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At least 217 records · Page 12

Integrative teaching of metabolic modeling and flux analysis with interactive python modules

Abstract The modeling of rates of biochemical reactions—fluxes—in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint‐based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to‐date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C‐metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands‐on computer laboratory component of a four‐day metabolic modeling workshop and participant survey results showed improvements in learners' self‐assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.

Kaste, Joshua A. M.↗

Considerations for quantitative in situ X-ray powder diffraction studies of solid-state reactions

The importance of sample preparation in collecting high-fidelity powder diffraction data suitable for quantitative structure and phase analysis is well established. Such powder diffraction experiments are increasingly being appliedin situ, during reactions, to explore solid-state reactivity. When appliedin situ, X-ray diffraction is widely used to gain insight into the mechanism and kinetics, and to identify dynamic intermediate states. Here, using a model ion-exchange reaction (NaFeO 2 + LiCl → LiFeO 2 + NaCl), we show that sample preparation not only influences the fidelity of powder diffraction analysis but also impacts the observed reaction progress. Specifically, we found that the observed reaction progress can differ by ∼50% depending on the capillary sample preparation. Thus, forin situdiffraction studies of solid-state reactions, packing fraction is an important and previously unrecognized consideration that impacts reproducibility and fidelity of the reaction study.

Chemistry↗

IVEM Contributions to CINR Penn State MT17-12797: In situ Ion Irradiation to Add Irradiation Assisted Grain Growth to the MARMOT Tool

In-situ TEM experiments were performed at the IVEM-Tandem Facility in Argonne National Laboratory to study the irradiation-induced grain growth of nanocrystalline UO 2 and CeO 2 thin films using 1 MeV Kr ions at various temperatures from 50K to 1073K. The grain growth kinetics was studied under both irradiation and thermal annealing conditions. Bright field and dark field TEM images and diffraction patterns were systematically recorded as a function of temperature, irradiation dose and annealing time. A comprehensive grain growth data of UO 2 was collected for further analysis and for the implementation to the MARMOT tool.

36 MATERIALS SCIENCE↗

Analysis of scale-dependent kinetic and potential energy in sheared, stably stratified turbulence

Budgets of turbulent kinetic energy (TKE) and turbulent potential energy (TPE) at different scales $\ell$ in sheared, stably stratified turbulence are analysed using a filtering approach. Competing effects in the flow are considered, along with the physical mechanisms governing the energy fluxes between scales, and the budgets are used to analyse data from direct numerical simulation at buoyancy Reynolds number $Re_b=O(100)$ . The mean TKE exceeds the TPE by an order of magnitude at the large scales, with the difference reducing as $\ell$ is decreased. At larger scales, buoyancy is never observed to be positive, with buoyancy always converting TKE to TPE. As $\ell$ is decreased, the probability of locally convecting regions increases, though it remains small at scales down to the Ozmidov scale. The TKE and TPE fluxes between scales are both downscale on average, and their instantaneous values are correlated positively, but not strongly so, and this occurs due to the different physical mechanisms that govern these fluxes. Moreover, the contributions to these fluxes arising from the sub-grid fields are shown to be significant, in addition to the filtered scale contributions associated with the processes of strain self-amplification, vortex stretching and density gradient amplification. Probability density functions (PDFs) of the $Q,R$ invariants of the filtered velocity gradient are considered and show that as $\ell$ increases, the sheared-drop shape of the PDF becomes less pronounced and the PDF becomes more symmetric about $R=0$ .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

$\overline{TKE}$ Parameterization and $\bar{v}$ Uncertainty Analysis for CGMF

Previous work was performed on tuning CGMF parameters for 235 U, 238 U, and Plutonium isotopes. Now work is being done to tune minor uranium isotopes. However, uranium isotopes like 232 U and 236 U have almost no experimental data. We are applying cross-isotope models to extrapolate and tune CGMF on isotopes that lack experimental data. There exist several internal CGMF physics quantities that affect the output of CGMF—multi-chance fission probability, excitation energy sharing, spin-cutoff factor, spin scaling, and fragment total kinetic energy to name a few. The mean fragment total kinetic energy, $\overline{TKE}$, is particularly interesting because of its strong anti-correlation with $\bar{v}$. We are most interested in the mean fragment total kinetic energy before neutron emissions. $\overline{TKE}$ is assumed to be pre-neutron emission unless otherwise stated. Currently in CGMF, the $\overline{TKE}$ model for 233,234,235,238 U are tuned independently to reproduce ν for the associated isotopes. In this report, we will tune a cross-isotope $\overline{TKE}$ model to experimental $\overline{TKE}$ data for 232,233,234,235,236,238 U. Because of the unreliable and sparse nature of $\overline{TKE}$ experimental data, future work will use more reliable experimental $\bar{v}$ data to infer the $\overline{TKE}$ model (and likely other internal CGMF parameters) for uranium isotopes. Such work has been performed previously using a sensitivity analysis and Kalman filter methods.

07 ISOTOPE AND RADIATION SOURCES↗

Prediction of curing kinetics of resorcinol‐added resole phenolic resins using differential scanning calorimetry for the fabrication of carbon/carbon composites

Phenolic resins are commonly used as carbon precursors for the fabrication of carbon/carbon composites due to their high carbon yield and aromatic nature. To decrease curing times, acid catalysts are generally used, but the addition of resorcinol was found to have a similar effect while being incorporated into the resin matrix with no contamination or corrosion issues. In this work, the curing kinetics of pure, 10, 20, and 30 wt% resorcinol-added phenolic resins were investigated through differential scanning calorimetry. Heating rates of 0.5, 1, 2.5, and 5°C min -1 were used with several curing models to predict isothermal curing. Averaged mean absolute error (MAE) for the isoconversional mathematical approaches namely Kissinger–Akahira–Sunose (MAE = 12.9 min), Flynn–Wall–Ozawa (15.8 min), and Vyazovkin (14 min) show that these methods provide the best predictions, attributed to their adoption of an activation energy that depends on the extent of cure (E a (α)). The Kissinger method (MAE = 36 min), which depends only on peak temperature with a constant activation energy assumption, and the data noise sensitive Friedman model (MAE = 1144.7 min) provide the least accurate results. Thermogravimetric analysis revealed that resorcinol decreases the curing times by up to 71% without lowering carbon yield.

36 MATERIALS SCIENCE↗

Characterization of a new ultra-high pressure shock tube facility for combustion and propulsion studies

A new shock tube facility has been designed, constructed, and characterized at the University of Central Florida. This facility is capable of withstanding pressures of up to 1000 atm, allowing for combustion diagnostics of extreme conditions, such as in rocket combustion chambers or in novel power conversion cycles. For studies with toxic gas impurities, the high initial pressures required the development of a gas delivery system to ensure the longevity of the facility and the safety of the personnel. Data acquisition and experimental propagation were implemented with remote access to ensure safety, paired with a LabVIEW- and Python-based user interface. Thus far, test pressures of 270 atm, blast pressures of 730 atm, and temperatures approaching 10 000 K have been achieved. The extreme limitations of this facility allow for emission spectroscopy to be performed during the oxidation of fuel mixtures, e.g., alkanes diluted in argon and carbon dioxide. Ignition delay times were determined and compared to simulations using chemical kinetic mechanisms. The design, experimental procedures, processes of analysis, and uncertainty determination are outlined, and typical pressure profiles are compared with a new gas dynamics solver and empirical correlations developed across multiple shock tube facilities. Preliminary reactive mixture analyses are included with further investigation of the mixtures outlined.

47 OTHER INSTRUMENTATION↗

Constraints on directionality effect of nuclear recoils in a liquid argon time projection chamber

The direct search for dark matter in the form of weakly interacting massive particles (WIMP) is performed by detecting nuclear recoils produced in a target material from the WIMP elastic scattering. The experimental identification of the direction of the WIMP-induced nuclear recoils is a crucial asset in this field, as it enables unmistakable modulation signatures for dark matter. The Recoil Directionality (ReD) experiment was designed to probe for such directional sensitivity in argon dual-phase time projection chambers (TPC), that are widely considered for current and future direct dark matter searches. The TPC of ReD was irradiated with neutrons at the INFN Laboratori Nazionali del Sud. Data were taken with nuclear recoils of known directions and kinetic energy of 72 keV, which is within the range of interest for WIMP-induced signals in argon. The direction-dependent liquid argon charge recombination model by Cataudella et al. was adopted and a likelihood statistical analysis was performed, which gave no indications of significant dependence of the detector response to the recoil direction. The aspect ratio R of the initial ionization cloud is $R < 1.072$ with 90 % confidence level.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Numerical Simulation of Biogenic Fluid Catalytic Cracking (BFCC) Regenerators at Different Scales with MFIX-Exa

Catalytic Fast Pyrolysis (CFP) is a process that converts biomass into liquid intermediates suitable for transportation fuels by rapidly heating it in the presence of a catalyst, aiming to produce stable oils with reduced oxygen content. During CFP, the catalyst can become deactivated by the accumulation of coke, a carbon-rich deposit formed from the decomposition of biomass components. Unlike in petroleum refining, regenerating coked catalysts from biomass pyrolysis requires specific approaches due to the different chemical nature of the coke formed. An experimental technique, Temperature Programmed Oxidation (TPO), was used to study the de-coking process by gradually increasing temperature while monitoring the production of CO and CO2, which provides data for kinetic modeling. Utilizing data from TPO experiments, coke combustion kinetic model was developed to describe the rate of coke removal at different temperatures, allowing for simulation of regeneration processes. Then kinetic model is integrated into MFIX-Exa for the simulation of Biogenic Fluid Catalytic Cracker (BFCC) regenerator at different scales, enabling analysis of catalyst flow, temperature distribution, and regeneration efficiency under various operating conditions.

biogenic fluid catalytic cracking↗

Functional Data Analysis in Wearable Body Sensor Networks

Improving response time of indirect room-size calorimeters is still an outstanding problem in metabolic research. Accurate estimates of instantaneous rates of gaseous exchange require numerical differentiation of measured gaseousgas concentrations. We propose a new method to estimate the instantaneous gaseousgas exchange rates in indirect calorimetry. In contrast to the previously developed techniques, the method addresses the problem of differentiation of gaseous concentrations as an ill-posed problem. By applying the method of regularization, the problem of differentiation is converted into a well-posed problem resulting in smooth and consistent gaseous exchange rates. The validity of the method is tested on a large dataset of calorimeter experiments which included 313 human experiments along with 231 alcohol combustion experiments. It is demonstrated that the method is able to reliably differentiate between the “unphysiological” process of alcohol combustion and physiological variations produced by human metabolism. The method also allowed unraveling the previously unreported relative kinetics of O2 consumption and Respiratory Quotient (RQ) in humans. It was found that the kinetics of oxidative fuel selection lags behind the energy expenditure in humans exhibiting some sort of oxidative inertia. The time lag varies from 2-3 min up to 30 min, depending on particular individual. No such lag was found in alcohol combustion experiments. In addition to the relative kinetics of substrate oxidation, two statistical indexes reflecting variability of minute-by-minute RQ were estimated. The indexes were the RQ’s standard deviation and RQ’s first-order derivative. Both indexes showed statistically significant difference between human experiments and alcohol combustion experiments. We conclude that the proposed method can consistently extract physiologically-relevant information from noisy calorimetry data and the aforesaid information can provide additional insights into the mechanism of metabolic fuel selection in humans.

54 ENVIRONMENTAL SCIENCES↗

Functional Data Analysis in Wearable Body Sensor Networks

Improving response time of indirect room-size calorimeters is still an outstanding problem in metabolic research. Accurate estimates of instantaneous rates of gaseous exchange require numerical differentiation of measured gaseousgas concentrations. We propose a new method to estimate the instantaneous gaseousgas exchange rates in indirect calorimetry. In contrast to the previously developed techniques, the method addresses the problem of differentiation of gaseous concentrations as an ill-posed problem. By applying the method of regularization, the problem of differentiation is converted into a well-posed problem resulting in smooth and consistent gaseous exchange rates. The validity of the method is tested on a large dataset of calorimeter experiments which included 313 human experiments along with 231 alcohol combustion experiments. It is demonstrated that the method is able to reliably differentiate between the “unphysiological” process of alcohol combustion and physiological variations produced by human metabolism. The method also allowed unraveling the previously unreported relative kinetics of O2 consumption and Respiratory Quotient (RQ) in humans. It was found that the kinetics of oxidative fuel selection lags behind the energy expenditure in humans exhibiting some sort of oxidative inertia. The time lag varies from 2-3 min up to 30 min, depending on particular individual. No such lag was found in alcohol combustion experiments. In addition to the relative kinetics of substrate oxidation, two statistical indexes reflecting variability of minute-by-minute RQ were estimated. The indexes were the RQ’s standard deviation and RQ’s first-order derivative. Both indexes showed statistically significant difference between human experiments and alcohol combustion experiments. We conclude that the proposed method can consistently extract physiologically-relevant information from noisy calorimetry data and the aforesaid information can provide additional insights into the mechanism of metabolic fuel selection in humans.

60 - APPLIED LIFE SCIENCES↗

Validation of Numerical Tools for Calculating Reactivity Feedback in Sodium Fast Reactors Using SEFOR Experimental Data

The Southwest Experimental Fast Oxide Reactor (SEFOR) was an experimental sodium-cooled fast breeder reactor operated from 1969 to 1972 with experiments designed to measure Doppler reactivity feedback in a wide temperature range from around 350 °F to temperatures approaching the melting point of mixed oxide fuel of around 5000 °F, providing valuable data for code validations. Co-supported by the Department of Energy (DOE) Fast Reactor Program (FRP) and the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the SEFOR benchmark project focused on using the experimental data to validate numerical tools that are used in industry and academia to design and license sodium-cooled fast reactors (SFRs). By the end of FY-25, substantial progress was achieved in the SEFOR benchmark study. A variety of numerical tools commonly used for modeling SFRs were applied to develop models for SEFOR core configurations I-D, I-E, I-I, and I-J. These included Monte Carlo codes such as MCNP, Serpent, and Shift; deterministic codes such as the legacy Argonne Reactor Computation (ARC) suite and the high-fidelity NEAMS code Griffin; and the system analysis code SAS4A/SASSYS-1 (SAS). Using these models, both SEFOR zero-power experiments and power-ascending tests were successfully simulated. Comparisons were performed against experimental measurements of core criticalities, reflector worth, kinetics parameters (Λ/βeff), isothermal reactivity feedback (from 350 °F to 760 °F at zero power), and power-ascending reactivity feedback (as power increased from 0.4 MW to 17 MW). In general, these comparisons demonstrated very good agreement between numerical results and experimental data. In Fiscal Year 26 (FY-26), the SEFOR benchmark project will continue to address the modeling issues identified in FY-25. Effort will focus on the simulation of reactivity insertion transients in SEFOR core II using the ARC/SAS model. Future work will also focus on incorporating BISON into the SEFOR core modeling process to enable the first Multiphysics simulations of the isothermal tests based on the MOOSE framework.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Biopolymer-Templated Titania Film Formation for Nanostructured Coatings Revealed by Machine Learning-Supported Time-Resolved Analysis

This study presents a machine learning approach to derive the film formation of biopolymer-templated titania nanostructures during spray deposition, in combination with in situ grazing-incidence small-angle X-ray scattering (GISAXS). A neural network trained on synthetic GISAXS data directly predicts domain-size distributions from experimental two-dimensional scattering patterns, capturing the full kinetics of nanostructure evolution with high temporal resolution. The predictions reveal hierarchical size distributions and periodic growth features, consistent with layer-by-layer spray deposition and validated by complementary scanning electron microscopy (SEM) imaging. Quantitative comparison with conventional parametric GISAXS fits shows good qualitative agreement, with systematic differences explained by domain-shape assumptions and resolved by applying a geometric scaling factor. Simulated SEM-like surfaces derived from neural network outputs reproduce the porous, foam-like nanoscale morphology observed experimentally, reinforcing the method’s credibility. This integrated approach enables real-time, nondestructive, statistically averaged monitoring of bulk nanostructure development in functional coatings, offering a scalable methodology to accelerate the characterization and process control of sustainably manufactured nanostructured titania films for energy-related applications such as photocatalysis and photovoltaics.

Heger, JulianEliah↗

Tafel Slope Analyses for Homogeneous Catalytic Reactions

Tafel analysis of electrocatalysts is essential in their characterization. This paper analyzes the application of Tafel-like analysis to the four-electron nonelectrochemical oxidation of water by the stoichiometric homogeneous 1-electron oxidant [Ru(bpy)3]3+ to dioxygen catalyzed by homogeneous catalysts, [Ru4O4(OH)2(H2O)4(γ-SiW10O36)2]10− (Ru4POM) and [Co4(H2O)2(PW9O34)2]10– (Co4POM). These complexes have slow electron exchange rates with electrodes due to the Frumkin effect, which precludes the use of known electrochemical methods to obtain Tafel plots at ionic strengths lower than 0.5 M. The application of an electron transfer catalyst, [Ru(bpy)3]3+/2+, increases the rates between the Ru4POM and electrode, but a traditional Tafel analysis of such a complex system is precluded due to a lack of appropriate theoretical models for 4-electron processes. Here, we develop a theoretical framework and experimental procedures for a Tafel-like analysis of Ru4POM and Co4POM, using a stoichiometric molecular oxidant [Ru(bpy)3]3+. The dependence of turnover frequency (TOF) as a function of electrochemical solution potential created by the [Ru(bpy)3]3+/[Ru(bpy)3]2+ redox couple (an analog of the Tafel plot) was obtained from kinetics data and interpreted based on the suggested reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase-space Energization of Ions in Oblique Shocks

Abstract Examining energization of kinetic plasmas in phase space is a growing topic of interest, owing to the wealth of data in phase space compared to traditional bulk energization diagnostics. Via the field-particle correlation (FPC) technique and using multiple means of numerically integrating the plasma kinetic equation, we have studied the energization of ions in phase space within oblique collisionless shocks. The perspective afforded to us with this analysis in phase space allows us to characterize distinct populations of energized ions. In particular, we focus on ions that reflect multiple times off the shock front through shock-drift acceleration, and how to distinguish these different reflected populations in phase space using the FPC technique. We further extend our analysis to simulations of three-dimensional shocks undergoing more complicated dynamics, such as shock ripple, to demonstrate the ability to recover the phase-space signatures of this energization process in a more general system. This work thus extends previous applications of the FPC technique to more realistic collisionless shock environments, providing stronger evidence of the technique’s utility for simulation, laboratory, and spacecraft analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of a data-driven neural network model for electron thermal transport in NSTX

A data-driven electron thermal transport neural network (ETT-NN) model, trained on TRANSP interpretative analysis results of National Spherical Torus Experiment (NSTX), was developed to enable faster and more accurate ETT computation for spherical tokamaks (STs). The model incorporates both convolutional NNs and recurrent NNs, allowing it to simultaneously account for the spatial and temporal non-localities and multi-scale features of turbulent transport, which have been considered only in a limited manner in conventional models. The model was validated through interpretative analysis and predictive simulations using Tokamak Reactor Integrated Automated Suite for Simulation and Computation, demonstrating relatively high accuracy. Additionally, parameter scans were performed on test discharges known to exhibit specific turbulent modes, such as microtearing mode, trapped electron mode, kinetic ballooning mode, and electron temperature gradient mode. The scanning results revealed that the ETT-NN model exhibits the same trends as those observed in conventional gyrokinetic simulations or theories, while also capturing the global nature of turbulent transport, indicating that the data-driven model accurately reflects the underlying physical characteristics. Furthermore, due to the dimensionless nature of the model, we can feasibly expand its applicability by incorporating data from other devices and uncovering the characteristics of ETT in STs in the future.

NSTX↗

An organogel library for solution NMR analysis of nanoparticle suspensions in non-aqueous samples

Surface contrast solution NMR methods (scNMR) are emerging as powerful tools to investigate the adsorption of small molecule ligands to the surface of nanoparticles (NP), returning fundamental insight into the kinetics and thermodynamics of sorption, as well as structural information on the adsorbed species. A prerequisite for the acquisition of high quality solution NMR data is the preparation of homogeneous and stable samples that return consistent NMR spectra and allow extensive signal averaging. Unfortunately, this condition does not apply to NMR samples containing NPs that often show a tendency to sediment and accumulate at the bottom of the NMR tube over the course of the experiment. We have recently shown that preparing NMR samples in an agarose gel matrix inhibits sedimentation and allows the characterization of small molecule-NP interactions by scNMR. Unfortunately, as the agarose gel only forms in aqueous solution, this sample preparation method cannot be used to stabilize NP suspensions in a non-aqueous environment. In this work, we introduce a library of 48 organogels, based on low molecular-mass organic gelators (LMOGs), to prepare NMR samples of small molecule/NP systems in a wide range of organic solvents. In addition, we present a simple method that takes advantage of 1H transverse relaxation (1H-R2) measurements to screen the library and identify the best gelator to characterize the small molecule-NP interaction of interest in the solvent of choice. We expect the results of this study will enable the preparation of homogeneous and stable samples of NPs in non-aqueous environments, therefore dramatically increasing the applicability of scNMR to the characterization of heterogeneous interactions and to the investigation of the role played by solvent molecules in regulating the kinetics and thermodynamics of sorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Study of Radiative Heat Transfer and Flow Physics from Medium-scale Methanol Pool Fire Simulations [Slides]

Analysis of methanol pool fire conducted as part of validation study for SIERRA/Fuego. Radiation model was effectively calibrated by modifying radiation model parameters for methanol. Computing integrated buoyancy flux, entrainment rate, and turbulent kinetic energy allowed for evaluation of less typical quantities in this validation study. Quantities were compared with experimental data or correlations and generally showed agreement. TKE needed fine mesh to be computed accurately. Predicted flame height less sensitive to variations in mixture fraction than temperature. Mixture fraction is a preferable threshold variable for this application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗