source for model uncertainty. Therefore, we develop a causal loop diagram (CLD) of the Arctic and boreal ecosystem that includes unquantified, and thus unmodeled, processes. We map model parameters to processes in the CLD and assess parameter vulnerability via the internal network structure. One important substructure, feed forward loops (FFLs), describe processes that are linked both directly and indirectly. When the model parameters are data-informed, these indirect processes might be implicitly included in the model, but if not, they have the potential to introduce significant model uncertainty. We find that the parameters describing the impact of local temperature on microbial activity are associated with a particularly high number of FFLs but are not constrained well by existing data. By employing ecological models of varying complexity, databases, and network methods, we identify the key parameters responsible for limited model accuracy. They should be prioritized for future data sampling to reduce model uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Region-Based Convolutional Neural Network for Wind Turbine Wake Characterization in Complex Terrain

We present a proof of concept of wind turbine wake identification and characterization using a region-based convolutional neural network (CNN) applied to lidar arc scan images taken at a wind farm in complex terrain. We show that the CNN successfully identifies and characterizes wakes in scans with varying resolutions and geometries, and can capture wake characteristics in spatially heterogeneous fields resulting from data quality control procedures and complex background flow fields. The geometry, spatial extent and locations of wakes and wake fragments exhibit close accord with results from visual inspection. The model exhibits a 95% success rate in identifying wakes when they are present in scans and characterizing their shape. To test model robustness to varying image quality, we reduced the scan density to half the original resolution through down-sampling range gates. This causes a reduction in skill, yet 92% of wakes are still successfully identified. When grouping scans by meteorological conditions and utilizing the CNN for wake characterization under full and half resolution, wake characteristics are consistent with a priori expectations for wake behavior in different inflow and stability conditions.

17 WIND ENERGY↗
DOE OSTI2021

Subsurface Characterization of Hydraulic Fracture Test Site-2 (HFTS-2), Delaware Basin

Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Wolfcamp Formation of the Permian (Delaware) Basin. This paper focuses on integration, advanced geological characterization, and 3D subsurface modeling of the comprehensive HFTS-2 dataset. The study showcases a multidisciplinary reservoir characterization approach that incorporates geology, petrophysics, geochemistry, geomechanics, microseismic, and subsurface engineering analysis. Subsurface characterization of organic-rich mudstone formations requires understanding complex hydraulic fracture network growth in relation to inherent lithology, geomechanical properties, and interaction with pre-existing natural fractures. This paper presents a characterization workflow incorporating pre- and post-stimulation subsurface data, unique to the HFTS-2 dataset. The study integrated: (1) rock properties from logs, cores, and thin sections; (2) natural and hydraulic fracture descriptions from cores and image logs; (3) local and regional stresses; (4) geomechanics; (5) microseismic; (6) fiber optic (FO) and bottomhole pressure gauge (BHPG) response; and (7) produced fluids analysis. During a stimulation treatment, creation of the stimulated rock volume (SRV) is influenced by several subsurface factors. Key contributing factors include structural context, stress conditions, lithology, facies architecture, pre-existing natural fractures, and geomechanical properties. The HFTS-2 subsurface data integration indicates that the SRV is comprised of a complex juxtaposition of hydraulic fracture swarms, as evidenced by image logs analysis, core description, and microseismic monitoring. The HFTS-2 microseismic event density was used to generate 3D heat maps that serve as a representative SRV footprint, corroborated by secondary datasets. These maps were further integrated with petrophysical and geomechanical characteristics, as well as responses from FO and BHPG, to estimate the lateral and vertical dimensions of the effective fractures. The geological characterization for the HFTS-2 dataset combined with 3D modeling for petrophysical and geomechanical properties provides a strong foundation for subsurface simulation and optimization studies. Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/1-21URTC/D011S005R001/2477501/urtec-2021-5243-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5243 The workflow improved our understanding of HFTS-2 hydraulic fracture propagation and characteristics in relation to offset pressure depletion and interaction with pre-existing natural fractures. Analysis showed that fracture geometry varies by stage and by well, and a complex fracture network is generated with varying fracture density. The multidisciplinary workflow presented herein for integration and characterization serves as a foundation to evaluate completion efficiency and estimate areal and vertical stimulation and depletion extent for the project. Furthermore, the workflow and learnings can also be transferred to other unconventional plays.

58 GEOSCIENCES↗
DOE OSTI2025

Spatiotemporal pattern detection, generation, and computation with circuits

Abstract Implementations of neurons, delays, and synapse circuits are presented with simulations. These neural elements are used to create two small spiking neural networks, the Rate-Window and Order-Biased clusters, which are capable of detecting simple two-spike spatiotemporal patterns. A simple pattern detecting network (SPDN) is created by combining the Rate-Window and Order-Biased clusters, where clusters are small spiking neural networks, and its simple pattern detection ability is demonstrated in simulation. The SPDN is used to implement a complex pattern detecting network (CPDN) and its complex pattern detection ability is demonstrated in simulation. Methods for generating arbitrary spatiotemporal patterns are presented. The CPDN and spatiotemporal pattern generation methods are then used to implement a novel spatiotemporal computing paradigm based on detecting and responding to spatiotemporal symbols. A simulation of a spatiotemporal half adder is presented to demonstrate the computing paradigm.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Benchmarking a Tunable Quantum Neural Network on Trapped-Ion and Superconducting Hardware

We implement a quantum generalization of a neural network on trapped-ion and IBM superconducting quantum computers to classify MNIST images, a common benchmark in computer vision. The network feedforward involves qubit rotations whose angles depend on the results of measurements in the previous layer. The network is trained via simulation, but inference is performed experimentally on quantum hardware. The classical-to-quantum correspondence is controlled by an interpolation parameter, $a$, which is zero in the classical limit. Increasing $a$ introduces quantum uncertainty into the measurements, which is shown to improve network performance at moderate values of the interpolation parameter. We then focus on particular images that fail to be classified by a classical neural network but are detected correctly in the quantum network. For such borderline cases, we observe strong deviations from the simulated behavior. We attribute this to physical noise, which causes the output to fluctuate between nearby minima of the classification energy landscape. Such strong sensitivity to physical noise is absent for clear images. We further benchmark physical noise by inserting additional single-qubit and two-qubit gate pairs into the neural network circuits. Our work provides a springboard toward more complex quantum neural networks on current devices: while the approach is rooted in standard classical machine learning, scaling up such networks may prove classically non-simulable and could offer a route to near-term quantum advantage.

FOS: Physical sciences↗
DOE OSTI2020

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗
DOE OSTI2022

Learning generative neural networks with physics knowledge

Deep generative neural networks have enabled modeling complex distributions, but incorporating physics knowledge into the neural networks is still challenging and is at the core of current physics-based machine learning research. To this end, we propose a physics generative neural network (PhysGNN), a new class of generative neural networks for learning unknown distributions in a physical system described by partial differential equations (PDE). PhysGNN couples PDE systems with generative neural networks. It is a fully differentiable model that allows back-propagation of gradients through both numerical PDE solvers and generative neural networks, and is trained by minimizing the discrete Wasserstein distance between generated and observed probability distributions of the PDE outputs using the stochastic gradient descent method. Moreover, PhysGNN does not require adversarial training like standard generative neural networks, which offers better stability than adversarial training. We show that PhysGNN can learn complex distributions in stochastic inverse problems, where conventional methods such as maximum likelihood estimation and momentum matching methods may be inapplicable when little knowledge is known about the form of unknown distributions or the physical model is too complex. Furthermore, our method allows physics-based generative neural network training for learning complex distributions in the context of differential equations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The Mycobacterium tuberculosis protein O -phosphorylation landscape

Bacterial phosphosignaling has long been synonymous with the histidine kinases of the two component systems (TCSs), but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignaling enzymes in eukaryotes, but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is unclear. Here, we explored the global signaling capacity of the STPKs in Mtb. We generated a panel of STPK loss- and gain-of-function strains and measured the resulting O-phosphorylation and transcriptional changes. This deep phosphoproteome shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >70% of the proteome. The substrate-kinase interactions of STPKs show an extensive interface with the transcriptional machinery, resulting in STPK regulation of gene expression of over 30% of Mtb genes. Finally, Mtb O-phosphorylation gives rise to an expansive, distributed, and cooperative network of a complexity that has previously only been associated with eukaryotic phosphosignaling networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Computationally Efficient Multiscale Neural Networks Applied to Fluid Flow in Complex 3D Porous Media

Abstract The permeability of complex porous materials is of interest to many engineering disciplines. This quantity can be obtained via direct flow simulation, which provides the most accurate results, but is very computationally expensive. In particular, the simulation convergence time scales poorly as the simulation domains become less porous or more heterogeneous. Semi-analytical models that rely on averaged structural properties (i.e., porosity and tortuosity) have been proposed, but these features only partly summarize the domain, resulting in limited applicability. On the other hand, data-driven machine learning approaches have shown great promise for building more general models by virtue of accounting for the spatial arrangement of the domains’ solid boundaries. However, prior approaches building on the convolutional neural network (ConvNet) literature concerning 2D image recognition problems do not scale well to the large 3D domains required to obtain a representative elementary volume (REV). As such, most prior work focused on homogeneous samples, where a small REV entails that the global nature of fluid flow could be mostly neglected, and accordingly, the memory bottleneck of addressing 3D domains with ConvNets was side-stepped. Therefore, important geometries such as fractures and vuggy domains could not be modeled properly. In this work, we address this limitation with a general multiscale deep learning model that is able to learn from porous media simulation data. By using a coupled set of neural networks that view the domain on different scales, we enable the evaluation of large ( $$>512^3$$ > 512 3 ) images in approximately one second on a single graphics processing unit. This model architecture opens up the possibility of modeling domain sizes that would not be feasible using traditional direct simulation tools on a desktop computer. We validate our method with a laminar fluid flow case using vuggy samples and fractures. As a result of viewing the entire domain at once, our model is able to perform accurate prediction on domains exhibiting a large degree of heterogeneity. We expect the methodology to be applicable to many other transport problems where complex geometries play a central role.

36 MATERIALS SCIENCE↗