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At least 1,783 records · Page 99

CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Monte Carlo techniques play a central role in statistical mechanics approaches that connect macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study of multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct phase diagrams from first principles. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples of increasing complexity. Additionally, an overview of the capabilities of the CASM software specific to Monte Carlo methods is given, and a new CASM software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations.

Cluster expansion↗

Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows

This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.

Herrick, Gregory P.↗

Floorspace.js

Floorspace.js is a 2D geometry editor. Users can define an explicit floor plan for each story of a building. A story-by-story interface makes it easy to develop space geometry and assign properties. Referencing satellite imagery or floor plan images, when available, speeds up geometry entry. Conversion of 2D to 3D geometry is currently out of scope for Floorspace.js, a reference implementation is available in the OpenStudio® SDK. Explicit floor plans allow more building-specific information than parameterized shoe-boxes but less information than a full 3D BIM model. Sloped walls, complex roofs, detailed shading structures, and other complex 3D structures are out of FloorspaceJS's scope. In general, if users have a 3D BIM model in a tool that can export a useful BEM representation then it is better to use that export than to recreate a new model using FloorspaceJS. Re-usability and minimal dependencies were key design considerations for software developers. Web technologies can be used in both online and desktop applications. The editor was written in pure JavaScript for maximum portability and re-usability. A custom JavaScript Object Notation (JSON) file format was developed to ease integration with other applications. Custom JSON schema design was a key part of FloorspaceJS development.

Noland, Katie↗

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 ‘loop’ structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 ‘loop’ is a stiff, α-helical ‘switchback’ structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore–microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding

The interaction between the receptor 4-1BB and its ligand 4-1BBL provides co-stimulatory signals for T-cell activation and proliferation. However, differences in the mouse and human molecules might result in differential engagement of this pathway. Here, we report the crystal structure of mouse 4-1BBL and of the mouse 4-1BB/4-1BBL complex, which together provided insights into the molecular mechanism by which m4-1BBL and its cognate receptor recognize each other. Unlike all human or mouse tumor necrosis factor ligands that form noncovalent and mostly trimeric assemblies, the m4-1BBL structure formed a disulfide-linked dimeric assembly. The structure disclosed that certain differences in the amino acid composition along the intramolecular interface, together with two specific residues (Cys-246 and Ser-256) present exclusively in m4-1BBL, are responsible for this unique dimerization. Unexpectedly, upon m4-1BB binding, m4-1BBL undergoes structural changes within each protomer; moreover, the individual m4-1BBL protomers rotate relative to each other, yielding a dimerization interface with more inter-subunit interactions. We also observed that in the m4-1BB/4-1BBL complex, each receptor monomer binds exclusively to a single ligand subunit with contributions of cysteine-rich domain 1 (CRD1), CRD2, and CRD3. Furthermore, structure-guided mutagenesis of the binding interface revealed that novel binding interactions with the GH loop, rather than the DE loop, are energetically critical and define the m4-1BB receptor selectivity for m4-1BBL. As a result, a comparison with the human 4-1BB/4-1BBL complex highlighted several differences between the ligand- and receptor-binding interfaces, providing an explanation for the absence of inter-species cross-reactivity between human and mouse 4-1BB and 4-1BBL molecules.

4-1BB↗

Terrace width variations in complex lunar craters

The widths of terrace structures in complex craters on the moon are compared to existing theoretical models of their origin. Terrace widths in an individual crater increase monotonically outward toward the crater rim. Similarly, the width W of the terraces lying closest to the rim of a crater of diameter D increases monotonically, obeying a least-squares power-law relation WS (km) = 0.09D exp 0.87 km). A simple model of slumping that ignores inertial forces and assumes a constant bedrock yield strength is in good agreement with the observations.

Pearce, Steven J.↗

Structure and ultrafast dynamics of tri-nuclear Ag-/Tl–Pt 2 POP 4 complexes in solution

The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt 2 (H 2 P 2 O 5 )$_4^{4−}$] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal–metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with $<$100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract ∼0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of ∼0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of ∼0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent (“wave-packet”) oscillations along the metal–Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal–metal bonding behavior in both the ground and excited state for both complexes.

Lenzen, Philipp [Technical Univ. of Denmark, Lyngb↗

A novel family of microporous uranyl germanates: Framework topology and complexity of the crystal structures

Five novel microporous uranyl germanates, Cs[(UO2)2(HGe2O7)] (1), Co2[(UO2)8(HGe2O7)4](H2O)6 (2), Ba2[(UO2)8(HGe2O7)4](H2O)3 (3), K4[(UO2)8(HGe2O7)4](H2O)2 (4), and Rb4[(UO2)8(HGe2O7)4](H2O)2 (5), have been synthesized under hydrothermal conditions. Single-crystal X-ray analyses indicate that 1 has an orthorhombic structure, space group Cmcm, while compounds 2-5 are isomorphous and have a tetragonal structure, space group I4/mcm. All compounds consist of heteropolyhedral frameworks that are based on chains of UO7 pentagonal bipyramids that share edges with GeO4 tetrahedra. These chains are either assembled into sheets (1) or nanotubules (2-5) to form a microporous framework characterized by the presence of [HGe2O7]5- dimers. The framework of 1 contains a channel with an effective channel dimension of 2.55 × 2.55 Å, and occupied by Cs atoms, whereas the unprecedented framework of 2-5 contains two channels of different dimensionality (1.88 × 1.88 and 3.82 × 5.59 Å of effective channel dimension) extending along the c crystallographic axis. In addition to water molecules, these channels accommodate mono- and divalent cations, with ionic radii ranging from 0.745 Å ([6]Co2+) to 1.61 Å ([8]Rb+). An extended structural comparison is provided between these compounds and similar compounds, as well as a discussion concerning the topology and the complexity of the uranyl germanates with framework-type structures.

nuclear (including radiation effects), materials a↗

One-dimensional Co(II)/Ni(II) complexes of 2-hydroxyisophthalate: Structures and magnetic properties

The solvothermal reactions of 2-hydroxyisophthalic acid (H{sub 3}ipO) with M(NO{sub 3}){sub 2}∙6H{sub 2}O (M=Co, Ni) afforded two complexes [Co{sub 2}(HipO){sub 2}(Py){sub 2}(H{sub 2}O){sub 2}] (1) and [Ni(HipO)(Py)H{sub 2}O] (2) (Py=pyridine). They exhibit similar zig-zag chain structures with the adjacent two metal centers connected by a anti-syn bridging carboxylate group from the HipO{sup 2−} ligand. The magnetic measurements reveal the dominant antiferromagnetic interactions and spin-canting in 1 while ferromagnetic interactions in 2. Both of them exhibit magnetocaloric effect (MCE) with the resulting entropy changes (−ΔS{sub m}) of 12.51 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 1 and 11.01 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 2, representing the rare examples of one-dimensional complexes with MCE. - Graphical abstract: Synopsis: Two Co(II)/Ni(II) complexes with zig-zag chain structures have been reported. 1-Co shows cant-antiferromagnetism while 2-Ni shows ferromagnetism. Magnetocaloric effect is also found in both of them. - Highlights: • Two one-dimensional Co(II)/Ni(II) complexes were solvothermally synthesized. • The Co-complex exhibits canted antiferromagnetism. • The Ni-complex exhibits ferromagnetism. • Both of the complexes display magnetocaloric effect.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local rare-earth dopant structure in a complex-oxide/semiconductor heterojunction: Molecular beam epitaxy grown Yb-doped SrTiO3 on Si(001)

We have investigated the structural and electronic properties of Yb-doped SrTiO3/Si(001) grown by molecular beam epitaxy. Other rare-earth donor dopants that result in n-type conductivity typically substitute for Sr at the A-sites in the perovskite lattice. In contrast, Yb has been found to substitute predominantly for Ti at the perovskite B-sites based on data from atomically resolved scanning transmission electron microscopy and spectroscopy, as well as extended x-ray absorption fine structure. Yb exhibits two distinct charge states as determined by x-ray absorption spectroscopy and associated modeling, +2.7 and +2.1. These aliovalent substitutional dopants are compensated by donor electrons from oxygen vacancies that form during epitaxial film growth. An atom beam flux mismatch was present during film depositions because it was assumed that Yb would occupy A-sites, leading to a flux matching formula given by Yb + Sr = Ti. However, the formation of YbTi rather than YbSr results in Sr vacancies and extraneous (i.e. non-lattice) Ti atoms in the films, or on the film surfaces. The presence of these defects, together with oxygen vacancies, leads to deep-level electron traps that were detected by resonant photoemission and much higher sheet resistance than that associated with, for instance, La-doped films.

Chambers, Scott A. (ORCID:000000025415043X)↗

Bond valence sum analysis of pyrochlore oxides including the novel dielectric Te 6+ pyrochlores: A Bi M TeO 7-y ( A = Cd, Ca; M = Cr, Ga, Sc, In, Fe)

Bond valence sum analysis is a powerful tool used in evaluating and validating crystal structures; especially when those structures are complex in nature. The pyrochlore structure type is versatile in not only the unique bonding that it exhibits, but also in the properties that results from the structure. Here this paper aims to center the discussion of evaluating the pyrochlore structure using the bond valence sum method. In this study, novel quaternary pyrochlores with a general stoichiometry of ABiMTeO 7 (A = Cd, Ca; M = Cr, Ga, Sc, In, Fe) were synthesized and characterized for their structural, magnetic, and dielectric properties. Two representative compounds within this series of pyrochlores, BiCaFeTeO7 and BiCdFeTeO 7 , were structurally characterized utilizing a combination of high-resolution synchrotron X-ray diffraction and neutron diffraction revealing oxygen deficient pyrochlore systems which were off from the expected stoichiometry with respect to the M site. The A site of both pyrochlores were found to be moved off-center from the expected 16d site to the 96h displaced position at a magnitude of 0.25 Å and 0.22 Å for the Bi/Ca and Bi/Cd systems, respectively. These structures were evaluated using the bond valence sum method and compared with trends in the literature. The properties are also reported for the Bi/Ca system for the first time, showing relatively high dielectric constants with a low dielectric loss which are primarily independent of frequency and temperature. The magnetic measurements for the Bi/Ca system for the magnetic substitutions reveal a paramagnet and antiferromagnetic properties for the Fe and Cr analogs, respectively. The novel BiCaMTeO 7 quaternary pyrochlore system shows great promise as an emerging dielectric material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elastic wave suppression through additively manufactured petal lattice metamaterials

Lattice-core sandwich structure metamaterials are lightweight alternatives to monolithic materials that can present better mechanical, thermal, and energy dampening performance. Manufacturing lattice metamaterials to follow curved surfaces can pose a challenge, as the lattices rely on their geometric orientation to the substrate for their mechanical properties. This work rationally designed a lattice structure where the surface is broken up into “petals” connected to the underlying lattice, which localizes the petals’ impact response. This design opens a pathway for implementation of lattice-core sandwich structures onto complex surface geometries. These petal structures were evaluated for their energy absorption efficiency experimentally by utilizing pressure waves generated with nanosecond lasers and computationally via finite element modeling. The lattice structures exhibited a two-orders-of-magnitude decrease in transmitted pressure compared to their constituent steel at equivalent mass. Furthermore, localizing energy absorption into petal structures provided a 44% reduction in peak load compared to a continuous “single-petal” design.

Sarracino, Alex↗

Squeezing quantum states in three-dimensional twisted crystals

Bloch's theorem provides a conventional starting point for describing wave propagation in periodic media, but in ordered materials where competing spatial periods coexist it is rendered ineffective, often with dramatic consequences. Here we develop an alternate approach that uses coherent free-particle vortex states to study quantum states in supertwisted crystals: three-dimensional stacks of atomically thin two-dimensional layers. Here, this formalism leads naturally to the representation of the spectrum using squeezed coherent states, and it reveals the crucial role of a Coriolis coupling in the equations of motion. This identifies an underlying noncommutative geometry and novel edge state structure in a family of complex ordered structures.

36 MATERIALS SCIENCE↗

Re-Defining Photovoltaic Efficiency Through Molecule Scale Control. Final Report

The direct conversion of sunlight into electricity represents one of the most important general means for sustainable energy production. Most modern photovoltaic cells are based on some form of semiconductor material such as silicon that is described by a characteristic energy or ''bandgap''. For solar rays with photon energy lower than the bandgap no absorption occurs and thus no energy is generated. For solar rays with photon energy greater than the bandgap, light may be absorbed to create a pair of electrical charges but only one bandgap of energy is created, leaving any additional energy lost as heat. Thus low bandgap materials can use a great part of the spectrum but can lose much of that energy; high bandgap materials fail to capture much of the spectrum. Thus there is a limit to the efficiency of such a solar cell that turns out to be about 32%. This limit is known as the Shockely-Queisser Limit. The Columbia EFRC program is dedicated to exploration of concepts that in principle can provide for efficiencies beyond this limit. One concept that this EFRC has explored for enhancing the efficiency of solar photovoltaic cells is called “Singlet Fission.” In this concept the absorption of light rays with photon energy at least twice the value of the basic bandgap for the system can produce two pairs of electrical charge carriers. If properly implemented this in principle can significantly reduce the energy lost as heat and give rise to solar cell efficiencies greater than the Shockley-Queisser limit. The problem is that there are virtually no materials that can undergo this process effectively. We have developed new materials that have demonstrated singlet fission efficiencies of almost 100%. We understand how these materials work and we have learned how to design many more systems in the future. So far we have only demonstrated the basic capability for efficient singlet fission. Much more work will be required to design and engineer specific materials that can be used practically in a solar cell system. In addition much work will be required to envision and demonstrate effective device structures that can utilize this concept. However these discoveries do provide the basis for an entirely new set of opportunities for more efficient solar energy generation moving beyond the Shockley-Queisser limit. A second part of the EFRC research program has been to investigate the material and device properties of an entirely new set of materials based on two-dimensional sheets (“ultra-thin”) with thicknesses of only one atom, or a single molecule or just a few atoms. These materials can exhibit conducting, insulating, and semiconducting character and thus they can form the basis for entirely new types of electrical devices. Recent fundamental investigations of these materials, at Columbia and elsewhere, demonstrate clearly that the flow of electrical charges in these systems is fundamentally different from the nature of electrical current flow in conventional materials. This fact presents many possibilities for new photovoltaic device concepts. The EFRC research team has achieved world leadership in the creation and understanding of these materials and in developing the fabrication techniques necessary to create useful devices from them. We have developed the basic fabrication methodology to build structures of these materials into complex device structures, layer by layer. Our EFRC research team has pioneered the synthesis and understanding for graphene, perhaps the simplest of these materials. Graphene can function as a highly transparent conducting material, capable of funneling an electrical charge over reasonable distances without significant energy loss. The EFRC program has also pioneered the development of ultra-thin sheets that function in a way analogous to semiconductor materials as well as sheets that act as electrical insulators. These developments therefore enable the construction of solar cells based on totally different physics from conventional cells. Because the electrons in these ultra-thin sheets interact strongly they will exhibit behaviors quite different from conventional materials with potential to operate at efficiencies beyond the Shockley-Queisser limit. In our EFRC program we have laid out many of the fundamental properties of these materials including the development of unique fabrication techniques. We discovered several new effects that demonstrate strong electron coupling. We have demonstrated the first solar cell that can actually generate electrical power at a high basic efficiency from these fundamentally new materials. There is much more science and technology required before these devices can become practical, but there is also very strong activity worldwide to build electronic devices from these materials, thus providing infrastructure and technical capability to develop these concepts.

14 SOLAR ENERGY↗

Thermally stable manganese(Ⅲ) peroxido complexes with hindered N3 tripodal ligands: Structures and their physicochemical properties

Mononuclear manganese(III) peroxido complexes are candidates for the reaction intermediates in manganese containing proteins, such as manganese superoxide dismutase (Mn-SOD) etc. In this study, manganese(III) peroxido complexes [Mn(O 2 )(L3)] and [Mn(O 2 )(L10)] ligated by anionic N3 type ligands with sterically hindered substituents, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (L3 - ) and hydrotris(3-adamantyl-5-isopropyl-1-pyrazolyl)borate (L10 - ), respectively, were structurally characterized. These complexes are the first examples of structurally characterized five-coordinate manganese(III) peroxido complexes. Their characteristic ν(O—O) and ν(Mn—O) stretchings were determined by using H 2 18 O 2 for the first time. Theoretical calculations were performed to obtain further insight into their structural parameters. The decomposed products were obtained as [{Mn III (μ-O)(L3)} 2 Mn IV ] and [Mn III (OH){L10(O)}] from [Mn(O 2 )(L3)] and [Mn(O 2 )(L10)], respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Paramagnetic Cu{sup II} complexes with 1-(hetarylmethyl)silatranes

The structures of paramagnetic complexes CuCl{sub 2}•L with L = HetCH{sub 2}Si(OCH{sub 2}CH{sub 2}){sub 3}N [Het = pyrrol-1-yl (1), indol-1-yl (2), carbazol-9-yl (3), imidazole-1-yl (4), 3,5-dimethylpyrazol-1-yl (5), 1,2,4-triazol-1-yl (6), benzimidazol-1-yl (7), and 1,2,3-benzotriazol-1-yl (8)] were studied by the ESR and quantum chemical methods in terms of the density functional theory (DFT) approximation. The difference in structures of complexes CuCl{sub 2}•1—CuCl{sub 2}•8 is mainly determined by the nature of the five-membered heterocycle. The ESR spectra at room temperature are typical of the mononuclear complexes of Cu{sup II} of axial symmetry with various types of distortions. In complexes CuCl{sub 2}•1—CuCl{sub 2}•3, narrow symmetric signals of zero-valent copper are recorded. These signals remain in the spectra for at least six months, which can characterize them as efficient stabilizing matrices of nanoparticles.

77 NANOSCIENCE AND NANOTECHNOLOGY↗