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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Temperature-Dependent Properties of Molten Li 2 BeF 4 Salt Using Ab Initio Molecular Dynamics

Molten lithium tetrafluoroberyllate (Li 2 BeF 4 ) salt, also known as FLiBe, with a 2:1 mixture of LiF and BeF 2 is being proposed as a coolant and solvent in advanced nuclear reactor designs, such as the molten salt reactor or the fluoride salt cooled high-temperature reactor. We present the results on the structure and properties of FLiBe over a wide range of temperatures, 0–2000 K, from high-throughput ab initio molecular dynamics simulation using a supercell model of 504 atoms. The variations in the local structures of solid and liquid FLiBe with temperature are discussed in terms of a pair distribution function, coordination number, and bond angle distribution. The temperature-dependent electronic structure and optical and mechanical properties of FLiBe are calculated. The optical and mechanical property results are reported for the first time. The results above and below the melting temperature (~732 K) are compared with the experimental data and with data for crystalline FLiBe. The electronic structure and interatomic bonding results are discussed in correlation with the mechanical strength. A novel concept of total bond order density (TBOD), an important quantum mechanical parameter, is used to characterize the internal cohesion and strength in the simulated models. The results show a variation in the rate of change in properties in solid and liquid phases with anomalous behavior across the melting region. The observed trend is the decrease in mechanical strength, band gap, and TBOD in a nonlinear fashion as a function of temperature. The refractive index shows a surprising minimum at 850 K, among the tested temperatures, which lies above the melting point. These findings provide a new platform to understand the interplay between the temperature-dependent structures and properties of FLiBe salt.

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

Short- to Intermediate-Range Structure, Transport, and Thermophysical Properties of LiF–NaF–ZrF4 Molten Salts

LiF–NaF–ZrF 4 multicomponent molten salts are identified as promising candidates for coolant salts in molten salt reactors and advanced high-temperature reactors. This study focused on low-melting point salt compositions of interest: 38LiF–51NaF–11ZrF 4 , 42LiF–29NaF–29ZrF 4 , and 26LiF–37NaF–37ZrF 4 . Ab-initio molecular dynamics (AIMD) calculations were performed and compared with available experimental data to assess the ability of rigid ion models (RIM) to reproduce short- to intermediate-range structure, transport, and thermophysical properties of the LiF–NaF–ZrF 4 salt mixtures. It is found that as ZrF 4 mol% increases, the average cation–anion coordination number (CN) of monovalent cations (Li + , Na + ) obtained from RIM calculations decreases, while multivalent Zr 4+ CN varied from 15% to 19% in comparison to corresponding AIMD values. In addition, RIM is found to predict the existence of 7, 8, and 9 coordinated fluorozirconate complexes, while AIMD and the available experimental data showed an occurrence of 6, 7, and 8 coordinated complexes in the melt. The intermediate-range structure analysis revealed that while the RIM parameters are able to reproduce a local structure for lower ZrF 4 mol% salts such as in 38LiF–51NaF–11ZrF 4 , an extensive fluorozirconate network formation is observed in RIM simulations for higher ZrF 4 mol% compositions. The network generated by RIM parameters is found to be mainly connected by “corner-sharing” fluorozirconate complexes as opposed to both “edge-sharing” and “corner-sharing” connectively portrayed by AIMD. It is found that a close agreement between AIMD and the RIM salt structure for the 11-mol% ZrF 4 salt resulted in good agreement in the calculated Zr diffusivities and the viscosity values. However, due to the inaccurate short- to intermediate-range structure prediction by RIM for higher ZrF 4 mol% compositions, thermophysical properties such as densities and heat capacity differ by up to 26% and 27%, respectively, upon comparison with AIMD and experimental values. Also, the network-dominated properties such as diffusion coefficients and viscosities differed by up to two and three orders of magnitude, respectively. This study signifies the importance of accurate salt structure generation for an accurate prediction of transport and thermophysical properties of multicomponent molten salts.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Revealing local order via high energy EELS

Short range order (SRO) is critical in determining the performance of many important engineering materials. However, accurate characterization of SRO with high spatial resolution – which is needed for the study of individual nanoparticles and at material defects and interfaces – is often experimentally inaccessible. Here, we locally quantify SRO via scanning transmission electron microscopy with extended energy loss fine structure analysis. Specifically, we use novel instrumentation to perform electron energy loss spectroscopy out to 12 keV, accessing energies which are conventionally only possible using a synchrotron. Our data is of sufficient energy resolution and signal-to-noise ratio to perform quantitative extended fine structure analysis, which allows determination of local coordination environments. To showcase this technique, we investigate a multicomponent metallic glass nanolaminate and locally quantify the SRO with <10 nm spatial resolution; this measurement would have been impossible with conventional synchrotron or electron microscopy methods. Finally, we discuss the nature of SRO within the metallic glass phase, as well as the wider applicability of our approach for determining processing–SRO–property relationships in complex materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Carboxylate binding prefers two cations to one

Almost all studies of specific ion binding by carboxylates (–COO - ) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li + , Na + , K + , Cs + ) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs + , which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na + and K + , and 3 for Li + and Cs + . There is a 4-fold coordination minimum just a few kcal mol -1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. Here we find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective ion transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1975

On the interaction structure of linear multi-input feedback control systems

The closely-related problems of designing reliable feedback stabilization strategy and coordinating decentralized feedbacks are considered. Two approaches are taken. A geometric characterization of the structure of control interaction (and its dual) was first attempted and a concept of structural homomorphism developed based on the idea of 'similarity' of interaction pattern. The idea of finding classes of individual feedback maps that do not 'interfere' with the stabilizing action of each other was developed by identifying the structural properties of nondestabilizing and LQ-optimal feedback maps. Some known stability properties of LQ-feedback were generalized and some partial solutions were provided to the reliable stabilization and decentralized feedback coordination problems. A concept of coordination parametrization was introduced, and a scheme for classifying different modes of decentralization (information, control law computation, on-line control implementation) in control systems was developed.

Wong, P. K.↗
DOE OSTI2022

Expanding and quantifying the crystal chemistry of the flexible ligand 15aneN5

Tetraazamacrocycles have been very extensively exploited as transition metal ligands for a variety of purposes, including catalysis, medical imaging, pharmaceuticals, etc. However, the pentaazamacrocycles are much less commonly used for similar purposes because of poor availability, difficulties in their synthesis, and less well-known metal coordination properties. 1,4,7,10,13-pentaazacyclopentadane (15aneN5) was initially synthesized by a published synthetic route, which we simplified and shortened with minimal drop in yield. Eight different transition metal complexes were made using typical complexation methods. X-ray crystallography of multiple novel complexes yielded insight into the flexibility in coordination geometry of this interesting macrocycle as well as the first crystal structures of 15aneN5 with Cr 3+ , Mn 3+ , Fe 3+ , Co 3+ , Cu 2+ , and Ru 2+ . A parameter to quantify the coordination geometry adopted by the ligand was devised and applied to all known crystal structures of its metal complexes. Lastly, oxidation of 15aneN5 to a novel diimine macrocycle was observed during complexation with ruthenium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics

Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the “spectral gap optimization of order parameters (SGOOP)” approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. Here, we believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Crystal structure of Cu2Zn(GexSi1−x)Se4 solid solution: the kesterite to wurtz–kesterite structural phase transition

Developing low-cost, sustainable, and environmentally friendly top absorber layers for tandem solar cells is essential to advancing photovoltaic technologies and accelerating the transition to renewable energy. In this work, we explore the potential of tetravalent (Cu2Zn(GexSi1−x)Se4) cation mutations in chalcogenide compound semiconductors with the aim of finding a material with increased band gap and reduced structural disorder. A combination of high-resolution synchrotron powder diffraction and neutron powder diffraction was used to determine the atomic positions and monoclinic angles in monoclinic wurtz–kesterite type Cu2Zn(GexSi1−x)Se4 mixed crystals as well as to determine the cation distribution in the crystal structure of Ge-rich kesterite-type and Si-rich wurtz–kesterite type mixed crystals. These investigations enabled us to deduce the structural transition scenario within the Cu2Zn(GexSi1−x)Se4 series. The transition occurs via a region where two phases with different crystal structures, tetragonal and monoclinic and thus a different distortion of the coordination tetrahedra, but the same cation distribution within the element specific cation sites co-exist. Thus, the structural transition between the kesterite and the wurtz–kesterite structure within the Cu2Zn(GexSi1−x)Se4 series is a distortion driven transition. The study identifies cation mutation in quaternary chalcogenides as a promising strategy beyond chalcopyrites and kesterites for low cost and environmentally friendly top absorbers in tandem solar cells.

Gurieva, Galina [Helmholtz Center Berlin for Mater↗
DOE OSTI2020

Materials Data on Rb(SiPt)4 by Materials Project

Rb(PtSi)4 crystallizes in the tetragonal I4 space group. The structure is three-dimensional. Rb1+ is bonded in a 8-coordinate geometry to eight equivalent Pt+0.25- atoms. There are four shorter (3.31 Å) and four longer (3.44 Å) Rb–Pt bond lengths. Pt+0.25- is bonded in a 5-coordinate geometry to two equivalent Rb1+ and five equivalent Si atoms. There are a spread of Pt–Si bond distances ranging from 2.42–2.57 Å. Si is bonded in a 5-coordinate geometry to five equivalent Pt+0.25- atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Constructing field-aligned coordinate systems for gyrokinetic simulations of tokamaks in X-point geometries

Structures in tokamak plasmas are elongated along the direction of the magnetic field and short in the directions perpendicular to the magnetic field. Many tokamak simulation codes take advantage of this by using a field-aligned coordinate system. However, field-aligned coordinate systems have a coordinate singularity at magnetic X-points where the poloidal magnetic field vanishes, which makes it difficult to use field-aligned coordinate systems when simulating the core and scrape-off layer simultaneously. Here, we present an algorithm for grid generation and computing geometric quantities in a standard field-aligned coordinate system that avoids the singularity and allows one to conduct two-dimensional gyrokinetic axisymmetric simulations in X-point geometries. Convergence tests of advection, boundary value problems and geometric quantities all show greater than first-order convergence even in the vicinity of the X-point. We also demonstrate the geometric consistency of our algorithm with an example simulation of the spherical tokamak for energy production, which shows machine-precision particle conservation.

fusion plasma↗
DOE OSTI2022

Luminescence and Scintillation in the Niobium Doped Oxyfluoride Rb4Ge5O9F6:Nb

A new niobium-doped inorganic scintillating oxyfluoride, Rb4Ge5O9F6:Nb, was synthesized in single crystal form by high-temperature flux growth. The host structure, Rb4Ge5O9F6, crystallizes in the orthorhombic space group Pbcn with lattice parameters a = 6.98430(10) Å, b = 11.7265(2) Å, and c = 19.2732(3) Å, consisting of germanium oxyfluoride layers made up of Ge3O9 units connected by GeO3F3 octahedra. In its pure form, Rb4Ge5O9F6 shows neither luminescence nor scintillation but when doped with niobium, Rb4Ge5O9F6:Nb exhibits bright blue luminescence and scintillation. The isostructural doped structure, Rb4Ge5O9F6:Nb, crystallizes in the orthorhombic space group Pbcn with lattice parameters a = 6.9960(3) Å, b = 11.7464(6) Å, and c = 19.3341(9) Å. X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) measurements suggest that the niobium is located in an octahedral coordination environment. Optical measurements inform us that the niobium dopant acts as the activator. The synthesis, structure, and optical properties are reported, including radioluminescence (RL) measurements under X-ray irradiation.

Carone, Darren (ORCID:0000000164014098)↗
NASA NTRS2003

The Effect of Spaceflight on the Ultrastructure of the Cerebellum

In weightlessness, astronauts and cosmonauts may experience postural illusions as well as motion sickness symptoms known as the space adaptation syndrome. Upon return to Earth, they have irregularities in posture and balance. The adaptation to microgravity and subsequent re-adaptation to Earth occurs over several days. At the cellular level, a process called neuronal plasticity may mediate this adaptation. The term plasticity refers to the flexibility and modifiability in the architecture and functions of the nervous system. In fact, plastic changes are thought to underlie not just behavioral adaptation, but also the more generalized phenomena of learning and memory. The goal of this experiment was to identify some of the structural alterations that occur in the rat brain during the sensory and motor adaptation to microgravity. One brain region where plasticity has been studied extensively is the cerebellar cortex-a structure thought to be critical for motor control, coordination, the timing of movements, and, most relevant to the present experiment, motor learning. Also, there are direct as well as indirect connections between projections from the gravity-sensing otolith organs and several subregions of the cerebellum. We tested the hypothesis that alterations in the ultrastructural (the structure within the cell) architecture of rat cerebellar cortex occur during the early period of adaptation to microgravity, as the cerebellum adapts to the absence of the usual gravitational inputs. The results show ultrastructural evidence for neuronal plasticity in the central nervous system of adult rats after 24 hours of spaceflight. Qualitative studies conducted on tissue from the cerebellar cortex (specifically, the nodulus of the cerebellum) indicate that ultrastructural signs of plasticity are present in the cerebellar zones that receive input from the gravity-sensing organs in the inner ear (the otoliths). These changes are not observed in this region in cagematched ground control animals. The specific changes include the formation of lamellar bodies, profoundly enlarged Purkinje cell mitochondria, the presence of inter-neuronal cellular protrusions in the molecular layer, and signs of degeneration in the distal dendrites of the Purkinje cells. Since these morphologic signs are not apparent in the control animals, they are not likely to be due to caging or tissue processing effects. The particular nature of the structural alterations in the nodulus, most notably the formation of lamellar bodies and the presence of degeneration, further suggests that excitotoxicity (damaging overstimulation of neurons) may play a role in the short-term neural response to spaceflight. These findings suggest a structural basis for the neuronal and synaptic plasticity accompanying the central nervous system response to altered gravity and help identify the cellular bases underlying the vestibular abnormalities experienced by astronauts during periods of adaptation and re-adaptation to different gravitational forces. Also, since the short- and long-term changes in neural structure occurring during such periods of adaptation resemble the neuronal alterations that occur in some neurologic disorders such as stroke, these findings may offer guidance in the development of strategies for rehabilitation and treatment of such disorders.

Holstein, Gay R.↗
DOE OSTI2023

Structurally Constrained Evolutionary Algorithm for the Discovery and Design of Metastable Phases

Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to determine a structure’s fitness, are not suitable for predicting the vast number of potentially synthesizable phases that represent a local minimum corresponding to a state in thermodynamic equilibrium. Here, we present a new approach for the prediction of metastable phases with specific structural features, and interface this method with the XTALOPT evolutionary algorithm. Our method relies on structural features that include the local crystalline order (e.g., the coordination number or chemical environment), and symmetry (e.g., Bravais lattice and space group) to filter the breeding pool of an evolutionary crystal structure search. The effectiveness of this approach is benchmarked on three known metastable systems: XeN 8 , with a two-dimensional polymeric nitrogen sublattice, brookite TiO 2 , and a high pressure BaH 4 phase that was recently characterized. Additionally, a newly predicted metastable melaminate salt, P1¯WC 3 N 6 , was found to possess an energy that is lower than two phases proposed in a recent computational study. Here, the method presented here could help in identifying the structures of compounds that have already been synthesized, and developing new synthesis targets with desired properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2006

In-Vacuum Photogrammetry of a Ten-Meter Square Solar Sail

Solar sailing is a promising, future in-space propulsion method that uses the small force of reflecting sunlight to accelerate a large, reflective membrane without expendable propellants. One of two solar sail configurations under development by NASA is a striped net approach by L'Garde, Inc. This design uses four inflatably deployed, lightweight booms supporting a network of thin strings onto which four quadrants of ultrathin aluminized membranes are attached. The NASA Langley Research Center (LaRC) provided both experimental and analytical support to L'Garde for validating the structural characteristics of this unique, ultralightweight spacecraft concept. One of LaRC's responsibilities was to develop and apply photogrammetric methods to measure sail shape. The deployed shape provides important information for validating the accuracy of finite-element modeling techniques. Photogrammetry is the science and art of calculating 3D coordinates of targets or other distinguishing features on structures using images. A minimum of two camera views of each target is required for 3D determination, but having four or more camera views is preferable for improved reliability and accuracy. Using retroreflective circular targets typically provides the highest measurement accuracy and automation. References 3 and 4 provide details of photogrammetry technology, and reference 5 discusses previous experiences with photogrammetry for measuring gossamer spacecraft structures such as solar sails. This paper discusses the experimental techniques used to measure a L Garde 10-m solar sail test in vacuum with photogrammetry. The test was conducted at the NASA-Glenn Space Power Facility (SPF) located at Plum Brook Station in Sandusky, Ohio. The SPF is the largest vacuum chamber in the United States, measuring 30 m in diameter by 37 m in height. High vacuum levels (10(exp -6) torr) can be maintained inside the chamber, and cold environments (-195 C) are possible using variable-geometry cryogenic cold walls. This test used a vacuum level of approximately 1 torr (sufficient for structural static/dynamic characterization) and instead of using the cryogenic cold walls, used local LN2 cold plates underneath each of the four cold-rigidizable solar sail booms instead.

Pappa, Richard S.↗
DOE OSTI2021

Distributed directory of named data elements in coordination namespace

An approach is described that provides a distributed directory structure within a storage of an information handling system (a local node). A request is received with the request corresponding to a shared virtual address. The shared virtual address that is shared amongst a number of nodes that includes the local node and some remote nodes. A Global Address Space Directory (GASD) is retrieved that corresponds to a global virtual address space. The GASD is stored in a Coordination Namespace that is stored in a memory that is distributed amongst the nodes. A mapping that is included in the GASD is used to determine the node where the shared virtual address currently resides. The shared virtual address is then accessed from the node where it currently resides.

Johns, Charles Ray↗
DOE OSTI2020

Rational Design and Synthesis of Hierarchical Porous Mn–N–C Nanoparticles with Atomically Dispersed MnNx Moieties for Highly Efficient Oxygen Reduction Reaction

Developing transition-metal excluding iron and cobalt–nitrogen–carbon (M–N–C) electrocatalysts for the oxygen reduction reaction (ORR) is critical to substantially promote the development of precious-metal-free metal–air batteries and fuel cells. In the work, Mn–N–C nanoparticles with atomically dispersed MnNx moieties were synthesized by pyrolyzing Mn-ion–dual-pyridine coordinated complex, which was obtained via a simple condensation reaction between 2,6-diamino-pyridine and 2,6-diacetyl-pyridine with MnCl 2 as the Mn source. The precursor features with a characteristic structure of dual-pyridine ligand, which possesses a strong coordinating capability for Mn 2+ , facilitating the formation of highly dispersed nitrogen-coordinated Mn sites (MnN x ). Attributed to the highly active atomic MnN x sites, hierarchical pore structure, and high surface area of the Mn–N–C derived from the new precursor, it exhibits outstanding ORR performance in 0.1 M KOH with an almost direct four-electron reaction path and high selectivity of O 2 into H 2 O (low H2O2 production <3.5%). The half-wave potential of Mn–N–C is 0.88 V vs RHE, which is 20 mV higher than that of commercial Pt/C catalyst and reaches to the level of Fe–N–C catalyst obtained by the same method. Meanwhile, the feasibility of Mn–N–C for practical application is validated by its higher-performance power output in Zn–air battery with a maximum power density of 132 mW cm –2 compared to that of Pt/C (121 mW cm –2 ) using the same catalyst loading of 1.0 mg cm –2 . This work develops a convenient route to develop non-Fe or Co–N–C electrocatalyst for the ORR.

36 MATERIALS SCIENCE↗