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At least 685 records · Page 38

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗

Search for pair production of heavy vector-like quarks decaying into high- p T W bosons and top quarks in the lepton-plus-jets final state in p p collisions at s = 13 TeV with the ATLAS detector

CERN-LHC, ATLAS. Limits on pair production of a heavy vector-like B quark together with its antiparticle, where the B quark decays to a W boson and a top quark. The search is based on 36.1 +\- 0.8 fb^{-1} of pp collisions at sqrt{s} = 13 TeV recorded in 2015 and 2016 with the ATLAS detector at the CERN Large Hadron Collider. Data are analysed in the lepton plus jets final state, including at least four small jets out of which at least one is required to be b-tagged jet and a large-radius jet. Mass limits on B production are set as a function of the decay branching ratios.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Conservative-variable average states for equilibrium gas multi-dimensional fluxes

Modern split component evaluations of the flux vector Jacobians are thoroughly analyzed for equilibrium-gas average-state determinations. It is shown that all such derivations satisfy a fundamental eigenvalue consistency theorem. A conservative-variable average state is then developed for arbitrary equilibrium-gas equations of state and curvilinear-coordinate fluxes. Original expressions for eigenvalues, sound speed, Mach number, and eigenvectors are then determined for a general average Jacobian, and it is shown that the average eigenvalues, Mach number, and eigenvectors may not coincide with their classical pointwise counterparts. A general equilibrium-gas equation of state is then discussed for conservative-variable computational fluid dynamics (CFD) Euler formulations. The associated derivations lead to unique compatibility relations that constrain the pressure Jacobian derivatives. Thereafter, alternative forms for the pressure variation and average sound speed are developed in terms of two average pressure Jacobian derivatives. Significantly, no additional degree of freedom exists in the determination of these two average partial derivatives of pressure. Therefore, they are simultaneously computed exactly without any auxiliary relation, hence without any geometric solution projection or arbitrary scale factors. Several alternative formulations are then compared and key differences highlighted with emphasis on the determination of the pressure variation and average sound speed. The relevant underlying assumptions are identified, including some subtle approximations that are inherently employed in published average-state procedures. Finally, a representative test case is discussed for which an intrinsically exact average state is determined. This exact state is then compared with the predictions of recent methods, and their inherent approximations are appropriately quantified.

Iannelli, G. S.↗

On the description of conical intersections—A continuous representation of the local topography of seams of conical intersection of three or more electronic states: A generalization of the two state result

For conical intersections of two states (I,J = I + 1) the vectors defining the branching or g-h plane, the energy difference gradient vector g{sup I,J}, and the interstate coupling vector h{sup I,J}, can be made orthogonal by a one parameter rotation of the degenerate electronic eigenstates. The representation obtained from this rotation is used to construct the parameters that describe the vicinity of the conical intersection seam, the conical parameters, s{sup I,J}{sub x} (R), s{sup I,J}{sub y} (R), g{sup I,J}(R), and h{sup I,J}(R). As a result of the orthogonalization these parameters can be made continuous functions of R, the internuclear coordinates. In this work we generalize this notion to construct continuous parametrizations of conical intersection seams of three or more states. The generalization derives from a recently introduced procedure for using non-degenerate electronic states to construct coupled diabatic states that represent adiabatic states coupled by conical intersections. The procedure is illustrated using the seam of conical intersections of three states in parazolyl as an example.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The MAGSAT vector magnetometer: A precision fluxgate magnetometer for the measurement of the geomagnetic field

A description of the precision triaxial fluxgate magnetometer to be flown aboard the MAGSAT spacecraft is presented. The instrument covers the range of + or - 64,000 nT with a resolution of + or - 0.5 nT, an intrinsic accuracy of + or - 0.001% of full scale and an angular alignment stability of the order of 2 seconds of arc. It was developed at NASA's Goddard Space Flight Center and represents the state-of-the-art in precision vector magnetometers developed for spaceflight use.

Acuna, M. H.↗

Simplified Two-Stage Model Predictive Control for a Hybrid Multilevel Converter With Floating H-Bridge

This paper proposes a simplified two-stage model predictive control (ST-MPC) for a hybrid multilevel converter, which is an active-neutral-point-clamped converter with floating H-bridge (ANPC-H). The objective of the first stage is to select the voltage vector that has the optimal current tracking performance by using a novel geometrical positioning approach in the complex plane. The second stage selects the best switching state among all the available switching states that belong to the same voltage vector obtained in the first stage, to balance dc capacitor voltages and reduce the common mode voltage. The proposed ST-MPC can dramatically reduce the computational burden and ensure the best current tracking by the two-stage structure, such that the execution time is much shorter compared with the conventional MPC. In addition, the geometrical positioning approach in the first stage is generic and can be applicable for any multilevel converters with N-level output; thus, this ST-MPC can be applied for both sevenand nine-level operation of the hybrid ANPC-H converter under different dc voltage ratios. Both simulation results and experimental results obtained on a silicon carbide hybrid ANPC-H converter prototype validate the feasibility and effectiveness of the proposed ST-MPC strategy.

42 ENGINEERING↗

Spin density wave and van Hove singularity in the kagome metal CeTi 3 Bi 4

Kagome metals with van Hove singularities near the Fermi level can host intriguing quantum phenomena such as chiral loop currents, electronic nematicity, and unconventional superconductivity. However, to our best knowledge, unconventional magnetic states driven by van Hove singularities–like spin-density waves–have not been observed experimentally in kagome metals. Here, we report the magnetic and electronic structure of the layered kagome metal CeTi 3 Bi 4 , where Ti kagome electronic structure interacts with a magnetic sublattice of Ce 3+ J eff = 1/2 moments. Neutron diffraction reveals an incommensurate spin-density wave ground state of the Ce 3+ moments, coexisting with commensurate antiferromagnetic order across most of the temperature-field phase diagram. The commensurate component is preferentially suppressed by thermal fluctuations and magnetic field, yielding a rich phase diagram involving an intermediate single-Q spin-density wave phase. First-principles calculations and angle-resolved photoemission spectroscopy identify van Hove singularities near the Fermi level, with the observed magnetic propagation vectors connecting their high density of states, strongly suggesting a van Hove singularity-assisted spin-density wave. These findings establish kagome metals LnTi 3 Bi 4 as a model platform where the characteristic electronic structure of the kagome lattice plays a pivotal role in magnetic order.

36 MATERIALS SCIENCE↗

A vectorized, finite-volume, adaptive-grid algorithm for Navier-Stokes calculations

An adaptive grid, finite-volume method has been used to solve the Navier-Stokes equations for complete (forebody and afterbody) flowfields around blunt bodies. The code, which is applicable for axisymmetric or two-dimensional flows, allows the mesh to adjust during the computation to provide a closer spacing of mesh points in regions of high gradients, thus minimizing the number of required computational points. The solution technique is explicit, utilizing a maximum time-step advancement at each grid point to accelerate convergence to the steady state. The code has been fully vectorized for efficient solution on the CYBER 203 computer. A very flexible rezoning routine is used to concentrate mesh points anywhere in the field, either by a user-defined weighting function or by allowing high gradient regions to adjust the grid. The grid adjustment routine is implicit in nature and represents a very small portion of the total computational cost. Currently, the code runs in approximately 0.000016 seconds per grid point per iteration.

Gnoffo, P. A.↗

Enhanced spin-triplet pairing in magnetic junctions with s -wave superconductors

A common path to superconducting spintronics, Majorana fermions, and topologically protected quantum computing relies on spin-triplet superconductivity. While naturally occurring spin-triplet pairing is elusive, and even common spin-triplet candidates, such as Sr 2 RuO 4 , support alternative explanations, proximity effects in heterostructures can overcome these limitations. It is expected that robust spin-triplet superconductivity in magnetic junctions should rely on highly spin-polarized magnets or complex magnetic multilayers. Instead, we predict that the interplay of interfacial spin-orbit coupling and the barrier strength in simple magnetic junctions, with only a small spin polarization and s -wave superconductors, can lead to nearly complete spin-triplet superconducting proximity effects. This peculiar behavior arises from an effective perfect transparency: interfacial spin-orbit coupling counteracts the native potential barrier for states of a given spin and wave vector. We demonstrate that the enhanced spin-triplet regime is characterized by a huge increase in conductance magnetoanisotropy, orders of magnitude larger than in the normal state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Phase transitions in the Rényi entropies of a 2+1D large- N interacting vector model

Here we consider the reduced density matrix for a disk in the ground state of the interacting fixed points of the large- N O(N) vector model in 2 + 1 dimensions. Using the map to the free energy on $\mathbb H_2 × S^1$, we show that there is an instability in the Rényi entropies at n = 1 in the N → ∞ limit, indicating a phase transition at or near this Rényi parameter. We close with a discussion of the finite- N case.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quasi-Two-Dimensional Antiferromagnetic Spin Fluctuations in the Spin-Triplet Superconductor Candidate CeRh 2 As 2

The tetragonal heavy-fermion superconductor CeRh 2 ⁢As 2 (T c = 0.3 K) exhibits an exceptionally high critical field of 14 T for B ∥ c. It undergoes a field-driven first-order phase transition between superconducting states, potentially transitioning from spin-singlet to spin-triplet superconductivity. To further understand these superconducting states and the role of magnetism, we probe spin fluctuations in CeRh 2 ⁢As 2 using neutron scattering. Here, we find dynamic (π, π) antiferromagnetic (AFM) spin correlations with an anisotropic quasi-two-dimensional correlation volume. Our data place an upper limit of 0.31 μ B on the staggered magnetization of corresponding Néel orders at T = 0.08 K. Density functional theory calculations, treating Ce 4⁢ƒ electrons as core states, show that the AFM wave vector connects significant areas of the Fermi surface. Our findings indicate that the dominant excitations in CeRh 2 ⁢As 2 for ℏω⁢ < 1.2 meV are magnetic and suggest that superconductivity in CeRh 2⁢ As 2 is mediated by AFM spin fluctuations associated with a proximate quantum critical point.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Antiferromagnetic order and its interplay with superconductivity in CaK(Fe$_{1-x}$Mn$_x$) 4 As 4

The magnetic order for several compositions of CaK(Fe$_{1-x}$Mn$_x$) 4 As 4 has been studied by nuclear magnetic resonance (NMR), Mössbauer spectroscopy, and neutron diffraction. Our observations for the Mn-doped 1144 compound are consistent with the hedgehog spin vortex crystal (hSVC) order which has previously been found for Ni-doped CaKFe 4 As 4 . The hSVC state is characterized by the stripe-type propagation vectors $(\pi\,0)$ and $(0\,\pi)$ just as in the doped 122 compounds. The hSVC state preserves tetragonal symmetry at the Fe site, and only this SVC motif with simple antiferromagnetic (AFM) stacking along $\ c$ is consistent with all our observations using NMR Mössbauer spectroscopy, and neutron diffraction. We find that the hSVC state in the Mn-doped 1144 compound coexists with superconductivity (SC), and by combining the neutron scattering and Mössbauer spectroscopy data we can infer a quantum phase transition, hidden under the superconducting dome, associated with the suppression of the AFM transition temperature ($T_N$) to zero for $x$ ≈ 0.01. In addition, unlike several 122 compounds and Ni-doped 1144, the ordered magnetic moment is not observed to decrease at temperatures below the superconducting transition temperature ($T_c$).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On the existence of touch points for first-order state inequality constraints

The appearance of touch points in state constrained optimal control problems with general vector-valued control is studied. Under the assumption that the Hamiltonian is regular, touch points for first-order state inequalities are shown to exist only under very special conditions. In many cases of practical importance these conditions can be used to exclude touch points a priori without solving an optimal control problem. The results are demonstrated on a simple example.

Seywald, Hans↗

Rescuing massive photons from the Swampland

Stringent Swampland conjectures aimed at effective theories containing massive abelian vectors have recently been proposed (arXiv:1808.09966), with striking phenomenological implications. In this article, we show how effective theories that parametrically violate the proposed conjectures can be UV-completed into theories that satisfy them. The UV-completion is accessible through both the Stückelberg and Higgs mechanisms, with all dimensionless parameters taking $\mathcal{O}$(1) values from the UV perspective. These constructions feature an IR limit containing a light vector that is parametrically separated from any other massive states, and from any cut-off scale mandated by quantum gravity consistency requirements. Moreover, the cut-off--to--vector--mass ratio remains parametrically large even in the decoupling limit in which all other massive states (including any scalar excitations) become arbitrarily heavy. We discuss how apparently strong constraints imposed by the proposed conjectures on phenomenologically interesting models, including specific production mechanisms of dark photon dark matter, are thereby circumvented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames

This dissertation presents research on addressing some of the contemporary challenges in the analysis of vector fields—an important type of scientific data useful for representing a multitude of physical phenomena, such as wind flow and ocean currents. In particular, new theories and computational frameworks to enable consistent feature extraction from vector fields are presented. One of the most fundamental challenges in the analysis of vector fields is that their features are defined with respect to reference frames. Unfortunately, there is no single “correct” reference frame for analysis, and an unsuitable frame may cause features of interest to remain undetected, thus creating serious physical consequences. This work develops new reference frames that enable extraction of localized features that other techniques and frames fail to detect. As a result, these reference frames objectify the notion of “correctness” of features for certain goals by revealing the phenomena of importance from the underlying data. An important consequence of using these local frames is that the analysis of unsteady (time-varying) vector fields can be reduced to the analysis of sequences of steady (timeindependent) vector fields, which can be performed using simpler and scalable techniques that allow better data management by accessing the data on a per-time-step basis. Nevertheless, the state-of-the-art analysis of steady vector fields is not robust, as most techniques are numerical in nature. The residing numerical errors can violate consistency with the underlying theory by breaching important fundamental laws, which may lead to serious physical consequences. This dissertation considers consistency as the most fundamental characteristic of computational analysis that must always be preserved, and presents a new discrete theory that uses combinatorial representations and algorithms to provide consistency guarantees during vector field analysis along with the uncertainty visualization of unavoidable discretization errors. Together, the two main contributions of this dissertation address two important concerns regarding feature extraction from scientific data: correctness and precision. The work presented here also opens new avenues for further research by exploring more-general reference frames and more-sophisticated domain discretizations.

97 MATHEMATICS AND COMPUTING↗

Accessing Photoredox Transformations with an Iron(III) Photosensitizer and Green Light

Efficient excited-state electron transfer between an iron(III) photosensitizer and organic electron donors was realized with green light irradiation. This advance was enabled by the use of the previously reported iron photosensitizer, [Fe(phtmeimb) 2 ]+ (phtmeimb = {phenyl[tris(3-methyl-imidazolin-2-ylidene)]borate}, that exhibited long-lived and luminescent ligand-to-metal charge transfer (LMCT) excited states. A benchmark dehalogenation reaction was investigated with catalytic yieldsthat exceed 90% and an enhanced stability relative to the prototypical photosensitizer [Ru(bpy) 3 ] 2+ . The initial catalytic step is electron transfer from an amine to the photoexcited iron sensitizer that is shown to occur with a large cage-escape yield. For LMCT excited states, this reductive electron transfer is vectoral and may be a general advantage of Fe(III) photosensitizers. In-depth time-resolved spectroscopic methods, that include transient absorption characterization from the ultraviolet to the infrared regions, provided a quantitative description of the catalytic mechanism with associated rate constants and yields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Connections between nonlocal operators: From vector calculus identities to a fractional Helmholtz decomposition

Nonlocal vector calculus, which is based on the nonlocal forms of gradient, divergence, and Laplace operators in multiple dimensions, has shown promising applications in fields such as hydrology, mechanics, and image processing. In this work, we study the analytical underpinnings of these operators. We rigorously treat compositions of nonlocal operators, prove nonlocal vector calculus identities, and connect weighted and unweighted variational frameworks. We combine these results to obtain a weighted fractional Helmholtz decomposition which is valid for sufficiently smooth vector fields. Our approach identifies the function spaces in which the stated identities and decompositions hold, providing a rigorous foundation to the nonlocal vector calculus identities that can serve as tools for nonlocal modeling in higher dimensions.

97 MATHEMATICS AND COMPUTING↗