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At least 1,243 records · Page 69

Transferring a Molecular Foundation Model for Polymer Property Predictions

Transformer-based large language models have remarkable potential to accelerate design optimization for applications such as drug development and material discovery. Self-supervised pretraining of transformer models requires large-scale data sets, which are often sparsely populated in topical areas such as polymer science. Further, state-of-the-art approaches for polymers conduct data augmentation to generate additional samples but unavoidably incur extra computational costs. In contrast, large-scale open-source data sets are available for small molecules and provide a potential solution to data scarcity through transfer learning. In this work, we show that using transformers pretrained on small molecules and fine-tuned on polymer properties achieves comparable accuracy to those trained on augmented polymer data sets for a series of benchmark prediction tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Representations of Materials for Machine Learning

High-throughput data generation methods and machine learning (ML) algorithms have given rise to a new era of computational materials science by learning the relations between composition, structure, and properties and by exploiting such relations for design. However, to build these connections, materials data must be translated into a numerical form, called a representation, that can be processed by an ML model. Data sets in materials science vary in format (ranging from images to spectra), size, and fidelity. Predictive models vary in scope and properties of interest. Here, we review context-dependent strategies for constructing representations that enable the use of materials as inputs or outputs for ML models. Furthermore, we discuss how modern ML techniques can learn representations from data and transfer chemical and physical information between tasks. Finally, we outline high-impact questions that have not been fully resolved and thus require further investigation.

36 MATERIALS SCIENCE↗

Search for New Physics via Low-Energy Electron Recoils with a 4.2 Tonne-Year Exposure from the LZ Experiment

We report results from searches for new physics models through electron recoils using data collected by the LUX-ZEPLIN experiment during its first two science runs, with a total exposure of 4.2 tonne−years. The observed data are consistent with a background-only hypothesis. Constraints are derived for electromagnetic interactions of solar neutrinos, solar axionlike particles (ALPs), mirror dark matter, and the absorption of bosonic dark matter candidates. The inverse Primakoff process for 57 Fe deexcitation solar ALPs is considered for the first time. These results represent the most stringent constraints to date on keV-scale Primakoff and 57 Fe solar ALPs, bosonic dark matter, mirror dark matter, and neutrino millicharge, while remaining competitive for the other signal models investigated.

Axion-like particles↗

Interlaboratory comparison of secondary ion mass spectrometry analysis results from the 7th international technical nuclear forensics working group collaborative material exercise

A review and interlaboratory comparison of secondary ion mass spectrometry (SIMS) data obtained by laboratories participating in the International Technical Nuclear Forensics Working Group (ITWG) 7th Collaborative Material Exercise (CMX-7) has been conducted. The analyzed materials were two uranium compounds in powder form and two pieces of uranium metal. The instruments used in this comparison were a small-geometry (SG) SIMS, CAMECA IMS 7f from the Research Centre Rez, and a large-geometry (LG) SIMS, CAMECA IMS 1280 from Los Alamos National Laboratory. Despite the differences in instruments and analytical procedures, e.g., sample preparation, SIMS setups, and data post-processing, there was good agreement for the 234 U/ 238 U, 235 U/ 238 U, and 236 U/ 238 U ratios in the analyzed materials. The main difference was in the precision, which was, as expected, higher for the LG-SIMS. In addition, a comparison between the laboratories was also made for the image processing algorithms applied to raw data acquired in automated particle measurement (APM) mode. In conclusion, the result of this comparison has led to identification of best practices for setting up parameters of the APM software.

and nuclear chemistry↗

MAPPRAISER: A massively parallel map-making framework for multi-kilo pixel CMB experiments

Forthcoming cosmic microwave background (CMB) polarized anisotropy experiments have the potential to revolutionize our understanding of the Universe and fundamental physics. The sought-after, tale-telling signatures will be however distributed over voluminous data sets which these experiments will collect. These data sets will need to be efficiently processed and unwanted contributions due to astrophysical, environmental, and instrumental effects characterized and efficiently mitigated in order to uncover the signatures. This poses a significant challenge to data analysis methods, techniques, and software tools which will not only have to be able to cope with huge volumes of data but to do so with unprecedented precision driven by the demanding science goals posed for the new experiments. A keystone of efficient CMB data analysis is solvers of very large linear systems of equations. Such systems appear in very diverse contexts throughout CMB data analysis pipelines, however they typically display similar algebraic structures and can therefore be solved using similar numerical techniques. Linear systems arising in the so-called map-making problem are one of the most prominent and common ones. In this work we present a massively parallel, flexible and extensible framework, comprised of a numerical library, MIDAPACK, and a high level code, MAPPRAISER, which provide tools for solving efficiently such systems. Here, the framework implements iterative solvers based on conjugate gradient techniques: enlarged and preconditioned using different preconditioners. We demonstrate the framework on simulated examples reflecting basic characteristics of the forthcoming data sets issued by ground-based and satellite-borne instruments, executing it on as many as 16,384 compute cores. The software is developed as an open source project freely available to the community at: https://github.com/B3Dcmb/midapack.

79 ASTRONOMY AND ASTROPHYSICS↗

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

Exploring MDSplus data-acquisition software and custom devices

MDSplus is a software tool designed for data acquisition, storage, and analysis of complex scientific experiments. Over the years, MDSplus has primarily been used for data management for fusion experiments. This paper demonstrates that MDSplus can be used for a much wider variety of systems and experiments. We present a step-by-step tutorial describing how to create a simple experiment, manage the data, and analyze it using MDSplus and Python. To this end, a custom example device was developed to be used as the data source. This device was built on an open-source electronic hardware platform, and it consists of a microcontroller and two sensors. Finally, we read data from these sensors, store it in MDSplus, and use JupyterLab to visualize and process it.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tikiri—Towards a lightweight blockchain for IoT

Internet of Things (IoT) platforms have been deployed in several domains to enhance efficiency of business process and improve productivity. Most IoT platforms comprise of heterogeneous software and hardware components which can potentially introduce security and privacy challenges. Blockchain technology has been proposed as one of the solutions to realize IoT security by leveraging the (a) Immutable ledger, (b) Decentralized architecture and (c) Strong cryptography primitives. However, integrating blockchain platforms with IoT based applications presents several challenges due to lack of (a) acceptable performance on resource-constrained devices, (b) high transaction throughput, (c) keyword-based search and retrieve, (d) transaction back pressure operations, and (e) real-time response. In this paper, we propose a lightweight blockchain platform, “Tikiri”, for resource-constrained IoT devices. Tikiri uses Apache Kafka for the consensus and proposes new blockchain architecture to handle real-time transaction execution on the blockchain. Tikiri is characterized by functional programming and actor-based smart contract platform that realizes concurrent execution of transactions in the blockchain. Tikiri realizes a lightweight and scalable blockchain that can provides performance on the resource-constrained IoT devices.

97 MATHEMATICS AND COMPUTING↗

Pass-efficient methods for compression of high-dimensional turbulent flow data

The future of high-performance computing, specifically on future Exascale computers, will presumably see memory capacity and bandwidth fail to keep pace with data generated, for instance, from massively parallel partial differential equation (PDE) systems. Current strategies proposed to address this bottleneck entail the omission of large fractions of data, as well as the incorporation of in situ compression algorithms to avoid overuse of memory. To ensure that post-processing operations are successful, this must be done in a way that a sufficiently accurate representation of the solution is stored. Moreover, in situations where the input/output system becomes a bottleneck in analysis, visualization, etc., or the execution of the PDE solver is expensive, the number of passes made over the data must be minimized. In the interest of addressing this problem, this work focuses on the utility of pass-efficient, parallelizable, low-rank, matrix decomposition methods in compressing high-dimensional simulation data from turbulent flows. Additionally, a particular emphasis is placed on using coarse representation of the data – compatible with the PDE discretization grid – to accelerate the construction of the low-rank factorization. This includes the presentation of a novel single-pass matrix decomposition algorithm for computing the so-called interpolative decomposition. The methods are described extensively and numerical experiments on two turbulent channel flow data are performed. In the first (unladen) channel flow case, compression factors exceeding 400 are achieved while maintaining accuracy with respect to first- and second-order flow statistics. In the particle-laden case, compression factors of 100 are achieved and the compressed data is used to recover particle velocities. These results show that these compression methods can enable efficient computation of various quantities of interest in both the carrier and disperse phases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Mechanical properties and deformation mechanisms of single crystal Mg micropillars subjected to high-strain-rate C-axis compression

Here, the mechanical properties and deformation mechanisms of single crystal magnesium under c-axis quasi-static and high-strain rate compressions are investigated through in situ scanning electron microscope (SEM) experiments and post-mortem transmission electron microscope (TEM) characterization. The findings revealed that ductility and high rates of hardening are preserved for pillars as large as 15 μm. Furthermore, rate effects result in a mild increase in flow stress with plastic deformations controlled primarily by the slip of type dislocations. Importantly and in contrast to other literature reports, plastic deformation occurs in the absence of twining. As the strain increases and plastic deformation exceeds about 4%, crystal rotation activates basal slip, <$\mathrm{a}$> type dislocations, resulting in a more rate independent flow stress. TEM observation on micropillars compressed at a strain rate of 250/s, revealed the activation of {${11}$$\bar{2}$$\bar{2}$} < $\bar{1}$$\bar{1}23$ > slip systems and high mobility of screw dislocations as major contributors to plastic strains in excess of 10% without fracture. These findings are relevant to the design of lightweight materials used in transportation systems, e.g., selection of material grain size. Moreover, the experimental data here reported provides the materials science community with a unique opportunity to validate discrete dislocation dynamics (DDD) formulations employed in multiscale design of materials.

36 MATERIALS SCIENCE↗

Predicting material microstructure evolution via data-driven machine learning

The recent rapid rise in data-driven practices in the materials science domain has led to the development of efficient, generalizable, and accurate approaches for several applications, including: material property prediction, mining (micro)structure- property and (micro)structure-processing relationships, and characterization of material microstructures. Central to the materials science domain is linking microstructure to properties and performance, and critical to building such linkages is understanding how microstructures evolve as a function of environmental exposure or processing conditions (e.g., time, temperature, applied stress or strain, irradiation). This preview article summarizes recent work on the development of recurrent neural networks for predicting spatio-temporal microstructure evolution detailed by Yang et al in their manuscript entitled 'Self-supervised Learning and Prediction of Microstructure Evolution with Recurrent Neural Networks'.

machine learning (ML), materials characterization↗

Nuclear data uncertainty propagation and modeling uncertainty impact evaluation in neutronics core simulation

Uncertainty analysis is a critical requirement in reactor simulation as it is used to quantify the reliability of best-estimate calculation. A comprehensive uncertainty analysis should characterize all sources of uncertainties in a computationally-feasible and scientifically-defendable manner. Here we employ a well-established reduced order modeling (ROM) based uncertainty quantification methodology to propagate uncertainties throughout neutronic calculations. ROM relies on recent advances in randomized data mining techniques applied to large data streams. In our proposed implementation, the nuclear data uncertainties are first propagated from multi-group level through lattice physics calculation to generate few-group parameter uncertainties, described using a vector of mean values and a covariance matrix. Employing an ROM-based compression of the covariance matrix, the few-group uncertainties are then propagated through downstream core simulation in a computationally efficient manner. This straightforward approach, albeit efficient as compared to brute force forward and/or adjoint-based methods, often employs a number of assumptions that have been unquestioned in the literature of neutronic uncertainty analysis. This manuscript argues that these assumptions could introduce another source of uncertainty referred to as modeling uncertainties, whose magnitude needs to be quantified in tandem with nuclear data uncertainties. Thus, our primary goal is to explore the interactions between these two uncertainty sources in order to assess whether modeling uncertainties have an impact on parameter uncertainties. To explore this endeavor, the impact of a number of modeling assumptions on core attributes uncertainties is quantified. The study employs a CANDU reactor model, with Serpent and NEWT as lattice physics solvers and NESTLE-C as core simulator. The modeling assumptions investigated include those related with the uncertainty propagation method employed, e.g., deterministic vs. stochastic, the few-group energy structure employed to represent the cross-sections, the resonance treatment in lattice physics calculation, the reference values for the cross-section, and the number of samples employed to render ROM compression. Results indicate that some of the modeling assumptions could have a non-negligible impact on the core responses propagated uncertainties, highlighting the need for a more comprehensive approach to combine parameter and modeling uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Unlocking Solutions: Innovative Approaches to Identifying and Mitigating the Environmental Impacts of Undocumented Orphan Wells in the United States

In the United States, hundreds of thousands of undocumented orphan wells have been abandoned, leaving the burden of managing environmental hazards to governmental agencies or the public. These wells, a result of over a century of fossil fuel extraction without adequate regulation, lack basic information like location and depth, emit greenhouse gases, and leak toxic substances into groundwater. For most of these wells, basic information such as well location and depth is unknown or unverified. Addressing this issue necessitates innovative and interdisciplinary approaches for locating, characterizing, and mitigating their environmental impacts. Our survey of the United States revealed the need for tools to identify well locations and assess conditions, prompting the development of technologies including machine learning to automatically extract information from old records (95%+ accuracy), remote sensing technologies like aero-magnetometers to find buried wells, and cost-effective methods for estimating methane emissions. Notably, fixed-wing drones equipped with magnetometers have emerged as cost-effective and efficient for discovering unknown wells, offering advantages over helicopters and quadcopters. Efforts also involved leveraging local knowledge through outreach to state and tribal governments as well as citizen science initiatives. These initiatives aim to significantly contribute to environmental sustainability by reducing greenhouse gases and improving air and water quality.

54 ENVIRONMENTAL SCIENCES↗

Estimating the Electric Fields Driving Lightning Dart Leader Development With BIMAP‐3D Observations

Abstract In this paper, a numerical dart leader model has been implemented to understand the leader's development and the corresponding electric field changes observed by the 3D broadband mapping and polarization (BIMAP‐3D) system. The model assumes the extending leader channel is equipotential and has a linear charge distribution induced by an ambient electric field. The charge distribution induced by the ambient field can be used to model the electric field change at the ground. We then find the ambient electric field which best fits the field change measurements at the two BIMAP stations. The estimated ambient electric field decreases in the direction of dart leader propagation. Our observations and modeling results are consistent with our earlier hypothesis that dart leader speed is proportional to the electric field at the leader tip. The model also supports our earlier analysis that leader speed variations near branch junctions were due to previous charge deposits near the junctions. The modeled tip electric field is generally lower than the breakdown field unless the pre‐dart‐leader channel has a significant temperature of 3,000 K. This is consistent with the fact that dart leaders typically do not form new branches into the virgin air. Furthermore, the tip field is generally close to the negative streamer stability field at ambient temperatures, explaining the nature of the narrow and well‐defined channel structure. In addition to the charge distribution and the ambient and tip electric field, the development of the channel potential and current distribution are also presented.

3D lightning mapping↗

Protein remote homology detection and structural alignment using deep learning

Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.

59 BASIC BIOLOGICAL SCIENCES↗

A dataset for understanding self-reported patterns influencing residential energy decisions

Household occupant behavior and decision-making dynamics substantially impact technology uptake and residential building energy performance. Although significant research underscores the importance of social science in energy studies, few public data with representative samples on household energy decision-making patterns are available. The dataset (UPGRADE-E: Understanding Patterns Guiding Residential Adoption and Decisions about Energy Efficiency) presents 9,919 responses from U.S. residents of single-family and small multifamily homes. Derived from a national-scale internet survey, the dataset contains 391 variables: demographics, building characteristics, home modifications, willingness to adopt new technologies, motivations for making changes, barriers, program participation, trusted information sources, and energy scenarios. Responses were validated via internal consistency checks and comparison with other U.S. national scale datasets. UPGRADE-E advances knowledge of household energy related decision-making, tying demographics, home modifications, and self-reported cognitive drivers together at a scale and breadth that has not been previously achieved. Policymakers and researchers at local, regional, and national levels may leverage this dataset to understand drivers influencing the adoption of key technologies in U.S. homes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗