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At least 505 records · Page 28

Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by ( R )-muscone and diverse other musk-smelling compounds

Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral ( R )-muscone and other musk-smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties. We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds. OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants. The experimentally found chiral selectivity of OR5AN1 to ( R )- over ( S )-muscone was also computationally confirmed for muscone and fluorinated ( R )-muscone analogs. Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane α-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194, and Phe207. As a result, the binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206. Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure–activity relationship model.

59 BASIC BIOLOGICAL SCIENCES↗

A non-intrusive parallel-in-time approach for simultaneous optimization with unsteady PDEs

This paper presents a non-intrusive framework for integrating existing unsteady partial differential equation (PDE) solvers into a parallel-in-time simultaneous optimization algorithm. The time-parallelization is provided by the non-intrusive software library XBraid [Parallel multigrid in time, software available at http://llnl.gov/casc/xbraid], which applies an iterative multigrid reduction technique to the time domain of existing time-marching schemes for solving unsteady PDEs. Its general user-interface has been extended in [S. Günther, N.R. Gauger, and J.B. Schroder, A non-intrusive parallel-in-time adjoint solver with the XBraid library, Comput. Vis. Sci. 19 (2018), pp. 85–95. Available at arXiv, math.OC/1705.00663] for computing adjoint sensitivities such that gradients of output quantities with respect to design changes can be computed parallel-in-time alongside with the primal PDE solution. In this paper, the primal and adjoint XBraid iterations are embedded into a simultaneous optimization framework, namely the One-shot method. In this method, design updates towards optimality are employed after each state and adjoint update such that optimality and feasibility of the design and the PDE solution are reached simultaneously. Finally, the time-parallel optimization method is validated on an advection-dominated flow control problem which shows significant speedup over a classical time-serial optimization algorithm.

97 MATHEMATICS AND COMPUTING↗

String instability mitigation of adaptive cruise control without modifying control laws: trajectory shaper and parameter estimation

Vehicle automation technologies equip vehicles with adaptive cruise control (ACC) systems, which relieve driving fatigue. However, recent studies have shown that the current ACC systems are string-unstable (i.e., exacerbate traffic congestion). To achieve string stability, most existing studies directly modify the control algorithms of ACC systems. Alternatively, this study proposes a trajectory shaper (TS)-based method, which only modifies the trajectory information of the predecessor vehicle, so that the ego vehicle driven by a string-unstable ACC system leverages the modified trajectory information to achieve string stability. To devise the TS-based method, an offline-online parameter estimation method integrating batch optimization and an extended Kalman filter is applied to estimate the parameters of an ACC system. The proposed TS-based method is cost-effective during implementation, as it avoids modifying existing ACC control algorithms (which entails a complex analysis of control systems and parameter tuning). In conclusion, the effectiveness of the proposed TS-based method is validated through extensive numerical experiments.

33 ADVANCED PROPULSION SYSTEMS↗

Understanding the electromagnetic topology during the ohmic breakdown in tokamaks considering self-generated electric fields

We report that the physical mechanisms of the ohmic breakdown in a tokamak have been understood based on the classical Townsend avalanche theory. However, a new systematic theory (Yoo et al 2018 Nat. Commun.9 3523) recently demonstrated that electron avalanches during the ohmic breakdown are completely different from the Townsend avalanche due to strong self-generated electric fields. In this study, we elucidate the multi-dimensional effects of the self-generated electric field on plasma dynamics during the ohmic breakdown. We also propose a novel electromagnetic topology analysis method that can easily predict the overall plasma behavior and where the main plasma is generated. The topology analysis method is validated by a state-of-art particle simulation for various magnetic configurations. New physical insights into the complex electromagnetic topology would facilitate designing more reliable and optimized ohmic breakdown scenarios in future tokamaks, such as ITER and beyond.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fast physics-based launcher optimization for electron cyclotron current drive

With the increased urgency to design fusion pilot plants, fast optimization of electron cyclotron current drive (ECCD) launchers is paramount. Traditionally, this is done by coarsely sampling the 4D parameter space of possible launch conditions consisting of (1) the launch location (constrained to lie along the reactor vessel), (2) the launch frequency, (3) the toroidal launch angle, and (4) the poloidal launch angle. For each initial condition, a ray-tracing simulation is performed to evaluate the ECCD efficiency. Unfortunately, this approach often requires a large number of simulations (sometimes millions in extreme cases) to build up a dataset that adequately covers the plasma volume, which must then be repeated every time the design point changes. Here we adopt a different approach. Rather than launching rays from the plasma periphery and hoping for the best, we instead directly reconstruct the optimal ray for driving current at a given flux surface using a reduced physics model coupled with a commercial ray-tracing code. Repeating this throughout the plasma volume requires only hundreds of simulations, constituting a significant speedup. The new method is validated on two separate example tokamak profiles, and is shown to reliably drive localized current at the specified flux surface with the same optimal efficiency as obtained from the traditional approach.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimizing the use of pressurized bladders for the assembly of HL-LHC MQXFB magnets

The use of pressurized bladders for stress control of superconducting magnets was firstly proposed at Lawrence Berkeley National Laboratory in the early 2000s. Since then, the so-called ‘bladders and keys’ procedure has become one of the reference techniques for the assembly of high-field accelerator magnets and demonstrators. Exploiting the advantages of this method is today of critical importance for Nb$_{3}$Sn-based accelerator magnets, whose production requires the preservation of tight stress targets in the superconducting coils to limit the effects of the strain sensitivity and brittleness of the conductor. The present manuscript reports on the results of an experimental campaign focused on the optimization of the ‘bladders and keys’ assembly process in the MQXFB quadrupoles. These 7.2 m long magnets shall be among the first Nb$_{3}$Sn cryomagnets to be installed in a particle accelerator as a part of the High Luminosity upgrade of the LHC. One of the main practical implications of the bladders technique, especially important when applied to long magnets like MQXFB, is that to insert the loading keys, the opening of a certain clearance in the support structure is required. The procedure used so far for MQXF magnets involved an overstress in the coils during bladder inflation. The work presented here shows that such an overshoot can be eliminated thanks to additional bladders properly positioned in the structure. This optimized method was validated in a short model magnet and in a full-length mechanical model, becoming the new baseline for the series production at CERN. Furthermore, the results are supported by numerical predictions using finite element models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measurement of the dipole in the cross-correlation function of galaxies

It is usually assumed that in the linear regime the two-point correlation function of galaxies contains only a monopole, quadrupole and hexadecapole. Looking at cross-correlations between different populations of galaxies, this turns out not to be the case. In particular, the cross-correlations between a bright and a faint population of galaxies contain also a dipole. In this paper we present the first attempt to measure this dipole. We discuss the four types of effects that contribute to the dipole: relativistic distortions, evolution effect, wide-angle effect and large-angle effect. We show that the first three contributions are intrinsic anti-symmetric contributions that do not depend on the choice of angle used to measure the dipole. On the other hand the large-angle effect appears only if the angle chosen to extract the dipole breaks the symmetry of the problem. We show that the relativistic distortions, the evolution effect and the wide-angle effect are too small to be detected in the LOWz and CMASS sample of the BOSS survey. On the other hand with a specific combination of angles we are able to measure the large-angle effect with high significance. We emphasise that this large-angle dipole does not contain new physical information, since it is just a geometrical combination of the monopole and the quadrupole. However this measurement, which is in excellent agreement with theoretical predictions, validates our method for extracting the dipole from the two-point correlation function and it opens the way to the detection of relativistic effects in future surveys like e.g. DESI.

79 ASTRONOMY AND ASTROPHYSICS↗

Weighted FFT estimators for 1D and 3D correlations of the Lyman- α forest

Correlations in the Lyman-α (Lyα) forest, both as a function of line of sight separation (1D) and 3D separation, provide a unique window to the distribution of matter at redshifts not accessible by current galaxy surveys. While optimal quadratic estimators have been used to measure 1D correlations, they are computationally expensive and difficult to extend to 3D analyses. On the other hand, estimators based on the Fast Fourier Transform (FFT) are significantly faster, but are affected by missing data in the spectra (masked pixels) and so far have not used pixel weights to reduce the uncertainties in the measurement. In this publication we describe how to compute the window matrix that enables forward-modelling the impact of masked pixels and weights on the FFT-based estimators. Here, we use Gaussian and hydrodynamical simulations with artificially masked pixels to validate the method on the measurement of 1D correlations. Finally, we show that the formalism can be extended to model the impact on 3D correlations, in particular on the cross-spectrum, the correlation of 1D Fourier modes as a function of transverse separation. This work will enable more precise clustering measurements with the Lyα forest dataset recently collected by the Dark Energy Spectroscopic Instrument (DESI).

Lokken, Martine [Univ. Autonoma de Barcelona (Spai↗

Summary of the 5th IAEA technical meeting on fusion data processing, validation and analysis (FDPVA)

The purpose of the 5th International Atomic Energy Agency technical meeting on fusion data processing, validation and analysis (FDPVA) (Ghent University, Ghent, Belgium, 12–15 June 2023) was to provide a platform during which a set of topics relevant to FDPVA were discussed with the view of meeting the needs of next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucial for a knowledge-based understanding of the physical processes governing the dynamics of these plasmas. This paper presents the recent progress and achievements in the domain of plasma diagnostics data analysis and synthetic diagnostics reported at the meeting, including concept description of new devices; fusion databases; integrated data analysis; inverse problems; uncertainty propagation, verification and validation; probabilistic methods and machine learning. The relevant results underline trends observed in the current major fusion confinement devices.

fusion databases↗

Identification of hadronic tau lepton decays using a deep neural network

A new algorithm is presented to discriminate reconstructed hadronic decays of tau leptons ($\tau_\mathrm{h}$) that originate from genuine tau leptons in the CMS detector against $\tau_\mathrm{h}$ candidates that originate from quark or gluon jets, electrons, or muons. The algorithm inputs information from all reconstructed particles in the vicinity of a $\tau_\mathrm{h}$ candidate and employs a deep neural network with convolutional layers to efficiently process the inputs. This algorithm leads to a significantly improved performance compared with the previously used one. For example, the efficiency for a genuine $\tau_\mathrm{h}$ to pass the discriminator against jets increases by 10-30% for a given efficiency for quark and gluon jets. Furthermore, a more efficient $\tau_\mathrm{h}$ reconstruction is introduced that incorporates additional hadronic decay modes. The superior performance of the new algorithm to discriminate against jets, electrons, and muons and the improved $\tau_\mathrm{h}$ reconstruction method are validated with LHC proton-proton collision data at $\sqrt{s} =$ 13 TeV.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with approximately 300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. Here, we assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. 405 samples of the four species, representing 57 populations, were subjected to RADseq. Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Differences in fitness between genets was estimated as the numbers of ramets each genet comprised. Degree of clonality (numbers of genets/numbers of ramets [samples]) within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but 2-8 ramets were detected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St. Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets, and sexes were not detected. Within S. divinum, however, female gametophytes harbored 2-3 times the number oi of microbial taxa as males. These four Sphagnum species all exhibit a similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns where genets abut one another but do not extensively mix, because of limited ramet fragmentation, and the guerrilla patterns where extensive genet fragmentation and dispersal results in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

59 BASIC BIOLOGICAL SCIENCES↗

Detection of small earthquakes with dense array data: example from the San Jacinto fault zone, southern California

We present a technique to detect small earthquakes not included in standard catalogues using data from a dense seismic array. The technique is illustrated with continuous waveforms recorded in a test day by 1108 vertical geophones in a tight array on the San Jacinto fault zone. Waveforms are first stacked without time-shift in nine non-overlapping subarrays to increase the signal-to-noise ratio. The nine envelope functions of the stacked records are then multiplied with each other to suppress signals associated with sources affecting only some of the nine subarrays. Running a short-term moving average/long-term moving average (STA/LTA) detection algorithm on the product leads to 723 triggers in the test day. Using a local P-wave velocity model derived for the surface layer from Betsy gunshot data, 5 s long waveforms of all sensors around each STA/LTA trigger are beamformed for various incident directions. Of the 723 triggers, 220 are found to have localized energy sources and 103 of these are confirmed as earthquakes by verifying their observation at 4 or more stations of the regional seismic network. This demonstrates the general validity of the method and allows processing further the validated events using standard techniques. The number of validated events in the test day is >5 times larger than that in the standard catalogue. Using these events as templates can lead to additional detections of many more earthquakes.

58 GEOSCIENCES↗

SPIDERS: an overview of the largest catalogue of spectroscopically confirmed x-ray galaxy clusters

SPIDERS is the spectroscopic follow-up effort of the Sloan Digital Sky Survey IV (SDSS-IV) project for the identification of X-ray selected galaxy clusters. We present our catalogue of 2740 visually inspected galaxy clusters as part of the SDSS Data Release 16 (DR16). Here we detail the target selection, our methods for validation of the candidate clusters, performance of the survey, the construction of the final sample, and a full description of what is found in the catalogue. Of the sample, the median number of members per cluster is approximately 10, with 818 having 15 or greater. We find that we are capable of validating over 99 per cent of clusters when five redshifts are obtained below z < 0.3 and when nine redshifts are obtained above z > 0.3. We discuss the improvements in this catalogue’s identification of cluster using 33 340 redshifts, with Δz phot /Δz spec ~100, over other photometric and spectroscopic surveys, as well as presenting an update to previous (σ–L X ) and (σ– λ ) relations. Finally, we present our cosmological constraints derived using the velocity dispersion function.

79 ASTRONOMY AND ASTROPHYSICS↗

Angular clustering properties of the DESI QSO target selection using DR9 Legacy Imaging Surveys

ABSTRACT The quasar target selection for the upcoming survey of the Dark Energy Spectroscopic Instrument (DESI) will be fixed for the next 5 yr. The aim of this work is to validate the quasar selection by studying the impact of imaging systematics as well as stellar and galactic contaminants, and to develop a procedure to mitigate them. Density fluctuations of quasar targets are found to be related to photometric properties such as seeing and depth of the Data Release 9 of the DESI Legacy Imaging Surveys. To model this complex relation, we explore machine learning algorithms (random forest and multilayer perceptron) as an alternative to the standard linear regression. Splitting the footprint of the Legacy Imaging Surveys into three regions according to photometric properties, we perform an independent analysis in each region, validating our method using extended Baryon Oscillation Spectroscopic Survey (eBOSS) EZ-mocks. The mitigation procedure is tested by comparing the angular correlation of the corrected target selection on each photometric region to the angular correlation function obtained using quasars from the Sloan Digital Sky Survey (SDSS) Data Release 16. With our procedure, we recover a similar level of correlation between DESI quasar targets and SDSS quasars in two-thirds of the total footprint and we show that the excess of correlation in the remaining area is due to a stellar contamination that should be removed with DESI spectroscopic data. We derive the Limber parameters in our three imaging regions and compare them to previous measurements from SDSS and the 2dF QSO Redshift Survey.

79 ASTRONOMY AND ASTROPHYSICS↗

Combined full shape analysis of BOSS galaxies and eBOSS quasars using an iterative emulator

ABSTRACT Standard full-shape clustering analyses in Fourier space rely on a fixed power spectrum template, defined at the fiducial cosmology used to convert redshifts into distances, and compress the cosmological information into the Alcock–Paczynski parameters and the linear growth rate of structure. In this paper, we propose an analysis method that operates directly in the cosmology parameter space and varies the power spectrum template accordingly at each tested point. Predictions for the power spectrum multipoles from the TNS model are computed at different cosmologies in the framework of $\Lambda \rm {CDM}$. Applied to the final eBOSS QSO and LRG samples together with the low-z DR12 BOSS galaxy sample, our analysis results in a set of constraints on the cosmological parameters Ωcdm, H0, σ8, Ωb, and ns. To reduce the number of computed models, we construct an iterative process to sample the likelihood surface, where each iteration consists of a Gaussian process regression. This method is validated with mocks from N-body simulations. From the combined analysis of the (e)BOSS data, we obtain the following constraints: σ8 = 0.877 ± 0.049 and $\Omega _{\rm m}=0.304^{+0.016}_{-0.010}$ without any external prior. The eBOSS quasar sample alone shows a 3.1σ discrepancy compared to the Planck prediction.

79 ASTRONOMY AND ASTROPHYSICS↗

Testing the lognormality of the galaxy and weak lensing convergence distributions from Dark Energy Survey maps

It is well known that the probability distribution function (PDF) of galaxy density contrast is approximately lognormal; whether the PDF of mass fluctuations derived from weak lensing convergence (kappa_WL) is lognormal is less well established. We derive PDFs of the galaxy and projected matter density distributions via the Counts in Cells (CiC) method. We use maps of galaxies and weak lensing convergence produced from the Dark Energy Survey (DES) Science Verification data over 139 deg^2. We test whether the underlying density contrast is well described by a lognormal distribution for the galaxies, the convergence and their joint PDF. We confirm that the galaxy density contrast distribution is well modeled by a lognormal PDF convolved with Poisson noise at angular scales from 10-40 arcmin (corresponding to physical scales of 3-10 Mpc). We note that as kappa_WL is a weighted sum of the mass fluctuations along the line of sight, its PDF is expected to be only approximately lognormal. We find that the kappa_WL distribution is well modeled by a lognormal PDF convolved with Gaussian shape noise at scales between 10 and 20 arcmin, with a best-fit chi^2/DOF of 1.11 compared to 1.84 for a Gaussian model, corresponding to p-values 0.35 and 0.07 respectively, at a scale of 10 arcmin. Above 20 arcmin a simple Gaussian model is sufficient. The joint PDF is also reasonably fitted by a bivariate lognormal. As a consistency check we compare the variances derived from the lognormal modelling with those directly measured via CiC. Our methods are validated against maps from the MICE Grand Challenge N-body simulation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Time Correlations from Steady-State Expectation Values

Recovering properties of correlation functions is typically challenging. On the one hand, experimentally, it requires measurements with a temporal resolution finer than the system’s dynamics. On the other hand, analytical or numerical analysis requires solving the system evolution. Here, we use recent results of quantum metrology with continuous measurements to derive general lower bounds on the relaxation and second-order correlation times that are both easy to calculate and measure. These bounds are based solely on steady-state expectation values and their derivatives with respect to a system parameter, and can be readily extended to the autocorrelation of arbitrary observables. We validate our method on two examples of critical quantum systems: a critical driven-dissipative resonator, where the bound matches analytical results for the dynamics, and the infinite-range Ising model, where only the steady state is solvable, and thus the bound provides information beyond the reach of existing analytical approaches. Our results can be applied to the experimental characterization of ultrafast systems and to the theoretical analysis of many-body models whose dynamics are hard to compute.

Górecki, Wojciech [INFN, Pavia] (ORCID:00000001991↗

Quarkonium Spectroscopy in the Quark-Gluon Plasma

The properties of bound states are fundamental to hadronic spectroscopy and play a central role in the transition from hadronic matter to a quark-gluon plasma (QGP). In a strongly coupled QGP (sQGP), the interplay of temperature, binding energy, and large collisional widths of the partons poses formidable challenges in evaluating the in-medium properties of hadronic states and their eventual melting. In particular, the existence of heavy quarkonia in the QGP is a long-standing problem that is hard to solve by considering their spectral properties on the real-energy axis. Here, we address this problem by analyzing in-medium thermodynamic quarkonium 𝑇 matrices in the complex energy plane. We first validate this method in vacuum, where the 𝑇-matrix poles of observed states are readily identified. When deploying this approach to recent self-consistently calculated 𝑇 matrices in the QGP, we find that poles in the complex energy plane can persist to surprisingly large temperatures, depending on the strength of the in-medium interactions. While the masses and widths of the pole positions are precisely defined, the notion of a binding energy is not due to the absence of thresholds caused by the (large) widths of the underlying quark or anti-quark spectral functions. Our method thus provides a new and definitive quantum-mechanical criterion to determine the melting temperature of hadronic states in the sQGP while increasing the accuracy in the theoretical determination of transport parameters.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗