SEARCH · Search NASA
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Not Available
The overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.
Purpose: Our assumption was that interfractional shape variations of target volumes could not be negligible for determination of clinical target volume (CTV)-to-planning target volume (PTV) margins. The aim of this study was to investigate this assumption as a simulation study by developing a computational framework of CTV-to-PTV margins with taking the interfractional shape variations into account based on point distribution model (PDM) Methods: The systematic and random errors for interfractional shape variations and translations of target volumes were evaluated for four types of CTV regions (only a prostate, a prostate plus proximal 1-cm seminal vesicles, a prostate plus proximal 2-cm seminal vesicles, and a prostate plus whole seminal vesicles). The CTV regions were delineated depending on prostate cancer risk groups on planning computed tomography (CT) and cone beam CT (CBCT) images of 73 fractions of 10 patients. The random and systematic errors for shape variations of CTV regions were derived from PDMs of CTV surfaces for all fractions of each patient. Systematic errors of shape variations of CTV regions were derived by comparing PDMs between planning CTV surfaces and average CTV surfaces. Finally, anisotropic CTV-to-PTV margins with shape variations in 6 directions (anterior, posterior, superior, inferior, right, and left) were computed by using a van Herk margin formula. Results: Differences between CTV-to-PTV margins with and without shape variations ranged from 0.7 to 1.7 mm in anterior direction, 1.0 to 2.8 mm in posterior direction, 0.8 to 2.8 mm in superior direction, 0.6 to 1.6 mm in inferior direction, 1.4 to 4.4 mm in right direction, and 1.3 to 5.2 mm in left direction. Conclusion: More than 1.0 mm additional margins were needed at least in 3 directions to guarantee CTV coverage due to shape variations. Therefore, shape variations should be taken into account for the determination of CTV-to-PTV margins.
X-ray photon correlation spectroscopy (XPCS) is a powerful technique for analyzing particle systems by investigating their dynamics in suspensions across a broad range of temporal and spatial scales. This is done by illuminating samples with coherent x-ray beams and calculating the correlation function of the obtained x-ray scattering images. XPCS is uniquely suited for studying Brownian dynamics, consisting of translational and rotational diffusion. While traditional XPCS image analysis techniques can extract translational diffusion components, they are unable to estimate rotational diffusion coefficients. Here, we introduce a methodology that combines the angular-temporal cross-correlation analysis and a algorithmic framework called Multi-Tiered Estimation for Correlation Spectroscopy in 3D for estimating three-dimensional rotational diffusion coefficients from XPCS images of three-dimensional particle systems. We demonstrate our methodology for extracting rotational diffusion coefficients from XPCS data by applying it to simulated noisy x-ray images of systems of crossing nanotubes and proteins that evolve under translational and rotational Brownian motion for different diffusion rates. Furthermore, our results show that our approach determines rotational diffusion coefficients within a few percent error.
Pyrometallurgical recovery of nonferrous metals involves a combination of thermally intensive transformations during exothermic gas-phase reactions, endothermic decomposition of solid charge, and melting of simpler solids. In the recovery of secondary lead, simultaneous thermal effects in a reverberatory-style furnace cause a melt pool to accumulate at the bottom, with lighter solids (slag) floating above and gaseous products from decomposition of the charge diffusing through the gas–slag interface. Species from oxy-fuel combustion of natural gas, species profiles from smelting reactions, and the formation of a melt pool consisting primarily of lead are simulated via a time-averaged formulation. Predictions of outflow are compared with preset inflow profiles to ensure conservation of mass. Thermal profiles for solid, liquid, and gas phases are presented by species. A novel method is implemented to model the latent heat of fusion using a heterogeneous chemical reaction. The simulation is conducted in Simcenter STAR-CCM+ v. 16.02.009-R8.
Assigning capacity value to renewable energy sources (RES) is a challenge faced in planning their integration with the grid. The difficulties stem from the natural characteristics of variability and intermittency of wind and solar sources. The capacity credit (CC) analysis evaluates the system’s actual power output compared with a constant capacity generator, i.e., conventional generator and determines an effective capacity to use for planning and operation. Herein this paper presents different factors that could affect the CC of a system. Two methods are proposed to determine the CC, namely equivalent firm capacity (EFC) and effective load carrying capability (ELCC). Since these methods are based on satisfying reliability criteria, daily loss of load expectation (LOLE), hourly loss of load (LOLH), and expected energy not served (EENS) have been employed as indices. To obtain the CC value, both methods apply two techniques: traditional and optimization. Genetic algorithm (GA) is the optimization approach used in this paper. Then, this work compares the two techniques and shows the superior performance of the optimization approach. Two hybrid systems, stand-alone (SA) and grid-connected (GC) modes, are proposed and used as case studies. The hybrid systems consist of photovoltaic (PV), wind turbine (WT), and battery energy storage system (BESS). In this work, three different scenarios are used to compare capacity credit: system as a whole, only wind, and no batteries. Finally, sensitivity analysis is carried out to examine the impact of varying the wind speed, solar irradiation, and load. It is demonstrated that the choice of reliability index plays an important role in determining the capacity credit and it is shown that EENS is a more comprehensive and consistent index of reliability.
Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.
Computational Fluid Dynamics (CFD) was used to investigate the CO2 capture by a novel PIM sorbent developed in National Energy Technology Laboratory (NETL) for direct air capture (DAC) applications. The CO2 adsorption kinetics used in the CFD was developed using isotherm data and CO2 breakthrough data obtained from experiments. Effect on humidity on the CO2 adsorption was also investigated and compared with the CO2 adsorption in dry conditions.
Abstract An extended version of the R -matrix methodology is presented for calculation of radiative parameters for improved plasma opacities. Contrast and comparisons with existing methods primarily relying on the distorted wave approximation are discussed to verify accuracy and resolve outstanding issues, particularly with reference to the opacity project (OP). Among the improvements incorporated are: (i) large-scale Breit–Pauli R -matrix calculations for complex atomic systems including fine structure, (ii) convergent close coupling wave function expansions for the ( e + ion) system to compute oscillator strengths and photoionization cross sections, (iii) open and closed shell iron ions of interest in astrophysics and experiments, (iv) a treatment for plasma broadening of autoionizing resonances as function of energy-temperature-density dependent cross sections, (v) a ‘top-up’ procedure to compare convergence with R -matrix calculations for highly excited levels, and (vi) spectroscopic identification of resonances and bound ( e + ion) levels. The present R -matrix monochromatic opacity spectra are fundamentally different from OP and lead to enhanced Rosseland and Planck mean opacities. An outline of the work reported in other papers in this series and those in progress is presented. Based on the present re-examination of the OP work, opacities of heavy elements might require revisions in high temperature-density plasma sources.
Metal–organic frameworks (MOFs) have premium exceptional properties for a variety of functions, such as gas separation and storage and catalysis. The large variety of possible inorganometallic nodes and organic linkers provide an almost unlimited number of combinations for assembling MOFs, which makes the experimental characterization and examination of all potentially useful combinations practically impossible. Furthermore, experimental studies of MOFs typically fall short in uncovering crucial details regarding their mechanisms of action or the molecular details responsible for their functional properties, such as the nature of adsorbate binding or the structures of transition states. Computational modeling has, therefore, become an efficient and important tool for strategizing the functionalization of MOFs and explicating the mechanisms of their functions. Furthermore, we review the computational methodologies used for computational studies of MOFs, especially Kohn–Sham density functional theory and combined quantum mechanical and molecular mechanical methods for calculating their structural, electronic, and magnetic properties, as well as for understanding the mechanisms of MOFs' applications to magetic devices, thermal conduction, gas adsorption, separation, storage, and sensing, thermal catalysis, photocatalysis, and electrocatalysis.
A novel multiphysics methodology for the computation of realistic plasma neutron sources has been developed. The approach is based on state-of-the-art plasma transport and neutron spectrum calculations, coupled with a Monte Carlo neutron transport code, bridging the gap between plasma physics and neutronics. In the paper two JET neutronics tokamak models are used to show the application of the developed plasma neutron sources and validate them. Diagnostic data for the record JET D discharge 92436 are used as input for the TRANSP code, modelling neutron emission in two external plasma heating scenarios, namely using only neutral beam injection and a combination of the latter and ion cyclotron resonance heating. Neutron spectra, based on plasma transport results, are computed using the DRESS code. The developed PLANET code package is employed to generate plasma neutron source descriptions and couple them with the MCNP code. The effects of using the developed sources in neutron transport calculations on the response of JET neutron diagnostic systems is studied and compared to the results obtained with a generic plasma neutron source. It is shown that, although there are significant differences in the emissivity profiles, spectra shape and anisotropy between the neutron sources, the integral response of the time-resolved ex-vessel neutron detectors is largely insensitive to source changes, with major relative deviations of up to several percent. However it is calculated that, because of the broadening of neutron spectra as a consequence of external plasma heating, larger differences may occur in activation of materials which have threshold reactions located at DD neutron peak energies. The PLANET plasma neutron source computational methodology is demonstrated to be suitable for detailed neutron source effect studies on JET during DT experiments and can be applied to ITER analyses.
Computational methodology is proposed to simulate time dependent temperature variations via thermostat approach. Here, the methodology is applied to study pyroelectricity under nonequilibrium conditions in prototypical ferroelectric PbTiO 3 . It is found that at room temperature the nonequilibrium effects in pyroelectricity begin manifesting above 1.0 THz and originate from the overlap with the intrinsic soft mode frequency. Therefore, the proposed computational methodology can be used to predict equilibrium pyroelectric response by choosing a frequency of temperature variation below the intrinsic polar mode frequencies for the material. Probing the dynamics of ferroelectric phase transition with the proposed methodology revealed that it takes about a nanosecond for the computational supercell to undergo phase transition. It is concluded that computational techniques capable of simulating picoseconds can be used to compute pyroelectric response from nonequilibrium dynamical approach while those that can reach nanoseconds are suitable for simulating phase transitions in ferroelectrics.
The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.
Numerous experiments have shown that the loads applied to Nb3Sn strands and cables can reduce their critical current. Experiments, performed on uniaxially loaded strands, allowed to define clear laws to describe the evolution of the critical surface as a function of the applied current, field, temperature and strain. It is, however, still unclear how these laws can be applied to superconducting magnets. The present paper proposes a methodology to estimate the critical current and temperature margin reduction on superconducting magnets due to stress on the superconducting material. The methodology is tested on the MQXF magnets, a quadrupole developed for the High Luminosity LHC project, and successfully validated by comparing computed strain with data from strain gauge measurements. Overall, results suggested that, because of the stresses arising in winding during assembly, cool-down and powering, the current limit of the magnet is lower than the expected short sample limit, and that the most critical region does not coincide with the peak field location.
Metal-organic frameworks (MOFs) have gained much attention as next generation porous media for various applications, especially gas separations/storage and catalysis. New MOFs are regularly reported; however, to develop better materials in a timely manner for specific applications, the interactions between guest molecules and the internal surface of the framework must first be understood. In this review, we present a combined experimental and theoretical approach that proves essential for the elucidation of small-molecule interactions in a model MOF system known as M 2 (dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Cu, or Zn), a material whose adsorption properties can be readily tuned via chemical substitution. Here, we additionally show that the study of extensive families like this one can provide a platform to test the efficacy and accuracy of developing computational methodologies in slightly varying chemical environments, a task that is necessary for their evolution into viable, robust tools for screening large numbers of materials.
The discharge rod internal pressure (RIP) and cladding hoop stress (CHS) distributions are quantified for Watts Bar Nuclear Unit 1 (WBN1) fuel rods by modeling core cycle design data, operation data, and as-built fuel enrichments and densities of each fuel rod in FRAPCON-3.5. A methodology is developed that tracks intercycle assembly movements and assembly batch fabrication information to build individual FRAPCON inputs for each evaluated WBN1 fuel rod. An alternate model for the amount of helium released from the zirconium diboride (ZrB 2 ) integral fuel burnable absorber (IFBA) layer is derived and applied to FRAPCON output data to quantify the RIP and CHS for these types of fuel rods. SCALE/Polaris is used to quantify fuel rod–specific spectral quantities and the amount of gaseous fission products produced in the fuel for use in FRAPCON inputs. Fuel rods with ZrB 2 IFBA layers (i.e., IFBA rods) are determined to have RIP predictions that are elevated when compared to fuel rods without IFBA layers (i.e., standard rods) despite the fact that IFBA rods often have reduced fill pressures and annular fuel pellets. The primary contributor to elevated RIP predictions at burnups less than and greater than 30 GWd/tonne U is determined to be the total fuel rod void volume and the amount of released fission gas in the fuel rod, respectively. Cumulative distribution functions (CDFs) are prepared from the distribution of RIP and CHS predictions for all standard and IFBA rods. The provided CDFs allow for the determination of the portion of WBN1 fuel rods that exceeds a specified RIP or CHS limit. Results are separated into IFBA and standard rods so that the two groups may be analyzed individually. FRAPCON results are provided in sufficient detail to enable the recalculation of the RIP while considering any desired plenum gas temperature, total void volume, or total amount of gas present in the void volume. A method to predict the CHS from a determined or assumed RIP is also proposed that is based on the approximately linear relationship between the CHS and the RIP. Finally, improvements to the computational methodology of FRAPCON are proposed.
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ~90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
The degradation of thermal conductivity in advanced nuclear fuels due to the accumulation of fission products and irradiation-induced defects is inevitable, and must be considered as part of safety and efficiency analyses of nuclear reactors. Here, this study examines the thermal conductivity of a zirconium-doped ThO 2 crystal, synthesized via the hydrothermal method using a spatial domain thermoreflectance technique. Zirconium is one of the soluble fission products in oxide fuels that can effectively scatter heat-carrying phonons in the crystalline lattice of fuel. Thus, thermal property measurements of zirconium-doped ThO 2 single crystals provide insights into the effects of substitutional zirconium doping, isolated from extrinsic factors such as grain boundary scattering. The experimental results are compared with first-principles calculations of the lattice thermal conductivity of ThO 2 , employing an iterative solution of the Peierls-Boltzmann transport equation. Additionally, the non-perturbative Green's function methodology is utilized to compute phonon-point defect scattering rates, accounting for local distortions around point defects, including mass difference changes, interatomic force constants, and structural relaxation. The congruence between the predicted results from first-principles calculations and the measured temperature-dependent thermal conductivity validates the computational methodology. Furthermore, the methodologies employed in this study enable systematic investigations of thermal conductivity reduction by fission products, potentially leading to the development of more accurate fuel performance codes.