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At least 19 records

Effect of Dietary Countermeasures and Impact of Gravity on Renal Calculi Size Distributions Predicted by PBE-System and PBE-CFD Models

Renal stone disease is not only a concern on earth but can conceivably pose a serious risk to the astronauts health and safety in Space. In this work, two different deterministic models based on a Population Balance Equation (PBE) analysis of renal stone formation are developed to assess the risks of critical renal stone incidence for astronauts during space travel. In the first model, the nephron is treated as a continuous mixed suspension mixed product removal crystallizer and the PBE for the nucleating, growing and agglomerating renal calculi is coupled to speciation calculations performed by JESS. Predictions of stone size distributions in the kidney using this model indicate that the astronaut in microgravity is at noticeably greater but still subcritical risk and recommend administration of citrate and augmented hydration as effective means of minimizing and containing this risk. In the second model, the PBE analysis is coupled to a Computational Fluid Dynamics (CFD) model for flow of urine and transport of Calcium and Oxalate in the nephron to predict the impact of gravity on the stone size distributions. Results presented for realistic 3D tubule and collecting duct geometries, clearly indicate that agglomeration is the primary mode of size enhancement in both 1g and microgravity. 3D numerical simulations seem to further indicate that there will be an increased number of smaller stones developed in microgravity that will likely pass through the nephron in the absence of wall adhesion. However, upon reentry to a 1g (Earth) or 38g (Mars) partial gravitational fields, the renal calculi can lag behind the urinary flow in tubules that are adversely oriented with respect to the gravitational field and grow agglomerate to large sizes that are sedimented near the wall with increased propensity for wall adhesion, plaque formation, and risk to the astronauts.

Renal Stones↗

Dryout and Rewetting in the Pool Boiling Experiment Flown on STS-72 (PBE-2 B) and STS-77 (PBE-2 A)

Experiments were conducted in the microgravity of space in which a pool of liquid (R-113), initially at a precisely defined pressure and temperature, is subjected to a step imposed heat flux from a semi-transparent thin-film heater forming part of one wall of the container such that boiling is initiated and maintained for a defined period of time at a constant pressure level. A total of nine tests were conducted at three levels of heat flux and three levels of subcooling in each of the two space experiments in a GAS canister on the STS-77, -72, respectively. Three (3) modes of propagation of boiling across the heater surface and subsequent vapor bubble growths were observed, in addition to the two (2) modes observed in the previous microgravity pool boiling space flights on STS-47, -57, and -60. Of particular interest were the extremely dynamic or "explosive" growths, which were determined to be the consequence of the large increase in the liquid-vapor interface area associated with the appearance of a corrugated or rough interface. Predictions of circumstances for its onset have been carried out. Assumptions were necessary regarding the character of disturbances necessary for the instabilities to grow. Also, a new vapor bubble phenomena was observed in which small vapor bubbles migrated toward a larger bubble, eventually coalescing with this larger bubble. The heat transfer was enhanced approximately 30% as a result of these migrating bubbles, which is believed to be a vapor bubble manifestation of Marangoni convection and/or molecular momentum effects, sometimes referred to as vapor recoil. The circumstances of heat flux and liquid subcooling necessary to produce heater surface dryout for an initially stagnant liquid subjected to an imposed heat flux have been more closely identified.

Merte, Herman, Jr.↗

PBE-HIL (Powering the Blue Economy Hardware-in-the-Loop models) [SWR-25-37]

Powering the Blue Economy Hardware-in-the-Loop models (PBE-HIL) is a repository of Power Hardware-in-the-loop models developed for typical Powering the Blue Economy market loads and power requirements. The HIL models were developed to be as generic and functional as possible, meaning that the user can easily configure these models to represent their unique PBE design. These PBE load and power requirement HIL models can then be used to inform marine energy converter (MEC) and power electronics design, as well as be used in laboratory testing using HIL equipment, leading to improved understanding of MEC performance and lower risk prior to open-water MEC deployment.

Labuschagne, Hannes [National Renewable Energy Lab↗

Coupled CFD-PBE Predictions of Renal Stone Size Distributions in the Nephron in Microgravity

In this paper, a deterministic model is developed to assess the risk of critical renal stone formation for astronauts during space travel. A Population Balance Equation (PBE) model is used to compute the size distribution of a population of nucleating, growing and agglomerating renal calculi as they are transported through different sections of the nephron. The PBE model is coupled to a Computational Fluid Dynamics (CFD) model that solves for steady state flow of urine and transport of renal calculi along with the concentrations of ionic species, calcium and oxalate, in the nephron using an Eulerian two-phase mathematical framework. Parametric simulation are performed to study stone size enhancement and steady state volume fraction distributions in the four main sections of the nephron under weightlessness conditions. Contribution of agglomeration to the stone size distribution and effect of wall friction on the stone volume fraction distributions are carefully examined. Case studies using measured astronaut urinary calcium and oxalate concentrations in microgravity as input indicate that under nominal conditions the largest stone sizes developed in Space will be still considerably below the critical range for problematic stone development. However, results also indicate that the highest stone volume fraction occurs next to the tubule and duct walls. This suggests that there is an increased potential for wall adhesion with the possibility of evolution towards critical stone sizes.

Microgravity↗

Coupled CFD-PBE Predictions of Renal Stone Size Distributions in the Nephron in Microgravity

In this paper, a deterministic model is developed to assess the risk of critical renal stone formation for astronauts during space travel. A Population Balance Equation (PBE) model is used to compute the size distribution of a population of nucleating, growing and agglomerating renal calculi as they are transported through different sections of the nephron. The PBE model is coupled to a Computational Fluid Dynamics (CFD) model that solves for steady state flow of urine and transport of renal calculi along with the concentrations of ionic species, calcium and oxalate, in the nephron using an Eulerian two-phase mathematical framework. Parametric simulation are performed to study stone size enhancement and steady state volume fraction distributions in the four main sections of the nephron under weightlessness conditions. Contribution of agglomeration to the stone size distribution and effect of wall friction on the stone volume fraction distributions are carefully examined. Case studies using measured astronaut urinary calcium and oxalate concentrations in microgravity as input indicate that under nominal conditions the largest stone sizes developed in Space will be still considerably below the critical range for problematic stone development. However, results also indicate that the highest stone volume fraction occurs next to the tubule and duct walls. This suggests that there is an increased potential for wall adhesion with the possibility of evolution towards critical stone sizes.

Crystal Growth↗

An evaluation for geometries, formation enthalpies, and dissociation energies of diatomic and triatomic (C, H, N, O), NO 3 , and HNO 3 molecules from the PAW DFT method with PBE and optB88-vdW functionals

The structural geometries, formation enthalpies, and dissociation energies of all diatomic and triatomic molecules consisting of the four basic elements C, H, N, and/or O are calculated using the projector augmented wave density functional theory (DFT) method with the Perdew–Burke–Ernzerhof and optB88-vdW exchange-correlation functionals. The calculations are also extended to two larger molecules NO 3 and HNO 3 , which consist of four and five atoms, respectively. In total, 82 molecules or isomers are considered in the calculations. The geometric parameters including 42 bond lengths and 15 bond angles of these molecules calculated using the planewave DFT method are highly satisfactory, relative to the available experimental data. The error analysis is also performed for 49 formation enthalpies and 138 dissociation energies (including 51 atomization energies as well as the corresponding bond dissociation energies). The results are also compared with the previous data from various atomic-orbital-based methods for molecules and from similar or different planewave DFT methods for various solids and other molecules. This provides an informative and instructive evaluation especially for calculating the large-size material systems containing these small molecules as well as for developing the DFT methods further.

74 ATOMIC AND MOLECULAR PHYSICS↗

PBE-GGA predicts the B8↔B2 phase boundary of FeO at Earth’s core conditions

FeO is a crucial component of the Earth’s core, and its thermodynamic properties are essential to developing more accurate core models. It is also a notorious correlated insulator in the NaCl-type (B1) phase at ambient conditions. It undergoes two polymorphic transitions at 300 K before it becomes metallic in the NiAs-type (B8) structure at ~100 GPa. Although its phase diagram is not fully mapped, it is well established that the B8 phase transforms to the CsCl-type (B2) phase at core pressures and temperatures. Here, we report a successful ab initio calculation of the B8↔B2 phase boundary in FeO at Earth’s core pressures. We show that fully anharmonic free energies computed with the Perdew–Burke–Ernzerhof-generalized gradient approximation coupled with thermal electronic excitations reproduce the experimental phase boundary within uncertainties at P > 255 GPa, including the largely negative Clapeyron slope of –52 MPa/K. This study validates the applicability of a standard density functional theory functional to FeO under Earth’s core conditions and demonstrates the theoretical framework that enables complex predictive studies of this region.

58 GEOSCIENCES↗

Charged point defect benchmark of Hybrid and GGA-PBE

Data used by the publication "High-throughput calculations of charged point defect properties with semi-local density functional theory - performance benchmarks for materials screening applications." This work presented an in-depth benchmark analysis of automated, semi-local point defect calculations with a-posteriori corrections, compared to 245 “gold standard” hybrid calculations previously published. We considered three different a-posteriori correction sets for semi-local calculations, implemented in a fully automated workflow, and consider the qualitative and quantitative differences for four different categories of defect information: thermodynamic transition levels, formation energies, fermi levels, and dopability limits. We highlighted the type of qualitative information about point defect properties that can be extracted from high-throughput calculations based on semi-local DFT methods, while also demonstrating the limits of quantitative accuracy that can be achieved by these approaches.

Broberg, Danny↗

Effect of XC functionals and dispersion corrections on the DFT‐computed structural and vibrational properties of SrCl 2 –NaCl and ZrF 4 –LiF

Density functional theory (DFT) calculations were performed to examine the impact of exchange–correlation (XC) functionals and van der Waals corrections (specifically the D3 method) on the structural and vibrational properties of the SrCl 2 –NaCl and ZrF 4 –LiF salt systems. Multiple XC functionals, including the local density approximation (LDA), the generalized gradient approximation using the Perdew–Burke–Ernzerhof (PBE) model, and its modified form suitable for solids (PBEsol), the dispersion-corrected PBE-D3 and PBEsol-D3, were considered. Of these functionals, LDA was found to exhibit the highest degree of error, while PBEsol and PBE-D3 displayed the least error. Underestimated lattice parameters compared with experimental values were observed to result in higher force constants, leading to an overprediction of vibrational frequencies. Conversely, an overestimation of lattice parameters was associated with lower vibrational frequencies. The methodology presented in this study yielded results that are in good agreement with experiment, irrespective of the method (finite differences vs. density functional perturbation theory) employed for calculating infrared and Raman spectra. It was further demonstrated that for alkali halides with weak Raman scattering, utilizing a supercell constructed from primitive cells better predicts Raman features than does the use of conventional cells.

Raman↗

Symmetry Breaking with the SCAN Density Functional Describes Strong Correlation in the Singlet Carbon Dimer

The SCAN (strongly constrained and appropriately normed) meta-generalized gradient approximation (meta-GGA), which satisfies all 17 exact constraints that a meta-GGA can satisfy, accurately describes equilibrium bonds that are normally correlated. With symmetry breaking, it also accurately describes some sd equilibrium bonds that are strongly correlated. While sp equilibrium bonds are nearly always normally correlated, the C 2 singlet ground state is known from correlated wave function theory to be a rare case of strong correlation in an sp equilibrium bond. Earlier work that calculated atomization energies of the molecular sequence B 2 , C 2 , O 2 , and F 2 in the local spin density approximation (LSDA), the Perdew–Burke–Ernzerhof (PBE) GGA, and the SCAN meta-GGA, without symmetry breaking in the molecule, found that only SCAN was accurate enough to reveal an anomalous under-binding for C 2 . Here, this work shows that spin symmetry breaking in singlet C 2 , which involves the appearance of net up- and down-spin densities on opposite sides (not ends) of the bond, corrects that underbinding, with a small SCAN atomization-energy error more like that of the other three molecules, suggesting that symmetry breaking with an advanced density functional might reliably describe strong correlation. This article also discusses some general aspects of symmetry breaking and the insights into strong correlation that symmetry breaking can bring. The normally correlated low-lying triplet excited state has the right vertical excitation energy in SCAN but not in LSDA or PBE, where the triplet is a false ground state. Fractional occupation numbers are found only for the symmetry-unbroken singlet and only in LSDA and PBE GGA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vertical detachment energies of ammonia cluster anions using self-interaction-corrected methods

Systems with weakly bound extra electrons impose great challenges to semilocal density functional approximations (DFAs), which suffer from self-interaction errors. Small ammonia clusters are one such example of weakly bound anions where the extra electron is weakly bound. We applied two self-interaction correction (SIC) schemes, viz., the well-known Perdew–Zunger and the recently developed locally scaled SIC (LSIC) with the local spin density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation (GGA), and the SCAN meta-GGA functionals to calculate the vertical detachment energies (VDEs) of small ammonia cluster anions (NH3)n–. Our results show that the LSIC significantly reduces the errors in calculations of VDE with LSDA and PBE-GGA functionals leading to better agreement with the reference values calculated with coupled cluster singles and doubles with perturbative triples [CCSD(T)]. Accurate prediction of VDE as an absolute of the highest occupied molecular orbital (HOMO) is challenging for DFAs. Our results show that VDEs estimated from the negative of HOMO eigenvalues with the LSIC-LSDA and Perdew–Zunger SIC-PBE are within 11 meV of the reference CCSD(T) results. Here, the LSIC method performs consistently well for the VDE estimates, from both the total energy differences and the absolute HOMO eigenvalues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the effect of density functional choice and van der Waals treatment on predicting the binding configuration, loading, and stability of amine-grafted metal organic frameworks

Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential’s (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections.

Chemistry↗

Oxygen–Chlorine Chemisorption Scaling for Seawater Electrolysis on Transition Metals: The Role of Redox

To clarify what controls species oxidation selectivity in seawater electrolysis, density functional theory (DFT) is used to identify chemisorption enthalpy trends and scaling relations for the simplest relevant adsorbates (O, Cl, and H) on relevant surfaces of 3d transition metals, as well as Pd and Pt, in face-centered-cubic and, if different, their ground-state crystal structures. Approximations are tested for electron exchange-correlation (XC) and van der Waals interactions to assess their ability to reproduce experimental adsorption enthalpies of H and O on Pt(111). The vdW-uncorrected generalized gradient approximation to XC of Perdew, Burke, and Ernzerhof (PBE) agrees most closely with experiments. Using DFT-PBE thereafter, it is determined that the O chemisorption enthalpy on this wide range of transition-metal surfaces is proportional to the sum of first and second atomic ionization energies, akin to a Born–Haber cycle for a redox reaction, indicating that metal redox activity controls O chemisorption strength. Then it is shown that the O and Cl chemisorption enthalpies are strongly correlated, suggesting that the transition metals considered will oxidize unselectively water and Cl – . This strong correlation appears also for crystal reduction potentials of binary oxides and chlorides, indicating a fundamental challenge for future seawater electrode materials design.

08 HYDROGEN↗

Dependence of predicted bulk properties of hexagonal hydroxyapatite on exchange-correlation functional

Hydroxyapatite (HA) is the main component of human bones and teeth. HA has also been widely applied in various technological fields due to its unique properties. Reliable computational simulations for this critical material often require input parameters obtained from the first-principles density functional theory (DFT) calculations with appropriate exchange–correlation functionals. Previous DFT calculations are insufficient to verify the reliabilities of various functionals, particularly as they fail to assess predictions for multiple properties of the material. In this paper, we first select 18 different functionals to calculate geometric, elastic, electronic, and thermodynamic properties of hexagonal HA bulk crystal. We find that the results from optB86b-vdW and optB88-vdW functionals with dispersion corrections have the overall best agreement with available experimental data. Then, we choose optB88-vdW functional, as well as PBE functional without dispersion corrections as a comparison, to perform extensive first-principles DFT phonon calculations under the quasiharmonic approximation. Various thermodynamic properties (including phonon contributions to internal energy, entropy, and Helmholtz free energy) and thermal parameters (including thermal expansions of volume, thermal expansion coefficients, heat capacities, isothermal bulk moduli, etc.) versus temperature are consequently obtained. By comparing these quantities, we report that the results from optB88-vdW functional have significantly better agreement with available experimental data than those from PBE functional although the latter has been widely used in previous DFT calculations for HA-based material systems.

36 MATERIALS SCIENCE↗

A comprehensive first-principles study of the effects of the exchange-correlation functional and magnetism on defect and diffusion properties of the CoCrNi medium-entropy alloy

The present work is a novel, systematic study of the effect of density functional theory input parameters on the vacancy formation energy (VFE), migration barrier for diffusion, and electronic structure for each element in the CoCrNi medium-entropy alloy (MEA). In particular, the novelties include: (1) calculating the aforementioned properties of Co, Cr, or Ni, in the CoCrNi MEA using magnetic and non-magnetic states, and two versions of the generalized gradient approximation: Perdew, Burke, and Ernzerhof (PBE) and the PBE version for solids (PBEsol), and (2) a detailed comparison of 0 K activation energy to experimental creep activation energies. First-principles calculations at 0 K are performed using the Vienna ab-initio simulation package. Special quasirandom structures (SQS) and Widom-type substitution are employed. For each element, Co, Cr, or Ni, non-magnetic calculations result in a higher VFE and larger range of calculated values for the configurations studied. The averaged migration barrier is the highest for Co in the CoCrNi for three of four sets of calculation parameters in the configurations studied. Finally, the results indicate that the average 0 K activation energy for diffusion makes up 70–80% of the experimental creep activation energy, depending on the exchange-correlation functional employed.

36 MATERIALS SCIENCE↗

A comparative analysis of different van der Waals treatments for molecular adsorption on the basal plane of 2H-MoS 2

The binding energy of hydrogen sulfide, ammonia, ethane, ethylene, butadiene, benzene, toluene, pyridine, pyrrole, and thiophene on the basal plane of the semi-conducting 2H-molybdenum sulfide (MoS 2 ) was calculated with the following flavors of Density Functional Theory (DFT): GGA-PW91, PBE-D3, vdW-DF, optPBE, optB86b, optB88, vdW-TS, and BEEF-vdW. The GGA-PW91 binding energies are negligible (<0.07 eV in magnitude) in all cases. The predictions with vdW-DF and PBE-D3 are the closest (error <0.05 eV) to the isosteric heats of adsorption calculated from reported temperature programmed desorption data for thiophene and butadiene. For all dispersion flavors examined here, the magnitude of the dispersion contribution to the binding energy increases linearly with the number of heavy atoms in the adsorbate, with each atom contributing 0.05 eV (BEEF-vdW) – 0.09 eV (optB88-vdW). Further, this implies that the calculated adsorption constants of molecules larger than acridine (i.e., comprising > 14 non-heavy atoms) can vary by more than four orders of magnitude at industrial conditions depending on the chosen method of dispersion correction. Further, dispersion effects fall off rapidly (>0.03 eV/ non-hydrogen atom/Å) as the adsorbate-surface distance increases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗