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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Thermodynamic versus kinetic control in self-assembly of zero-, one-, quasi-two-, and two-dimensional metal-organic coordination structures

Four types of metal-organic structures exhibiting specific dimensionality were studied using scanning tunneling microscopy and Monte Carlo simulations. The four structures were self-assembled out of specifically designed molecular building blocks via the same coordination motif on an Au(111) surface. We found that the four structures behaved differently in response to thermal annealing treatments: The two-dimensional structure was under thermodynamic control while the structures of lower dimension were under kinetic control. Monte Carlo simulations revealed that the self-assembly pathways of the four structures are associated with the characteristic features of their specific heat. These findings provide insights into how the dimensionality of supramolecular coordination structures affects their thermodynamic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

From hydrogen bonding to metal coordination and back: Porphyrin-based networks on Ag(111)

The self-assembly of a metal-free porphyrin bearing two pyridyl coordinating sites and two pentyl chains at trans meso positions was investigated under ultrahigh vacuum on a Ag(111) surface by scanning tunneling microscopy (STM). The STM measurements revealed a well-ordered close-packed structure with a rhombic unit cell for coverages ≤1 monolayer with their molecular plane parallel to the surface. The growth direction of the molecular islands is aligned along the step edges, which are restructured due to molecule-substrate interactions. The shorter unit cell vector of the molecular superstructure follows the 〈1-10〉 direction of the Ag(111) substrate. Hydrogen bonds between pyridyl and pyrrole groups of neighboring molecules as well as weak van der Waals forces between the pentyl chains stabilize the superstructure. Deposition of cobalt atoms onto the close-packed structure at room temperature leads to the formation of a hexagonal porous network stabilized by metal-ligand bonding between the pyridyl ligands and the cobalt atoms. Thermal annealing of the Co-coordination network at temperatures >450 K results in the transformation of the hexagonal network into a second close-packed structure. Changes in the molecule-substrate interactions due to metalation of the porphyrin core with Co as well as intermolecular interactions can explain the observed structural transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

A reactant-coordinate-based approach to state-to-state differential cross sections for tetratomic reactions

A new algorithm is proposed to compute quantum mechanically state-to-state differential cross sections for reactions involving four atoms in full dimensionality. This algorithm, which is based on the propagation of an initial state specific wave packet exclusively in reactant coordinates, extracts the S-matrix elements in the product channel by first interpolating the time-dependent wave packet using a collocation method at selected time intervals on the product coordinate grid and then projecting out the contributions of all final product states. Here, this approach is efficient and accurate, particularly for reactions that are dominated by a product well or long-range interactions. Validation of this approach is demonstrated for the H 2 + OH → H + H 2 O reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

A multilayer multiconfiguration time-dependent Hartree simulation of the reaction-coordinate spin-boson model employing an interaction picture

The multilayer multiconfiguration time-dependent Hartree method is applied in an interaction picture to simulate dynamics of the spin-boson model in the reaction-coordinate representation. The use of the interaction picture allows a more effective description of correlation effects, especially when the coupling strength between the reaction coordinate and the bath is very strong. Examples show that in most physical regimes the efficiency is improved significantly, in some cases up to several orders of magnitude. This opens up new avenues for studying quantum dynamical problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Coordination changes in liquid tin under shock compression determined using in situ femtosecond x-ray diffraction

Little is known regarding the liquid structure of materials compressed to extreme conditions, and even less is known about liquid structures undergoing rapid compression on nanosecond timescales. Here, we report on liquid structure factor and radial distribution function measurements of tin shock compressed to 84(19) GPa. High-quality, femtosecond x-ray diffraction measurements at the Linac Coherent Light Source were used to extract the liquid diffuse scattering signal. From the radial distribution function, we find that the structural evolution of the liquid with increasing pressure mimics the evolution of the solid phase. With increasing pressure, we find that the liquid structure evolves from a complex structure, with a low coordination number, to a simple liquid structure with a coordination number of ~12. We provide a pathway for future experiments to study liquids at elevated pressures using high-energy lasers to shock compress materials beyond the reach of static diamond anvil cell techniques.

X-ray diffraction↗
DOE OSTI2020

Photophysics of graphene quantum dot assemblies with axially coordinated cobaloxime catalysts

We report a study of chromophore-catalyst assemblies composed of light harvesting hexabenzocoronene (HBC) chromophores axially coordinated to two cobaloxime complexes. The chromophore-catalyst assemblies were prepared using bottom-up synthetic methodology and characterized using solid-state NMR, IR, and x-ray absorption spectroscopy. Detailed steady-state and time-resolved laser spectroscopy was utilized to identify the photophysical properties of the assemblies, coupled with time-dependent DFT calculations to characterize the relevant excited states. The HBC chromophores tend to assemble into aggregates that exhibit high exciton diffusion length (D = 18.5 molecule 2 /ps), indicating that over 50 chromophores can be sampled within their excited state lifetime. We find that the axial coordination of cobaloximes leads to a significant reduction in the excited state lifetime of the HBC moiety, and this finding was discussed in terms of possible electron and energy transfer pathways. By comparing the experimental quenching rate constant (1.0 × 10 9 s -1 ) with the rate constant estimates for Marcus electron transfer (5.7 × 10 8 s -1 ) and Förster/Dexter energy transfers (8.1 × 10 6 s -1 and 1.0 × 10 10 s -1 ), we conclude that both Dexter energy and Marcus electron transfer process are possible deactivation pathways in CoQD-A. No charge transfer or energy transfer intermediate was detected in transient absorption spectroscopy, indicating fast, subpicosecond return to the ground state. Finally, these results provide important insights into the factors that control the photophysical properties of photocatalytic chromophore-catalyst assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Testing the conservative character of particle simulations: I. Canonical and noncanonical guiding center model in Boozer coordinates

The guiding center (GC) Lagrangian in Boozer coordinates for toroidally confined plasmas can be cast into canonical form by eliminating terms containing the covariant component B Ψ P of the magnetic field vector with respect to the poloidal flux function Ψ P . In an unperturbed plasma, B Ψ P can be eliminated via exact coordinate transformations, but, in general, one relies on approximations, assuming that the effect of B Ψ P is small. In this work, we are interested in the question whether Hamiltonian conservation laws are still satisfied when B Ψ P is retained in the presence of fluctuations. Considering fast ions in the presence of a shear Alfvén wave field with fixed amplitude, fixed frequency, and a single toroidal mode number n, we show that simulations using the code ORBIT with and without B Ψ P yield practically the same resonant and nonresonant GC orbits. The numerical results are consistent with theoretical analyses (presented in the appendix), which show that the unabridged GC Lagrangian with B Ψ P retained yields equations of motion that possess two key properties of Hamiltonian flows: (i) phase space conservation and (ii) energy conservation. As counter-examples, we also show cases where energy conservation (ii) or both conservation laws (i) and (ii) are broken by omitting certain small terms. When testing the conservative character of the simulation code, it is found to be beneficial to apply perturbations that do not resemble normal (eigen) modes of the plasma. The deviations are enhanced and, thus, more easily spotted when one inspects wave-particle interactions using nonnormal modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Pressure–strain interaction. II. Decomposition in magnetic field-aligned coordinates

In weakly collisional and collisionless magnetized plasmas, the pressure–strain interaction describes the rate of conversion between bulk flow and thermal energy density. In this study, we derive an analytical expression for the pressure–strain interaction in a coordinate system with an axis aligned with the local magnetic field. The result is eight groups of terms corresponding to different physical mechanisms that can contribute to the pressure–strain interaction. We provide a physical description of each term. Here, the results are immediately of interest to weakly collisional and collisionless magnetized plasmas and the fundamental processes that happen therein, including magnetic reconnection, magnetized plasma turbulence, and collisionless shocks. The terms in the field-aligned coordinate decomposition are likely accessible to measurement with satellite observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase

Significance The φ29 DNA packaging motor can be thought of as a five-cylinder engine, where each cylinder (subunit) catalyzes ATP hydrolysis to power DNA translocation. The motor operates in two phases: first, the subunits load fuel (ATP) sequentially one at a time; second, all subunits rapidly hydrolyze ATP in sequential fashion. How the subunits coordinate their activities remained unknown. Here, we show that the subunits use regulatory features observed in signaling pathways, a very different biological context, to coordinate their activities. Moreover, one of the subunits is stimulated by a contact with the DNA, transforming it into a “timer” element that paces the activity of the remaining cylinders. Similar mechanisms are likely present in other molecular machines.

Tafoya, Sara↗
DOE OSTI2022

Ultrahigh-pressure disordered eight-coordinated phase of Mg 2 GeO 4 : Analogue for super-Earth mantles

Mg 2 GeO 4 is important as an analog for the ultrahigh-pressure behavior of Mg 2 SiO 4 , a major component of planetary interiors. In this study, we have investigated magnesium germanate to 275 GPa and over 2,000 K using a laser-heated diamond anvil cell combined with in situ synchrotron X-ray diffraction and density functional theory (DFT) computations. The experimental results are consistent with the formation of a phase with disordered Mg and Ge, in which germanium adopts eightfold coordination with oxygen: the cubic, Th 3 P 4 -type structure. DFT computations suggest partial Mg-Ge order, resulting in a tetragonal $I\bar{4}2d$ structure indistinguishable from $I\bar{4}3d$ Th 3 P 4 in our experiments. If applicable to silicates, the formation of this highly coordinated and intrinsically disordered phase may have important implications for the interior mineralogy of large, rocky extrasolar planets.

58 GEOSCIENCES↗
DOE OSTI2022

Exact reaction coordinates for flap opening in HIV-1 protease

The primary goal of protein science is to understand how proteins function, which requires understanding the functional dynamics responsible for transitions between different functional structures of a protein. A central concept is the exact reaction coordinates that can determine the value of committor for any protein configuration, which provide the optimal description of functional dynamics. Despite intensive efforts, identifying the exact reaction coordinates (RCs) in complex molecules remains a formidable challenge. Using the recently developed generalized work functional, we report the discovery of the exact RCs for an important functional process—the flap opening of HIV-1 protease. Our results show that this process has six RCs, each one is a linear combination of ~240 backbone dihedrals, providing the precise definition of collectivity and cooperativity in the functional dynamics of a protein. Applying bias potentials along each RC can accelerate flap opening by 10 3 to 10 4 folds. The success in identifying the RCs of a protein with 198 residues represents a significant progress beyond that of the alanine dipeptide, currently the only other complex molecule for which the exact RCs for its conformational changes are known. Our results suggest that the generalized work functional (GWF) might be the fundamental operator of mechanics that controls protein dynamics.

Science & Technology - Other Topics↗
DOE OSTI2017

Coordination chemistry controls the thiol oxidase activity of the B 12 -trafficking protein CblC

The cobalamin or B 12 cofactor supports sulfur and one-carbon metabolism and the catabolism of odd-chain fatty acids, branched-chain amino acids, and cholesterol. CblC is a B 12 -processing enzyme involved in an early cytoplasmic step in the cofactor-trafficking pathway. It catalyzes the glutathione (GSH)-dependent dealkylation of alkylcobalamins and the reductive decyanation of cyanocobalamin. CblC from Caenorhabditis elegans (ceCblC) also exhibits a robust thiol oxidase activity, converting reduced GSH to oxidized GSSG with concomitant scrubbing of ambient dissolved O2. The mechanism of thiol oxidation catalyzed by ceCblC is not known. In this study, we demonstrate that novel coordination chemistry accessible to ceCblC-bound cobalamin supports its thiol oxidase activity via a glutathionyl-cobalamin intermediate. Deglutathionylation of glutathionyl-cobalamin by a second molecule of GSH yields GSSG. The crystal structure of ceCblC provides insights into how architectural differences at the α- and β-faces of cobalamin promote the thiol oxidase activity of ceCblC but mute it in wild-type human CblC. The R161G and R161Q mutations in human CblC unmask its latent thiol oxidase activity and are correlated with increased cellular oxidative stress disease. In summary, we have uncovered key architectural features in the cobalamin-binding pocket that support unusual cob(II)alamin coordination chemistry and enable the thiol oxidase activity of ceCblC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Coordinate parameterisation and spectral method optimisation for Beltrami field solver in stellarator geometry

The numerical solution of the stepped pressure equilibrium (Hudson et al 2012 Phys. Plasmas 19 112502) requires a fast and robust solver to obtain the Beltrami field in three-dimensional geometry such as stellarators. The spectral method implemented in the stepped pressure equilibrium code (SPEC) is efficient when the domain is a hollow torus, but ill-conditioning of the discretised linear equations occurs in the (solid) toroid due to the artificially singular coordinate parameterisation near the axis. Here, we propose an improved choice for the reference axis to prevent coordinates surfaces from overlapping. Then, we examine the parity and asymptotics of the magnetic vector potential near the axis and suggest the use of recombined and rescaled Zernike radial basis functions. The maximum relative error in the magnetic field of the Wendelstein 7-X geometry is shown to reach 10 –9 at high resolution in a series of convergence tests and benchmarks against the boundary integral equation solver for Taylor states. The new method is also reported to significantly improve the accuracy of multi-volume SPEC calculations. A comparison between free-boundary SPEC and the analytical Dommaschk potential is presented with higher-than-usual Fourier resolution. It is illustrated that we are able to resolve low amplitude current sheets when an interface is placed where there is no flux surface in the analytic solution. This was previously concealed because of insufficient numerical resolution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Construction of quasisymmetric stellarators using a direct coordinate approach

In this work, optimized stellarator configurations and their analytical properties are obtained using a near-axis expansion approach. Such configurations are associated with good confinement as the guiding center particle trajectories and neoclassical transport are isomorphic to those in a tokamak. This makes them appealing as fusion reactor candidates. Using a direct coordinate approach, where the magnetic field and flux surface functions are found explicitly in terms of the position vector at successive orders in the distance to the axis, the set of ordinary differential equations for first and second order quasisymmetry is derived. Examples of quasi-axisymmetric shapes are constructed using a pseudospectral numerical method. Finally, the direct coordinate approach is used to independently verify two hypotheses commonly associated with quasisymmetric magnetic fields, namely that the number of equations exceeds the number of parameters at third order in the expansion and that the near-axis expansion does not prohibit exact quasisymmetry from being achieved on a single flux surface.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Energetic lanthanide complexes: coordination chemistry and explosives applications

Here, we report that metals are generally added to organic molecular explosives in a heterogeneous composite to improve overall heat and energy release. In order to avoid creating a mixture that can vary in homogeneity, energetic organic molecules can be directly bonded to high molecular weight metals, forming a single metal complex with Angstrom-scale separation between the metal and the explosive. To probe the relationship between the structural properties of metal complexes and explosive performance, a new series of energetic lanthanide complexes has been prepared using energetic ligands such as NTO (5-nitro-2,4-dihydro-1,2,4-triazole-3-one). These are the first examples of lanthanide NTO complexes where no water is coordinated to the metal, demonstrating novel control of the coordination environment. The complexes have been characterized by X-ray crystallography, NMR and IR spectroscopies, photoluminescence, and sensitivity testing. The structural and energetic properties are discussed in the context of enhanced blast effects and detection. Cheetah calculations have been performed to fine-tune physical properties, creating a systematic method for producing explosives with 'tailor made' characteristics. In conclusion, these new complexes will be benchmarks for further study in the field of metalized high explosives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A path to intelligent watersheds: coordinating the data to decision pipeline

Operations of multi-reservoir systems are challenged in-part by the interplay of complex physical processes functioning within the watershed. The employment of intelligent systems can be of aid by linking environmental sensing, information technology, data analytics, simulation and decision support to achieve a data-to-decision flow of information. A further challenge is that watershed resources are managed for multiple purposes requiring some level of coordination among numerous resource managers, asset operators and users. System intelligence in this context relies on shared community platforms (data portals, community models), and coordinated communication between decision makers. Opportunities to enrich watershed intelligence has been the subject of a roadmapping exercise for the Department of Energy’s Water Power Technologies Office which has relied on broad stakeholder engagement. Initial phases of engagement involved personal interviews and a series of virtual group meetings, which focused on identifying opportunities to improve the intelligence of the physical infrastructure within our watersheds—examples of feedback include improved sensing of snowpack and runoff, data standards for facilitated data sharing, and better forecasting tools. The latter phase of engagement involved the conduct of a case study in the Upper Colorado River basin where key stakeholders were interviewed to map how their decisions are informed by intelligence from other basin stakeholders. Our presentation will highlight the interdisciplinary flow of information in complex watershed systems and identify physical and institutional opportunities toward the strategic operation of water infrastructure.

Colorado River↗
DOE OSTI2021

Application of an efficient generator-coordinate subspace-selection algorithm to neutrinoless double- β decay

The generator coordinate method begins with the variational construction of a set of nonorthogonal mean-field states that span a subspace of the full many-body Hilbert space. These states are then often projected onto states with good quantum numbers to restore symmetries, leading to a set with members that can be similar to one another, and it is sometimes possible to reduce this set without greatly affecting results. Here, we propose a greedy algorithm that we call the energy-transition-orthogonality procedure (ENTROP) to select subsets of important states. As applied here, the approach selects on the basis of diagonal energy, orthogonality, and contribution to the matrix element that governs neutrinoless double-β decay. We present both shell-model and preliminary ab initio calculations of this matrix element for the decay of 76Ge, with quadrupole deformation parameters and the isoscalar pairing strength as generator coordinates. ENTROP converges quickly, reducing significantly the number of basis states needed for an accurate calculation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗