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At least 289 records · Page 16

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DOE OSTI2023

Multi-level parallelization of quantum-chemical calculations

Here, strategies for multiple-level parallelizations of quantum-mechanical calculations are discussed, with an emphasis on using groups of workers for performing parallel tasks. These parallel programming models can be used for a variety ab initio quantum chemistry approaches, including the fragment molecular orbital method and replica-exchange molecular dynamics. Strategies for efficient load balancing on problems of increasing granularity are introduced and discussed. A four-level parallelization is developed based on a multi-level hierarchical grouping, and a high parallel efficiency is achieved on the Theta supercomputer using 131 072 OpenMP threads.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Effect of boron concentration on local structure and spontaneous polarization in AlBN thin films

The discovery of ferroelectricity in polar wurtzite-based ternary materials, such as Al 1–x B x N, has attracted attention due to their compatibility with complementary metal–oxide–semiconductor processes and potential use in integrated non-volatile memory devices. However, the origin of ferroelectricity and the fundamental control of the polarization switching in these materials are still under intensive investigation but appear to be related to local disorder induced from the alloying. In this work, we report the effect of boron alloying on the local structure of Al 1–x B x N films deposited by magnetron sputtering. Our results reveal a diminished crystalline order as a function of boron concentration, accompanied by a reduction in the spontaneous polarization. The film disorder is primarily associated with the dissimilar bond lengths between Al–N and B–N and the formation of threading dislocations induced by B incorporation in the structure.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Planarization of p -GaN surfaces on MOCVD grown V-defect engineered GaN-based LEDs

The large polarization barriers between the quantum wells and quantum barriers in long-wavelength GaN-based light-emitting diodes (LEDs) inhibit their performance by requiring excess driving voltages to reach standard operating current densities. Lateral injection of carriers directly into quantum wells is required to circumvent this issue. V-defects are naturally occurring inverted hexagonal defects with semipolar {$10\bar{1}1$}-plane sidewalls generated on surface depressions from threading dislocations. LEDs engineered to intentionally generate V-defects below the active region of the LED can achieve lateral carrier injection through the V-defect sidewalls and have already been able to demonstrate world record wall-plug efficiencies for LEDs in the green-red wavelengths. V-defects can be enlarged during kinetically limited growth where the growth rate of the c-plane GaN is faster than that of their sidewalls, leaving them unfilled. We report on the metal organic chemical vapor deposition growth conditions required to fill in V-defects with p-GaN during epitaxial growth of the LED post the active region. Circular transmission length measurements of Pd/Au contacts processed on p-GaN surfaces with various amounts of unfilled V-defects showed no significant difference in their sheet resistance and specific contact resistance. J–V measurements of LEDs grown with varying unfilled V-defect densities showed no significant difference in the forward bias regime. However, in the reverse bias regime, catastrophic breakdown occurred at markedly lower voltages for samples with larger unfilled V-defect densities. This suggests that unfilled V-defects may act as hotspots for device failure, and planarizing LED surfaces may help prevent early degradation of LED devices.

Chemical vapor deposition↗

DOE OSTI2022

Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor

Hearing is a fundamental sense of many animals, including all mammals, birds, some reptiles, amphibians, fish, and arthropods. The auditory organs of these animals are extremely diverse in anatomy after hundreds of millions of years of evolution, yet all are made up of cellular tissue and are morphologically part of the bodies of animals. Here, we show that hearing in the orb-weaving spider Larinioides sclopetarius is not constrained by the organism’s body but is extended through outsourcing hearing to its extended phenotype, the proteinaceous, self-manufactured orb web. We find that the wispy, wheel-shaped orb web acts as a hyperacute acoustic antenna to capture the sound-induced air particle movements that approach the maximum physical efficiency better than the acoustic responsivity of all previously known eardrums. By sensing the motion of web threads, the spider remotely detects and localizes the source of an incoming airborne acoustic wave, such as those emitted by approaching prey or predators. By outsourcing its acoustic sensors to its web, the spider is released from body size constraints and permits the araneid spider to increase its sound-sensitive surface area enormously, up to 10,000 times greater than the spider itself. The spider also enables the flexibility to functionally adjust and regularly regenerate its external "eardrum" according to its needs. The outsourcing and supersizing of auditory function in spiders provides unique features for studying extended and regenerative sensing and designing novel acoustic flow detectors for precise fluid dynamic measurement and manipulation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Review: knots and other new topological effects in liquid crystals and colloids

Abstract Humankind has been obsessed with knots in religion, culture and daily life for millennia, while physicists like Gauss, Kelvin and Maxwell already involved them in models centuries ago. Nowadays, colloidal particles can be fabricated to have shapes of knots and links with arbitrary complexity. In liquid crystals, closed loops of singular vortex lines can be knotted by using colloidal particles and laser tweezers, as well as by confining nematic fluids into micrometer-sized droplets with complex topology. Knotted and linked colloidal particles induce knots and links of singular defects, which can be interlinked (or not) with colloidal particle knots, revealing the diversity of interactions between topologies of knotted fields and topologically nontrivial surfaces of colloidal objects. Even more diverse knotted structures emerge in nonsingular molecular alignment and magnetization fields in liquid crystals and colloidal ferromagnets. The topological solitons include hopfions, skyrmions, heliknotons, torons and other spatially localized continuous structures, which are classified based on homotopy theory, characterized by integer-valued topological invariants and often contain knotted or linked preimages, nonsingular regions of space corresponding to single points of the order parameter space. A zoo of topological solitons in liquid crystals, colloids and ferromagnets promises new breeds of information displays and a plethora of data storage, electro-optic and photonic applications. Their particle-like collective dynamics echoes coherent motions in active matter, ranging from crowds of people to schools of fish. This review discusses the state of the art in the field, as well as highlights recent developments and open questions in physics of knotted soft matter. We systematically overview knotted field configurations, the allowed transformations between them, their physical stability and how one can use one form of knotted fields to model, create and imprint other forms. The large variety of symmetries accessible to liquid crystals and colloids offer insights into stability, transformation and emergent dynamics of fully nonsingular and singular knotted fields of fundamental and applied importance. The common thread of this review is the ability to experimentally visualize these knots in real space. The review concludes with a discussion of how the studies of knots in liquid crystals and colloids can offer insights into topologically related structures in other branches of physics, with answers to many open questions, as well as how these experimentally observable knots hold a strong potential for providing new inspirations to the mathematical knot theory.

Physics↗

DOE OSTI2019

A tunneling current measurement scheme to observe Majorana-zero-mode-induced crossed Andreev reflection

We propose a scheme to observe the Majorana-zero-mode-induced crossed Andreev reflection by measuring tunneling current directly. In this scheme a metallic ring structure is utilized to separate electron and hole signals. Since tunneling electrons and holes have different propagating wave vectors, the conditions for them to be constructively coherent in the ring differ. We find that when the magnetic flux threading the ring varies, it is possible to observe adjacent positive and negative tunneling current peaks of about equal amplitudes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

QSHS: an axion dark matter resonant search apparatus

We describe a resonant cavity search apparatus for axion dark matter constructed by the quantum sensors for the hidden sector collaboration. The apparatus is configured to search for QCD axion dark matter, though also has the capability to detect axion-like particles, dark photons, and some other forms of wave-like dark matter. Initially, a tuneable cylindrical oxygen-free copper cavity is read out using a low noise microwave amplifier feeding a heterodyne receiver. The cavity is housed in a dilution refrigerator (DF) and threaded by a solenoidal magnetic field, nominally 8 T. The apparatus also houses a magnetic field shield for housing superconducting electronics, and several other fixed-frequency resonators for use in testing and commissioning various prototype quantum electronic devices sensitive at a range of axion masses in the range 2.0–40 μ eV c -2 . The apparatus as currently configured is intended as a test stand for electronics over the relatively wide frequency band attainable with TM 010 the cavity mode used for axion searches. We present performance data for the resonator, DF, and magnet, and plans for the first science run.

Physics - Physics of elementary particles and fiel↗

DOE OSTI2023

Constraints on early dark energy from the axion weak gravity conjecture

A popular proposal for resolving the Hubble tension involves an early phase of dark energy, driven by an axion field with a periodic potential. Here, in this paper, we argue that these models are tightly constrained by the axion weak gravity conjecture: for typical parameter values, the axion decay constant must satisfy f < 0.008,M Pl , which is smaller than the axion decay constants appearing in the vast majority of early dark energy models to date. We discuss possible ways to evade or loosen this constraint, arguing that its loopholes are small and difficult to thread. This suggests that it may prove challenging to realize early dark energy models in a UV complete theory of quantum gravity.

string theory and cosmology↗

DOE OSTI2022

Optimizing the hit finding algorithm for liquid argon TPC neutrino detectors using parallel architectures

Neutrinos are particles that interact rarely, so identifying them requires large detectors which produce lots of data. Processing this data with the computing power available is becoming even more difficult as the detectors increase in size to reach their physics goals. Liquid argon time projection chamber (LArTPC) neutrino experiments are expected to grow in the next decade to have 100 times more wires than in currently operating experiments, and modernization of LArTPC reconstruction code, including parallelization both at data- and instruction-level, will help to mitigate this challenge. The LArTPC hit finding algorithm is used across multiple experiments through a common software framework. In this paper we discuss a parallel implementation of this algorithm. Using a standalone setup we find speedup factors of two times from vectorization and 30–100 times from multi-threading on Intel architectures. The new version has been incorporated back into the framework so that it can be used by experiments. On a serial execution, the integrated version is about 10 times faster than the previous one and, once parallelization is enabled, more speedups comparable to the standalone program are achieved.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool

Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data are not readily available. In this work, we present amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences using a random forest classifier.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Linear complexity

We present factorization and solution phases for a new linear complexity direct solver designed for concurrent batch operations on fine-grained parallel architectures, for matrices amenable to hierarchical representation. We focus on the strong-admissibility-based $\mathscr{H}^{2}$ format, where strong recursive skeletonization factorization compresses remote interactions. We build upon previous implementations of $\mathscr{H}^{2}$ matrix construction for efficient factorization and solution algorithm design, which are illustrated graphically in stepwise detail. The algorithms are ‘blackbox’ in the sense that the only inputs are the matrix and right-hand side, without analytical or geometrical information about the origin of the system. We demonstrate linear complexity scaling in both time and memory on four representative families of dense matrices up to one million in size. Parallel scaling up to 16 threads is enabled by a multi-level matrix graph coloring and avoidance of dynamic memory allocations thanks to prefix-sum memory management. An experimental backward error analysis is included. We break down the timings of different phases, identify phases that are memory-bandwidth limited, and discuss alternatives for phases that may be sensitive to the trend to employ lower precisions for performance.

Boukaram, Wajih↗

DOE OSTI2023

Magnetorotational instability in a swirling partially ionized gas

ABSTRACT The magnetorotational instability (MRI) has been proposed as the method of angular momentum transport that enables accretion in astrophysical discs. However, for weakly ionized discs, such as protoplanetary discs, it remains unclear whether the combined non-ideal magnetohydrodynamic (MHD) effects of Ohmic resistivity, ambipolar diffusion, and the Hall effect make these discs MRI stable. While much effort has been made to simulate non-ideal MHD MRI, these simulations make simplifying assumptions and are not always in agreement with each other. Furthermore, it is difficult to directly observe the MRI astrophysically because it occurs on small scales. Here, we propose the concept of a swirling gas experiment of weakly ionized argon gas between two concentric cylinders threaded with an axial magnetic field that can be used to study non-ideal MHD MRI. For our proposed experiment, we derive the hydrodynamic equilibrium flow and a dispersion relation for MRI that includes the three non-ideal effects. We solve this dispersion relation numerically for the parameters of our proposed experiment. We find it should be possible to produce a non-ideal MRI in such an experiment because of the Hall effect, which increases the MRI growth rate when the vertical magnetic field is anti-aligned with the rotation axis. As a proof of concept, we also present experimental results for a hydrodynamic flow in an unmagnetized prototype. We find that our prototype has a small, but non-negligible, α-parameter that could serve as a baseline for comparison to our proposed magnetized experiment, which could be subject to additional turbulence from the MRI.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Proposal for superconducting quantum networks using multioctave transduction to lower frequencies

We propose networking superconducting quantum circuits by transducing their excitations (typically 4–8 GHz) to 200–500 MHz photons for transmission via superconducting cryogenic coaxial cables. This frequency down-conversion reduces transmission losses and, counterintuitively, reduces noise. We introduce a multioctave asymmetrically threaded superconducting quantum interference device circuit capable of the required efficient, high-rate transduction. For a 100-meter cable with 𝑄 𝑖 = 10 5 at 10 mK, we theoretically show that our approach achieves single-photon fidelities of 0.962 at 200 MHz versus 0.772 at 8 GHz, and triples the lower bound on quantum channel capacity. In conclusion, this method enables highly efficient networking of superconducting qubits while maintaining high fidelities, combining improved performance with the practical advantages of flexible, compact coaxial cables.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Dark magnetohydrodynamics: Black hole accretion in superradiant dark photon clouds

Black holes threaded by massive vector fields can be subject to a superradiant instability, growing a cloud of massive vector particles around it. In this work, we consider what happens if such a dark matter candidate field mimicking a dark photon interacts with an accretion flow onto the black hole. By including a kinetic mixing term with the standard model photon, we extend the commonly used equations of general-relativistic magnetohydrodynamics to a dark photon constituent. The coupling to the dark photon then appears as an effective dynamo term together with a dark Lorentz force acting on the accreting matter. We numerically study the interactions between the superradiant dark photon cloud and the inner accretion flow by solving the coupled system in full numerical relativity. By parameterically varying the mixing parameter between the dark and standard model sector, we provide a first investigation of how the accretion flow could be modified. In conclusion, depending on the coupling strength, our solutions exhibit increased wind launching, as well as oscillation modes in the disk.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Hofstadter Topology: Noncrystalline Topological Materials at High Flux

he Hofstadter problem is the lattice analog of the quantum Hall effect and is the paradigmatic example of topology induced by an applied magnetic field. Conventionally, the Hofstadter problem involves adding ~10 4 T magnetic fields to a trivial band structure. In this work, we show that when a magnetic field is added to an initially topological band structure, a wealth of possible phases emerges. Remarkably, we find topological phases that cannot be realized in any crystalline insulators. We prove that threading magnetic flux through a Hamiltonian with a nonzero Chern number or mirror Chern number enforces a phase transition at fixed filling and that a 2D Hamiltonian with a nontrivial Kane–Mele invariant can be classified as a 3D topological insulator (TI) or 3D weak TI phase in periodic flux. We then study fragile topology protected by the product of twofold rotation and time reversal and show that there exists a higher order TI phase where corner modes are pumped by flux. We show that a model of twisted bilayer graphene realizes this phase. Our results rely primarily on the magnetic translation group that exists at rational values of the flux. The advent of Moiré lattices renders our work relevant experimentally. Due to the enlarged Moiré unit cell, it is possible for laboratory-strength fields to reach one flux per plaquette and allow access to our proposed Hofstadter topological phase.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Measuring Topological Constraint Relaxation in Ring-Linear Polymer Blends

Polymers are an effective test bed for studying topological constraints in condensed matter due to a wide array of synthetically available chain topologies. When linear and ring polymers are blended together, emergent rheological properties are observed as the blend can be more viscous than either of the individual components. This emergent behavior arises since ring-linear blends can form long-lived topological constraints as the linear polymers thread the ring polymers. Here, in this work, we demonstrate how the Gauss linking integral can be used to efficiently evaluate the relaxation of topological constraints in ring-linear polymer blends. For majority-linear blends, the relaxation rate of topological constraints depends primarily on reptation of the linear polymers, resulting in the diffusive time τ d,R for rings of length N R blended with linear chains of length N l to scale as τ d,R ~ N$^2_R$N$^{3.4}_L$.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗