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At least 199 records · Page 11

Artificial Intelligence Transforming Post-Translational Modification Research

Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs are compared. Finally, our high-throughput PTM-data-generation pipeline, which formats data suitably for AI training and predictions is described. We hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.

59 BASIC BIOLOGICAL SCIENCES

Classification of Clouds and Deep Convection from GEOS-5 Using Satellite Observations

With the increased resolution of global atmospheric models and the push toward global cloud resolving models, the resemblance of model output to satellite observations has become strikingly similar. As we progress with our adaptation of the Goddard Earth Observing System Model, Version 5 (GEOS-5) as a high resolution cloud system resolving model, evaluation of cloud properties and deep convection require in-depth analysis beyond a visual comparison. Outgoing long-wave radiation (OLR) provides a sufficient comparison with infrared (IR) satellite imagery to isolate areas of deep convection. We have adopted a binning technique to generate a series of histograms for OLR which classify the presence and fraction of clear sky versus deep convection in the tropics that can be compared with a similar analyses of IR imagery from composite Geostationary Operational Environmental Satellite (GOES) observations. We will present initial results that have been used to evaluate the amount of deep convective parameterization required within the model as we move toward cloud system resolving resolutions of 10- to 1-km globally.

Putman, William

The star formation history of the Large Magellanic Cloud

Deep photometric observations of stars in three fields of the LMC are presented, and these data are interpreted using synthetic CMDs and LFs generated from overshoot models. The field CMDs and LFs with a star formation rate that experienced a large increase (4 +/- 0.5) x 10 exp 9 yr ago is successfully modeled. The precise age of this 'burst' depends sensitively on the characteristics of the models. Classical (i.e., nonovershoot) models yield a burst age about 2 x 10 exp 9 yr younger than the value obtained. An initial mass function with slope of 2.35 (the Salpeter value) and a mean field star metallicity of Fe/H of about -0.7 are consistent with the photometric data and LFs. It is suggested that the star formation rate in the LMC was globally quite low during at least the first half of its lifetime, and that a major event triggered a substantial and relatively sudden increase in the star formation rate throughout the entire LMC which persisted for several 10 exp 9 yr and even up to the present epoch in some parts of that galaxy.

Bertelli, Gianpaolo

Discrete fracture network model benchmarks developed and applied in a DECOVALEX-2023 repository performance assessment study

This study presents newly developed benchmarks for modeling flow and transport within discrete fracture networks (DFNs) and useful methods for analyzing the results. The new benchmarks are designed to test modeling approaches for use in probabilistic performance assessment models of deep geologic repositories in fractured rock. The benchmarks simulate flow and transport through a 1 km 3 block of fractured rock. The first simulates migration of a short pulse of tracer through a simple network of four intersecting fractures. The second adds 1089 stochastically generated fractures. The third changes the pulse to a continuous point source. Evaluation of model performance relies on moment analysis and comparison of the results of different models. The expected nondimensional first moment of the conservative tracer for each benchmark is 1. The benchmarks were simulated by teams from Canada, Czechia, Germany, Korea, Sweden, Taiwan, and the United States as part of a DECOVALEX-2023 study (decovalex.org). The teams used various approaches, including explicit DFN modeling, DFN upscaling to an equivalent continuous porous medium (ECPM), and a combination of both methods. Transport mechanisms are modeled using either the advection-dispersion equation or particle tracking. Results demonstrate strong agreement among the models in breakthrough behavior up to the 75th percentile. Significant deviations in first moments and well-clustered outputs led to the identification of inaccuracies in several models. Such findings exemplify the benefit of exercising these benchmarks and using the presented methods to test DFN flow and transport models.

Benchmark

Probing ExoMiner for Effectiveness against False Alarms in Kepler Data

We present a study on the effectiveness of ExoMiner against False Alarms in Kepler data. ExoMiner is a deep learning model that was used to validate around 370 Kepler Objects of Interest. We follow the analysis conducted in Coughlin et al (2017) “DR25 Robovetter Completeness and Effectiveness” for Robovetter, a rule-based model used to vet TCEs for this data release and automatically generate the Q1-Q17 DR 25 KOI Table. The ExoMiner model is trained on observed transit data from Kepler Q1-Q17 DR25 and evaluated on Kepler inverted and scrambled data. The results provide a more comprehensive insight into the capacities and limitations of ExoMiner, especially the vetting of not-transit-like signals and, more generally, the use of deep learning models to model transit photometry data for vetting and validation purposes.

exoplanet

Irreducible Tests for Space Mission Sequencing Software

As missions extend further into space, the modeling and simulation of their every action and instruction becomes critical. The greater the distance between Earth and the spacecraft, the smaller the window for communication becomes. Therefore, through modeling and simulating the planned operations, the most efficient sequence of commands can be sent to the spacecraft. The Space Mission Sequencing Software is being developed as the next generation of sequencing software to ensure the most efficient communication to interplanetary and deep space mission spacecraft. Aside from efficiency, the software also checks to make sure that communication during a specified time is even possible, meaning that there is not a planet or moon preventing reception of a signal from Earth or that two opposing commands are being given simultaneously. In this way, the software not only models the proposed instructions to the spacecraft, but also validates the commands as well.To ensure that all spacecraft communications are sequenced properly, a timeline is used to structure the data. The created timelines are immutable and once data is as-signed to a timeline, it shall never be deleted nor renamed. This is to prevent the need for storing and filing the timelines for use by other programs. Several types of timelines can be created to accommodate different types of communications (activities, measurements, commands, states, events). Each of these timeline types requires specific parameters and all have options for additional parameters if needed. With so many combinations of parameters available, the robustness and stability of the software is a necessity. Therefore a baseline must be established to ensure the full functionality of the software and it is here where the irreducible tests come into use.

sequencing test

The glass-ceiling convective regime and the origin and diversity of coronae on Venus

Venus and Earth are rocky planets of roughly the same size and bulk density, yet their surface volcanic and tectonic features appear substantially different. On Venus, the coexistence of large volcanic highlands—interpreted as the surface expression of long-lived mantle plumes—alongside coronae, smaller features thought to be caused by transient thermal diapirs, remains enigmatic. Using two-dimensional numerical models of mantle convection with sharp and broad mineral phase transitions for pyrolite, we show that both scales of upwellings can be generated in a stagnant lid planet with an interior temperature 250 to 400 K warmer than Earth’s. The smaller plumes originate from a ~600 km deep internal layer that exists as a consequence of the different sequence of mineral phase transitions that occur in warmer mantles less processed and differentiated by partial melting and volcanism. Future models that include melting will provide further tests of our hypothesis.

Science & Technology - Other Topics

DeepAndes: A Self-Supervised Vision Foundation Model for Multispectral Remote Sensing Imagery of the Andes

By mapping sites at large scales usingremotely sensed data, archaeologists can generate unique insights into long-term demographic trends, interregional social networks, and human adaptations in the past. Remote sensing surveys complement field-based approaches, and their reach can be especially great when combined with deep learning and computer vision techniques. However, conventional supervised deep learning methods face challenges in annotating fine-grained archaeological features at scale. In addition, while recent vision foundation models have shown remarkable success in learning large-scale remote sensing data with minimal annotations, most off-the-shelf solutions are designed for RGB images rather than multispectral satellite imagery, such as the eight-band data used in our study. In this article, we introduce DeepAndes, a transformer-based vision foundation model trained on three million multispectral satellite images, specifically tailored for Andean archaeology. DeepAndes incorporates a customized DINOv2 self-supervised learning algorithm optimized for eight-band multispectral imagery, marking the first foundation model designed explicitly for the Andes region. We evaluate its image understanding performance through imbalanced image classification, image instance retrieval, and pixel-level semantic segmentation tasks. Our experiments show that DeepAndes achieves superior F1 scores, mean average precision, and Dice scores in few-shot learning scenarios, significantly outperforming models trained from scratch or pretrained on smaller datasets. This underscores the effectiveness of large-scale self-supervised pretraining in archaeological remote sensing.

Guo, Junlin [Vanderbilt Univ., Nashville, TN (Unit

A Quantitative Investigation of Entrainment and Detrainment in Numerically Simulated Convective Clouds: Simulations of Cumulonimbus Clouds - Pt. 2

Deep cumulonimbus clouds are simulated using a model that makes accurate diagnoses of entrainment and detrainment rates and of the properties of entrained and detrained air. Clouds generated by a variety of initial thermodynamic soundings are compared. In the simulations, updraft entrainment rates are large near and above cloud base, through the entire depth of the conditionally unstable layer. Stronger updrafts in a more unstable environment are better able to entrain relatively undisturbed environmental air, while weaker updrafts can entrain only air that has been modified by the clouds. When the maximum buoyancy is large, the updraft includes parcels with a wide range of buoyancies, while weaker clouds are more horizontally uniform. Strong downdrafts originate from levels at which updrafts detrain, and their mass flux depends on the mass flux of the updraft. The magnitude of mixing between cloud and environment, not the entrainment rate, varies inversely with the cloud radius. How much of the mixed air is entrained depends on the buoyancy.

Cohen, Charles

Global tuning of hadronic interaction models with accelerator-based and astroparticle data

In high-energy and astroparticle physics, event generators play an essential role, even in the simplest data analyses. As analysis techniques become more sophisticated, e.g. based on deep neural networks, their correct description of the observed event characteristics becomes even more important. Physical processes occurring in hadronic collisions are simulated within a Monte Carlo framework. A major challenge is the modeling of hadron dynamics at low momentum transfer, which includes the initial and final phases of every hadronic collision. QCD-inspired phenomenological models used for these phases cannot guarantee completeness or correctness over the full phase space. These models usually include parameters which must be tuned to suitable experimental data. Until now, event generators have been developed and tuned mainly on the basis of data from high-energy physics experiments at accelerators. The wealth of data available from the latest generation of astroparticle experiments has not yet been fully exploited, and in many cases is not satisfactorily described. Both kinds of data sets are complementary as astroparticle experiments provide sensitivity especially to hadrons produced nearly parallel to the collision axis and cover center-of-mass energies up to several hundred TeV, well beyond those reached at colliders so far. In this report, we provide an overview of state-of-the-art event generators and their tuning, including the most relevant inputs from high-energy accelerator and astroparticle experiments. We present a road map that shows, for the first time, how the unified tuning of event generators with accelerator-based and astroparticle data can be performed.

Albrecht, J. [Ruhr U., Bochum, RAPP Ctr.; Ruhr U.,

LAF-Net: A Deep Residual and Cross-Attention Framework for Day-Ahead Load Forecasting: Preprint

Accurate day-ahead load forecasting is essential for reliable power system operations and market efficiency. System operators such as the Midcontinent Independent System Operator (MISO) rely on forecasts from multiple vendors, yet combining them effectively remains a persistent challenge due to vendor-specific biases. This paper presents a novel LSTM-Attention Fusion Network with Error Representation (LAF-Net) that enhances day-ahead hourly load forecasting through deep residual learning and multi-modal cross-attention. The proposed model builds a historical error memory from past vendor performance and dynamically queries it with future hour context to generate adaptive, hour-specific trust weights for each vendor. A bounded residual correction further refines forecasts by mitigating systematic and temporally localized errors. Tested on real MISO LBA data with multi-vendor forecasts, LAF-Net consistently outperforms the best vendor baseline across all 38 LBAs, achieving more than a 40% reduction in system-level mean absolute error (MAE) during peak load hours relative to the best vendor baseline.

24 POWER TRANSMISSION AND DISTRIBUTION

Observations and models of inertial waves in the deep ocean

A study of the structure of the inertial peak in deep ocean kinetic energy is presented, based on records taken from Polymode arrays deployed in the western North Atlantic Ocean. Results are interpreted in terms of both local sources and turning point effects on internal waves generated at lower latitudes, and it is found that three classes of environment and their corresponding spectra emerge from peak height variations: (1) the 1500-m level near the Mid-Atlantic Ridge, with the greatest peak height of 18 dB; (2) the upper and deep ocean over rough topography and the deep ocean underneath the Gulf Stream, with the intermediate peak height of 11.5 dB; and (3) the deep ocean over smooth topography, with the lowest peak height of 7.5 dB. Using the globally valid wave functions obtained by Munk and Phillips (1968), frequency spectra near f are calculated numerically. The model is latitudinally dependent, with the frequency shift and bandwidth of the inertial peak decreasing with latitude.

Fu, L.-L.

Rapid Turnaround of Costing/Designing of Space Missions Operations

The Ground Segment Team (GST), at NASA's Jet Propulsion Laboratory in Pasadena, California, provides high-level mission operations concepts and cost estimates for projects that are in the formulation phase. GST has developed a tool to track costs, assumptions, and mission requirements, and to rapidly turnaround estimates for mission operations, ground data systems, and tracking for deep space and near Earth missions. Estimates that would often take several weeks to generate are now generated in minutes through the use of an integrated suite of cost models. The models were developed through interviews with domain experts in areas of Mission Operations, including but not limited to: systems engineering, payload operations, tracking resources, mission planning, navigation, telemetry and command, and ground network infrastructure. Data collected during interviews were converted into parametric cost models and integrated into one tool suite. The tool has been used on a wide range of missions from small Earth orbiters, to flagship missions like Cassini. The tool is an aid to project managers and mission planners as they consider different scenarios during the proposal and early development stages of their missions. The tool is also used for gathering cost related requirements and assumptions and for conducting integrated analysis of multiple missions.

Cost estimation

Ma'adim Vallis Estuarine Delta in Elysium Basin and Its Relevance as a Landing Site for Exobiology Exploration on Mars

The debouche of Ma'adim Vallis in the Elysium Basin generated a transitional transported sediment structure, which planimetric shape is controlled by the enclosing topography of a deep reentrant gulf of the Basin into the highland. We defined it as an estuarine delta. The location and the importance of this estuarine delta is supported by the theoretical model of graded profile constructed for Ma'adim Vallis, and by two approaches: (i) the reconstruction of Ma'adim Vallis downstream course from Gusev to Elysium Basin, and (ii) the survey of the sediment deposit in the alleged estuary. The longitudinal graded profile of Ma'adim Vallis finds its base-level in the Elysium Basin, at a about 1000 m elevation, which is in agreement with the observed Basin shoreline. This model is supported by observational evidence of flow between the northern rim of Gusev crater, and the Elysium Basin shoreline. This downstream course of Ma'adim Vallis can be divided into three hydrogeologic regions. into three hydrogeologic regions. (a) The first region is a flooded plain (Zephiria Mensae), consisting in chaotic terrain formed by highland rocks, and disintegrated lava of the western flank of Apollinaris. Morphologic indicators of the flood process are: (1) the sediment deposit over the Gusev crater northern rim that reflects the overspilling of the crater-lake water through a 40-km wide gap provided by an ancient impact crater, (2) the tear-drop shaped feature on the northeastern flank of Apollinaris Patera, and (3) the chaotic terrain that suggest the emergence of ground water generated by the seepage of the crater lake through high-permeable broken rampart material. This underground water circulation sustained by the hydrostatic pressure of the crater-lake has likely generated a hydrothermal system in the volcanic environment of Apollinaris Patera. The stratigraphy of the flooded area is identified as Hesperian age, with occurrences of Noachian hilly individual features, and as Amazonian flooded plain and chaotic material, (b) The second region is located on the western flank of Apollinaris Patera. It is surrounded by relics of deep valleys that suggest a former downstream course of Ma'adim Vallis. The geologic setting of this region (Lucus Planum) is interpreted to be an Amazonian formation composed by the middle and lower members of the Medusae Formation., c) The third region corresponds to the convergence of the west and east branches of Ma'adirn Vallis into a deep re-entrant wide gulf that penetrates about 100 km into the highland. This topographic depression is delineated by the 1000 in elevation contour. This gulf has formed an estuarine configuration centered at 3S/190W within the Elysium Basin. This configuration has favored the formation of a estuarine sedimentary delta, because of topographically controlled lateral migration. This estuarine structure is strongly dominated by the incoming supply of Ma'adim Vallis fluvial sediment extracted from Zephiria Mensae and Lucus Planum. The obtuse-angle geometry of the estuary increases the sedimentation rate, which is higher than in the course of the channel. The sediment deposition process is governed by the estuarine water circulation. The inflowing loaded fluvial water enters the estuary as a bottom current, and mixes with the relatively less-loaded water of the receiving basin. When they mixed. the inflowing fluvial material, and the landward basin circulating water generate an accumulation of highly-diversified estuarine deposit stratification. This accumulation of material is mostly centered in the transitional zone of the delta. The sediment trapping efficiency of the estuary is function of the energy balance between the inflowing fluvial water, and the ingoing basin current. The submergence of the delta by the rising of the water-level increases the estuary water-depth, and consequently the sediment entrapment is favored. The locus of sediment accumulation moves landward in the zone of inflowing fluvial water. This results in the rising of the channel base-level, thus in the increase of the length of the longitudinal graded-profile. The sediment deposit facies of the zone A shows a generally smooth surface. The longitudinal deposit is bordered by alluvial terraces that reflect the variations of the channel level. The waning of the Elysium Basin caused the erosion of the Basin estuarine zone by small channels, this episode being characterized by dissected tear-drop shaped mesa-like morphologies in the delta. Our estuarine delta model predicts a lithostratigraphic depositional sequence associated with the water submergence and the transgression of Elysium Basin. The thickness of the estuarine sediment corresponds to the Elysium Basin levels changes relatively to the bed floor of the estuary, The depositional sequence of Ma'adim Vallis are described: (1) a pro-current filled region (A), where fluvial are longitudinally accumulated by the inflowing water, (2) inverse current from Elysium Basin (B), where fluvial and lacustrine sediments are accumulated, and (3) zone of current equilibrium (C), where the sediments are distributed as a shoreline at the boundary of the estuarine delta. The estuary sedimentology dynamics collects and keeps the record of the geologic unit material crossed by Ma'adim Vallis, and those of the lakebed deposit of Elysium Basin. The predicted mixed stratigraphic sequence from fluvial and lacustrine sediment makes this site an exceptional environment to concentrate potential multi-origin biologic records. We envision four possible strategies to explore this sedimentologic record: (1) longitudinal surface and subsurface traverses in region A to investigate outcrop levees, (2) exploration of the mesa walls in region B, (3) deep drilling hole lodging of the sequential deposits in the zones A and B, and (4) surface and subsurface exploration of the shoreline delta. The expected results for each of these strategies are: (1) in the deepest layers of region A are predicted frequent and abundant coarse material, sandy lenses lamination grading downward from sand to cobbles. Volcanic debris from the Noachian crustal Plateau unit material, hydrothermal altered rocks, carbonates, Hesperian and possibly Amazonian volcanic material, from Apollinaris Patera, altered rocks and carbonates from Zephiria Mensae are expected. As a favorable environment for inception of life, possible biological records are expected in transported rock, (2) At the surface, and subsurface (<=100 m), large deposits sandy to silted material from Elysium paleolake basin mixed with fine-grained sediments from Ma'adim Vallis are expected mostly in the upstream part of region B, (3) on the shoreline of the estuarine delta, abundant fine material from Elysium paleolake basin (evaporites, carbonates), mostly Amazonian in age are expected. The Ma'adini estuary is a favorable landing site for all the above mentioned science aspects, and .for its location. The site lies near the equator, which is favorable for the rover solar power supply, and at 1000m elevation, which is a favorable configuration for the descent system braking. Another advantage is the extent of the area of high scientific interest (33,000 sq km), which provides a good ellipse, and potential long study traverses.

Grin, E. A.

Decomposing sources of value for electricity and negative emissions technologies in net-zero power systems

Deep decarbonization of the US power system would require rapid deployment of variable renewable energy (VRE) resources, which are projected to provide a substantial share of electricity generation at the time of net-zero emissions. However, the exact share of generation met by VRE and the roles of other technologies in supplying key electricity services—energy and firm capacity—remain uncertain. This study employs a detailed model of the US power sector to decompose the provision and value of electricity services, including negative emissions, by technology across a range of deep decarbonization scenarios. Results indicate that while technology deployment and the share of services provided by each technology vary significantly depending on future technological and market conditions, the value composition and future roles of individual technologies remain consistent. These findings offer guidance for research and development priorities and provide insights to inform electricity policy and planning.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Prospects for a breakthrough in field-dependent 'propulsion'

If sufficient justification exists to start the development of a field physics laboratory, attention might well be given to the development of two advanced types of field-independent propulsion systems. These are gravimagnetic systems and field resonance systems. The first are multipurpose propulsion systems employing the 'gravitational' effects of coherent electromagnetic energy configurations. The second are deep-space propulsion systems which artificially generate an energy pattern that matches precisely, or resonates with, a virtual pattern associated with a distant space-time point. A new model of space-time/field interactions is used in the present paper to describe the potential characteristics of electromagnetic/gravitational field interactions and the performance capabilities of these two propulsion systems.

Holt, A. C.

Accelerated CO2 Storage Optimization Using Multi-Resolution Fourier Neural Operator at the Illinois Basin Decatur Project (IBDP)

This paper presents a deep learning-based approach for optimizing CO2 injection in carbon capture and storage (CCS) operations. We developed a multi-resolution machine learning model to significantly reduce data generation costs. Utilizing this proxy model, we implemented a multi-objective genetic algorithm to optimize well control during the CO2 injection process. The proposed approach was applied to the Illinois Basin Decatur Project (IBDP), successfully optimizing the CO2 injection schedule based on three key objectives: maximizing the amount of CO2 stored, maximizing sweep efficiency, and minimizing pressure increase. The use of the proxy model accelerated the optimization workflow by two orders of magnitude, while the cost of data generation for the proxy model was reduced by 90% by utilizing a coarse-scale model.

accelerated CO2 storage optimization

On the generation and evolution of internal gravity waves

The tidal generation and evolution of internal gravity waves is investigated experimentally and theoretically using a two-dimensional two-layer model. Time-dependent flow is created by moving a profile of maximum submerged depth 7.7 cm through a total stroke of 29 cm in water above a freon-kerosene mixture in an 8.6-m-long 30-cm-deep 20-cm-wide transparent channel, and the deformation of the fluid interface is recorded photographically. A theoretical model of the interface as a set of discrete vortices is constructed numerically; the rigid structures are represented by a source distribution; governing equations in Lagrangian form are obtained; and two integrodifferential equations relating baroclinic vorticity generation and source-density generation are derived. The experimental and computed results are shown in photographs and graphs, respectively, and found to be in good agreement at small Froude numbers. The reasons for small discrepancies in the position of the maximum interface displacement at large Froude numbers are examined.

Lansing, F. S.