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At least 1,747 records · Page 97

Defect Complexes and Optical Properties of Doubly Doped Lithium Niobate Crystals

The effect of defect complexes related to the presence of protons on the optical properties of LiNbO{sub 3}:Y(0.24):Mg(0.63) and LiNbO{sub 3}:Gd(0.25):Mg(0.75) (wt %) crystals has been studied using IR absorption spectroscopy, photoinduced light scattering, and laser conoscopy. The results indicate that the absorption bands at frequencies of 3483 and 3486 cm{sup –1} correspond to vibrations of a V{sub Li}{sup -}–OH{sup −} defect complex. To a Mg {sub Li}{sup +} - Mg {sub Nb}{sup 3-}–OH{sup −}defect complex in the LiNbO{sub 3}:Gd(0.25):Mg(0.75) crystal correspond bands at frequencies of 3526 and 3535 cm{sup –1}. In the LiNbO{sub 3}:Y(0.24):Mg(0.63) crystal, we have detected an anomalous opening of the speckle structure of the photoinduced light scattering indicatrix.

36 MATERIALS SCIENCE↗

Synthesis and crystal structure of the iridium(I) carbene complex with a pair of hydrogen wing tips

The iridium(I) cyclooctadiene complex with two (3-tert-butylimidazol-2-ylidene) ligands [(H-Im{sup t}Bu){sub 2}Ir(COD)]{sup +}PF{sub 6}{sup −} (C{sub 22}H{sub 32}PF{sub 6}IrN{sub 4}) has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal atom, which is coordinated by two H-Im{sup t}Bu ligands and one cyclooctadiene group. The new iridium carbene complex has a pair of hydrogen wing tips. The Ir−C{sub carbene} bond lengths are 2.066(5) and 2.052(5) Å, and the bond angle C−Ir−C between these bonds is 95.54(19)°. The dihedral angle between two imidazol-2-ylidene rings is 86.42°.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Fourth-Order Embedded Boundary Finite Volume Method for the Unsteady Stokes Equations with Complex Geometries

A fourth-order finite volume embedded boundary (EB) method is presented for the unsteady Stokes equations. The algorithm represents complex geometries on a Cartesian grid using EB, employing a technique to mitigate the ``small cut-cell"" problem without mesh modifications, cell merging, or state redistribution. Spatial discretizations are based on a weighted least-squares technique that has been extended to fourth-order operators and boundary conditions, including an approximate projection to enforce the divergence-free constraint. Solutions are advanced in time using a fourth-order additive implicit-explicit Runge-Kutta method, with the viscous and source terms treated implicitly and explicitly, respectively. Formal accuracy of the method is demonstrated with several grid convergence studies, and results are shown for an application with a complex bio-inspired material. In conclusion, the developed method achieves fourth-order accuracy and is stable despite the pervasive small cells arising from complex geometries.

97 MATHEMATICS AND COMPUTING↗

Accelerating the Mining of Influential Nodes in Complex Networks through Community Detection

Computing the set of influential nodes with a given size to ensure maximal spread of influence on a complex network is a challenging problem impacting multiple applications. A rigorous approach to influence maximization involves utilization of optimization routines that comes with a high computational cost. In this work, we propose to exploit the existence of communities in complex networks to accelerate the mining of influential seeds. We provide intuitive reasoning to explain why our approach should be able to provide speedups without significantly degrading the extent of the spread of influence when compared to the case of influence maximization without using the community information. Additionally, we have parallelized the complete workflow by leveraging an existing parallel implementation of the Louvain community detection algorithm. We then conduct a series of experiments on a dataset with three representative graphs to first verify our implementation and then demonstrate the speedups. Our method achieves speedups ranging from 3x - 28x for graphs with small number of communities while nearly matching or even exceeding the activation performance on the entire graph. Complexity analysis reveals that dramatic speedups are possible for larger graphs that contain a correspondingly larger number of communities. In addition to the speedups obtained from the utilization of the community structure, scalability results show up to 6.3x speedup on 20 cores relative to the baseline run on 2 cores. Finally, current limitations of the approach are outlined along with the planned next steps.

community detection↗

A Study of Complex Deep Learning Networks on High-Performance, Neuromorphic, and Quantum Computers

Current deep learning approaches have been very successful using convolutional neural networks trained on large graphical-processing-unit-based computers. Three limitations of this approach are that (1) they are based on a simple layered network topology, i.e., highly connected layers, without intra-layer connections; (2) the networks are manually configured to achieve optimal results, and (3) the implementation of the network model is expensive in both cost and power. In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. We use the MNIST dataset for our experiment, due to input size limitations of current quantum computers. Our results show the feasibility of using the three architectures in tandem to address the above deep learning limitations. Finally, we show that a quantum computer can find high quality values of intra-layer connection weights in a tractable time as the complexity of the network increases, a high performance computer can find optimal layer-based topologies, and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware.

97 MATHEMATICS AND COMPUTING↗

On the Fundamental and Practical Aspects of Modeling Complex Electrochemical Kinetics and Transport

Numerous technologies, such as batteries and fuel cells, depend on electrochemical kinetics. In some cases, the responsible electrochemistry and charged-species transport is complex. However, to date, there are essentially no general-purpose modeling capabilities that facilitate the incorporation of thermodynamic, kinetic, and transport complexities into the simulation of electrochemical processes. A vast majority of the modeling literature uses only a few (often only one) global charge-transfer reactions, with the rates expressed using Butler-Volmer approximations. The objective of the present paper is to identify common aspects of electrochemistry, seeking a foundational basis for designing and implementing software with general applicability across a wide range of materials sets and applications. The development of new technologies should be accelerated and improved by enabling the incorporation of electrochemical complexity (e.g., multi-step, elementary charge-transfer reactions and as well as supporting ionic and electronic transport) into the analysis and interpretation of scientific results. The spirit of the approach is analogous to the role that Chemkin has played in homogeneous chemistry modeling, especially combustion. The Cantera software, which already has some electrochemistry capabilities, forms the foundation for future capabilities expansion.

30 DIRECT ENERGY CONVERSION↗

Large-Eddy Simulation over Complex Terrain Using an Improved Immersed Boundary Method in the Weather Research and Forecasting Model

Abstract The Weather Research and Forecasting (WRF) Model is increasingly being used for higher-resolution atmospheric simulations over complex terrain. With increased resolution, resolved terrain slopes become steeper, and the native terrain-following coordinates used in WRF result in numerical errors and instability. The immersed boundary method (IBM) uses a nonconformal grid with the terrain surface represented through interpolated forcing terms. Lundquist et al.’s WRF-IBM implementation eliminates the limitations of WRF’s terrain-following coordinate and was previously validated with a no-slip boundary condition for urban simulations and idealized terrain. This paper describes the implementation of a log-law boundary condition into WRF-IBM to extend its applicability to general atmospheric complex terrain simulations. The implementation of the improved WRF-IBM boundary condition is validated for neutral flow over flat terrain and the complex terrain cases of Askervein Hill, Scotland, and Bolund Hill, Denmark. First, comparisons are made to similarity theory and standard WRF results for the flat terrain case. Then, simulations of flow over the moderately sloped Askervein Hill are used to demonstrate agreement between the IBM and terrain-following WRF results, as well as agreement with observations. Finally, Bolund Hill simulations show that WRF-IBM can handle steep topography (standard WRF fails) and compares well to observations. Overall, the new WRF-IBM boundary condition shows improved performance, though the leeside representation of the flow can be potentially further improved.

54 ENVIRONMENTAL SCIENCES↗

The ECP SICM project: Managing complex memory hierarchies for exascale applications

The Exascale Computing Project (ECP)’s Simplified Interface to Complex Memories (SICM) effort focuses on developing universal interfaces for discovering, managing, and sharing data across complex memory hierarchies. These facilitate the exploitation of emerging memory technologies and support precise control over their various trade-offs such as high-bandwidth versus low-latency, persistent versus ephemeral, high-capacity versus low-capacity, and near-CPU versus near-GPU. SICM comprises three interrelated components: a low-level interface, a high-level interface, and a persistent-heap interface. The low-level SICM interface is intended for system and run-time developers as well as expert application developers who prefer full control of the memory objects used within their application. The high-level SICM interface builds upon the low-level interface, employing application-level profiling and analysis to optimize data management for complex memory hierarchies. The persistent-heap interface provides applications with a persistent memory allocator that can allocate custom C++ data structures in both block-storage and byte-addressable persistent memories.

97 MATHEMATICS AND COMPUTING↗

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Abstract Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗

Performance and community structure dynamics of microbial electrolysis cells operated on multiple complex feedstocks

Microbial electrolysis is a promising technology for converting aqueous wastes into hydrogen. However, substrate adaptability is an important feature, seldom documented in microbial electrolysis cells (MECs). In addition, the correlation between substrate composition and community structure has not been well established. This study used an MEC capable of producing over 10 L/L-day of hydrogen from a switchgrass-derived bio-oil aqueous phase and investigated four additional substrates, tested in sequence on a mature biofilm. The additional substrates included a red oak-derived bio-oil aqueous phase, a corn stover fermentation product, a mixture of phenol and acetate, and acetate alone. The MECs fed with the corn stover fermentation product resulted in the highest performance among the complex feedstocks, producing an average current density of 7.3 ± 0.51 A/m 2 , although the acetate fed MECs outperformed complex substrates, producing 12.3 ± 0.01 A/m 2 . 16S rRNA gene sequencing showed that community structure and community diversity were not predictive of performance, and replicate community structures diverged despite identical inoculum and enrichment procedure. The trends in each replicate, however, were indicative of the influence of the substrates. Geobacter was the most dominant genus across most of the samples tested, but its abundance did not correlate strongly to current density. High-performance liquid chromatography (HPLC) showed that acetic acid accumulated during open circuit conditions when MECs were fed with complex feedstocks and was quickly degraded once closed circuit conditions were applied. The largest net acetic acid removal rate occurred when MECs were fed with red oak bio-oil aqueous phase, consuming 2.93 ± 0.00 g/L-day. Principal component analysis found that MEC performance metrics such as current density, hydrogen productivity, and chemical oxygen demand removal were closely correlated. Net acetic acid removal was also found to correlate with performance. However, no bacterial genus appeared to correlated to these performance metrics strongly, and the analysis suggested that less than 70% of the variance was accounted for by the two components. This study demonstrates the robustness of microbial communities to adapt to a range of feedstocks and conditions without relying on specific species, delivering high hydrogen productivities despite differences in community structure. The results indicate that functional adaptation may play a larger role in performance than community composition. Further investigation of the roles each microbe plays in these communities will help MECs to become integral in the 21st-century bioeconomy to produce zero-emission fuels.

09 BIOMASS FUELS↗

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13 >C and 1 H NMR spectra with respect to experimentally measured values. This leads us to the question–what accuracy is required in predicted 13 C and 1 H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1 H and 13 C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical analysis of the role of complex transition dipole phase in XUV transient-absorption probing of charge migration

We theoretically investigate the role of complex dipole phase in the attosecond probing of charge migration. The iodobromoacetylene ion (ICCBr + ) is considered as an example, in which one can probe charge migration by accessing both the iodine and bromine ends of the molecule with different spectral windows of an extreme-ultraviolet (XUV) pulse. The analytical expression for transient absorption shows that the site-specific information of charge migration is encoded in the complex phase of cross dipole products for XUV transitions between the I-4 d and Br-3 d spectral windows. Ab-initio quantum chemistry calculations on ICCBr + reveal that there is a constant π phase difference between the I-4 d and Br-3 d transient-absorption spectral windows, irrespective of the fine-structure energy splittings. Transient absorption spectra are simulated with a multistate model including the complex dipole phase, and the results correctly reconstruct the charge-migration dynamics via the quantum beats in the two element spectral windows, exhibiting out-of-phase oscillations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5

Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis and structural characterization of a series of uranyl-betaine coordination complexes

Abstract Trimethylglycine and betainium class ionic liquids were employed in synthesizing six uranyl-betaine coordination complexes: [(μ 2 -(CH 3 )N 2 C 3 H 3 (CH 2 COO)) 2 (UO 2 (Cl)((CH 3 )N 2 C 3 H 3 (CH 2 COO))) 2 ] 2[N(SO 2 CF 3 ) 2 ] ( 1 ), [K][UO 2 (Cl) 3 ((CH 3 ) 3 NCH 2 COO)] ( 2 ), [(CH 3 ) 3 NCH 2 COOH][UO 2 (Cl) 3 ((CH 3 ) 3 NCH 2 COO)]·H 2 O ( 3 ), [LiUO 2 (μ 2 -(CH 3 ) 3 NCH 2 COO) 4 ] 3[N(SO 2 CF 3 ) 2 ] ( 4 ) {(μ 2 -(CH 3 ) 3 NCH 2 COO)UO 2 (NO 3 ) 2 ((CH 3 ) 3 NCH 2 COO)} 2 UO 2 (NO 3 ) 2 , UO 2 (NO 3 ) 2 (H 2 O) 2 ·H 2 O ( 5 ), and UO 2 (Cl) 2 (H 2 O)(μ 2 -(CH 3 ) 3 NCH 2 COO) ( 6 ). These complexes expound upon the variability of mono carboxyl-functionalized uranyl coordination complexes, providing an enhanced framework for investigations into the structural chemistry of analogous actinyl systems.

Crystallography↗

Models of dislocation glide and strengthening mechanisms in bcc complex concentrated alloys

Abstract The mechanical response of complex concentrated alloys (CCAs) deviates from that of their pure and dilute counterparts due to the introduction of a combinatorially sized chemical concentration dimension. Compositional fluctuations constantly alter the energy landscape over which dislocations move, leading to line roughness and the appearance of defects such as kinks and jogs under stress and temperature conditions where they would ordinarily not exist in pure metals and dilute alloys. The presence of such chemical defects gives rise to atomic-level mechanisms that fundamentally change how CCAs deform plastically at meso- and macroscales. In this article, we provide a review of recent advances in modeling dislocation glide processes in CCAs, including atomistic simulations of dislocation glide using molecular dynamics, kinetic Monte Carlo simulations of edge and screw dislocation motion in refractory CCAs, and phase-field models of dislocation evolution over complex energy landscapes. We also discuss pathways to develop comprehensive simulation methodologies that connect an atomic-level description of the compositional complexity of CCAs with their mesoscopic dislocation-mediated plastic response with an eye toward improved design of CCA with superior mechanical response. Graphical abstract

36 MATERIALS SCIENCE↗

Nanoparticle self-assemblies with modern complexity

Thanks to decades of tireless efforts, nanoparticle assemblies have reached at an extremely high level of controllability, sophistication, and complexity, with new insights provided by integration with graph theory, cutting-edge characterization, and machine learning (ML)-based computation and modeling, as well as with ever-diversifying applications in energy, catalysis, biomedicine, optics, electronics, magnetics, organic biosynthesis, and quantum technology. Nanoparticle assemblies can be crystalline, known as superlattices or supracrystals. Their assembly entails a transition from disorder—dispersed nanoparticles—to order, which can be achieved through classical nucleation pathways or nonclassical pathways via prenucleation precursors or particle aggregation. Further, the periodic lattices allow facile manipulations of electrons, phonons, photons, and even spins, leading to advanced device components and metamaterials. Meanwhile, aperiodic assemblies out of nanoparticles, such as gels, networks, and amorphous solids, also start to attract attentions. Despite the loss of periodicity, symmetry-lowering or symmetry-breaking three-dimensional (3D) structures emerge with unique properties, such as chiroptical activity, topological mechanical strength, and quantum entanglement. Real-space imaging such as electron microscopy and X-ray based tomography methods are utilized to characterize these complex structures, while mathematical tools such as graph theories are in need to describe such complex structures. This issue aims to provide a timely review of the efforts in this greatly broadened materials design space including experiment, simulation, theory, and applications. Nine top experts (and their teams) from four countries deliver six review papers, summarizing fundamental mechanistic understandings of nanoparticle assemblies, highlighted with the developments of state-of-the-art in situ characterization tools and ML-assisted reverse engineering, and newly emergent applications of nanoarchitectures.

36 MATERIALS SCIENCE↗

Rupture Jumping and Seismic Complexity in Models of Earthquake Cycles for Fault Stepovers with Off-Fault Plasticity

ABSTRACT Fault stepovers are prime examples of geometric complexity in natural fault zones that may affect seismic hazard by determining whether an earthquake rupture continues propagating or abruptly stops. However, the long-term pattern of seismicity near-fault stepovers and underlying mechanisms of rupture jumping in the context of earthquake cycles are rarely studied. Leveraging a hybrid numerical scheme combining the finite element and the spectral boundary integral methods, FEBE, we carry out fully dynamic simulations of sequences of earthquakes and aseismic slip for both compressive and tensile stepovers with off-fault plasticity. We consider a rate-and-state friction law for the fault friction and pressure-sensitive Drucker–Prager plasticity for the off-fault bulk response. We observe that the accumulation of plastic deformation, an indication of off-fault damage, is significantly different in the two cases, with more plastic deformation projected in the overlapping region for the tensile stepover. The seismic pattern for a tensile stepover is more complex than for a compressive stepover, and incorporating plasticity also increases complexity, relative to the elastic case. A tensile stepover with off-fault plasticity shows rupture segmentation, temporal clustering, and frequent rupture jumping from one fault to another. These results shed light on possible mechanisms of rupture jumping in fault stepovers as well as the long-term evolution of the fault zone.

Geochemistry & Geophysics↗

The multi-faceted inverted harmonic oscillator: Chaos and complexity

The harmonic oscillator is the paragon of physical models; conceptually and computationally simple, yet rich enough to teach us about physics on scales that span classical mechanics to quantum field theory. This multifaceted nature extends also to its inverted counterpart, in which the oscillator frequency is analytically continued to pure imaginary values. In this article we probe the inverted harmonic oscillator (IHO) with recently developed quantum chaos diagnostics such as the out-of-time-order correlator (OTOC) and the circuit complexity. In particular, we study the OTOC for the displacement operator of the IHO with and without a non-Gaussian cubic perturbation to explore genuine and quasi scrambling respectively. In addition, we compute the full quantum Lyapunov spectrum for the inverted oscillator, finding a paired structure among the Lyapunov exponents. We also use the Heisenberg group to compute the complexity for the time evolved displacement operator, which displays chaotic behaviour. Finally, we extended our analysis to N-inverted harmonic oscillators to study the behaviour of complexity at the different timescales encoded in dissipation, scrambling and asymptotic regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗