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At least 919 records · Page 51

Vibronic mixing enables ultrafast energy flow in light-harvesting complex II

Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from electronic-vibrational mixing, however, it remains uncertain if such mixing significantly influences energy transport. Here, we examine the interplay between the electronic and nuclear degrees of freedom (DoF) during the excitation energy transfer (EET) dynamics of light-harvesting complex II (LHCII) with two-dimensional electronic-vibrational spectroscopy. Particularly, we show the involvement of the nuclear DoF during EET through the participation of higher-lying vibronic chlorophyll states and assign observed oscillatory features to specific EET pathways, demonstrating a significant step in mapping evolution from energy to physical space. These frequencies correspond to known vibrational modes of chlorophyll, suggesting that electronic-vibrational mixing facilitates rapid EET over moderately size energy gaps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Programmable interactions and emergent geometry in an array of atom clouds

Interactions govern the flow of information and the formation of correlations between constituents of many-body quantum systems, dictating phases of matter found in nature and forms of entanglement generated in the laboratory. Typical interactions decay with distance and thus produce a network of connectivity governed by geometry—such as the crystalline structure of a material or the trapping sites of atoms in a quantum simulator. However, many envisioned applications in quantum simulation and computation require more complex coupling graphs including non-local interactions, which feature in models of information scrambling in black hole, and mappings of hard optimization problems onto frustrated classical magnets. Here we describe the realization of programmable non-local interactions in an array of atomic ensembles within an optical cavity, in which photons carry information between atomic spins. By programming the distance dependence of the interactions, we access effective geometries for which the dimensionality, topology and metric are entirely distinct from the physical geometry of the array. As examples, we engineer an antiferromagnetic triangular ladder, a Möbius strip with sign-changing interactions and a treelike geometry inspired by concepts of quantum gravity. The tree graph constitutes a toy model of holographic duality, in which the quantum system lies on the boundary of a higher-dimensional geometry that emerges from measured correlations. Overall, our work provides broader prospects for simulating frustrated magnets and topological phases, investigating quantum optimization paradigms and engineering entangled resource states for sensing and computation.

74 ATOMIC AND MOLECULAR PHYSICS↗

Physics consistent machine learning framework for inverse modeling with applications to ICF capsule implosions

In high energy density physics (HEDP) and inertial confinement fusion (ICF), predictive modeling is complicated by uncertainty in parameters that characterize various aspects of the modeled system, such as those characterizing material properties, equation of state (EOS), opacities, and initial conditions. Typically, however, these parameters are not directly observable. What is observed instead is a time sequence of radiographic projections using X-rays. In this work, we define a set of sparse hydrodynamic features derived from the outgoing shock profile and outer material edge, which can be obtained from radiographic measurements, to directly infer such parameters. Our machine learning (ML)-based methodology involves a pipeline of two architectures, a radiograph-to-features network (R2FNet) and a features-to-parameters network (F2PNet), that are trained independently and later combined to approximate a posterior distribution for the parameters from radiographs. We show that the machine learning architectures are able to accurately infer initial conditions and EOS parameters, and that the estimated parameters can be used in a hydrodynamics code to obtain density fields, shocks, and material interfaces that satisfy thermodynamic and hydrodynamic consistency. Finally, we demonstrate that features resulting from an unknown EOS model can be successfully mapped onto parameters of a chosen analytical EOS model, implying that network predictions are learning physics, with a degree of invariance to the underlying choice of EOS model. To the best of our knowledge, our framework is the first demonstration of recovering both thermodynamic and hydrodynamic consistent density fields from noisy radiographs.

97 MATHEMATICS AND COMPUTING↗

Cis-regulatory evolution shapes facial diversity in birds and mammals

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Kyomen, Stella [Max Planck Institute for Evolution↗

CEGANN: CRYSTAL EDGE GRAPH ATTENTION NEURAL NETWORK

SF-22-156 Machine learning (ML) models and applications in materials design and discovery typically involve the use of feature representations or descriptors followed by a learning algorithm that maps them to user desired properties of interest. Most popular mathematical formulation-based descriptors are not unique across atomic environments and suffer from transferability issues across different application domains and/or material classes. The CEGANN code provides a unified interface to facilitate material characterization across materials across multiple scales (from atomic to mesoscale) and diverse classes of materials ranging from metals oxides, non-metals, and even hierarchical materials such as zeolites and semi ordered materials such as mesophases. CEGANN implements a Graph Attention Network (GAT) type convolution architecture. The details of network architecture can be found in the paper https://doi.org/10.48550/arXiv.2207.10168. The software comes with pretrained examples and dataset for the classification of the following representative systems: (1) Structure-level representation such as space group (2) Structural dimensionality (e.g., bulk, 2D, clusters etc.) (3) Grain boundary identification (4) Nucleation and growth of a zeolite polymorph (5) Characterization of binary mesophases and their phase transitions (6) Growth of ice. The code is written in python programming language.

CHAN, HENRYT↗

classLog: Logistic regression for the classification of genetic sequences

Introduction Sequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in realtime genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference. Methods We present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output rapidly, even with incomplete data. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A virus (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%. Results When applied to a poor-quality sequence data, the classifier achieved between >85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations. Discussion Our approach is implemented as a python package with code available at https://github.com/flu-crew/classLog .

Zeller, Michael A.↗

Open-Source Data Analysis Tool for Spectral Small-Angle X-ray Scattering Using Spectroscopic Photon-Counting Detector

Spectral small-angle X-ray scattering (sSAXS) is a powerful technique for material characterization from thicker samples by capturing elastic X-ray scattering data in angle- and energy-dispersive modes at small angles. This approach is enabled by the use of a 2D spectroscopic photon-counting detector that provides energy and position information of scattered photons when a sample is irradiated by a polychromatic X-ray beam. Here, we describe an open-source tool with a graphical interface for analyzing sSAXS data obtained from a 2D spectroscopic photon-counting detector with a large number of energy bins. The tool takes system geometry parameters and raw detector data to output 1D scattering patterns and a 2D spatially-resolved scattering map in the energy range of interest. We validated these features using data from samples of caffeine powder with well-known scattering peaks. This open-source tool will facilitate sSAXS data analysis for various material characterization applications.

Chemistry↗

MEGASIM: Distribution and Detection of Earth Trojan Asteroids

Abstract Using N -body simulation results from the MEGASIM data set, we present spatial distributions of Earth Trojan Asteroids and assess the detectability of the population in current and next-generation ground-based astronomical surveys. Our high-fidelity Earth Trojan Asteroid (ETA) distribution maps show never-before-seen high-resolution spatial features that evolve over timescales up to 1 Gyr. The simulation was synchronized to start times and timelines of two observational astronomy surveys: (1) the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST) and (2) the Zwicky Transient Facility (ZTF). We calculate upper limits for the number of ETAs potentially observable with both the ZTF and LSST surveys. Due to the Yarkovsky Effect, we find no stable ETAs on billion-year timescales likely to be detected by any ETA survey, as no C-type or S-type ETAs (with H < 22 and H < 24, respectively) are likely to be stable on billion-year timescales, and ETAs large enough to remain stable on billion-year timescales are very rare relative to the rest of the ETA population. We find that a twilight ETA survey will not drastically increase the likelihood of individual ETA detection, but it would provide orders of magnitude more observations of select ETA populations. The null detection to date from ZTF restricts the potential ETA population to hundreds of objects larger than 100 m (at H ≈ 22), while a null detection by LSST will further restrict the ETA population to tens of objects larger than 100 m.

79 ASTRONOMY AND ASTROPHYSICS↗

An interdisciplinary analysis of ERTS data for Colorado mountain environments using ADP techniques. An early analysis of ERTS-1 data

There are no author-identified significant results in this report. The principal problem encountered has been the lack of good quality, small scale baseline photography for the test areas. Analysis of the ERTS-1 data for the San Juan Site will emphasize development of a preliminary spectral classification defining grass cover categories, and then selection of subframes for intensive investigation of the forestry, geologic, and hydrologic properties of the area. Primary work has been devoted to the selection and digitization of areas for topographic modeling, and compilation of ground based data maps necessary for computer analysis. Study effort has emphasized: geomorphic features; macro-vegetation; micro-vegetation; snow-hydrology; insect/disease damage; and blow-down. Analysis of a frame of the Lake Texoma area indicates a great deal of potential in the analysis and interpretation of ERTS imagery. Preliminary results of investigations of geologic, forest, range, cropland, and water resources of the area are summarized.

Hoffer, R. M.↗

ERTS-1 evaluation of natural resources management applications in the Great Basin

The relatively cloud free weather in the Great Basin has allowed the accumulation of several dates of excellent ERTS-1 imagery. Mountains, valleys, playas, stream courses, canyons, alluvial fans, and other landforms are readily delineated on ERTS-1 imagery, particularly with MSS-5. Each band is useful for identifying and studying one or more natural resource features. For example, crested wheatgrass seedings were most easily identified and measured on MSS-7. Color enhancements simulating CIR were useful for depicting meadow and phreatophytic vegetation along water bodies and stream courses. Work is underway to inventory and monitor wildfire areas by age and successional status. Inventories have been completed on crested wheatgrass seedings over the entire State of Nevada, and inventories of playa surfaces, water surfaces, phreatophytic vegetation, snow cover, meadows, and other features is continuing. Vegetation ecotones are being delineated for vegetation mapping. The pinyon/juniper-northern desert shrub ecotone has been identified with considerable success. Phenology changes can be used to describe vegetation changes for management.

Tueller, P. T.↗

An evaluation of machine processing techniques of ERTS-1 data for user applications

A broad study is described to evaluate a set of machine analysis and processing techniques applied to ERTS-1 data. Based on the analysis results in urban land use analysis and soil association mapping together with previously reported results in general earth surface feature identification and crop species classification, a profile of general applicability of this procedure is beginning to emerge. Put in the hands of a user who knows well the information needed from the data and also is familiar with the region to be analyzed it appears that significantly useful information can be generated by these methods. When supported by preprocessing techniques such as the geometric correction and temporal registration capabilities, final products readily useable by user agencies appear possible. In parallel with application, through further research, there is much potential for further development of these techniques both with regard to providing higher performance and in new situations not yet studied.

Landgrebe, D.↗

The mixture problem in computer mapping of terrain: Improved techniques for establishing spectral signature, atmospheric path radiance, and transmittance

The results of LANDSAT and Skylab research programs on the effects of the atmosphere on computer mapping of terrain include: (1) the concept of a ground truth map needs to be drastically revised; (2) the concept of training areas and test areas is not as simple as generally thought because of the problem of pixels that represent a mixture of terrain classes; (3) this mixture problem needs to be more widely recognized and dealt with by techniques of calculating spectral signatures of mixed classes, or by other methods; (4) atmospheric effects should be considered in computer mapping of terrain and in monitoring changes; and (5) terrain features may be used as calibration panels on the ground, from which atmospheric conditions can be determined and monitored. Results are presented of a test area in mountainous terrain of south-central Colorado for which an initial classification was made using simulated mixture-class spectral signatures and actual LANDSAT-1-MSS data.

Smedes, H. W.↗

Field trip stop descriptions

Fifteen sites within the channeled scabland were selected as stops with the dual aim of visiting locations critical to the arguments for a catastrophic flood origin of the scablands, as well as permitting an examination of the variability in both erosional and depositional features. The stop locations are plotted on a generalized geologic map and their coordinates are given in table form.

Nummedal, D.↗

Submillimeter observations of the galactic center

A 15 by 15 arcmin region surrounding Sgr A has been mapped at a mean wavelength of 540 microns. The principal feature is a ridge about 10 arcmin long running parallel to the galactic equator and approximately centered on Sgr A but with no peak at that point. The ridge coincides with the 25- and 55-km/s clouds seen in molecular line observations. The mass of the clouds is estimated, and their positions with respect to the galactic center are discussed.

Hildebrand, R. H.↗

Image restoration of high resolution observations of the M87 jet

Image-restoration techniques are applied to high-resolution (FWHM 0.5-1.0 arcsec) plates of the M87 jet obtained with the CFH telescope by Nieto and Lelievre (1982), and their description of the optical jet is confirmed. Most of the features detected are similar to those shown by the VLA map of Biretta et al. (1982), having a resolution of 0.12 arcsec. In particular, the restored images show evidence for an elongated nucleus and for a very sharp discontinuity in knot A which is not perpendicular to the jet axis. It also seems that the start of the oscillations and this discontinuity are not related. This similarity at a 0.2-arcsec scale suggests no relativistic motion (v less than 25,000 km/sec) throughout the jet.

Lorre, J. J.↗

Analysis of data acquired by synthetic aperture radar and LANDSAT Multispectral Scanner over Kershaw County, South Carolina, during the summer season

Data acquired by synthetic aperture radar (SAR) and LANDSAT multispectral scanner (MSS) were processed and analyzed to derive forest-related resources inventory information. The SAR data were acquired by using the NASA aircraft X-band SAR with linear (HH, VV) and cross (HV, VH) polarizations and the SEASAT L-band SAR. After data processing and data quality examination, the three polarization (HH, HV, and VV) data from the aircraft X-band SAR were used in conjunction with LANDSAT MSS for multisensor data classification. The results of accuracy evaluation for the SAR, MSS and SAR/MSS data using supervised classification show that the SAR-only data set contains low classification accuracy for several land cover classes. However, the SAR/MSS data show that significant improvement in classification accuracy is obtained for all eight land cover classes. These results suggest the usefulness of using combined SAR/MSS data for forest-related cover mapping. The SAR data also detect several small special surface features that are not detectable by MSS data.

Wu, S. T.↗

On the use of potential vorticity for the diagnosis of stratospheric synoptics

According to quasi-geostrophic approximation, regions of strong cross flow gradient of geopotential vortivity support Rossby wave propagation. Using potential vorticity as a dynamical tracer, the polar vortex can be considered as a material entity. In addition to synoptic charts of geopotential heights and temperatures, maps of potential vorticity are used to describe some distinct features of the circulation of the winter stratosphere.

Rose, K.↗