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A Survey of Collectives

Due to the increasing sophistication and miniaturization of computational components, complex, distributed systems of interacting agents are becoming ubiquitous. Such systems, where each agent aims to optimize its own performance, but where there is a well-defined set of system-level performance criteria, are called collectives. The fundamental problem in analyzing/designing such systems is in determining how the combined actions of self-interested agents leads to 'coordinated' behavior on a iarge scale. Examples of artificial systems which exhibit such behavior include packet routing across a data network, control of an array of communication satellites, coordination of multiple deployables, and dynamic job scheduling across a distributed computer grid. Examples of natural systems include ecosystems, economies, and the organelles within a living cell. No current scientific discipline provides a thorough understanding of the relation between the structure of collectives and how well they meet their overall performance criteria. Although still very young, research on collectives has resulted in successes both in understanding and designing such systems. It is eqected that as it matures and draws upon other disciplines related to collectives, this field will greatly expand the range of computationally addressable tasks. Moreover, in addition to drawing on them, such a fully developed field of collective intelligence may provide insight into already established scientific fields, such as mechanism design, economics, game theory, and population biology. This chapter provides a survey to the emerging science of collectives.

Tumer, Kagan↗

Asteroid 2008 TC3 Breakup and Meteorite Fractions

The recovery of meteorites from the impact of asteroid 2008 TC3 in the Nubian Desert of Sudan on October 7, 2008, marked the first time meteorites were collected from an asteroid observed in space by astronomical techniques before impacting. Search teams from the University of Khartoum traced the location of the strewn field and collected about 660 meteorites in four expeditions to the fall region, all of which have known fall coordinates. Upon further study, the Almahata Sitta meteorites proved to be a mixed bag of mostly ureilites (course grained, fine grained, and sulfide-metal assemblages), enstatite chondrites (EL3-6, EH3, EH5, breccias) and ordinary chondrites (H5-6, L4-5). One bencubbinite-like carbonaceous chondrite was identified, as well as one unique Rumuruti-like chondrite and an Enstatite achondrite. New analysis: The analysed meteorites so far suggest a high 30-40 percent fraction of non-ureilites among the recovered samples, but that high fraction does not appear to be in agreement with the meteorites in the University of Khartoum (UoK) collection. Ureilites dominate the meteorites that were recovered by the Sudanese teams. To better understand the fraction of recovered materials that fell to Earth, a program has been initiated to type the meteorites in the UoK collection in defined search areas. At this meeting, we will present some preliminary results from that investigation.

Goodrich, C.↗

Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon

Abstract Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

High-order cumulants and correlation functions near the critical point from molecular dynamics

We present a systematic investigation of particle-number fluctuations in the crossover region near the critical end point of a first-order phase transition using molecular dynamics simulations of the classical Lennard-Jones fluid. We extend our prior studies to third- and fourth-order cumulants in both coordinate- and momentum-space acceptances and integrated correlation functions (factorial cumulants). We find that, even near the critical point, non-Gaussian cumulants equilibrate on timescales comparable to those of the second-order cumulants, but show stronger finite-size effects. The presence of interactions and of the critical point leads to strong deviations of the cumulants from the ideal-gas baseline in coordinate space; these deviations are expected to persist in momentum space in the presence of collective expansion. In particular, the kurtosis becomes strongly negative, κσ 2 ≪ − 1 , on the crossover side of the critical point. However, this signal is significantly diluted once an efficiency cut used to distinguish protons from baryons is applied, leading to |κσ 2 | ≲ 1 even in the presence of the critical point. We discuss our results in the context of ongoing measurements of proton-number cumulants in heavy-ion collisions in RHIC-BES-II.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SeaWiFS Technical Report Series. Volume 8: Proceedings of the First SeaWiFS Science Team Meeting

The first meeting of the SeaWiFS Science Team was held in preparation for a launch of the SeaStar satellite carrying the SeaWiFS ocean color scanner in the October 1993 time frame. The primary goals of the meeting were: (1) to brief Science Team members, agency representatives, and international collaborators on the status of the mission by representatives from the SeaWiFS Project, the prime contractor Orbital Sciences Corporation (OSC), and the Goddard Distributed Active Archive Center (DAAC); (2) to provide for briefings on the science investigations undertaken by Science Team members and to solicit comments and recommendations from meeting attendees for improvements; and (3) to improve coordination of research and validation activities both inter- and intra-nationally with respect to collection, validation, and application of ocean color data from the SeaWiFS mission. Presentations and recommendations are summarized.

Hooker, Stanford B.↗

A study of lightning in winter thunderstorms and the analysis of thunderstorm overflight data

Thunderstorms and the activities associated with them was the emphasis of this final report. The primary goal of the investigation of the dynamics, microphysics, and the electrical properties of tropical thunderstorms, was to understand the process or processes which initiate the precipitation in various convective clouds. A concept that the degree of atmospheric instability that determines the updraft velocity is different between those storms that generate electrical activity and those that do not. This is apparent in temperate latitudes, but in tropical regions, little knowledge of these interactions is available. Several ground monitoring stations have been set up and, along with a waveform recorder at one of the stations, the data collected from these stations will be analyzed in conjunction with other data collected from ship and airborne radars and airborne in situ measurements of electrical activity in coordination with the TOGA-COARE program.

Brook, Marx↗

GPS Modeling and Analysis. Summary of Research: GPS Satellite Axial Ratio Predictions

This report outlines the algorithms developed at the Colorado Center for Astrodynamics Research to model yaw and predict the axial ratio as measured from a ground station. The algorithms are implemented in a collection of Matlab functions and scripts that read certain user input, such as ground station coordinates, the UTC time, and the desired GPS (Global Positioning System) satellites, and compute the above-mentioned parameters. The position information for the GPS satellites is obtained from Yuma almanac files corresponding to the prescribed date. The results are displayed graphically through time histories and azimuth-elevation plots.

Axelrad, Penina↗

Space Reclamation for Uncoordinated Checkpointing in Message-Passing Systems

Checkpointing and rollback recovery are techniques that can provide efficient recovery from transient process failures. In a message-passing system, the rollback of a message sender may cause the rollback of the corresponding receiver, and the system needs to roll back to a consistent set of checkpoints called recovery line. If the processes are allowed to take uncoordinated checkpoints, the above rollback propagation may result in the domino effect which prevents recovery line progression. Traditionally, only obsolete checkpoints before the global recovery line can be discarded, and the necessary and sufficient condition for identifying all garbage checkpoints has remained an open problem. A necessary and sufficient condition for achieving optimal garbage collection is derived and it is proved that the number of useful checkpoints is bounded by N(N+1)/2, where N is the number of processes. The approach is based on the maximum-sized antichain model of consistent global checkpoints and the technique of recovery line transformation and decomposition. It is also shown that, for systems requiring message logging to record in-transit messages, the same approach can be used to achieve optimal message log reclamation. As a final topic, a unifying framework is described by considering checkpoint coordination and exploiting piecewise determinism as mechanisms for bounding rollback propagation, and the applicability of the optimal garbage collection algorithm to domino-free recovery protocols is demonstrated.

Wang, Yi-Min↗

Laboratory time series moisture manipulative experiment from sediment across the contiguous US: time series aerobic respiration and geochemistry (v2)

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration across the contiguous United States (CONUS). The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS CONUS-Scale Model-Sample Study (CM). This study was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. The data package associated with the CM study is available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689. CM sampling began in April 2022 and ended in October 2023. This study uses subsamples from a subset of CM samples collected between June 2022 and June 2023. The original field samples were labeled as CM_###. Subsequent subsamples for this study were labeled as EC_###. The labels from the field samples and the EC subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EC_001 is a subsample from CM_001). See the critical details section below for more details on sample naming. This data package was originally published in August 2024. It was updated in February 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate this data package, see this infographic from the River Corridor SFA https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) adenosine triphosphate (ATP); (4) percent carbon and nitrogen; (5) effect size; (6) iron (II); (7) gravimetric moisture; (8) respiration rates and raw dissolved oxygen values; (9) specific conductance; (10) pH; (11) temperature; (12) a summary containing median values of each data type for each treatment (wet and dry); (13) methods codes; (14) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla FTICR-MS data. This folder contains three subfolders, one containing the sediment .xml data files, one containing the sediment CoreMS output files, the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

Assimilation of a Coordinated Fleet of Uncrewed Aircraft System Observations in Complex Terrain: EnKF System Design and Preliminary Assessment

Abstract Uncrewed aircraft system (UAS) observations collected during the 2018 Lower Atmospheric Process Studies at Elevation—a Remotely Piloted Aircraft Team Experiment (LAPSE-RATE) field campaign were assimilated into a high-resolution configuration of the Weather Research and Forecasting Model using an ensemble Kalman filter. The benefit of UAS observations was assessed for a terrain-driven (drainage and upvalley) flow event that occurred within Colorado’s San Luis Valley (SLV) using independent observations. The analysis and prediction of the strength, depth, and horizontal extent of drainage flow from the Saguache Canyon and the subsequent transition to upvalley and up-canyon flow were improved relative to that obtained both without data assimilation (benchmark) and when only surface observations were assimilated. Assimilation of UAS observations greatly improved the analyses of vertical variations in temperature, relative humidity, and winds at multiple locations in the northern portion of the SLV, with reductions in both bias and the root-mean-square error of roughly 40% for each variable relative to the benchmark run. Despite these noted improvements, some biases remain that were tied to measurement error and/or the impact of the boundary layer parameterization on vertically spreading the observations, both of which require further exploration. The results presented here highlight how observations obtained with a fleet of profiling UAS improve limited-area, high-resolution analyses and short-term forecasts in complex terrain.

54 ENVIRONMENTAL SCIENCES↗

ORNL_AISD_NiPt

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for three different sizes of the crystal structure: 256 atoms, 864 atoms, and 2,048 atoms, each of which contains 1900 configurations. For each size of the crystal structure, the data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in three compressed zipped folders: atoms256.zip, atoms864.zip, atoms2048.zip Each zipped folder contains the data that describes crystals of size 256 atoms, 864 atoms, and 2,048 atoms respectively. Each one of the three zipped folders contains the data structured in the following way: -Ni_ground_state.cfg --> atomic configuration for the pure nickel -Pt_ground_state.cfg --> atomic configuration for the pure platinum -Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder. Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms256.zip is 65,046. The total number of atomic configurations contained in atoms864.zip is 63,936. The total number of atomic configurations contained in atoms2048.zip is 61,997. The total number of atomic configurations spanned by the entire dataset is 190,979. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büccchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D

36 MATERIALS SCIENCE↗

ORNL_AISD_NiPt_108atoms

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for crystal structures with 108 atoms with 1,900 configurations. The data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system 'MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001' [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in a compressed zipped folders atoms108.zip. The zipped folder contains the data structured in the following way: - Ni_ground_state.cfg --> atomic configuration for the pure nickel - Pt_ground_state.cfg --> atomic configuration for the pure platinum - Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder - Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms108.zip is 66,132. This dataset is an extension to the dataset ORNL_AISD_NiPt [5] that has been previously released with crystal structures of 256 atoms, 864 atoms, and 2,048 atoms, with the same methodology for data collection. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D [5] M. Karabin, M. Lupo Pasini, and M. Eisenbach. ORNL_AISD_NiPt. United States: N. p., 2023. Web. doi:10.13139/OLCF/1958172.

36 MATERIALS SCIENCE↗

Highly Elliptic Circular Dichroism of Copper Aspartate One-Dimensional Nanostructures across the Ultraviolet to Terahertz Ranges

Since the discovery of chirality, circular dichroism (CD) of mirror-asymmetric molecules has been studied across the ultraviolet, visible, and near-infrared ranges. Recently, chiroptical activity studies have expanded to the terahertz (THz) range, where resonance peaks originate from collective vibrations of tens and hundreds of atoms. Here, in this study, we synthesized Cu 2+ coordination complexes with L- and D-aspartic acid as nanowires and nanorods and characterized their chiroptical activity across multiple frequency ranges. Both chiral nanostructures exhibit strong electronic CD (ECD), primarily from Cu 2+ d-d transitions, while vibrational CD (VCD) spectra show sharp C=O, C–H, and O–H vibronic peaks, indicating higher atomic defect densities in nanorods than nanowires. Although THz CD (TCD) spectra are broad, they exhibit ∼1000× greater ellipticity than ECD and VCD, perhaps warranting previous references to circular dichroism of nanostructures as giant. Comparative TCD analysis highlights strong chiral phonon sensitivity, underscoring its potential for probing defect densities and structural changes for various chiral nanostructures and (bio)crystals.

THz spectroscopy↗

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm’s behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl .

Gorstein, Evan↗

Deriving inertial wave characteristics from surface drifter velocities - Frequency variability in the tropical Pacific

Two techniques were developed for estimating statistics of inertial oscillations from satellite-tracked drifters that overcome the difficulties inherent in estimating such statistics from data dependent upon space coordinates that are a function of time. Application of these techniques to tropical surface drifter data collected during the NORPAX, EPOCS, and TOGA programs reveals a latitude-dependent, statistically significant 'blue shift' of inertial wave frequency. The latitudinal dependence of the blue shift is similar to predictions based on 'global' internal-wave spectral models, with a superposition of frequency shifting due to modification of the effective local inertial frequency by the presence of strongly sheared zonal mean currents within 12 deg of the equator.

Poulain, Pierre-Marie↗

Development of high-accuracy convection schemes for sequential solvers

An exploration is conducted of the applicability of such high resolution schemes as TVD to the resolving of sharp flow gradients using a sequential solution approach borrowed from pressure-based algorithms. It is shown that by extending these high-resolution shock-capturing schemes to a sequential solver that treats the equations as a collection of scalar conservation equations, the speed of signal propagation in the solution has to be coordinated by assigning the local convection speed as the characteristic speed for the entire system. A higher amount of dissipation is therefore needed to eliminate oscillations near discontinuities.

Thakur, Siddharth↗

Comparative measurement of visual stability in Earth and cosmic space (L-4)

The frequency and the intensity of space motion sickness was reviewed and investigated. Unusual induced-gravity situations, such as rotation, linear acceleration, parallel swinging etc. were investigated as well. Visually-induced motion sensation or distorted perception were evaluated with respect to visual stability by many investigators. These studies are all concerned with the effect of gravity and the induction of motion sickness through human visual perception. Direct investigation under the microgravity situation, such as parabolic flight, Skylab, and Spacelab, was carried out. These studies focused on how human visual stability is established through various sensory afferents in specific gravity conditions. Results from these investigations indicate that sensory mismatch probably plays an important role in space motion sickness. The interaction of visual, vestibular, and somatosensory perception is smoothly coordinated under normal gravitational conditions on the Earth in our daily life. When the cooperation is destroyed or a mismatch occurs among them, motion sickness may develop not only on the Earth but also in microgravity. The latter case may be the cause of space motion sickness or space adaption syndrome. How human beings obtain visual stability even with posture changes on the ground was investigated. Visual stability can be categorized as static or dynamic. Static visual stability is concerned with orientation and dynamic stability is concerned with object motion perception. The perception of visual stability is modified by many other sensations, such as somatosensory, vestibular, and muscle tension. We will mainly focus on modifications by vestibular inputs to visual perception produced by eye movements in microgravity. The Vestibular-Oscular Reflex (VOR) is a well-known characteristic which results from the relationship between eye mobility and vestibular afferent inputs. Eye movements also modify dynamic visual perception, such as perceived object motion velocity. The VOR is constantly simulated under 1-g conditions on Earth. In fact, human beings have been habituated and 'programmed' for orientation (visual stability) in their everyday, 1-g environment. When humans are exposed to a different gravity situation, this programmed behavior must change; that is, it is reprogrammed. This is called habituation or familiarization. We hope to examine how object motion perception is perturbed and subsequently adapted in the microgravity environment. This experiment is focused on the cooperation of visual, vestibular, and somatosensory perception coordination and how it is changed or reduced in space compared to 1-g environment. We will obtain information on the coordination between eye movement and neck muscle activity by using EOG and EMG. We will also collect data from Payload Specialists using a self-diagnostic questionnaire concerned with perceptual abnormality. When each sensory input function and its integration in the higher nervous system are well-characterized, then more effective techniques to control SAS may be developed.

Koga, Kazugo↗