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At least 379 records · Page 21

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DOE OSTI2021

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple sequence alignments (MSAs) of a pair of interacting proteins (dimers) as input, which are often difficult to obtain because there are not many known protein complexes available to generate MSAs of sufficient depth for a pair of proteins. In recognizing that multiple sequence alignments of a monomer that forms homomultimers contain the co-evolutionary signals of both intrachain and interchain residue pairs in contact, we applied DNCON2 (a deep learning-based protein intrachain residue-residue contact predictor) to predict both intrachain and interchain contacts for homomultimers using multiple sequence alignment (MSA) and other co-evolutionary features of a single monomer followed by discrimination of interchain and intrachain contacts according to the tertiary structure of the monomer. We name this tool DNCON2_Inter. Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers. In some instances, especially where interchain contact densities are high, DNCON2_Inter predicted interchain contacts with 100% precision. We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex. Using Con_Complex, we show that the predicted contacts can be used to accurately construct the structure of some complexes. Our experiment demonstrates that monomeric multiple sequence alignments can be used with deep learning to predict interchain contacts of homomeric proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Multiple resource use efficiency (mRUE): A new concept for ecosystem production

The resource-driven concept, which is an important school for investigating ecosystem production, has been applied for decades. However, the regulatory mechanisms of production by multiple resources remain unclear. We formulated a new algorithm model that integrates multiple resource uses to study ecosystem production and tested its applications on a water-availability gradient in semi-arid grassland. The result of our experiment showed that changes in water availability significantly affected the resources of light and nitrogen, and altered the relationships among multiple resource absorption rate (ε), multiple resource use efficiency (mRUE), and available resource (R avail ). The increased water availability suppressed ecosystem mRUE (i.e., “declining marginal returns”); The changes in mRUE had a negative effect on ε (i.e., “inverse feedback”). These two processes jointly regulated that the stimulated single resource availability would promote ecosystem production rather than suppress it, even when mRUE was reduced. This study illustrated the use of the mRUE model in exploring the coherent relationships among the key parameters on regulating the ecosystem production for future modeling, and evaluated the sensitivity of this conceptual model under different dataset properties. Furthermore, this model needs extensive validation by the ecological community before it can extrapolate this method to other ecosystems in the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Co-orchestration of multiple instruments to uncover structure–property relationships in combinatorial libraries

The rapid growth of automated and autonomous instrumentation brings forth opportunities for the co-orchestration of multimodal tools that are equipped with multiple sequential detection methods or several characterization techniques to explore identical samples. This is exemplified by combinatorial libraries that can be explored in multiple locations via multiple tools simultaneously or downstream characterization in automated synthesis systems. In co-orchestration approaches, information gained in one modality should accelerate the discovery of other modalities. Correspondingly, an orchestrating agent should select the measurement modality based on the anticipated knowledge gain and measurement cost. Herein, we propose and implement a co-orchestration approach for conducting measurements with complex observables, such as spectra or images. The method relies on combining dimensionality reduction by variational autoencoders with representation learning for control over the latent space structure and integration into an iterative workflow via multi-task Gaussian Processes (GPs). This approach further allows for the native incorporation of the system's physics via a probabilistic model as a mean function of the GPs. We illustrate this method for different modes of piezoresponse force microscopy and micro-Raman spectroscopy on a combinatorial Sm-BiFeO3 library. However, the proposed framework is general and can be extended to multiple measurement modalities and arbitrary dimensionality of the measured signals.

47 OTHER INSTRUMENTATION↗

DOE OSTI2014

On the possibility of the multiple inductively coupled plasma and helicon plasma sources for large-area processes

In this study, we attempted to determine the possibility of multiple inductively coupled plasma (ICP) and helicon plasma sources for large-area processes. Experiments were performed with the one and two coils to measure plasma and electrical parameters, and a circuit simulation was performed to measure the current at each coil in the 2-coil experiment. Based on the result, we could determine the possibility of multiple ICP sources due to a direct change of impedance due to current and saturation of impedance due to the skin-depth effect. However, a helicon plasma source is difficult to adapt to the multiple sources due to the consistent change of real impedance due to mode transition and the low uniformity of the B-field confinement. As a result, it is expected that ICP can be adapted to multiple sources for large-area processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Mechanism of hole injection enhancement in light-emitting diodes by inserting multiple hole-reservoir layers in electron blocking layer

In this study, gallium nitride (GaN) based light-emitting diodes (LEDs) with single and multiple hole-reservoir layers (HRLs) inserted in the electron-blocking layer (EBL) have been investigated numerically and experimentally. According to simulation results, a better electron confinement and a higher hole injection level can be achieved by the multiple HRLs inserted in the EBL region. To further reveal the underlying mechanism of hole injection enhancement experimentally, the active regions were intentionally designed to emit photons with three different wavelengths of 440 nm, 460 nm, and 480 nm, respectively. Based on the experimental results of photoluminescence (PL) and time-resolved PL (TRPL) measurements conducted at 298 K, the remarkable enhancement (148%) of PL intensities and significant increase in the decay times of the quantum wells close to p-GaN can be obtained. Therefore, the mechanism is proposed that carriers are able to reserve in the EBL region with multiple HRLs for a much longer time. Meanwhile, carriers could diffuse into the active region by tunnelling and/or thermo-electronic effect and then recombine efficiently, leading to the better carrier reservoir effect and higher hole injection in LEDs. As a result, by inserting multiple HRLs in the EBL region instead of single HRL, the experimental external quantum efficiency is enhanced by 19.8%, while the serious droop ratio is markedly suppressed from 37.0% to 27.6% at the high current injection of 100 A/cm{sup 2}.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

Generating multiple orbital angular momentum vortex beams using a metasurface in radio frequency domain

In this paper, an electromagnetic metasurface is designed, fabricated, and experimentally demonstrated to generate multiple orbital angular momentum (OAM) vortex beams in radio frequency domain. Theoretical formula of compensated phase-shift distribution is deduced and used to design the metasurface to produce multiple vortex radio waves in different directions with different OAM modes. The prototype of a practical configuration of square-patch metasurface is designed, fabricated, and measured to validate the theoretical analysis at 5.8 GHz. The simulated and experimental results verify that multiple OAM vortex waves can be simultaneously generated by using a single electromagnetic metasurface. The proposed method paves an effective way to generate multiple OAM vortex waves in radio and microwave wireless communication applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

Repetition rate multiplication of frequency comb using all-pass fiber resonator

We propose a stable method for repetition rate multiplication of a 250-MHz Er-fiber frequency comb by a phase-locked all-pass fiber ring resonator, whose phase-locking configuration is simple. The optical path length of the fiber ring resonator is automatically controlled to be accurately an odd multiple of half of the original cavity length using an electronical phase-locking unit with an optical delay line. As for shorter cavity length of the comb, high-order odd multiple is preferable. Because the power loss depends only on the net-attenuation of the fiber ring resonator, the energetic efficiency of the proposed method is high. The input and output optical spectrums show that the spectral width of the frequency comb is clearly preserved. Besides, experimental results show less pulse intensity fluctuation and 35 dB suppression ratio of side-modes while providing a good long-term and short-term frequency stability. Higher-order repetition rate multiplication to several GHz can be obtained by using several fiber ring resonators in cascade configuration.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2013

CCD MEASUREMENTS OF DOUBLE AND MULTIPLE STARS AT NAO ROZHEN AND ASV IN 2011. FIVE LINEAR SOLUTIONS

Using the 2 m telescope of the Bulgarian National Astronomical Observatory at Rozhen, observations of 222 double or multiple stars were carried out during three nights in 2011. This is the sixth series of measurements of CCD frames of double and multiple stars obtained at Rozhen. Also in 2011, using the 0.6 m telescope of the Serbian Astronomical Station on the mountain of Vidojevica, observations of 208 double or multiple stars were carried out during six nights. This is the first series of measurements of CCD frames of double and multiple stars obtained at this station. In this paper, we present the results for the position angle and angular separation for 337 pairs and residuals for 72 pairs with published orbital elements or linear solutions. These observations have angular separations in the range from 1.''37 to 172.''81, with a median angular separation of 7.''66. We also present the recalculated linear solutions for four pairs and one linear solution that has been calculated for the first time.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Multiplicity functions of quasars: predictions from the MassiveBlackII simulation

ABSTRACT We examine multiple active galactic nucleus (AGN) systems (triples and quadruples, in particular) in the MassiveBlackII simulation over a redshift range of 0.06 ≲ z ≲ 4. We identify AGN systems (with bolometric luminosity $L_{\mathrm{bol}}\gt 10^{42}~\mathrm{erg\, s}^{-1}$) at different scales (defined by the maximum distance between member AGNs) to determine the AGN multiplicity functions. This is defined as the volume/surface density of AGN systems per unit richness R, the number of AGNs in a system. We find that gravitationally bound multiple AGN systems tend to populate scales of ${\lesssim}0.7~\mathrm{cMpc}\, h^{-1}$; this corresponds to angular separations of ≲100 arcsec and a line-of-sight velocity difference ${\lesssim}200~\mathrm{km\, s}^{-1}$. The simulation contains ∼10 and ∼100 triples/quadruples per deg2 up to depths of DESI (g ≲ 24) and LSST (g ≲ 26) imaging, respectively; at least $20{{\ \rm per\ cent}}$ of these should be detectable in spectroscopic surveys. The simulated quasar ($L_{\mathrm{bol}}\gt 10^{44}~\mathrm{erg\, s}^{-1}$) triples and quadruples predominantly exist at 1.5 ≲ z ≲ 3. Their members have black hole masses $10^{6.5}\lesssim M_{\mathrm{ bh}}\lesssim 10^{9}~\mathrm{M}_{\odot }\, h^{-1}$ and live in separate (one central and multiple satellite) galaxies with stellar masses $10^{10}\lesssim M_{*}\lesssim 10^{12}~\mathrm{M}_{\odot }\, h^{-1}$. They live in the most massive haloes (e.g. ${\sim}10^{13}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 2.5; ${\sim}10^{14}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 1) in the simulation. Their detections provide an exciting prospect for understanding massive black hole growth and their merger rates in galaxies in the era of multimessenger astronomy.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Stellar multiplicity and stellar rotation: insights from APOGEE

ABSTRACT We measure rotational broadening in spectra taken by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey to characterize the relationship between stellar multiplicity and rotation. We create a sample of 2786 giants and 24 496 dwarfs with stellar parameters and multiple radial velocities from the APOGEE pipeline, projected rotation speeds vsin i determined from our own pipeline, and distances, masses, and ages measured by Sanders & Das. We use the statistical distribution of the maximum shift in the radial velocities, ΔRVmax, as a proxy for the close binary fraction to explore the interplay between stellar evolution, rotation, and multiplicity. Assuming that the minimum orbital period allowed is the critical period for Roche Lobe overflow and rotational synchronization, we calculate theoretical upper limits on expected vsin i and ΔRVmax values. These expectations agree with the positive correlation between the maximum ΔRVmax and vsin i values observed in our sample as a function of log(g). We find that the fast rotators in our sample have a high occurrence of short-period [log(P/d) ≲ 4] companions. We also find that old, rapidly rotating main-sequence stars have larger completeness-corrected close binary fractions than their younger peers. Furthermore, rapidly rotating stars with large ΔRVmax consistently show differences of 1–10 Gyr between the predicted gyrochronological and measured isochronal ages. These results point towards a link between rapid rotation and close binarity through tidal interactions. We conclude that stellar rotation is strongly correlated with stellar multiplicity in the field, and caution should be taken in the application of gyrochronology relations to cool stars.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Observation of strangeness enhancement with charmed mesons in high-multiplicity p Pb collisions at s NN = 8.16 TeV

The production of prompt D s + and D + mesons is measured by the LHCb experiment in proton-lead ( p Pb ) collisions in both the forward ( 1.5 < y * < 4.0 ) and backward ( − 5.0 < y * < − 2.5 ) rapidity regions at a nucleon-nucleon center-of-mass energy of s NN = 8.16 TeV . The nuclear modification factors of both D s + and D + mesons are determined as a function of transverse momentum, p T , and rapidity. In addition, the D s + to D + cross section ratio is measured as a function of the primary charged particle multiplicity in the event. An enhanced D s + to D + production in high-multiplicity events is observed for the whole measured p T range, in particular at low p T and backward rapidity, where the significance exceeds six standard deviations. This constitutes the first observation of strangeness enhancement in charm quark hadronization in high-multiplicity p Pb collisions. The results are also qualitatively consistent with the presence of quark coalescence as an additional charm quark hadronization mechanism in high-multiplicity proton-lead collisions. © 2024 CERN, for the LHCb Collaboration 2024 CERN

Aaij, R. (ORCID:0000000305331952)↗

DOE OSTI2013

Multiple transient memories in sheared suspensions: Robustness, structure, and routes to plasticity

Multiple transient memories, first discovered in charge-density-wave conductors, are a remarkable and initially counterintuitive example of how a system can store information about its driving. In this class of memories, a system can learn multiple driving inputs, nearly all of which are eventually forgotten despite their continual input. If sufficient noise is present, the system regains plasticity so that it can continue to learn new memories indefinitely. Recently, Keim and Nagel [Phys. Rev. Lett. 107, 010603 (2011)] showed how multiple transient memories could be generalized to a generic driven disordered system with noise, giving as an example simulations of a simple model of a sheared non-Brownian suspension. Here, we further explore simulation models of suspensions under cyclic shear, focusing on three main themes: robustness, structure, and overdriving. We show that multiple transient memories are a robust feature independent of many details of the model. The steady-state spatial distribution of the particles is sensitive to the driving algorithm; nonetheless, the memory formation is independent of such a change in particle correlations. Finally, we demonstrate that overdriving provides another means for controlling memory formation and retention.

42 ENGINEERING↗

DOE OSTI2023

Evidence for Modification of $b$ Quark Hadronization in High-Multiplicity $pp$ Collisions at $\sqrt{s}$ = 13 TeV

The production rate of $B^{0}_{s}$ mesons relative to $B^0$ mesons is measured by the LHCb experiment in $pp$ collisions at a center-of-mass energy $\sqrt{s}$ = 13 TeV over the forward rapidity interval 2 < $y$ < 4.5 as a function of the charged particle multiplicity measured in the event. Evidence at the 3.4$σ$ level is found for an increase of the ratio of $B^{0}_{s}$ to $B^0$ cross sections with multiplicity at transverse momenta below 6 GeV /$c$, with no significant multiplicity dependence at higher transverse momentum. Comparison with data from $e^+$ $e^–$ collisions implies that the density of the hadronic medium may affect the production rates of $B$ mesons. This is qualitatively consistent with the emergence of quark coalescence as an additional hadronization mechanism in high-multiplicity collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Emergence of Long-Range Angular Correlations in Low-Multiplicity Proton-Proton Collisions

This Letter presents the measurement of near-side associated per-trigger yields, denoted ridge yields, from the analysis of angular correlations of charged hadrons in proton-proton collisions at s = 13 TeV . Long-range ridge yields are extracted for pairs of charged particles with a pseudorapidity difference of 1.4 < | Δ η | < 1.8 and a transverse momentum of 1 < p T < 2 GeV / c , as a function of the charged-particle multiplicity measured at midrapidity. This Letter extends the measurements of the ridge yield to the low multiplicity region, where in hadronic collisions it is typically conjectured that a strongly interacting medium is unlikely to be formed. The precision of the new low multiplicity results allows for the first direct quantitative comparison with the results obtained in e + e − collisions at s = 91 GeV and s = 183 – 209 GeV , where initial-state effects such as preequilibrium dynamics and collision geometry are not expected to play a role. In the multiplicity range 8 ≲ ⟨ N ch ⟩ ≲ 24 where the e + e − results have good precision, the measured ridge yields in p p collisions are substantially larger than the limits set in e + e − annihilations. Consequently, the findings presented in this Letter suggest that the processes involved in e + e − annihilations do not contribute significantly to the emergence of long-range correlations in p p collisions. © 2024 CERN, for the ALICE Collaboration 2024 CERN

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Chaotic roots of the modular multiplication dynamical system in Shor's algorithm

Shor's factoring algorithm, believed to provide an exponential speedup over classical computation, relies on finding the period of an exactly periodic quantum modular multiplication operator. This exact periodicity is the hallmark of an integrable system, which is paradoxical from the viewpoint of quantum chaos, given that the classical limit of the modular multiplication operator is a highly chaotic system that occupies the “maximally random” Bernoulli level of the classical ergodic hierarchy. In this work, we approach this apparent paradox from a quantum dynamical systems viewpoint, and consider whether signatures of ergodicity and chaos may indeed be encoded in such an “integrable” quantization of a chaotic system. We show that Shor's modular multiplication operator, in specific cases, can be written as a superposition of quantized 𝐴-baker's maps exhibiting more typical signatures of quantum chaos and ergodicity. This work suggests that the integrability of Shor's modular multiplication operator may stem from the interference of other “chaotic” quantizations of the same family of maps, and paves the way for deeper studies on the interplay of integrability, ergodicity, and chaos in and via quantum algorithms.

Dynamical systems↗

DOE OSTI2026

Flavor, transverse momentum, and azimuthal dependence of charged pion multiplicities in semi-inclusive deep-inelastic scattering with 10.6 GeV electrons

Measurements of semi-inclusive deep-inelastic scattering multiplicities for 𝜋 + and 𝜋 − from proton and deuteron targets are reported on a grid of hadron kinematic variables 𝑧, 𝑃 𝑇 , and 𝜙* for leptonic kinematic variables in the range 0.3<𝑥<0.6 and 3<𝑄 2 <5GeV 2 . Data were acquired in 2018 and 2019 at Jefferson Lab Hall C with a 10.6 GeV electron beam impinging on 10-cm-long liquid hydrogen and deuterium targets. Scattered electrons and charged pions were detected in the High Momentum Spectrometer and Super High Momentum Spectrometer, respectively. The multiplicities were fitted for each bin in (𝑥,𝑄 2 ,𝑧,𝑃𝑡) to extract the 𝜙*—independent 𝑀 0 and the azimuthal modulations ⟨cos⁡(𝜙*)⟩ and ⟨cos⁡(2⁢𝜙*)⟩. The 𝑃𝑡 dependence of the 𝑀 0 results was found to be remarkably consistent for the four cases studied: 𝑒⁢𝑝→𝑒⁢𝜋 + ⁢𝑋, 𝑒⁢𝑝→𝑒⁢𝜋 − ⁢𝑋, 𝑒⁢𝑑→𝑒⁢𝜋 + ⁢𝑋, 𝑒⁢𝑑→𝑒⁢𝜋 − ⁢𝑋 over the range 0GeV<𝑃 𝑡 <0.4GeV, as were the multiplicities evaluated near 𝜙*=180∘ over the extended range 0GeV<𝑃 𝑡 <0.7GeV. The Gaussian widths of the 𝑃 𝑡 dependence exhibit a quadratic increase with 𝑧. The cos⁡(𝜙*) modulations were found to be consistent with zero for 𝜋 + , in agreement with previous world data, while the 𝜋 − moments were, in many cases, significantly greater than zero. The cos⁡(2⁢𝜙*) modulations were found to be consistent with zero. The higher statistical precision of this dataset of about 20 000 individual multiplicity values, compared with previously published data, should allow improved determinations of quark transverse momentum distributions and higher twist contributions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2016

Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication

Multiplication of a sparse matrix with a dense matrix is a building block of an increasing number of applications in many areas such as machine learning and graph algorithms. However, most previous work on parallel matrix multiplication considered only both dense or both sparse matrix operands. This paper analyzes the communication lower bounds and compares the communication costs of various classic parallel algorithms in the context of sparse-dense matrix-matrix multiplication. We also present new communication-avoiding algorithms based on a 1D decomposition, called 1.5D, which - while suboptimal in dense-dense and sparse-sparse cases - outperform the 2D and 3D variants both theoretically and in practice for sparse-dense multiplication. Our analysis separates one-time costs from per iteration costs in an iterative machine learning context. Experiments demonstrate speedups up to 100x over a baseline 3D SUMMA implementation and show parallel scaling over 10 thousand cores.

Koanantakool, Penporn↗

DOE OSTI2020

Cooperative Load Scheduling for Multiple Aggregators Using Hierarchical ADMM

Demand response (DR) serves an important role in improving the efficiency and stability of power systems. In recent years, with advances in communication and smart device technologies, many aggregators have emerged to facilitate end customer participation in DR programs. These aggregators, equipped with customized optimal control algorithms, are capable of providing various grid services. Among them is load scheduling during DR events, namely following a load signal provided by the utility company while minimizing overall customer discomfort. However, as the number of aggregators keeps increasing, it becomes challenging for utility companies to conduct load scheduling for multiple aggregators and generate reference signals for each of them. This paper proposes an optimization framework using hierarchical alternating direction method of multipliers (H-ADMM) to optimally generate load following signals for multiple aggregators. Under this framework, utility and multiple aggregators work in a cooperative manner, aiming at minimizing an overall system cost from different levels of the power system hierarchy, while protecting user privacy. A case study has been conducted in a system with multiple aggregators, based on control of HVAC loads. Experimental results validate the effectiveness of the proposed algorithm.

ADMM↗