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DOE OSTI2019

Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems

Abstract In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modeling approaches that are currently used assume ideal conditions and that each cell is identical, limiting their application to pure cultures in well-mixed vessels. Here we describe our development of Multiscale Multiobjective Systems Analysis (MiMoSA), a metabolic modeling approach that can track individual cells in both space and time, track the diffusion of nutrients and light and the interaction of cells with each other and the environment. As a proof-of concept study, we used MiMoSA to model the growth of Trichodesmium erythraeum , a filamentous diazotrophic cyanobacterium which has cells with two distinct metabolic modes. The use of MiMoSA significantly improves our ability to predictively model metabolic changes and phenotype in more complex cell cultures.

09 BIOMASS FUELS↗

DOE OSTI2014

Isothermal dehydration of thin films of water and sugar solutions

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Radiation feedback in ULIRGs: are photons movers and shakers?

We perform multidimensional radiation hydrodynamics simulations to study the impact of radiation forces on atmospheres composed of dust and gas. Our setup closely follows that of Krumholz and Thompson, assuming that dust and gas are well-coupled and that the radiation field is characterized by blackbodies with temperatures ≳ 80 K, as might be found in ultraluminous infrared galaxies (ULIRGs). In agreement with previous work, we find that Rayleigh-Taylor instabilities develop in radiation supported atmospheres, leading to inhomogeneities that limit momentum exchange between radiation and dusty gas, and eventually providing a near balance of the radiation and gravitational forces. However, the evolution of the velocity and spatial distributions of the gas differs significantly from previous work, which utilized a less accurate flux-limited diffusion (FLD) method. Our variable Eddington tensor simulations show continuous net acceleration of the gas and never reach a steady state. In contrast, our FLD results show little net acceleration of the gas and settle into a quasi-steady, turbulent state with low velocity dispersion. The discrepancies result primarily from the inability of FLD to properly model the variation of the radiation field around structures that are less than a few optical depths across. We consider the effect of varying the optical depth and study the differences between two-dimensional and three-dimensional runs. We conclude that radiation feedback remains a plausible mechanism for driving high-Mach number turbulence in ULIRGs with sufficiently high optical depths. We discuss implications for observed systems and galactic-scale numerical simulations of feedback.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Diffuse X-ray scattering from polished silicon: application of the distorted wave Born approximation

Measured diffuse X-ray scattering data for a `smooth' as well as for a `rough' silicon sample were fit to theoretical expressions within the distorted wave Born approximation (DWBA). Data for the power spectral density (PSD) for both samples were also obtained by means of atomic force microscopy and optical interferometry. The Fourier transforms of trial correlation functions were fit to the PSD data and then applied to the DWBA formalism. The net correlation functions needed to fit the PSD data for each sample comprised the sum of two terms with different cutoff lengths and different self-affine fractal exponents. At zero distance these correlation functions added up to yield net values of σ 2 = (2) 2 and (71) 2 Å 2 for the smooth and rough samples, respectively. X-ray scattering data were obtained at beamline 1-BM of the Advanced Photon Source. Data and fits at values of q z = 0.05 and 0.10 Å −1 for the smooth sample are reported. Good fits for the smooth sample were obtained at both q z values simultaneously, that is, identical fitting parameters were applied at both values of q z . The smooth sample also exhibited weak Yoneda wings and a clear distinction between the strong specular scattering and the weak diffuse scattering. Data for the rough sample were qualitatively different and exhibited very weak scattering at the specular condition in contrast to extremely large Yoneda wings. Fits for the rough sample are reported for q z = 0.04, 0.05, and 0.06 Å −1 . Although the large Yoneda wings could be fit quite well in both position and amplitude, scattering near the specular condition could not be equally well fit by applying the same fitting parameters at all values of q z . Albeit imperfect, best-fitting results at the specular condition were obtained by invoking only diffuse scattering, that is, without including a separate theoretical expression for specular scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Ab Initio Design of High-Entropy Thermal/ Environmental Barrier Coatings

Next generation thermal/environmental barrier coatings (TEBC) require carefully balancing various properties including phase stability, thermal conductivity, coefficient of thermal expansion (CTE), mechanical properties, and resistance against hot corrosion and water vapor recession. This work mainly focuses on rapid design of cost-effective high entropy rare-earth disilicates and aluminum garnets to protect SiC-based ceramic matrix composites and nickel-based superalloys in the hot section of gas turbine engines using density functional theory methods. Our calculations identify several low-cost high entropy TEBC exhibiting ultralow thermal conductivity at 1500 K and desirable CTE while maintaining good mechanical properties, including Er1/2Y3/4Yb3/4Si2O7, Gd1/4Er1/4Y3/4Yb3/4Si2O7, Eu1/4Er1/4Y3/4Yb3/4Si2O7, and (Y1/4Gd1/4Er1/4Yb1/4)3Al5O12. This work also aims to gain fundamental understanding of oxygen diffusion in model disilicates. Minimizing oxidizer (such as water vapor and oxygen) permeability through the EBC layer can significantly decrease the growth rate of thermally grown oxide and extend the service life of the coating system. Oxygen diffusion mechanisms including formation energy of defects under varying oxygen conditions and defect migration energy barriers will be presented.

coefficient of thermal expansion↗

DOE OSTI2017

Simple Analytical Forms of the Perpendicular Diffusion Coefficient for Two-component Turbulence. III. Damping Model of Dynamical Turbulence

In several astrophysical applications one needs analytical forms of cosmic-ray diffusion parameters. Some examples are studies of diffusive shock acceleration and solar modulation. In the current article we explore perpendicular diffusion based on the unified nonlinear transport theory. While we focused on magnetostatic turbulence in Paper I, we included the effect of dynamical turbulence in Paper II of the series. In the latter paper we assumed that the temporal correlation time does not depend on the wavenumber. More realistic models have been proposed in the past, such as the so-called damping model of dynamical turbulence. In the present paper we derive analytical forms for the perpendicular diffusion coefficient of energetic particles in two-component turbulence for this type of time-dependent turbulence. We present new formulas for the perpendicular diffusion coefficient and we derive a condition for which the magnetostatic result is recovered.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1982

Importance of heterogeneous processes to tropospheric chemistry - Studies with a one-dimensional model

A one-dimensional, time-dependent model of tropospheric air composition is developed which incorporates several heterogeneous physical and chemical processes. The model includes the interaction of gases, aerosols, and hydrometeors through the physical mechanisms of nucleation, condensation, evaporation, coagulation, coalescence, and deliquescence. Precipitation, sedimentation, and dry deposition act to remove material from the atmosphere, while chemical transformations occur both in the vapor and the condensed phases. The model also incorporates the sources and vertical diffusion of gases and particles, as well as changes in the solar intensity caused by light-scattering from aerosols and clouds. Preliminary simulations made using this model indicate that rainout and washout processes strongly influence the distributions of tropospheric gases and aerosols under certain conditions.

Turco, R. P.↗

NASA NTRS2010

Ares I Reaction Control System Propellant Feedline Decontamination Modeling

The objective of the work presented here is to quantify the effects of purge gas temperature, pressure, and mass flow rate on Hydrazine (Hz) decontamination rates of the Ares I Roll Control System and Reaction Control System. A survey of experts in this field revealed the absence of any decontamination rate prediction models. Three basic decontamination methods were identified for analysis and modeling. These include low pressure eduction, high flow rate purge, and pulse purge. For each method, an approach to predict the Hz mass transfer rate, as a function of system pressure, temperature, and purge gas mass flow rate, is developed based on the applicable physics. The models show that low pressure eduction is two orders of magnitude more effective than the high velocity purge, which in turn is two orders of magnitude more effective than the pure diffusion component of pulse purging of deadheads. Eduction subjects the system to low pressure conditions that promote the extraction of Hz vapors. At 120 F, Hz is saturated at approximately 1 psia. At lower pressures and 120 F, Hz will boil, which is an extremely efficient means to remove liquid Hz. The Hz boiling rate is predicted by equating the rate at which energy is added to the saturated liquid Hz through heaters at the tube outer wall with the energy removed from the liquid through evaporation. Boil-off fluxes were predicted by iterating through the range of local pressures with limits set by the minimum allowed pressure of 0.2 psia and maximum allowed wall temperature of 120 F established by the heaters, which gives a saturation pressure of approximately 1.0 psia. Figure 1 shows the resulting boil-off fluxes as a function of local eduction pressure. As depicted in figure 1, the flux is a strong inverse function of eduction pressure, and that minimizing the eduction pressure maximizes the boil-off flux. Also, higher outer wall temperatures lead to higher boil-off fluxes and allow for boil-off over a greater range of eduction pressures.

Pasch, James J.↗

DOE OSTI2014

Electron and ion transport equations in computational weakly-ionized plasmadynamics

A new set of ion and electron transport equations is proposed to simulate steady or unsteady quasi-neutral or non-neutral multicomponent weakly-ionized plasmas through the drift–diffusion approximation. The proposed set of equations is advantaged over the conventional one by being considerably less stiff in quasi-neutral regions because it can be integrated in conjunction with a potential equation based on Ohm's law rather than Gauss's law. The present approach is advantaged over previous attempts at recasting the system by being applicable to plasmas with several types of positive ions and negative ions and by not requiring changes to the boundary conditions. Several test cases of plasmas enclosed by dielectrics and of glow discharges between electrodes show that the proposed equations yield the same solution as the standard equations but require 10 to 100 times fewer iterations to reach convergence whenever a quasi-neutral region forms. Further, several grid convergence studies indicate that the present approach exhibits a higher resolution (and hence requires fewer nodes to reach a given level of accuracy) when ambipolar diffusion is present. Because the proposed equations are not intrinsically linked to specific discretization or integration schemes and exhibit substantial advantages with no apparent disadvantage, they are generally recommended as a substitute to the fluid models in which the electric field is obtained from Gauss's law as long as the plasma remains weakly-ionized and unmagnetized.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2017

Tortuosity Computations of Porous Materials using the Direct Simulation Monte Carlo

Low-density carbon fiber preforms, used as thermal protection systems (TPS) materials for planetary entry systems, have permeable, highly porous microstructures consisting of interlaced fibers. Internal gas transport in TPS is important in modeling the penetration of hot boundary-layer gases and the in-depth transport of pyrolysis and ablation products. The gas effective diffusion coefficient of a porous material must be known before the gas transport can be modeled in material response solvers; however, there are very little available data for rigid fibrous insulators used in heritage TPS.The tortuosity factor, which reflects the efficiency of the percolation paths, can be computed from the effective diffusion coefficient of a gas inside a porous material and is based on the micro-structure of the material. It is well known, that the tortuosity factor is a strong function of the Knudsen number. Due to the small characteristic scales of porous media used in TPS applications (typical pore size of the order of 50 micron), the transport of gases can occur in the rarefied and transitional regimes, at Knudsen numbers above 1. A proper way to model the gas dynamics at these conditions consists in solving the Boltzmann equation using particle-based methods that account for movement and collisions of atoms and molecules.In this work we adopt, for the first time, the Direct Simulation Monte Carlo (DSMC) method to compute the tortuosity factor of fibrous media in the rarefied regime. To enable realistic simulations of the actual transport of gases in the porous medium, digitized computational grids are obtained from X-ray micro-tomography imaging of real TPS materials. The SPARTA DSMC solver is used for simulations. Effective diffusion coefficients and tortuosity factors are obtained by computing the mean-square displacement of diffusing particles.We first apply the method to compute the tortuosity factors as a function of the Knudsen number for computationally designed materials such as random cylindrical fibers and packed bed of spheres with prescribed porosity. Results are compared to literature values obtained using random walk methods in the rarefied and transitional regime and a finite-volume method for the continuum regime. We then compute tortuosity factors for a real carbon fiber material with a transverse isotropic structure (FiberForm), quantifying differences between through-thickness and in-plain tortuosities at various Knudsen regimes.

Tortuosity↗

NASA NTRS1999

Growing wheat in Biosphere 2 under elevated CO2: observations and modeling

Spring wheat (Triticum aestivum L., cv. Yecora Rojo) was grown in the intensive agricultural biome (IAB) of Biosphere 2 during the l995-l996 winter/spring season. Environmental conditions were characterized by a day/night temperature regime of 27/17 degrees C, relative humidity (RH) levels around 45%, mean atmospheric CO2 concentration of 450 ppmv, and natural light conditions with mean intensities about half of outside levels. Weekly samples of above-ground plant matter were collected throughout the growing season and phenological events recorded. A computer model, CERES-Wheat, previously tested under both field and controlled conditions, was used to simulate the observed crop growth and to help in data analysis. We found that CERES-Wheat simulated the data collected at Biosphere 2 to within 10% of observed, thus suggesting that wheat growth inside the IAB was comparable to that documented in other environments. The model predicts phenological stages and final dry matter (DM) production within l0% of the observed data. Measured DM production rates, normalized for light absorbed by the crop. suggested photosynthetic efficiencies intermediate between those observed under optimal field conditions and those recorded in NASA-Controlled Ecological Life-Support Systems (CELSS). We suggest that such a difference can be explained primarily in terms of low light levels inside the IAB, with additional effects due to elevated CO2 concentrations and diffuse light fractions.

Non-NASA Center↗

DOE OSTI2023

Reacceleration of Galactic Cosmic Rays beyond the Knee at the Termination Shock of a Cosmic-Ray-driven Galactic Wind

The origin of cosmic rays (CRs) above the knee in the spectrum is an unsolved problem. We present a wind model in which interstellar gas flows along a nonrotating, expanding flux tube with a changing speed and cross-sectional area. CRs from Galactic sources, such as supernova remnants, which are coupled to the plasma via Alfvén waves, provide the main pressure source for driving this outflow. These CRs are then subject to diffusive shock reacceleration at the Galactic wind termination shock, which is located at a distance ~200 kpc. Some of the highest-energy reaccelerated particles propagate upstream against the wind and can contribute to the petaelectronvolt to exaelectronvolt range of the spectrum. We analyze the conditions under which efficient reacceleration can occur and find that rigidities ~10–40 PV can be obtained and that the termination shock may account for between 10% and 50% of the proton spectrum measured in IceCube/IceTop experiment. In our model, the termination shock is unable to fully explain the CR spectrum in the petaelectronvolt to exaelectronvolt range. The highest-energy particles that escape downstream from our termination shock, and similar shocks surrounding most galaxies, can be further accelerated by intergalactic shock fronts.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2018

Reynolds-Stress Budgets in an Impinging Shock Wave/Boundary-Layer Interaction

Implicit large-eddy simulation (ILES) of a shock wave/boundary-layer interaction (SBLI) was performed. Comparisons with experimental data showed a sensitivity of the current prediction to the modeling of the sidewalls. This was found to be common among various computational studies in the literature where periodic boundary conditions were used in the spanwise direction, as was the case in the present work. Thus, although the experiment was quasi-two-dimensional, the present simulation was determined to be two-dimensional. Quantities present in the exact equation of the Reynolds-stress transport, i.e., production, molecular diffusion, turbulent transport, pressure diffusion, pressure strain, dissipation, and turbulent mass flux were calculated. Reynolds-stress budgets were compared with past large-eddy simulation and direct numerical simulation datasets in the undisturbed portion of the turbulent boundary layer to validate the current approach. The budgets in SBLI showed the growth in the production term for the primary normal stress and energy transfer mechanism was led by the pressure strain term in the secondary normal stresses. The pressure diffusion term, commonly assumed as negligible by turbulence model developers, was shown to be small but non-zero in the normal stress budgets, however it played a key role in the primary shear stress budget.

shock wave/boundary-layer interactio↗

DOE OSTI2018

Assessment of uncertainty in the numerical simulation of solar irradiance over inclined PV panels: New algorithms using measurements and modeling tools

Development of accurate transposition models to simulate plane-of-array (POA) irradiance from horizontal measurements or simulations is a complex process mainly because of the anisotropic distribution of diffuse solar radiation in the atmosphere. The limited availability of reliable POA measurements at large temporal and spatial scales leads to difficulties in the comprehensive evaluation of transposition models. This paper proposes new algorithms to assess the uncertainty of transposition models using both surface-based observations and modeling tools. We reviewed the analytical derivation of POA irradiance and the approximation of isotropic diffuse radiation that simplifies the computation. Two transposition models are evaluated against the computation by the rigorous analytical solution. We proposed a new algorithm to evaluate transposition models using the clear-sky measurements at the National Renewable Energy Laboratory's (NREL's) Solar Radiation Research Laboratory (SRRL) and a radiative transfer model that integrates diffuse radiances of various sky-viewing angles. We found that the radiative transfer model and a transposition model based on empirical regressions are superior to the isotropic models when compared to measurements. We further compared the radiative transfer model to the transposition models under an extensive range of idealized conditions. Our results suggest that the empirical transposition model has slightly higher cloudy-sky POA irradiance than the radiative transfer model, but performs better than the isotropic models under clear-sky conditions. Significantly smaller POA irradiances computed by the transposition models are observed when the photovoltaics (PV) panel deviates from the azimuthal direction of the sun. The new algorithms developed in the current study have opened the door to a more comprehensive evaluation of transposition models for various atmospheric conditions and solar and PV orientations.

14 SOLAR ENERGY↗

DOE OSTI2023

Selective Uptake of Ethane/Ethylene Mixtures by UTSA-280 is Driven by Reversibly Coordinated Water Defects

The metal–organic framework (MOF) UTSA-280 has been shown previously to separate ethane/ethylene mixtures. We show that this separation is kinetic; if full equilibrium is reached, the MOF is not selective. The time scales associated with this kinetic separation are sufficient to make the material potentially interesting for practical separations. The observation of kinetic separation is surprising because the MOF’s one-dimensional (1D) channels are small enough that molecular motion along the channels would be expected to take place by single-file diffusion, which is not observed. We show using a combination of experimental and modeling techniques that diffusion of molecules between adjacent 1D channels through local defects associated with coordinated water molecules allows net mixing of molecules and, moreover, that this process is potentially responsible for the selective nature of the observed kinetic separation. We show how activation and regeneration conditions play an essential role in controlling the density of these local defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

The shard test and nanoporomechanics reverse classical paradigm of cement hydration being contractive

Le Chatelier in 1887 and Powers in 1947 demonstrated that the volume of nanoscale C-S-H (calcium silicate hydrate) particles formed during hydration is smaller than the combined volume of the reactants—the anhydrous Portland cement and water. Hydration has thus been considered as contractive. An experiment shows that the opposite is true above the nanoscale. The porous skeleton of cement paste expands as the growing C-S-H particles push each other apart, similar to crystal growth pressure. This is significant for high-performance concretes (HPC) with low water-cement ratios (w/c ≤ 0.4), where chemical self-desiccation lowers pore relative humidity by 40%, compared to just 1% in traditional concretes (w/c ≈ 0.5). Standard American Society for Testing and Materials (ASTM) C1608 tests, using 10 mm thick water-immersed specimens, show large shrinkage because the half-time of water ingress is many decades, unable to offset shrinkage-causing self-desiccation. The present experiment, using a laser microscopy-topography technique, proves the opposite—expansion, evidenced by measuring the length changes of water-immersed HPC shards 0.5 mm thick in which the diffusion halftime, only about one hour, allows continuous resaturation of pores, canceling self-desiccation. The faster diffusion (halftime of one hour) enables continuous pore resaturation, preventing shrinkage. When sealed with paraffin oil, the shards self-desiccate and shrink. These findings align with studies since 2015, showing that models excluding hydration expansion cannot fit test data across various specimen sizes and sealing conditions. The results suggest that standardized ASTM tests for the so-called chemical shrinkage in modern concretes with very low water-cement ratios are misleading and need revision.

Science & Technology - Other Topics↗

DOE OSTI2024

Spectroscopy-guided discovery of three-dimensional structures of disordered materials with diffusion models

Spectroscopy techniques such as x-ray absorption near edge structure (XANES) provide valuable insights into the atomic structures of materials, yet the inverse prediction of precise structures from spectroscopic data remains a formidable challenge. In this study, we introduce a framework that combines generative artificial intelligence models with XANES spectroscopy to predict three-dimensional atomic structures of disordered systems, using amorphous carbon (a-C) as a model system. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method, to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of a-C as a representative material system from the target XANES spectra. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e. with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Examination of Legacy Metallic Fuel Pins (U-10Zr) Tested in FFTF

The MFF series of metallic fuel (U-10wt%Zr) tests performed in the Fast Fuel Test Facility (FFTF) were the beginning tests to qualify the fuel as a driver fuel for FFTF. They all performed very well, to relatively high burnup and with no pin breaches. Tests MFF-3 and MFF-5 were chosen to be destructively examined because they were run at high peak cladding temperatures, 643 and 649°C respectively, and to modest to high burnup (138 and 101 MWd/kgM respectively). They were the only sodium fast reactor (SFR) metallic tests, with long (91.4 cm) fuel columns and clad in HT9, to be operated at these high temperatures. Extensive operating condition reconstruction was performed to accompany the examination, providing detailed operating conditions axially along the pins. In addition, detailed ORIGEN calculations provided fuel burnup along the pin length. These calculations and detailed cross-section metallography allowed a PhD dissertation to be performed where the fuel/cladding chemical interaction (FCCI) was modeled using Fickian and Soret Effect driven diffusion of rare earth fission products to the cladding surface and interact with the cladding. The examination of the MFF-3 and MFF-5 pins included neutron radiography, axial profilometry including pin bow and length measurements, precision gamma scanning, plenum gas puncturing to measure fission gas release, detailed chemical/isotopic analyses of fuel samples to confirm burnup calculations, and metallography of pin cross-sections, including micro-hardness measurements of fuel and cladding.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗