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At least 433 records · Page 24

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Pusey, Marc Lee↗

In-situ High-energy X-ray Diffraction Study of the Local Structure of Supercooled Liquid Si

While changes in the coordination number for liquid silicon upon supercooling, signaling an underlying liquid-liquid phase transition, have been predicted, x-ray and neutron measurements have produced conflicting reports. In particular some studies have found an increase in the first shell coordination as temperature decreases in the supercooled regime, while others have reported increases in the coordination number with decreasing temperature. Employing the technique of electrostatic levitation coupled with high energy x-ray diffraction (125 keV), and rapid data acquisition (100ms collection times) using an area detector, we have obtained high quality structural data more deeply into the supercooled regime than has been possible before. No change in coordination number is observed in this temperature region, calling into question previous experimental claims of structural evidence for the existence of a liquid-liquid phase transition.

Lee, G. W.↗

Atomically dispersed metal–nitrogen–carbon catalysts for fuel cells: advances in catalyst design, electrode performance, and durability improvement

The urgent need to address the high-cost issue of proton-exchange membrane fuel cell (PEMFC) technologies, particularly for transportation applications, drives the development of simultaneously highly active and durable platinum group metal-free (PGM-free) catalysts and electrodes. The past decade has witnessed remarkable progress in exploring PGM-free cathode catalysts for the oxygen reduction reaction (ORR) to overcome sluggish kinetics and catalyst instability in acids. Among others, scientists have identified the newly emerging atomically dispersed transition metal (M: Fe, Co, or/and Mn) and nitrogen co-doped carbon (M–N–C) catalysts as the most promising alternative to PGM catalysts. Here, we provide a comprehensive review of significant breakthroughs, remaining challenges, and perspectives regarding the M–N–C catalysts in terms of catalyst activity, stability, and membrane electrode assembly (MEA) performance. A variety of novel synthetic strategies demonstrated effectiveness in improving intrinsic activity, increasing active site density, and attaining optimal porous structures of catalysts. Rationally designing and engineering the coordination environment of single metal MN x sites and their local structures are crucial for enhancing intrinsic activity. Increasing the site density relies on the innovative strategies of restricting the migration and agglomeration of single metal sites into metallic clusters. Relevant understandings provide the correlations among the nature of active sites, nanostructures, and catalytic activity of M–N–C catalysts at the atomic scale through a combination of experimentation and theory. Current knowledge of the transferring catalytic properties of M–N–C catalysts to MEA performance is limited. Rationally designing morphologic features of M–N–C catalysts play a vital role in boosting electrode performance through exposing more accessible active sites, realizing uniform ionomer distribution, and facilitating mass/proton transports. We outline future research directions concerning the comprehensive evaluation of M–N–C catalysts in MEAs. The most considerable challenge of current M–N–C catalysts is the unsatisfied stability and rapid performance degradation in MEAs. Therefore, we further discuss practical methods and strategies to mitigate catalyst and electrode degradation, which is fundamentally essential to make M–N–C catalysts viable in PEMFC technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating molecular scale interactions underlying the freezing behavior of salt solutions in silica nanopores

Elucidating the influence of nanoscale confinement on the freezing behavior of salt solutions is of fundamental interest to environmental security and materials science and engineering. Specific structural information such as the coordination environment of ions in confined aqueous medium, effects on the extended hexagonal network of water molecules and their mutual non-bonding interactions in confinement are sparse in the literature along with the change in the dynamical characteristics of water in the presence of ions. To address these knowledge gaps, the current study is focused on investigating the influence of reduced dimensionality arising from nanoscale confinement on the structural evolution of salt solutions on freezing and the associated fluid–surface interactions. In this regard, operando wide-angle X-ray scattering (WAXS) measurements and classical molecular dynamics (MD) simulations are conducted with water and 0.5 M CaCl 2 , MgCl 2 and KCl solutions confined in 4 nm sized SBA-15 silica pores upon cooling from 300 K to 200 K. The freezing point of the salt solutions is depressed to 235 K which is about 10 K lower than that of confined water. The translational dynamics of confined salt solutions indicates shifts in the fragile-to-strong dynamical crossover to a lower temperature compared to pure water. The strong electrostatic attraction between the cations and the surrounding water molecules contributes to the freezing point depression in confined salt solutions. These insights unlock the molecular-scale basis and mechanisms underlying the freezing behavior of confined salt solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First-Principles Approach to Extracting Chemical Information from X-ray Absorption Near-Edge Spectra of Ga-Containing Materials

The X-ray absorption near-edge structure (XANES) can provide uniquely detailed information on the coordination environments of important Ga-containing materials with unknown structures, including catalytically active materials. In this work, the Ga K-edge XANES was simulated using first-principles-based methods for seven molecular Ga complexes as well β-Ga 2 O 3 , in order to explore the chemical origins of the experimentally observed features. The theoretical spectra were computed using FEFF, CASTEP, and StoBe, to assess the sensitivity of the results to the computational approach. While the XANES features depend on the Ga coordination environment, they are also sensitive to the electronegativity of the ligands and the symmetry at Ga. The white line position responds to changes in both the core state (due to differential screening) and the valence “p” states (arising from differences in ligand coordination).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Thermo‐Flow‐Mechanics‐Fracture Model Coupling a Phase‐Field Interface Approach and Thermo‐Fluid‐Structure Interaction

This work proposes a novel approach for coupling non-isothermal fluid dynamics with fracture mechanics to capture thermal effects within fluid-filled fractures accurately. This method addresses critical aspects of calculating fracture width in enhanced geothermal systems, where the temperature effects of fractures are crucial. The proposed algorithm features an iterative coupling between an interface-capturing phase-field fracture method and interface-tracking thermo-fluid-structure interaction using arbitrary Lagrangian–Eulerian coordinates. We use a phase-field approach to represent fractures and reconstruct the geometry to frame a thermo-fluid-structure interaction problem, resulting in pressure and temperature fields that drive fracture propagation. We developed a novel phase-field interface model accounting for thermal effects, enabling the coupling of quantities specific to the fluid-filled fracture with the phase-field model through the interface between the fracture and the intact solid domain. We provide several numerical examples to demonstrate the capabilities of the proposed algorithm. In particular, we analyze mesh convergence of our phase-field interface model, investigate the effects of temperature on crack width and volume in a static regime, and highlight the method's potential for modeling slowly propagating fractures.

fracture↗

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sub-domain decomposition methods and computational controls for multibody dynamical systems

This paper presents a concurrent methodology to simulate the dynamics of flexible multibody systems with a large number of degrees of freedom. A general class of open-loop structures is treated and a redundant coordinate formulation is adopted. A range space method is used in which the constraint forces are calculated using a preconditioned conjugate gradient method. By using a preconditioner motivated by the regular ordering of the directed graph of the structures, it is shown that the method is order N in the total number of coordinates of the system. The overall formulation has the advantage that it permits fine parallelization and does not rely on system topology to induce concurrency. It can be efficiently implemented on the present generation of parallel computers with a large number of processors. Validation of the method is presented via numerical simulations of space structures incorporating large number of flexible degrees of freedom.

Menon, R. G.↗

CSD 2374310: Experimental Crystal Structure Determination

An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Cell Parameters↗

Space Launch System Vibration Analysis Support

The ultimate goal for my efforts during this internship was to help prepare for the Space Launch System (SLS) integrated modal test (IMT) with Rodney Rocha. In 2018, the Structural Engineering Loads and Dynamics Team will have 10 days to perform the IMT on the SLS Integrated Launch Vehicle. After that 10 day period, we will have about two months to analyze the test data and determine whether the integrated vehicle modes/frequencies are adequate for launching the vehicle. Because of the time constraints, NASA must have newly developed post-test analysis methods proven well and with technical confidence before testing. NASA civil servants along with help from rotational interns are working with novel techniques developed and applied external to Johnson Space Center (JSC) to uncover issues in applying this technique to much larger scales than ever before. We intend to use modal decoupling methods to separate the entangled vibrations coming from the SLS and its support structure during the IMT. This new approach is still under development. The primary goal of my internship was to learn the basics of structural dynamics and physical vibrations. I was able to accomplish this by working on two experimental test set ups, the Simple Beam and TAURUS-T, and by doing some light analytical and post-processing work. Within the Simple Beam project, my role involves changing the data acquisition system, reconfiguration of the test set up, transducer calibration, data collection, data file recovery, and post-processing analysis. Within the TAURUS-T project, my duties included cataloging and removing the 30+ triaxial accelerometers, coordinating the removal of the structure from the current rolling cart to a sturdy billet for further testing, preparing the accelerometers for remounting, accurately calibrating, mounting, and mapping of all accelerometer channels, and some testing. Hammer and shaker tests will be performed to easily visualize mode shapes at low frequencies. Short analytical projects using MATLAB were also assigned to aid in research efforts. These included integration of acceleration data for comparison to measured displacement data. Laplace and Fourier transforms were also investigated to determine viability as a method of modal decoupling. In addition to these projects, I was also able contribute work that would benefit future interns and the division as a whole. I gave a short presentation and answered questions to aid in the recruitment of subsequent interns and co-ops for the division. I also assisted in revisions and additions to Intern/Co-Op Handbook to provide incoming employees with background information on the organization they are about to work for. I further developed tutorial on Pulse software, which was used for data acquisition for both experiments and will be helpful to interns and engineers that may be unfamiliar to the software. I gained a diverse range of experience throughout my internship. I was introduced to advanced dynamics and analytical techniques. This was through new experience with both hands on experimentation and analytical post processing methods. I was exposed to the benefits of interdepartmental collaboration and developed stronger skills in time management by coordinating two different tests at once. This internship provided an excellent opportunity to see how engineering theories applied to real life scenarios, and an introduction to how NASA/JSC solves technical problems.

Johnson, Katie↗

Understanding the Instability of the Halide Perovskite CsPbI 3 through Temperature-Dependent Structural Analysis

Despite the tremendous interest in halide perovskite solar cells, the structural reasons that cause the all-inorganic perovskite CsPbI 3 to be unstable at room temperature remain mysterious, especially since many tolerance-factor-based approaches predict CsPbI 3 should be stable as a perovskite. Here single-crystal X-ray diffraction and X-ray pair distribution function (PDF) measurements characterize bulk perovskite CsPbI3 from 100 to 295 K to elucidate its thermodynamic instability. While Cs occupies a single site from 100 to 150 K, it splits between two sites from 175 to 295 K with the second site having a lower effective coordination number, which, along with other structural parameters, suggests that Cs rattles in its coordination polyhedron. PDF measurements reveal that on the length scale of the unit cell, the Pb-I octahedra concurrently become greatly distorted, with one of the I-Pb-I angles approaching 82° compared to the ideal 90°. The rattling of Cs, low number of Cs-I contacts, and high degree of octahedral distortion cause the instability of perovskite-phase CsPbI 3 . These results reveal the limitations of tolerance factors in predicting perovskite stability and provide detailed structural information that suggests methods to engineer stable CsPbI 3 -based solar cells.

36 MATERIALS SCIENCE↗

Model reduction in the physical coordinate system

In the dynamics modeling of a flexible structure, finite element analysis employs reduction techniques, such as Guyan's reduction, to remove some of the insignificant physical coordinates, thus producing a dynamics model that has smaller mass and stiffness matrices. But this reduction is limited in the sense that it removes certain degrees of freedom at a node points themselves in the model. From the standpoint of linear control design, the resultant model is still too large despite the reduction. Thus, some form of the model reduction is frequently used in control design by approximating a large dynamical system with a fewer number of state variables. However, a problem arises from the placement of sensors and actuators in the reduced model, because a model usually undergoes, before being reduced, some form of coordinate transformations that do not preserve the physical meanings of the states. To correct such a problem, a method is developed that expresses a reduced model in terms of a subset of the original states. The proposed method starts with a dynamic model that is originated and reduced in finite element analysis. Then the model is converted to the state space form, and reduced again by the internal balancing method. At this point, being in the balanced coordinate system, the states in the reduced model have no apparent resemblance to those of the original model. Through another coordinate transformation that is developed, however, this reduced model is expressed by a subset of the original states.

Yae, K. Harold↗

Active learning of ternary alloy structures and energies

Abstract Machine learning models with uncertainty quantification have recently emerged as attractive tools to accelerate the navigation of catalyst design spaces in a data-efficient manner. Here, we combine active learning with a dropout graph convolutional network (dGCN) as a surrogate model to explore the complex materials space of high-entropy alloys (HEAs). We train the dGCN on the formation energies of disordered binary alloy structures in the Pd-Pt-Sn ternary alloy system and improve predictions on ternary structures by performing reduced optimization of the formation free energy, the target property that determines HEA stability, over ensembles of ternary structures constructed based on two coordinate systems: (a) a physics-informed ternary composition space, and (b) data-driven coordinates discovered by the Diffusion Maps manifold learning scheme. Both reduced optimization techniques improve predictions of the formation free energy in the ternary alloy space with a significantly reduced number of DFT calculations compared to a high-fidelity model. The physics-based scheme converges to the target property in a manner akin to a depth-first strategy, whereas the data-driven scheme appears more akin to a breadth-first approach. Both sampling schemes, coupled with our acquisition function, successfully exploit a database of DFT-calculated binary alloy structures and energies, augmented with a relatively small number of ternary alloy calculations, to identify stable ternary HEA compositions and structures. This generalized framework can be extended to incorporate more complex bulk and surface structural motifs, and the results demonstrate that significant dimensionality reduction is possible in thermodynamic sampling problems when suitable active learning schemes are employed.

Chemistry↗

Predicting the Dissolution Rate of Borosilicate Glasses using QSPR analysis based on molecular dynamics simulations

Quantitative Structure Property Relationship (QSPR) analysis based on molecular dynamics (MD) simulations is a promising approach for establishing the composition-property relationships of glass and other materials with complex structures. A series of 20 borosilicate and boroaluminosilicate glasses have been modeled by using MD simulations with recently developed effective potentials. Short- and medium-range structures of these glasses were analyzed and, based on these structural information, QSPR analysis of the initial dissolution rate (r0) was made and compared with measured r0 at 90°C and pH 9 using various structural descriptors such as percentage of bridging oxygen species, network connectivity and average ring size. The structural descriptors, Fnet, containing energetic information such as single bond strength and other structural information were also used. It was found that overall network connectivity, average ring size and Fnet give reasonable predictions of the r0 of studied glasses, given the conditions that the glasses are homogeneous and dissolve congruently. Modifying glass compositions to account preferential release of modifiers gives a better prediction for incongruently dissolving glasses. The results were compared with our recent work of predicting glass dissolution behavior from compositions using the topological-constraints-based models.

Du, Jincheng↗

Anisotropic Structural Collapse of Mg 3 Sb 2 and Mg 3 Bi 2 at High Pressure

Alloys between Mg 3 Sb 2 and Mg 3 Bi 2 have recently been shown to be exceptional thermoelectric materials due in part to their anomalously low thermal conductivity. In the present study, in situ high-pressure synchrotron X-ray diffraction was used to investigate the structure and bonding in Mg 3 Sb 2 and Mg 3 Bi 2 at pressures up to 50 GPa. Our results confirm prior predictions of isotropic in-plane and out-of-plane compressibility but reveal large disparities between the bond strength of the two distinct Mg sites. Using single-crystal diffraction, we show that the octahedral Mg–Sb bonds are significantly more compressible than the tetrahedral Mg–Sb bonds in Mg 3 Sb 2 , which lends support to prior arguments that the weaker octahedral Mg bonds are responsible for the anomalous thermal properties of Mg 3 Sb 2 and Mg 3 Bi 2 . Further, we report the discovery of a displacive and reversible phase transition in both Mg 3 Sb 2 and Mg 3 Bi 2 above 7.8 and 4.0 GPa, respectively. Furthermore, the transition to the high-pressure structure involves a highly anisotropic volume collapse, in which the out-of-plane axis compresses significantly more than the in-plane axes. Single-crystal diffraction at high pressure was used to solve the monoclinic high-pressure structure ( C 2/ m ), which is a distorted variant of the ambient-pressure structure containing four unique Mg coordination environments.

36 MATERIALS SCIENCE↗

Oxygen Deficiency and Migration-Mediated Electric Polarization in Magnetic Fe,Co-Substituted SrTiO3−δ

We use density functional theory (DFT) calculations to show that oxygen vacancies (vO) and mobility induce noncentrosymmetric polar structures in SrTi1−x−yFexCoyO3−δ (STFC, x=y=0.125) with δ={0.125,0.25}, enhance the saturation magnetization, and give rise to large changes in the electric polarization |ΔP|. We present an intuitive set of rules to describe the properties of STFC, which are based on the interplay between (Co/Fe)-vO defects, magnetic cation coordination, and topological vacancy disorder. STFC structures consist of layered crystals with sheets of linearly organized O4,5,6-coordinated Fe–Co pairs, sandwiched with layers of O5-coordinated Ti. (Co/Fe)-vO defects are the source of crystal distortions, cation off-centering and bending of the oxygen octahedra which, considering the charge redistribution mediated by vO and the cations’ electronegativity and valence states, triggers an effective electric polarization. Oxygen migration for δ=0.125 leads to |ΔP|>∼10 µC/cm2 due to quantum-of-polarization differences between δ=0.125 structures. Increasing the oxygen deficiency to δ=0.25 yields |ΔP|, the O migration of which resolved polarization for δ=0.25 is >∼3 µC/cm2. Magnetism is dominated by the Fe,Co spin states for δ=0.125, and there is a contribution from Ti magnetic moments (∼1 μB) for δ=0.25. Magnetic and electric order parameters change for variations of δ or oxygen migration for a given oxygen deficiency. Our results capture characteristics observed in the end members of the series SrTi(Co,Fe)O3, and suggest the existence of a broader set of rules for oxygen-deficient multiferroic oxides.

36 MATERIALS SCIENCE↗

Configuration space representation in parallel coordinates

By means of a system of parallel coordinates, a nonprojective mapping from R exp N to R squared is obtained for any positive integer N. In this way multivariate data and relations can be represented in the Euclidean plane (embedded in the projective plane). Basically, R squared with Cartesian coordinates is augmented by N parallel axes, one for each variable. The N joint variables of a robotic device can be represented graphically by using parallel coordinates. It is pointed out that some properties of the relation are better perceived visually from the parallel coordinate representation, and that new algorithms and data structures can be obtained from this representation. The main features of parallel coordinates are described, and an example is presented of their use for configuration space representation of a mechanical arm (where Cartesian coordinates cannot be used).

Fiorini, Paolo↗