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At least 325 records · Page 18

Physics-informed latent neural operator for real-time predictions of time-dependent parametric PDEs

Deep operator network (DeepONet) has shown significant promise as surrogate models for systems governed by partial differential equations (PDEs), enabling accurate mappings between infinite-dimensional function spaces. However, when applied to systems with high-dimensional input-output mappings arising from large numbers of spatial and temporal collocation points, these models often require heavily overparameterized networks, leading to long training times. Latent DeepONet addresses some of these challenges by introducing a two-step approach: first learning a reduced latent space using a separate model, followed by operator learning within this latent space. While efficient, this method is inherently data-driven and lacks mechanisms for incorporating physical laws, limiting its robustness and generalizability in data-scarce settings. Here, in this work, we propose PI-Latent-NO, a physics-informed latent neural operator framework that integrates governing physics directly into the learning process. Our architecture features two coupled DeepONets trained end-to-end: a Latent-DeepONet that learns a low-dimensional representation of the solution, and a Reconstruction-DeepONet that maps this latent representation back to the physical space. By embedding PDE constraints into the training via automatic differentiation, our method eliminates the need for labeled training data and ensures physics-consistent predictions. The proposed framework is both memory and compute-efficient, exhibiting near-constant scaling with problem size and demonstrating significant speedups over traditional physics-informed operator models. We validate our approach on a range of parametric PDEs, showcasing its accuracy, scalability, and suitability for real-time prediction in complex physical systems.

Latent representations↗

An atlas of ECMWF analyses (1980-1987). Part 1: First moment quantities

This document is an atlas of the European Center for Medium Range Weather Forecasts (ECMWF) initialized analyses for 1980 to 1987. Various first moment quantities are presented for monthly, seasonal, and annual averages on a global cylindrical projection, as well as, cross section maps of zonal averages. Global maps of winds, temperature, stream function, and velocity potential are presented at 850 and 200 mb. In addition, global maps of the 300 mb height field (total and eddy), the 500 mb vertical velocity, the 850 mb moisture field, and sea level pressure are presented. The average seasonal cycle and anomalies during the 8 year period are presented for selected quantities.

Schubert, S.↗

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Abstract Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited. Here, we report ECNet (evolutionary context-integrated neural network), a deep-learning algorithm that exploits evolutionary contexts to predict functional fitness for protein engineering. This algorithm integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe. As such, it enables accurate mapping from sequence to function and provides generalization from low-order mutants to higher-order mutants. We show that ECNet predicts the sequence-function relationship more accurately as compared to existing machine learning algorithms by using ~50 deep mutational scanning and random mutagenesis datasets. Moreover, we used ECNet to guide the engineering of TEM-1 β-lactamase and identified variants with improved ampicillin resistance with high success rates.

59 BASIC BIOLOGICAL SCIENCES↗

Radio sky mapping from satellites at very low frequencies

Wave Distribution Function (WDF) analysis is a procedure for making sky maps of the sources of natural electromagnetic waves in space plasmas, given local measurements of some or all of the three magnetic and three electric field components. The work that still needs to be done on this subject includes solving basic methodological problems, translating the solution into efficient algorithms, and embodying the algorithms in computer software. One important scientific use of WDF analysis is to identify the mode of origin of plasmaspheric hiss. Some of the data from the Japanese satellite Akebono (EXOS D) are likely to be suitable for this purpose.

Storey, L. R. O.↗

6.7 radio sky mapping from satellites at very low frequencies

Wave Distribution Function (WDF) analysis is a procedure for making sky maps of the sources of natural electromagnetic waves in space plasmas, given local measurements of some or all of the three magnetic and three electric field components. The work that still needs to be done on this subject includes solving basic methodological problems, translating the solution into efficient algorithms, and embodying the algorithms in computer software. One important scientific use of WDF analysis is to identify the mode of origin of plasmaspheric hiss. Some of the data from the Japanese satellite Akebono (EXOS D) are likely to be suitable for this purpose.

Storey, L. R. O.↗

High-Throughput Nanoindentation Mapping of Additively Manufactured T91 Steel

Here, this work aims to adapt nanoindentation mapping combined with a k-means algorithm as a high-throughput technique to study the nano-scale spatial changes in mechanical properties for a heterogeneous material. This technique can also classify the individual data points based on their properties. Hundreds to thousands of indents were performed on additively manufactured T91 at room temperature, 300°C, 400°C, and 500°C across a square area with a side length of 120 μm to 400 μm. From this data, the hardness and reduced modulus at each point could be calculated and mapped. Using k-means clustering, we were able to arrange the data into three or four clusters corresponding roughly to the ferritic and martensitic phases as well as one or two intermediate clusters sampling both the phases. The hardness of these two phases appears to be quite stable as a function of temperature. Nanoindentation mapping and the k-means algorithm can therefore be used to rapidly assess the feasibility of heterogeneous materials under extreme conditions, such as nuclear reactor steels.

36 MATERIALS SCIENCE↗

PAVC: The foundation for a Pan-Arctic Vegetation Cover database

Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and “other” vegetation, as well as absolute cover for litter and top cover for water and bare ground.

Steckler, Morgan R. [Oak Ridge National Laboratory↗

An Einstein survey of the 1 keV soft X-ray background in the Galactic plane

We have analyzed 56 Einstein Observatory Imaging Proportional Counter (IPC) observations within +/- 3 deg of the Galactic plane in order to determine the low-latitude soft X-ray background flux in the 0.56-1.73 keV band. Any detected X-ray point source which fell within our regions of study was removed from the image, enabling us to present maps of the background flux as a function of Galactic latitude along 18 meridians. These maps reveal considerable structure to the background in the Galactic plane on an angular scale of approximately 1 deg. Our results are compared with those of an earlier study of the 1 keV X-ray background along l = 25 deg by Kahn & Caillault. The double-peaked structure they found is not discernible in our results, possibly because of the presence of solar backscattered flux in their data. A model which takes into account contributions to the background by extragalactic and stellar sources, the distribution of both atomic and molecular absorbing material with the Galaxy, the energy dependence of the cross section for absorption of X-rays, and the energy dependence of the detector has been constructed and fitted to these new data to derive constraints on the scale height, temperature, and volume emissivity of the unaccounted-for X-ray-emitting material. The results of this model along l = 25 deg are roughly similar to those of the model of Kahn & Caillault along the same meridian.

Stanford, John M.↗

Namibia Dashboard Enhancements

The purpose of this presentation is for a Technical Interchange Meeting with the Namibia Hydrological Services (NHS) in Namibia. The meeting serves as a capacity building exercise. This presentation goes over existing software functionality developed in collaboration with NHS over the past five years called the Namibia Flood Dashboard. Furthermore, it outlines new functionality developed over the past year and future functionality that will be developed. The main purpose of the Dashboard is to assist in decision support for flood warning. The Namibia Flood Dashboard already exists online in a cloud environment and has been used in prototype mode for the past few years.Functionality in the Dashboard includes river gauge hydrographs, TRMM estimate rainfall, EO-1 flood maps, infrastructure maps and other related functions. Future functionality includes attempting to integrate interoperability standards and crowd-sourcing capability. To this end, we are adding OpenStreetMap compatibility and an Applications Program Interface (API) called a GeoSocial API to enable discovery and sharing of data products useful for decision support via social media.

Disaster Decision Support↗

A resolution independent neural operator

The Deep operator network (DeepONet) is a powerful yet simple neural operator architecture that utilizes two deep neural networks to learn mappings between infinite-dimensional function spaces. This architecture is highly flexible, allowing the evaluation of the solution field at any location within the desired domain. However, it imposes a strict constraint on the input space, requiring all input functions to be discretized at the same locations; this limits its practical applications. Here, in this work, we introduce a general framework for operator learning from input–output data with arbitrary number and locations of sensors. This begins by introducing a resolution-independent DeepONet (RI-DeepONet), enabling it to handle input functions that are arbitrarily, but sufficiently finely, discretized. To this end, we propose two dictionary learning algorithms to adaptively learn a set of appropriate continuous basis functions, parameterized as implicit neural representations (INRs), from correlated signals defined on arbitrary point cloud data. These basis functions are then used to project arbitrary input function data as a point cloud onto an embedding space (i.e., a vector space of finite dimensions) with dimensionality equal to the dictionary size, which can be directly used by DeepONet without any architectural changes. In particular, we utilize sinusoidal representation networks (SIRENs) as trainable INR basis functions. The introduced dictionary learning algorithms are then used in a similar way to learn an appropriate dictionary of basis functions for the output function data, which defines a new neural operator architecture referred to as the R esolution I ndependent N eural O perator (RINO). In the RINO, the operator learning task simplifies to learning a mapping from the coefficients of input basis functions to the coefficients of output basis functions. We demonstrate the robustness and applicability of RINO in handling arbitrarily (but sufficiently richly) sampled input and output functions during both training and inference through several numerical examples.

Deep operator network (DeepONet)↗

Uncertainty quantification in scientific machine learning: Methods, metrics, and comparisons

Neural networks (NNs) are currently changing the computational paradigm on how to combine data with mathematical laws in physics and engineering in a profound way, tackling challenging inverse and ill-posed problems not solvable with traditional methods. However, quantifying errors and uncertainties in NN-based inference is more complicated than in traditional methods. This is because in addition to aleatoric uncertainty associated with noisy data, there is also uncertainty due to limited data, but also due to NN hyperparameters, overparametrization, optimization and sampling errors as well as model misspecification. Although there are some recent works on uncertainty quantification (UQ) in NNs, there is no systematic investigation of suitable methods towards quantifying the total uncertainty effectively and efficiently even for function approximation, and there is even less work on solving partial differential equations and learning operator mappings between infinite-dimensional function spaces using NNs. In this work, we present a comprehensive framework that includes uncertainty modeling, new and existing solution methods, as well as evaluation metrics and post-hoc improvement approaches. Further, to demonstrate the applicability and reliability of our framework, we present an extensive comparative study in which various methods are tested on prototype problems, including problems with mixed input-output data, and stochastic problems in high dimensions. In the Appendix, we include a comprehensive description of all the UQ methods employed. Further, to help facilitate the deployment of UQ in Scientific Machine Learning research and practice, we present and develop in [1] an open-source Python library (github.com/Crunch-UQ4MI/neuraluq), termed NeuralUQ, that is accompanied by an educational tutorial and additional computational experiments.

11 physics-informed neural networks↗

Predicting nonequilibrium Green’s function dynamics and photoemission spectra via nonlinear integral operator learning

Understanding the dynamics of nonequilibrium quantum many-body systems is an important research topic in a wide range of fields across condensed matter physics, quantum optics, and high-energy physics. However, numerical studies of large-scale nonequilibrium phenomena in realistic materials face serious challenges due to intrinsic high-dimensionality of quantum many-body problems and the absence of time-invariance. The nonequilibrium properties of many-body systems can be described by the dynamics of the correlator, or the Green's function of the system, whose time evolution is given by a high-dimensional system of integro-differential equations, known as the Kadanoff–Baym equations (KBEs). The time-convolution term in KBEs, which needs to be recalculated at each time step, makes it difficult to perform long-time numerical simulation. In this paper, we develop an operator-learning framework based on recurrent neural networks (RNNs) to address this challenge. We utilize RNNs to learn the nonlinear mapping between Green's functions and convolution integrals in KBEs. By using the learned operators as a surrogate model in the KBE solver, we obtain a general machine-learning scheme for predicting the dynamics of nonequilibrium Green's functions. Besides significant savings per each time step, the new methodology reduces the temporal computational complexity from $O(N_t^3)$ to $O(N_t)$ where N t is the number of steps taken in a simulation, thereby making it possible to study large many-body problems which are currently infeasible with conventional KBE solvers. Through various numerical examples, we demonstrate the effectiveness of the operator-learning based approach in providing accurate predictions of physical observables such as the reduced density matrix and time-resolved photoemission spectra. Moreover, our framework exhibits clear numerical convergence and can be easily parallelized, thereby facilitating many possible further developments and applications.

97 MATHEMATICS AND COMPUTING↗

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Depth-Dependent Emission from Silver Dopants in Single CdSe Nanoplatelets

Dopants in semiconductor nanostructures offer tremendous control over electronic, optical, and magnetic properties beyond what is achievable in bulk materials. We demonstrate that the broad dopant emission in semiconductor nanoplatelets effectively maps the electron wave function across the nanoplatelet thickness. Both the emission energy and lifetime of the dopant transition depend strongly on the depth of the dopant within the nanoplatelet. This dependence arises from the electrostatic self-interaction of the charged dopant, which varies with proximity to the dielectric discontinuity at the nanoplatelet surface. Through comprehensive single-particle spectroscopy of silver-doped CdSe nanoplatelets, we verify that acceptors near the center emit at higher energies with shorter lifetimes, while those near the surface emit at lower energies with longer lifetimes. This spatial mapping also reveals unusual two-color emission from individual nanoplatelets, with enhanced Auger recombination yielding exceptional photon antibunching (>90% purity) at room temperature, suggesting potential applications in quantum information technologies.

cadmium selenide↗

Incorporating UAS Traffic Management into Wildland Firefighting Operations: Initial Findings of Subject Matter Expert Interviews

Uncrewed Aircraft Systems (UASs) are being utilized throughout the disaster and emergency response domain, including in wildland firefighting operations. While UASs can offer safety benefits in comparison to crewed aircraft, such as removing the human pilot from the vehicle so that they are not exposed to the same risks and the ability to operate in low-visibility conditions, they are not without tradeoffs. For example, it can be challenging for UAS pilots (UASPs) to build situation awareness of the airspace in which their UAS is operating. In order to address some of the challenges associated with using UASs and provide greater assistance to the firefighters and incident personnel in the wildland firefighting environment, the National Aeronautics and Space Administration (NASA) launched the Advanced Capabilities for Emergency Response Operations (ACERO) project. Building on previous NASA research, ACERO will explore the implementation of a traffic management system in the wildland fire environment to enhance safety and support situation awareness. ACERO draws on the UAS Traffic Management (UTM) system previously demonstrated in an urban environment. However, a traffic management system implemented in the wildland fire environment is expected to look and function much differently in order to meet the unique needs of this domain. At the outset of the ACERO project, interviews were conducted with five UASPs who operate UASs at wildland fire incidents. The interviews focused on exploring UASPs’ initial insights about the application of a traffic management system in wildland firefighting and understanding the unique needs of this environment. The UASPs discussed a range of topics including, the shape, size, and organization of UAS operations in the wildland fire environment, information needs for a user interface, such as traffic and map information, an alerting function when other traffic nears their operation area, and the importance of conformance monitoring. The UASPs also discussed their willingness to share operational information to support safety. In this paper, we describe the foundational work upon which ACERO will build and summarize the information and insights gathered during the UASP interviews, some of which have already informed the development of the ACERO work.

Uncrewed Aircraft System (UAS)↗

Incorporating UAS Traffic Management into Wildland Firefighting Operations: Initial Findings of Subject Matter Expert Interviews

Uncrewed Aircraft Systems (UASs) are being utilized throughout the disaster and emergency response domain, including in wildland firefighting operations. While UASs can offer safety benefits in comparison to crewed aircraft, such as removing the human pilot from the vehicle so that they are not exposed to the same risks and the ability to operate in low-visibility conditions, they are not without tradeoffs. For example, it can be challenging for UAS pilots (UASPs) to build situation awareness of the airspace in which their UAS is operating. In order to address some of the challenges associated with using UASs and provide greater assistance to the firefighters and incident personnel in the wildland firefighting environment, the National Aeronautics and Space Administration (NASA) launched the Advanced Capabilities for Emergency Response Operations (ACERO) project. Building on previous NASA research, ACERO will explore the implementation of a traffic management system in the wildland fire environment to enhance safety and support situation awareness. ACERO draws on the UAS Traffic Management (UTM) system previously demonstrated in an urban environment. However, a traffic management system implemented in the wildland fire environment is expected to look and function much differently in order to meet the unique needs of this domain. At the outset of the ACERO project, interviews were conducted with five UASPs who operate UASs at wildland fire incidents. The interviews focused on exploring UASPs’ initial insights about the application of a traffic management system in wildland firefighting and understanding the unique needs of this environment. The UASPs discussed a range of topics including, the shape, size, and organization of UAS operations in the wildland fire environment, information needs for a user interface, such as traffic and map information, an alerting function when other traffic nears their operation area, and the importance of conformance monitoring. The UASPs also discussed their willingness to share operational information to support safety. In this presentation, we describe the foundational work upon which ACERO will build and summarize the information and insights gathered during the UASP interviews, some of which have already informed the development of the ACERO work.

Uncrewed Aircraft Systems (UAS)↗

MnRhBi3: A Cleavable Antiferromagnetic Metal

This dataset contains DFT input and output files supporting the theoretical modeling in the associated publication (Chem. Mater. 2024, 36, 11306-11316). The calculations characterize MnRhBi3, an orthorhombic (Cmmm) van der Waals-layered intermetallic compound that cleaves easily between neighboring Bi layers. The dataset is organized into three calculation types: (i) Bulk: Structural relaxations of the periodic MnRhBi3 crystal in antiferromagnetic (AFM) and ferromagnetic (FM) configurations, using the vdW-DF-optB86b functional. These provide the equilibrium lattice constants, magnetic energy differences (AFM is 0.5 meV/f.u. lower than FM), and magnetic moments (4.4 µB/Mn, 0.17 µB/Rh, 0.18 µB/Bi) reported in Table 1 of the main text. (ii) Slab: Same magnetic configurations computed with an 18 Ang vacuum layer introduced between Bi layers, used to calculate the cleavage energy Ec = 0.56 J/m2 (AFM) and 0.57 J/m2 (FM), establishing MnRhBi3 as a van der Waals-layered material comparable to graphite, MoS2, and CrI3. (iii) ELF: Single-point calculation on the relaxed bulk AFM geometry with LELF=.TRUE., producing the ELFCAR file used to generate electron localization function isosurfaces and contour maps (Fig. 2, main text) showing Bi lone pairs directed into the van der Waals gaps. All folders contain CONTCAR, INCAR, KPOINTS, OUTCAR, and POSCAR. The ELF/ folder additionally contains ELFCAR. Calculations were performed using VASP 6.3.2 with PBE + vdW-DF-optB86b, PAW potentials, and an energy cutoff of 800 eV.

36 MATERIALS SCIENCE↗

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗