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At least 73 records · Page 4

Metamodeling Time-Temperature Creep Parameters

Abstract There exist many time-temperature parameter (TTP) models for creep rupture prediction of components including the Larson–Miller (LM), Manson–Haferd (MH), Manson–Brown (MB), Orr–Sherby–Dorn (OSD), Manson–Succop (MS), Graham–Walles (GW), Chitty–Duval (CD), Goldhoff–Sherby (GS) models. It remains a challenge to determine which model is “best”, capable of accurate interpolation and physically realistic extrapolation of creep rupture data for a given material. In this study, metamodeling is applied to create a unified TTP metamodel that combines and regresses into twelve TTP models (eight existing and four newly derived). An analysis of the mathematical problems that exist in TTP models is provided. A matlab code is written that can: (1) calibrate the material constants of any of the twelve TTP models (using the metamodel); (2) determine the most suitable stress-parameter function; (3) and report the normalized mean square error (NMSE) of rupture predictions for a given material database. Using the metamodel, and code, a design engineer can make an intelligent selection of the “best” TTP model for creep resistant design. This process is demonstrated using four isotherms of alloy P91 creep rupture data. To assess the influence of material, further validation is performed on alloys Hastelloy X, 304SS, and 316SS. It is determined that the “best” model is dependent on material type and the quality and quantity of available data.

Engineering↗

Fault Diagnosis of Double Pitch Time-Sharing Meshing Toothed Conveyor Chain Transmission System Based on Neural Network

With the rapid development of industry, the production and demand of automobiles have increased significantly. The generation of cars often requires tens of thousands of processes, consisting of hundreds of assembly lines to complete. Chain conveyors are widely used in the transportation of automobile assembly lines. The existing conveyor chains are roller chains. With the improvement of the requirements for conveyor reliability, synchronization, and environmental friendliness, the characteristics of roller conveyor chains restrict the further development of chain conveyors. It is urgent to study a new conveyor chain system to improve the synchronization, reliability, and environmental friendliness of chain conveyors on hundreds of assembly lines. In this paper, the mathematical modeling, meshing analysis, reliability, and environmental friendliness of the parameters of the components of the double pitch time-sharing meshing toothed conveyor chain system are studied. In addition, a novel fault diagnosis method of double pitch time-sharing meshing toothed conveyor chain transmission system based on neural network model is proposed in this paper.

Ding, Song↗

Phase-curve Pollution of Exoplanet Transit Depths

The next generation of space telescopes will enable transformative science to understand the nature and origin of exoplanets. In particular, transit spectroscopy will reveal the chemical composition of the exoplanet atmospheres with unprecedented detail thanks to precise measurements of the visible-to-infrared transit depths down to 10 parts per million. Such a level of instrumental precision raises the challenge to obtain even more precise astrophysical models so as not to significantly influence the interpretation of the observed data. We must therefore critically revisit some of the commonly accepted assumptions that were adequate for analyzing past and current observations. A common approximation in the analysis of exoplanetary primary transits is that the planet does not contribute to the recorded flux, so-called dark planet hypothesis. In this paper, we investigate the impact of the dark planet hypothesis on the parameters obtained from the analysis of transits with particular attention to the transit depth. We develop mathematical formulae and release new software to estimate the magnitude of the potential bias. These tools will be useful in the preparation of observing proposals, as well as within the scientific consortia of the James Webb Space Telescope (JWST) and the Atmospheric Remote-sensing Infrared Exoplanet Large-survey (ARIEL) missions. We probe the accuracy of the mathematical formulae through the analysis of synthetic observations with the JWST Mid-InfraRed Instrument. We find that self-blending from nightside emission attenuates the transit depth by >3σ for some of the known exoplanet systems, in agreement with previous work. An additional unreported effect caused by the nightside rotating into view can also impart a significant effect, but in the opposite direction (increasing the transit depth); this effect can largely be removed with conventional detrending practices, at the expense of a slight increase in noise, and mixing astrophysical variations and instrumental drifts.

79 ASTRONOMY AND ASTROPHYSICS↗

Analysis of tumor-immune functional responses in a mathematical model of neoantigen cancer vaccines

Cancer neoantigen vaccines have emerged as a promising approach to stimulating the immune system to fight cancer. We propose a simple model including key elements of cancer-immune interactions and conduct a phase plane analysis to understand the immunological mechanisms of cancer neoantigen vaccines. Analytical results are obtained for two widely used functional forms that represent the killing rate of tumor cells by immune cells: the law of mass action (LMA) and the dePillis-Radunskaya Law (LPR). Using the LMA, our results reveal that a slowly growing tumor can escape the immune surveillance and that there is a unique periodic solution. The LPR offers richer dynamics, in which tumor elimination and uncontrolled tumor growth are both present. We show that tumor elimination requires sufficient number of initial activated T cells in relationship to the malignant cells, which lends support to using the neoantigen cancer vaccine as an adjuvant therapy after the primary tumor is surgically removed or treated using radiotherapy. We also derive a sufficient condition for uncontrolled tumor growth under the assumption of the LPR. Here, the juxtaposition of analyses with these two different choices for the killing rate function highlights their importance on model behavior and biological implications, by which we hope to spur further theoretical and experimental work to understand mechanisms underlying different functional forms for the killing rate.

60 APPLIED LIFE SCIENCES↗

Modeling and control of cascaded bridgeless multilevel rectifier under unbalanced load conditions

The goal of this project is to model and control a novel unidirectional cascaded multilevel bridgeless rectifier as an active front end in medium and high voltage applications. This topology has many advantages over a conventional cascaded H-bridge rectifier, such as lower implementation cost, higher reliability, and greater flexibility with similar power quality. The complete design process of the proposed converter is developed step by step in order to meet all the desired objectives. The steady-state mathematical model is used to develop a method for the voltage balancing of dc cells. Power factor analysis is discussed to mathematically derive requirements for the number of partially controlled and fully controlled H-bridges in the proposed H-bridge converter. Power loss, efficiency, and cost comparison studies between the traditional cascaded H-Bridge converter and the proposed bridgeless converter demonstrate the advantages. After exploring various well-established control methods, a novel control strategy is proposed to achieve dc voltage balancing, fast and robust grid synchronization, power factor correction, and elimination of zero crossing current distortion under both balanced and unbalanced load conditions. The converter can also be used for reactive power compensation in a grid tied power system if a sufficient number of fully controlled H-bridge modules are included. Processor-In-the-Loop (PIL) simulation has been the utilized to validate the performance of discrete control structure. Simulation and experimental results validate the models and control method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Practical Guide to Chemometric Analysis of Optical Spectroscopic Data

The methodology and mathematical treatment of several classic multivariate methods for the analysis of spectroscopic data is demonstrated in a straightforward way that can be used as a basis for teaching an undergraduate introductory course on chemometric analysis. The multivariate techniques of classical least squares (CLS), principal component regression (PCR), and partial least squares (PLS), as well as the univariate Beer’s law method have been described and compared, building students’ understanding by starting with the univariate method and progressing step by step into the multivariate methods. Equations for the production of regression vectors from training set spectral data is described and their use demonstrated for the prediction of constituent concentrations on a separate validation set of spectra. Extreme care is taken to ensure consistency in variable formatting of data matrices. This provides a key foundation to understanding how spectral data are manipulated using these different mathematical approaches for building quantitative regression models. Each method is applied to a real-world data set, and the results are discussed to show students the types of information that can be gleaned from each method. A training set comprised of 20 infrared absorbance spectra containing 3 constituents (benzene, polystyrene, and gasoline) of known composition are used to demonstrate the matrix operations for each regression method. A separate set of 12 real-world napalm samples (containing benzene, polystyrene and gasoline) are used as a validation set to demonstrate the ability to utilize the regression models on an unknown dataset. A toolbox (PNNL Chemometric Toolbox) written in MATLAB language is supplied in the Supplemental Information file and can be used as a companion for understanding the development and deployment of the chemometric algorithms described in this paper. The datasets of the infrared spectra are also supplied, allowing users to build and inspect the chemometric models on their own. Finally, the Toolbox includes scripts to assist users in loading their own datasets into MATLAB and performing CLS, PCR, and PLS on their data.

Upper-Division Undergraduate, Analytical Chemistry↗

FPDetect: Efficient Reasoning About Stencil Programs Using Selective Direct Evaluation

We present FPDetect, a low-overhead approach for detecting logical errors and soft errors affecting stencil computations without generating false positives. We develop an offline analysis that tightly estimates the number of floating-point bits preserved across stencil applications. This estimate rigorously bounds the values expected in the data space of the computation. Violations of this bound can be attributed with certainty to errors. FPDetect helps synthesize error detectors customized for user-specified levels of accuracy and coverage. FPDetect also enables overhead reduction techniques based on deploying these detectors coarsely in space and time. Experimental evaluations demonstrate the practicality of our approach.

97 MATHEMATICS AND COMPUTING↗

Combining PCA and nonlinear fitting of peak models to re-evaluate C 1s XPS spectrum of cellulose

Cellulose is an example of a material that responds to XPS by the creation of new chemistry not present in the as-received sample. While improvements in instrumentation may be seen in general as beneficial to surface science, recent studies have shown that the consequences for some materials are detrimental. Here, in this work, these problems are illustrated through an analysis of cellulose spectra obtained during a degradation study. C 1s spectra are decomposed into two well-formed component curves that are open to chemical interpretation. In particular, a component-curve representative of pure cellulose is obtained as well as a second component curve that implies cellulose is degraded through the creation of carbon chemistry involving C—O, C$=$O and O—C$=$O. Since cellulose is a crystalline material, formed through the alignment of molecules under the influence of hydrogen bonds, the analysis and findings presented in this paper are relevant to any material analyzed by XPS whose properties are dependent on hydrogen bonds. The analysis techniques are based on an informed vectorial approach, which extracts directly from data spectral shapes that are used to monitor sample degradation via linear least squares optimization. Related mathematics of Principal Component Analysis and linear analysis are presented.

36 MATERIALS SCIENCE↗

Topological Data Analysis for Particulate Gels

Soft gels, formed via the self-assembly of particulate materials, exhibit intricate multiscale structures that provide them with flexibility and resilience when subjected to external stresses. Here, this work combines particle simulations and topological data analysis (TDA) to characterize the complex multiscale structure of soft gels. Our TDA analysis focuses on the use of the Euler characteristic, which is an interpretable and computationally scalable topological descriptor that is combined with filtration operations to obtain information on the geometric (local) and topological (global) structure of soft gels. We reduce the topological information obtained with TDA using principal component analysis (PCA) and show that this provides an informative low-dimensional representation of the gel structure. We use the proposed computational framework to investigate the influence of gel preparation (e.g., quench rate, volume fraction) on soft gel structure and to explore dynamic deformations that emerge under oscillatory shear in various response regimes (linear, nonlinear, and flow). Our analysis provides evidence of the existence of hierarchical structures in soft gels, which are not easily identifiable otherwise. Moreover, our analysis reveals direct correlations between topological changes of the gel structure under deformation and mechanical phenomena distinctive of gel materials, such as stiffening and yielding. In summary, we show that TDA facilitates the mathematical representation, quantification, and analysis of soft gel structures, extending traditional network analysis methods to capture both local and global organization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PSUADE

PSUADE (Problem Solving testbed for Uncertainty Analysis and Design Exploration) is a mathematical software useful for performing uncertainty quantification and sensitivity analysis.

Tong, CharlesH↗

Field Validation of Thermoelectric Generation System at Holcim Cement Plant in Alpena, Michigan

Executive Summary Project Background The Industrial Technology Validation (ITV) program aims to identify and demonstrate the performance of new, emerging, and underutilized energy-saving technologies in the industrial sector to help inform decisions to help accelerate their commercialization and deployment, as well as to help make industries more competitive. This ITV demonstration evaluated a thermoelectric generation (TEG) technology at a cement plant, aiming to reduce energy demand in the cement industry. A median cement plant consumes 5.73 million British thermal units per ton of clinker production (resulting in 0.838 metric tons of carbon dioxide [CO₂] emissions per ton of clinker) (Boyd and Zhang 2011, EPA 2021), equivalent to approximately 6.9 trillion British thermal units (TBtu) per year in energy consumption at a cement plant producing 3,300 tons of clinker per day.¹ Collaborating with Holcim, Advanced Thermovoltaic Systems (ATS) developed and deployed a pilot-scale thermoelectric power system to efficiently capture and convert waste heat to electricity. The system leverages the Seebeck effect to convert temperature differences on two sides of semiconductor cartridges into electrical power (ScienceDirect, n.d.). This generation is realized with minimal moving parts compared to existing waste-heat-to-generation solutions and allows capture from heat sources with temperatures as low as 150°C. This project aimed to validate a scalable solution applicable for capturing medium-temperature waste heat, including ambient losses from other high-temperature processes, and high-temperature sources less suitable for other waste-heat-to-power solutions. By recovering this otherwise wasted heat, this project intends to validate improvements to overall process efficiency through reduction in purchased electricity, thereby reducing operational costs while enhancing resiliency and competitiveness. Description and Scope This study evaluated the performance of a TEG system from ATS as a solution to convert waste heat into useful power at a Holcim cement plant in Alpena, Michigan. This plant is a fully integrated cement plant that has been operating since 1907. The facility operates continuously (24/7/365) with approximately 250 employees and five long dry kilns, yielding a total production capacity of 7,852 tons of cement per day (EPA 2023). Currently, the Alpena plant uses waste heat boilers to convert waste heat from the exhaust of each kiln into steam, which drives steam turbine generators. The ATS TEG is being evaluated for its potential to supplement the steam turbines by capturing the remaining lower grade heat. This technology is also being considered for other Holcim plants where steam turbines are not a viable option. ATS installed a pilot-scale TEG unit with an array of 582 individual thermoelectric semiconductor cartridges, of which 573 were operational. The cartridges are sandwiched between 48 hot plates and 49 cold plates. Each cartridge is designed to generate 20 watts (W) of gross power at a hot-side temperature of 240°C and cold-side temperature of 20°C. As such, the total gross generation capacity of the installed system is 11.5 kilowatts (kW) at design conditions. The system configuration for the evaluation was designed to prioritize convenience of installation and minimize disruption to production at the site, while ensuring that the heat required can be obtained for evaluating the TEG system at various operational conditions. To accomplish this, a portion of the steam supplied to Alpena’s steam turbine generation system was diverted to be used as the heat source for the TEG system, while water was supplied to the cold side of the system from nearby Lake Huron. This configuration was designed for the evaluation of the pilot-scale system to assess the performance at different conditions. A commercial-scale system will likely vary from the pilot system depending on typical configurations, including both scale and application. Future commercial applications of the ATS system would involve integrating the system into the exhaust from kiln preheaters, clinker coolers, or radiant heat capture from kiln shells for the heat source. For the cold source, a range of cooling solutions can be considered, including a mechanical cooling system, depending on the location and the application. To increase the generation capacity for commercial applications, the technology provider is working toward developing a commercial-scale TEG system, which would combine multiple TEG units (each similar in design to the pilot system) together. The scope of this evaluation includes the pilot-scale TEG system and all impacted equipment including pumps, controllers, and power handling equipment. Study Objectives The evaluation's goal was to assess the potential of the ATS TEG system to generate useful electrical power by capturing waste heat from cement production kilns. The objectives of this study are to evaluate and verify the following claims made by ATS regarding the pilot-scale system installed at the Holcim Alpena plant. The following design parameters and claims are also outlined in Table ES- 1 and Table ES- 2: • Gross Power: The thermoelectric system converts heat into power to create gross power, the total measured power generated by the system. The 573 active cartridge pilot-scale system is expected to generate 11.5 kW of gross power at the designed hot-side temperature of 240°C and cold-side temperature of 20°C. Power production is dependent on the temperature difference between the heat source (ultimately from the waste heat) and cold temperature supply source. • Net Power: The net power is the total usable power provided to the site by the TEG system after deducting parasitic power loads from the gross generated power. Supplementary equipment is required to operate the TEG system including pumps, controllers, and, in certain anticipated applications, mechanical cooling, which introduce parasitic loads to system operation. After deducting the parasitic loads from the gross power generation, ATS anticipates achieving a net power generation of 7.5 kW from the pilot-scale system. • Thermal Efficiency: The thermal efficiency is the percent of the total heat transferred to the TEG system that is converted to gross power. Historically, TEGs have a thermal efficiency of 2%–5% (DOE 2008). Prior industrial-scale TEG systems, such as the E1 TEG offered by Alphabet Energy, operated at an efficiency of 2.5% (Lamonica, 2014). ATS anticipates achieving an average efficiency of 4.8% or higher in converting heat energy to usable electricity. • Cartridge Performance: The TEG system comprises 573 active individual semiconductor cartridges, each of which generates a portion of the total power. Cartridge optimization and selection is an important design consideration for potential future TEG system design performance. Therefore, understanding the distribution of gross power and efficiency within the pilot system is vital to understanding what is achievable. At a design hot-side temperature of 240°C and cold-side temperature of 20°C, ATS anticipates a cartridge performance of 20 W of gross power per cartridge at an efficiency of 4.8% per cartridge. In addition to evaluating the claimed performance of the TEG pilot-scale unit, the study estimated the potential annual impacts of a scaled-up commercial system used to capture kiln waste heat over annual operations. The evaluation estimated the gross and net annual electric generation achievable by capturing heat from the two proposed tap-in points: the kiln exhaust and the clinker cooler exhaust; see Section 2.1 for details. Two use cases were examined: • Holcim Alpena: The Holcim Alpena site consists of long dry kilns with superheater boilers, which differs from the rest of Holcim’s cement plant portfolio and results in lower waste heat temperatures. The study estimates gross and net annual generation using the superheater boiler exhaust and clinker cooler exhaust, based on 2023 operational data. • Typical Installation: Common cement plants have preheater kilns with higher exhaust temperatures than Holcim Alpena across a range of production rates. The study estimates gross and net annual generation using the preheater exhaust and clinker cooler exhaust, with a sensitivity analysis to account for the typical range of preheater exhaust temperatures, clinker cooler exhaust temperatures, and clinker production rates. Methodology The evaluation methodology followed a measurement and verification (M&V) strategy based on the International Performance Measurement and Verification Protocol Option B through comprehensive measurements and analyses of the affected systems. Evaluation data was collected from March 9 to March 11, 2024, the test period of the pilot TEG system. During the test period, in coordination with the ITV team, the ATS team adjusted system operations to capture the range of variability expected for each of the variables pertinent to performance of the system. The methodology consisted of two parts: evaluating the performance of the pilot unit's TEG system and estimating the annual TEG impact in terms of gross and net power based on a given waste heat profile. First, the evaluation of the thermoelectric generation performance of the pilot unit relative to the claims was performed by analyzing the collected test data. Gross power of the pilot TEG system was directly measured. Net power was determined by deducting the measured parasitic power from the gross power. The gross power generation was compared to heat transferred to the system by the working fluid (which was heated by steam generated from the kiln waste heat) to calculate the thermal efficiency achieved by the system. Performance of individual semiconductor cartridges within the pilot array was also assessed in terms of measured gross cartridge power and calculated cartridge thermal efficiency. The second part of the evaluation estimated the annual TEG impacts in terms of gross power and net power (calculated from the difference between gross power and parasitic power). This analysis comprised development of mathematical regression models for gross power and parasitic power, with assessment of each model’s goodness-of-fit characteristics to ensure satisfaction of statistical requirements. The models predicted the gross power generation, the parasitic load based on the temperature difference between the hot working fluid and the cold-side fluid (cold water from Lake Huron) entering the system, the volumetric flow rate of the cold-side fluid at the inlet, and the volumetric flow rate of the hot working fluid at the inlet. The annual impact analysis considered a theoretical commercial-scale system sized to capture the available waste heat at a cement plant, consisting of linked pilot-scale units that receive heat from a theoretical gas-to-working-fluid heat exchanger. To estimate annual impacts at the Alpena plant, the gross power and parasitic power regression models were applied to the arrays in the theoretical commercial-scale system. The heat supplied to the unit was calculated based on the kiln run time, annual production, kiln exhaust waste heat, and clinker cooler waste heat derived from 2023 Holcim Alpena kiln operational data. Net power impacts were calculated by deducting the resulting parasitic power from the estimated gross power. Inputs for the model were generated from a combination of hourly data, assumed design considerations for TEG system scale-up from the pilot-scale unit, and assumptions regarding TEG system operations. This analysis was then used as the basis for estimating annual impacts of typical TEG installation at cement plants, by applying sensitivity analyses to key kiln operational characteristics including kiln preheater exhaust temperatures, cooler clinker exhaust temperatures, and plant daily production rates across a range of expected values. Project Results/Findings Table ES- 2 and Table ES- 2 provide a summary of the operating conditions and evaluation results compared to the stated claims from the technology provider. Key takeaways include: • Gross Power: The peak gross power achieved during the testing period was 10.0 kW, compared to the 11.5 kW expected for 573 active cartridges. The claimed gross power was associated with a target hot side of 240°C; however, the system only received a maximum hot-side mean plate temperature of 212°C during the testing period. • Net Power: The pilot-scale unit exceeded the claims for net power, achieving a peak of 7.7 kW net compared to a claim of 7.5 kW. One factor contributing to the higher achieved net power is the relatively high water pressure available through Lake Huron. The pilot TEG system did not require cold-side pumps during the test, whereas most installations would. This reduced the parasitic loads on the system, ultimately contributing to higher net power relative to the gross power. • Thermal Efficiency: The pilot-scale unit outperformed the claimed efficiency, achieving a peak system efficiency of 5.0% thermal efficiency compared to the stated 4.8%. • Cartridge Performance: To compare cartridge performance against claims, the study focused on the third day of testing, which aimed for conditions closest to the design specifications, with a hot side of 240°C and cold-side exit temperature of 6.4°–30°C. On this day, the mean gross power observed in the cartridges within the TEG array was 18.1 W/cartridge, and the peak performance was 34.7 W/cartridge. The estimated mean cartridge efficiency was 5.2%, and the estimated efficiency at peak gross cartridge power was 10%. The regression models developed for gross power generation and parasitic loads were used to estimate the generation impact for given heat input to the TEG from the working fluid (captured from the waste heat) and from the cold loop (Lake Huron) on an hourly basis for a year of operation. Based on this analysis, installation of a commercial-scale TEG system at the Holcim cement plant in Alpena, Michigan, with a waste heat exchanger of 0.85 effectiveness, would generate up to 391 kW of net power, translating to between 920,000 and 1,800,000 kilowatt-hours (kWh) in net electricity per year. Based on typical grid emissions for Alpena, this would avoid estimated net emissions by 752 metric tons of CO₂ annually.² The sensitivity analysis estimated that typical TEG system installations at cement plants could generate an average of 56–1,040 kW of net power, or between 488,000 and 9,110,000 kWh of net energy. This generation potential is most significantly affected by plant production rates and also influenced by preheater and clinker cooler exhaust temperatures. Applying the national average emission rate, typical commercial-scale installations at Holcim plants are projected to avoid between 182 and 3,401 metric tons of CO₂ annually per site. Table ES- 3 shows a summary of the estimated annual impacts.³ While parasitic loads are significant and vary by application, this analysis assumed the use of heating loop pumps and access to Lake Huron as a cold sink. This setup assumed no need for cooling loop pumps due to the available water pressure at the test site. Applications that require cooling towers or additional equipment are likely to experience higher parasitic loads. Therefore, the study’s estimates are most applicable to scenarios with similar parasitic load configurations—namely, access to a high-pressure cold sink. Applicability to other locations may be limited, as differing conditions could necessitate additional pumps and cooling systems, potentially impacting performance significantly.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Affine Transformations to Enable Machine Learning for Semi-Quantitative EDS Analysis

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Within-Host Phenotypic Evolution and the Population-Level Control of Chronic Viral Infections by Treatment and Prophylaxis

Chronic viral infections can persist for decades spanning thousands of viral generations, leading to a highly diverse population of viruses with its own complex evolutionary history. We propose an expandable mathematical framework for understanding how the emergence of genetic and phenotypic diversity affects the population-level control of those infections by both non-curative treatment and chemo-prophylactic measures. Our frameworks allows both neutral and phenotypic evolution, and we consider the specific evolution of contagiousness, resistance to therapy, and efficacy of prophylaxis. We compute both the controlled and uncontrolled, population-level basic reproduction number accounting for the within-host evolutionary process where new phenotypes emerge and are lost in infected persons, which we also extend to include both treatment and prophylactic control efforts. We used these results to discuss the conditions under which the relative efficacy of prophylactic versus therapeutic methods of control are superior. Finally, we give expressions for the endemic equilibrium of these models for certain constrained versions of the within-host evolutionary model providing a potential method for estimating within-host evolutionary parameters from population-level genetic sequence data.

sensitivity analysis↗

Bifurcation Analysis Reveals Solution Structures of Phase Field Models

The phase field method is playing an increasingly important role in understanding and predicting morphological evolution in materials and biological systems. Here, in this study, we develop a new analytical approach based on the bifurcation analysis to explore the mathematical solution structure of phase field models. Revealing such solution structures not only is of great mathematical interest but also may provide guidance to experimentally or computationally uncover new morphological evolution phenomena in materials undergoing electronic and structural phase transitions. To elucidate the idea, we apply this analytical approach to three representative phase field equations: the Allen-Cahn equation, the Cahn-Hilliard equation, and the Allen-Cahn-Ohta-Kawasaki system. The solution structures of these three phase field equations are also verified numerically by the homotopy continuation method.

97 MATHEMATICS AND COMPUTING↗

Segmentation of tomography datasets using 3D convolutional neural networks

Dendritic microstructures are ubiquitous in nature and are the primary solidification morphologies in metallic materials. Techniques such as X-ray computed tomography (XCT) have provided new insights into dendritic phase transformation phenomena. However, manual identification of dendritic morphologies in microscopy data can be both labor intensive and potentially ambiguous. The analysis of 3D datasets is particularly challenging due to their large sizes (terabytes) and the presence of artifacts scattered within the imaged volumes. Here, in this study, we trained 3D convolutional neural networks (CNNs) to segment 3D datasets. Three CNN architectures were investigated, including a new version of FCDenseNet which we extended to 3D. We show that using hyperparameter optimization (HPO) and fine-tuning techniques, both 2D and 3D CNN architectures outperform the previous state of the art. The 3D U-Net architecture trained in this study produced the best segmentations according to quantitative metrics (intersection-over-union of 95.56% and a boundary displacement error of 0.58 pixels), while 3D FCDense produced the smoothest boundaries and best segmentations according to visual inspection. The trained 3D CNNs are able to segment entire 852 × 852 × 250 voxel 3D volumes in only ~60 s, thus hastening the progress towards a deeper understanding of phase transformation phenomena such as dendritic solidification.

36 MATERIALS SCIENCE↗

Advances in genome-scale metabolic models of industrially important fungi

Many fungal species have been used in industrial production for biofuels and bioproducts. Developing strains with better performance in biomanufacturing requires systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated in several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. In this report we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test- learn cycles, ultimately advancing the field of fungal biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

Numerical fluid dynamics for FRG flow equations: Zero-dimensional QFTs as numerical test cases. II. Entropy production and irreversibility of RG flows

Herein we demonstrate that the reformulation of renormalization group (RG) flow equations as nonlinear heat equations has severe implications on the understanding of RG flows in general. We demonstrate by explicitly constructing an entropy function for a zero-dimensional Z 2 -symmetric model that the dissipative character of generic nonlinear diffusion equations is also hard-coded in the functional RG equation. This renders RG flows manifestly irreversible, revealing the semigroup property of RG transformations on the level of the flow equation itself. Additionally, we argue that the dissipative character of RG flows, its irreversibility and the entropy production during the RG flow may be linked to the existence of a so-called C– / A-function. In total, this introduces an asymmetry in the so-called RG time—in complete analogy to the thermodynamic arrow of time—and allows for an interpretation of infrared actions as equilibrium solutions of dissipative RG flows equations. The impossibility of resolving microphysics from macrophysics is evident in this framework. Furthermore, we directly link the irreversibility and the entropy production in RG flows to an explicit numerical entropy production, which is manifest in diffusive and non-linear partial differential equations (PDEs) and a standard mathematical tool for the analysis of PDEs. Using exactly solvable zero-dimensional Z 2 -symmetric models, we explicitly compute the (numerical) entropy production related to the total variation nonincreasing property of the PDE during RG flows toward the infrared limit. Finally, we discuss generalizations of our findings and relations to the C– / A-theorem as well as how our work may help to construct truncations of RG flow equations in the future, including numerically stable schemes for solving the corresponding PDEs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗