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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.

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At least 19 records

Statistical mechanics based on fractional classical and quantum mechanics

The purpose of this work is to study some problems in statistical mechanics based on the fractional classical and quantum mechanics. At first stage we have presented the thermodynamical properties of the classical ideal gas and the system of N classical oscillators. In both cases, the Hamiltonian contains fractional exponents of the phase space (position and momentum). At the second stage, in the context of the fractional quantum mechanics, we have calculated the thermodynamical properties for the black body radiation, studied the Bose-Einstein statistics with the related problem of the condensation and the Fermi-Dirac statistics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well‐known codes—NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.

Pirojsirikul, Teerapong↗

Combined quantum mechanical and molecular mechanical method for metal–organic frameworks: proton topologies of NU-1000

Metal–organic frameworks (MOFs) are materials with applications in catalysis, gas separations, and storage. Quantum mechanical (QM) calculations can provide valuable guidance to understand and predict their properties. In order to make the calculations faster, rather than modeling these materials as periodic (infinite) systems, it is useful to construct finite models (called cluster models) and use subsystem methods such as fragment methods or combined quantum mechanical and molecular mechanical (QM/MM) methods. Here we employ a QM/MM methodology to study one particular MOF that has been of widespread interest because of its wide pores and good solvent and thermal stability, namely NU-1000, which contains hexanuclear zirconium nodes and 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy 4- ) linkers. A modified version of the Bristow–Tiana–Walsh transferable force field has been developed to allow QM/MM calculations on NU-1000; we call the new parametrization the NU1T force field. We consider isomeric structures corresponding to various proton topologies of the [Zr 6 (μ 3 -O) 8 O 8 H 16 ] 8+ node of NU-1000, and we compute their relative energies using a QM/MM scheme designed for the present kind of problem. We compared the results to full quantum mechanical (QM) energy calculations and found that the QM/MM models can reproduce the full QM relative energetics (which span a range of 334 kJ mol -1 ) with a mean unsigned deviation (MUD) of only 2 kJ mol-1. Furthermore, we found that the structures optimized by QM/MM are nearly identical to their full QM optimized counterparts.

Wu, Xin-Ping↗

Deformation mechanism study of a hot rolled Zr-2.5Nb alloy by transmission electron microscopy. II. In situ transmission electron microscopy study of deformation mechanism change of a Zr-2.5Nb alloy upon heavy ion irradiation

The effect of heavy-ion irradiation on deformation mechanisms of a Zr-2.5Nb alloy was investigated by using the in situ transmission electron microscopy deformation technique. The gliding behavior of prismatic 〈a〉 dislocations has been dynamically observed before and after irradiation at room temperature and 300 °C. Irradiation induced loops were shown to strongly pin the gliding dislocations. Unpinning occurred while loops were incorporated into or eliminated by 〈a〉 dislocations. In the irradiated sample, loop depleted areas with a boundary parallel to the basal plane trace were found by post-mortem observation after room temperature deformation, supporting the possibility of basal channel formation in bulk neutron irradiated samples. Strong activity of pyramidal slip was also observed at both temperatures, which might be another important mechanism to induce plastic instability in irradiated zirconium alloys. Finally, (011{sup ¯}1)〈01{sup ¯}12〉 twinning was identified in the irradiated sample deformed at 300 °C.

36 MATERIALS SCIENCE↗

Characterizing the Mechanisms of Ca and Mg Carbonate Ion-Pair Formation with Multi-Level Molecular Dynamics/Quantum Mechanics Simulations

The carbonate minerals of Ca and Mg are abundant throughout the lithosphere and have recently garnered significant research interest as possible long-term carbon sinks in the sequestration of atmospheric carbon dioxide. Nonetheless, an understanding of the atomic-level processes comprising their mineralization remains limited. Furthermore, we characterize and contrast the mechanisms of contact ion-pair formation in aqueous Ca and Mg carbonate systems, which represents the most fundamental step leading to the formation of their mineral solids. Utilizing multilevel embedded correlated wavefunction-based ab initio molecular dynamics/quantum mechanics simulations, we characterize not only the dynamics of these processes but also factors arising from the electronic structure of the involved species, revealing further details of the fundamentally different mechanisms for the interconversion between the contact ion-pairs and solvent-shared ion-pairs of Ca versus Mg carbonate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces

Performing reliable computer simulations of elementary processes occurring at metal–water interfaces is pivotal for novel catalyst design in sustainable energy applications. Computational catalyst design hinges on the ability to reliably and efficiently compute the potential energy surface (PES) of the system. Here, due to the large system sizes needed for studying processes at liquid water–metal interfaces, these systems can currently not be described using density functional theory (DFT). In this work, we used a hybrid quantum mechanical, molecular mechanical, and machine learning potential for studying the adsorption behavior of phenol, atomic hydrogen, 2-butanol, and 2-butanone on the (0001) facet of Ru under reducing conditions when Ru is not oxidized. Specifically, we describe the adsorbate and the surrounding metal atoms at the DFT level of theory. Here, we also considered the electrostatic field effect of the water molecules on adsorbate–metal interactions. Next, for the water–water and water–adsorbate interactions, we used established classical force fields. Finally, for the water–Ru surface interaction, for which no reliable force fields have been published, we used Behler–Parrinello high-dimensional neural network potentials (HDNNPs). Employing this setup, we used our explicit solvation for metal surface (eSMS) approach to compute the aqueous-phase effect on the low-coverage adsorption of selected molecules and atoms on the (0001) facet of Ru. In agreement with previous experimental and computational studies of oxygenated molecules over transition metal facets, we found that liquid water destabilizes the tested adsorbates on Ru(0001). Interestingly, our findings indicate that adsorbates on Ru are less affected by the presence of an aqueous phase than on other transition metals (e.g., Pt), highlighting the necessity of experimental investigations of Ru-based catalytic systems in liquid water.

Adsorption↗

Pellet cladding mechanical interaction as a potential failure mechanism during a control rod drop accident in a boiling water reactor

Boiling water reactors (BWRs) represent approximately one-third of the operating fleet in the United States, contributing significantly towards the global effort in reducing carbon emissions. Even though most of the operating fleet has been in operation for quite some time, continued advancements in new nuclear fuel (such as accident tolerant fuel) or operating regimes (such as power up-rates and higher burnup operation) necessitates similar advancements in modeling and simulation capabilities. Bison, a component of the Virtual Environment for Reactor Applications (VERA), is a high-fidelity fuel performance code able to explore the fuel performance of a wide variety of fuel types in one-, two-, and three-dimensions. Until recently, the code had not been used for analyses of BWRs. Modeling capabilities have been added for Gd-bearing UO{sub 2} and pure zirconium liners. New models have been added based upon the U.S. Nuclear Regulatory Commission (NRC) guide-lines for hydrogen pickup in Zircaloy-2 claddings and pellet-clad mechanical interaction (PCMI) failure during a reactivity insertion accident (RIA), known as a rod drop accident (CRDA) in BWRs. Implementing and/or improving Bison modeling capabilities extended its analytical reach to areas beyond its original intended purpose. This paper demonstrates one of these capabilities as a proof of concept. Recently developed models enable Bison to provide an alternate approach for cladding integrity determination in CRDA evaluations, which currently use bounding conservative estimates. As part of this demonstration, NRC guidance on hydrogen-pickup and PCMI failure models were utilized in this research. Even though more research is needed in establishing right inputs and process in this area, this paper demonstrates Bison's ability to determine cladding integrity in a CRDA evaluation. This first of a kind demonstration is a proof of concept in this area, which could potentially be extended to a number of other areas where a more accurate cladding integrity determination would be needed. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The Structure and Catalytic Mechanism of Sorghum bicolor Caffeoyl-CoA O-Methyltransferase

Caffeoyl-coenzyme A 3-O-methyltransferase (CCoAOMT) is an S-adenosyl methionine (SAM)-dependent O-methyltransferase responsible for methylation of the meta-hydroxyl group of caffeoyl-coenzyme A (CoA) on the pathway to monolignols, with their ring methoxylation status characteristic of guaiacyl or syringyl units in lignin. In order to better understand the unique class of type 2 O-methyltransferases from monocots, we have characterized CCoAOMT from sorghum (Sorghum bicolor; SbCCoAOMT), including the SAM binary complex crystal structure and steady-state enzyme kinetics. Key amino acid residues were validated with site-directed mutagenesis. Isothermal titration calorimetry data indicated a sequential binding mechanism for SbCCoAOMT, wherein SAM binds prior to caffeoyl-CoA, and the enzyme showed allosteric behavior with respect to it. 5-Hydroxyferuloyl-CoA was not a substrate for SbCCoAOMT. We propose a catalytic mechanism in which lysine-180 acts as a catalytic base and deprotonates the reactive hydroxyl group of caffeoyl-CoA. This deprotonation is facilitated by the coordination of the reactive hydroxyl group by Ca 2+ in the active site, lowering the pK a of the 3'-OH group. Collectively, these data give a new perspective on the catalytic mechanism of CCoAOMTs and provide a basis for the functional diversity exhibited by type 2 plant OMTs that contain a unique insertion loop (residues 208–231) conferring affinity for phenylpropanoid-CoA thioesters. The structural model of SbCCoAOMT can serve as the basis for protein engineering approaches to enhance the nutritional, agronomic, and industrially relevant properties of sorghum.

Walker, Alexander M.↗

Data integration reveals key homeostatic mechanisms following low dose radiation exposure

The goal of this study was to define pathways regulated by low dose radiation to understand how biological systems respond to subtle perturbations in their environment and prioritize pathways for human health assessment. Using an in vitro 3-D human full thickness skin model, we have examined the temporal response of dermal and epidermal layers to 10 cGy X-ray using transcriptomic, proteomic, phosphoproteomic and metabolomic platforms. Bioinformatics analysis of each dataset independently revealed potential signaling mechanisms affected by low dose radiation, and integrating data shed additional insight into the mechanisms regulating low dose responses in human tissue. We examined direct interactions among datasets (top down approach) and defined several hubs as significant regulators, including transcription factors (YY1, MYC and CREB1), kinases (CDK2, PLK1) and a protease (MMP2). These data indicate a shift in response across time — with an increase in DNA repair, tissue remodeling and repression of cell proliferation acutely (24–72 h). Pathway-based integration (bottom up approach) identified common molecular and pathway responses to low dose radiation, including oxidative stress, nitric oxide signaling and transcriptional regulation through the SP1 factor that would not have been identified by the individual data sets. Significant regulation of key downstream metabolites of nitrative stress was measured within these pathways. Among the features identified in our study, the regulation of MMP2 and SP1 was experimentally validated. Our results demonstrate the advantage of data integration to broadly define the pathways and networks that represent the mechanisms by which complex biological systems respond to perturbation. - Highlights: • Low dose ionizing radiation altered homeostasis in 3D skin tissue model. • Global gene/protein/metabolite data integrated using complementary statistical approaches • Time and location-specific change in matrix regulation, ROS/RNS and DNA repair pathways detected • Low dose exposure alters metabolites involved in nitric oxide biosynthesis and wound healing. • Computationally predicted regulators of primary mechanisms were experimentally validated.

60 APPLIED LIFE SCIENCES↗

Deformation mechanisms in a precipitation-strengthened ferritic super alloy revealed by in situ neutron dffraction studies at elevated temperatures

The ferritic superalloy Fe–10Ni–6.5Al–10Cr–3.4Mo strengthened by ordered (Ni,Fe)AlB2-type precipitates is a candidate material for ultra-supercritical steam turbine applications above 923 K. Despite earlier success in improving its room-temperature ductility, the creep resistance of this material at high temperatures needs to be further improved, which requires a fundamental understanding of the high-temperature deformation mechanisms at the scales of individual phases and grains. In situ neutron diffraction has been utilized to investigate the lattice strain evolution and the microscopic load-sharing mechanisms during tensile deformation of this ferritic superalloy at elevated temperatures. Finite-element simulations based on the crystal plasticity theory are employed and compared with the experimental results, both qualitatively and quantitatively. Based on these interphase and intergranular load-partitioning studies, it is found that the deformation mechanisms change from dislocation slip to those related to dislocation climb, diffusional flow and possibly grain boundary sliding, below and above 873 K, respectively. Insights into microstructural design for enhancing creep resistance are also discussed.

nuclear (including radiation effects), defects, me↗

Mechanical behaviors and phase transition of Ho{sub 2}O{sub 3} nanocrystals under high pressure

Mechanical properties and phase transition often show quite large crystal size dependent behavior, especially at nanoscale under high pressure. Here, we have investigated Ho{sub 2}O{sub 3} nanocrystals with in-situ x-ray diffraction and Raman spectroscopy under high pressure up to 33.5 GPa. When compared to the structural transition routine cubic -> monoclinic -> hexagonal phase in bulk Ho{sub 2}O{sub 3} under high pressure, the nano-sized Ho{sub 2}O{sub 3} shows a much higher onset transition pressure from cubic to monoclinic structure and followed by a pressure-induced-amorphization under compression. The detailed analysis on the Q (Q = 2π/d) dependent bulk moduli reveals the nanosized Ho{sub 2}O{sub 3} particles consist of a clear higher compressible shell and a less compressible core. Insight into these phenomena shed lights on micro-mechanism studies of the mechanical behavior and phase evolution for nanomaterials under high pressure, in general.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Band or Polaron: The Hole Conduction Mechanism in the p-Type Spinel Rh 2ZnO4

Given the emerging role of oxide spinels as hole conductors, we discuss in this article the traditional vs. new methodologies of determining the type of conduction mechanism at play - localized polaronic vs. band-like transport. Applying (i) traditional small polaron analysis to our in-situ high temperature four-point conductivity and thermopower measurements, we previously found an activated mobility, which is indicative of the small polaron mechanism. However, (ii) employing the recent developments in correcting density functional methodologies for hole localization, we predict that the self-trapped hole is unstable and that Rh{sub 2}ZnO{sub 4} is instead a band conductor with a large effective mass. The hole mobility measured by high-field room temperature Hall effect also suggests band rather than polaron conduction. The apparent contradiction between the conclusion of the traditional procedure (i) and first-principles theory (ii) is resolved by taking into account in the previous transport analysis the temperature dependence of the effective density of states, which leads to the result that the mobility is actually temperature-independent in Rh{sub 2}ZnO{sub 4}. Our case study on Rh{sub 2}ZnO{sub 4} illustrates the range of experimental and theoretical approaches at hand to determine whether the transport mechanism of a semiconductor is band or small polaron conduction.

14 SOLAR ENERGY↗

Failure Mechanism of Fast-Charged Lithium Metal Batteries in Liquid Electrolyte

In recent years, lithium anode has re-attracted broad interest because of the necessity of employing lithium metal in the next-generation battery technologies such as lithium sulfur (Li-S) and lithium oxygen (Li-O2) batteries. Fast capacity degradation and safety issue associated with rechargeable lithium metal batteries have been reported, although the fundamental understanding on the failure mechanism of lithium metal at high charge rate is still under debate due to the complicated interfacial chemistry between lithium metal and electrolyte. Herein, we demonstrate that, at high current density, the quick growth of porous solid electrolyte interphase towards bulk lithium, instead of towards the separator, dramatically builds up the cell impedance that directly leads to the cell failure. Understanding the lithium metal failure mechanism is very critical to gauge the various approaches used to address the stability and safety issues associated with lithium metal anode. Otherwise, all cells will fail quickly at high rates before the observation of any positive effects that might be brought from adopting the new strategies to protect lithium.

Environmental Molecular Sciences Laboratory↗