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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments

mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mechanistic modelling of SARS-CoV-2 and other infectious diseases and the effects of therapeutics

Modern viral kinetic modeling and its application to therapeutics is a field that attracted the attention of the medical, pharmaceutical and modeling communities during the early days of the AIDS epidemic. Its successes lead to applications of modeling methods not only to HIV but a plethora of other viruses, such as hepatitis C virus (HCV), hepatitis B virus (HBV) and cytomegalovirus (CMV), which along with HIV cause chronic diseases, and viruses such as influenza, respiratory syncytial virus (RSV), West Nile virus (WNV), Zika virus, and SAR-CoV-2, which generally cause acute infections. Here we first review the historical development of mathematical models to understand HIV and HCV infections and the effects of treatment by fitting the models to clinical data. Furthermore, we then focus on recent efforts and contributions of applying these models towards understanding SARS-CoV-2 infection and highlight outstanding questions where modeling can provide crucial insights and help to optimize non-pharmaceutical and pharmaceutical interventions of the COVID-19 pandemic. The review is written from our personal perspective emphasizing the power of simple target cell limited models that provided important insights and then their evolution into more complex models that captured more of the virology and immunology. To quote Albert Einstein “Everything should be made as simple as possible, but not simpler”, and this idea underlies the modeling we describe below.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mechanistic modeling of CO 2 well leakage in a generic abandoned well through a bridge plug cement-casing gap

Both known and unmapped plugged and abandoned wells are potential leakage pathways for CO 2 from geologic carbon sequestration (GCS) sites. Although many abandoned wells have cement bridge plugs installed to prevent leakage, the seal between the cement and the inner casing wall is subject to failure. In this study, we carried out detailed T2Well simulations of cases of sudden non-Darcy flow of CO 2 and brine leakage up the gap between a cement plug and the inner steel casing wall that becomes a fully connected flow path during the post-injection period. The goal of our study was two-fold: (1) to understand the dynamics, rates, and the characteristic temporal signals associated with the onset of leakage through various gap-aperture sizes, and (2) to suggest potential monitoring strategies based on the findings. Simulation results show that the leakage of CO 2 and brine upward is transient with interesting phase interference behavior. Time-dependent oscillatory flows with varying pressure, temperature, and flow rates of CO 2 and brine show strong dependence on gap aperture. Phase-change and decompression lead to very low temperatures at the top of the well for gap apertures larger than 4 mm suggesting that remote thermal monitoring at the ground surface may be an effective way of monitoring even if well locations are not known a priori. Pressure in the well is also indicative of CO 2 leakage. The temporal patterns of changing temperature and pressure may be useful diagnostic signals for leakage detection. Finally, these transient leakage signals may provide information on the cause of leakage and/or characteristics of the flow path that could inform effective remediation design and execution approaches.

58 GEOSCIENCES↗
DOE OSTI2025

Removal of Selenium Oxyanions from Aqueous Solutions by Ion Exchange: Equilibrium, Kinetics, and Mechanistic Modeling

Selenium (Se) is an essential micronutrient but toxic at high concentrations, posing challenges for water treatment. This study investigated the removal of selenate (SeO 4 2– ) and selenite (SeO 3 2– ) using the strong-base anion-exchange resin IRA-900, particularly in the presence of competing sulfate (SO 4 2– ). The performance of the commercially available resin IRA-900 was systematically investigated. The batch equilibrium behavior was studied in both single- and binary-component systems, and the kinetic behavior was investigated in single-component systems. Results confirmed a selectivity order of SeO 4 2– > SO 4 2– > SeO 3 2– , indicating preferential SeO 4 2– removal over competing SO 4 2– but lower affinity for SeO 3 2– . The maximum total exchange capacity was determined to be 2.04 mequiv/g. Furthermore, SeO 3 2– uptake was found to be pH-dependent, whereas SeO 4 2– uptake remained stable across a broad pH range. From a modeling perspective, the Law of Mass Action model effectively described equilibrium data, and a transport–reaction modeling framework captured removal kinetics of oxyanions including film and intraparticle diffusion. Finally, X-ray photoelectron spectroscopy confirmed ion exchange between chloride and Se oxyanions as the primary removal mechanism. These findings provide fundamental insights into the removal of Se oxyanions from aqueous solutions by ion exchange.

IRA-900↗
DOE OSTI2023

Linking stem rehydration kinetics to hydraulic traits using a novel method and mechanistic model

Background: Despite the recognized importance of hydraulic capacitance as a mechanism used by plants to maintain hydraulic functioning during high transpiration, characterizing the dynamics of capacitance remains a challenge. Methods: For this work, we used a novel ‘two-balance method’ to investigate relationships between stem rehydration kinetics and other hydraulic traits in multiple tree species, and we developed a model to explore stem rehydration kinetics further. Key Results: We found that: (1) rehydration time constants and the amount of water uptake occurring during rehydration differed significantly across species; (2) time constants did not change with declining water potential (Ψ), while water uptake increased at lower Ψ in some species; (3) longer time constants were associated with lower wood density, higher capacitance and less negative stem pressures causing 50 % loss of hydraulic conductivity (P 50 ); (4) greater water uptake occurred in stems with lower wood density and less negative P 50 values; and (5) the model could estimate the total hydraulic resistance of the rehydration path, which cannot be measured directly. Conclusions: Overall, the two-balance method can be used to examine rehydration dynamics quickly and thoroughly in detached woody stems. This method has the potential to improve our understanding of how capacitance functions across tree species, which is an often-overlooked component of whole-plant hydraulics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Mechanistic modeling of lifetime distribution of SiC/SiC composite claddings

Silicon carbide (SiC) fiber-reinforced SiC matrix (SiC/SiC) composites have emerged as a new material candidate for fuel claddings in light water reactors. Recent studies showed that the load capacity of SiC/SiC materials exhibits a considerable statistical variation. Therefore, reliability analysis plays a critical role in design of SiC/SiC composite claddings. Here, this paper presents a probabilistic model for the lifetime distribution of SiC/SiC composites. The model is anchored by a multiaxial stress-based failure criterion and subcritical damage accumulation mechanism. Based on the kinetics of subcritical damage growth, the lifetime distribution of a laboratory test specimen for any given loading history can be calculated. A finite weakest-link model is used to extrapolate the lifetime distribution of test specimens to full-length claddings. It is shown that the damage accumulation mechanism has a strong influence on the lifetime distribution of the cladding. This finding highlights the importance of understanding the static fatigue behavior of SiC/SiC composites. The present analysis also demonstrates an intricate length effect on the failure probability of the cladding, which is expected to play a crucial role in design extrapolation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A mechanistic model of a PWR-based nuclear power plant in response to external hazard-induced station blackout accidents

Natural hazard-induced nuclear accidents, such as the Fukushima Daiichi Accident that occurred in Japan in 2011, have significantly increased reactor safety studies in understanding nuclear power plant (NPP) responses to external hazard events such as earthquakes and floods. Natural hazards could cause the loss of offsite power in nuclear power plants, potentially leading to a Station Blackout (SBO) accident that significantly contributes to the overall risk of nuclear power plant accidents. Despite the fact that extensive research has been conducted on the station blackout accident for nuclear power plant, further understanding of these events is needed, particularly in the context of the dynamic nature of external hazards such as external flooding. This paper estimates the progression of station blackout events for a generic pressurized water reactor (PWR) in response to external flooding events. The original RELAP5-3D model of the Westinghouse four-loop design pressurized water reactor was adopted and modified to simulate the external flood-induced station blackout accident, including the short-term and long-term station blackout scenarios. A sensitivity analysis of long-term station blackout, examining reactor operation times and analyzing key parameters over time, was also conducted in this work. The results of the analyses, especially the critical timing parameters of key event sequences, provide useful insights about the time during the external flooding event, which is important for plant operators to make timely decisions to prevent potential core damage. This paper represents significant progress toward developing an integrated risk assessment framework for further identifying and assessing the effects of the critical sources of uncertainties of nuclear power plant under external hazard-induced events.

Liu, Tao↗
DOE OSTI2020

An improved mechanistic model for ammonia volatilization in Earth system models: Flow of Agricultural Nitrogen version 2 (FANv2)

Abstract. Volatilization of ammonia (NH 3 ) from fertilizers and livestock wastes forms a significant pathway of nitrogen losses in agricultural ecosystems and constitutes the largest source of atmospheric emissions of NH 3 . This paper describes a major update to the process model FAN (Flow of Agricultural Nitrogen), which evaluates NH 3 emissions interactively within an Earth system model; in this work, the Community Earth System Model (CESM) is used. The updated version (FANv2) includes a more detailed treatment of both physical and agricultural processes, which allows the model to differentiate between the volatilization losses from animal housings, manure storage, grazed pastures, and the application of manure and different types of mineral fertilizers. The modeled ammonia emissions are first evaluated at a local scale against experimental data for various types of fertilizers and manure, and they are subsequently run globally to evaluate NH3 emissions for 2010–2015 based on gridded datasets of fertilizer use and livestock populations. Comparison of regional emissions shows that FANv2 agrees with previous inventories for North America and Europe and is within the range of previous inventories for China. However, due to higher NH 3 emissions in Africa, India, and Latin America, the global emissions simulated by FANv2 (48 Tg N) are 30 %–40 % higher than in the existing inventories.

Vira, Julius↗
DOE OSTI2020

A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm

Neither the disease mechanism nor treatments for COVID-19 are currently known. Here, we present a novel molecular mechanism for COVID-19 that provides therapeutic intervention points that can be addressed with existing FDA-approved pharmaceuticals. The entry point for the virus is ACE2, which is a component of the counteracting hypotensive axis of RAS. Bradykinin is a potent part of the vasopressor system that induces hypotension and vasodilation and is degraded by ACE and enhanced by the angiotensin 1-9 produced by ACE2. Here, we perform a new analysis on gene expression data from cells in bronchoalveolar lavage fluid (BALF) from COVID-19 patients that were used to sequence the virus. Comparison with BALF from controls identifies a critical imbalance in RAS represented by decreased expression of ACE in combination with increases in ACE2, renin, angiotensin, key RAS receptors, kinogen and many kallikrein enzymes that activate it, and both bradykinin receptors. This very atypical pattern of the RAS is predicted to elevate bradykinin levels in multiple tissues and systems that will likely cause increases in vascular dilation, vascular permeability and hypotension. These bradykinin-driven outcomes explain many of the symptoms being observed in COVID-19.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A mechanistic damage model for solid oxide fuel cell ceramic materials - Part I: Constitutive modeling

A multiscale mechanistic damage model for solid oxide fuel cell (SOFC) ceramics that combines micromechanics of stiffness reduction due to material porosity change and microcracking with a continuum damage mechanics (CDM) description for the evolution of microcracks up to fracture is developed in this work. The model also accounts for volumetric swelling of the anode due to redox cycling. Porosity change and swelling during redox combined with normal operating thermomechanical loads could increase the stress, strain and damage distributions in SOFC stacks leading them to failure. The proposed model involves three governing parameters: (i) the porosity in terms of the pore or void volume fraction, (ii) material swelling magnitude prescribed at a given loading step, and (iii) the damage variable that describes microcracking caused by thermomechanical loads and swelling. Pores and microcracks in the ceramics are modeled as randomly distributed ellipsoidal inclusions with negligible stiffness by an Eshelby-Mori-Tanaka formulation combined with an inclusion orientation distribution method. Microcracking damage evolution is described by a CDM formulation. Volumetric swelling is treated in a similar way to thermal expansion in the constitutive relations. After validation and numerical checks, the damage model is used to analyze a simplified SOFC positive-electrode/electrolyte/negative-electrode (PEN) structure subjected a redox cycle in addition to thermomechanical loads experienced during normal operation of a SOFC stack.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2025

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Bayesian discovery of optimal reduced order models from mechanistic and experimental data: A case study of Pd penetration in TRISO fuels using BISON

TRistructural ISOtropic (TRISO) particles rely on a silicon carbide (SiC) layer as the primary structural material and barrier to metallic fission products (FPs) release. Accurate prediction of palladium (Pd) transport and penetration is therefore critical for qualifying TRISO fuels for advanced reactors. The empirical correlation for Pd penetration in BISON is derived from historical particle-fuel data, but cannot explain the large scatter in the experimental data that arises from varying experimental conditions. To aid fuel qualification, we previously developed a mechanistic reduced order model (ROM) using BISON that resolves these dependencies. Here, in this work we build on that mechanistic ROM and perform validation and quantify its uncertainty using Bayesian uncertainty quantification (UQ). calibration against a suite of in-pile and out-of-pile experiments spanning particle compositions, geometries, and operating conditions, and we benchmark it against the empirical correlation. Bayesian UQ identifies influential parameters, calibrates them to data, and yields predictive intervals. Results show that while the empirical correlation can be tuned to fit a single experiment type, it transfers poorly; the mechanistic ROM sustains accuracy with credible uncertainty across disparate conditions. This demonstrates a practical path—via Bayesian UQ applied to mechanistic ROMs—to leverage single-effect experiments for inferring in-reactor behavior and supporting TRISO fuel qualification.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗