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At least 271 records · Page 15

Data-driven learning of Mori–Zwanzig operators for isotropic turbulence

Developing reduced-order models for turbulent flows, which contain dynamics over a wide range of scales, is an extremely challenging problem. In statistical mechanics, the Mori–Zwanzig (MZ) formalism provides a mathematically exact procedure for constructing reduced-order representations of high-dimensional dynamical systems, where the effects due to the unresolved dynamics are captured in the memory kernel and orthogonal dynamics. Turbulence models based on MZ formalism have been scarce due to the limited knowledge of the MZ operators, which originates from the difficulty in deriving MZ kernels for complex nonlinear dynamical systems. In this work, we apply a recently developed data-driven learning algorithm, which is based on Koopman's description of dynamical systems and Mori's linear projection operator, on a set of fully resolved isotropic turbulence datasets to extract the Mori–Zwanzig operators. With data augmentation using known turbulence symmetries, the extracted Markov term, memory kernel, and orthogonal dynamics are statistically converged and the generalized fluctuation–dissipation relation can be verified. The properties of the memory kernel and orthogonal dynamics, and their dependence on the choices of observables are investigated to address the modeling assumptions that are commonly used in MZ-based models. A series of numerical experiments are then constructed using the extracted kernels to evaluate the memory effects on prediction. The results show that the prediction errors are strongly affected by the choice of observables and can be further reduced by including the past history of the observables in the memory kernel.

97 MATHEMATICS AND COMPUTING↗

KG-Hub—building and exchanging biological knowledge graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

59 BASIC BIOLOGICAL SCIENCES↗

DeepFreeze: Towards Scalable Asynchronous Checkpointing of Deep Learning Models

In the age of big data, deep learning has emerged as a powerful tool to extract insight and exploit its value, both in industry and scientific applications. One common pattern emerging in such applications is frequent checkpointing of the state of the learning model during training, needed in a variety of scenarios: analysis of intermediate states to explain features and correlations with training data, exploration strategies involving alternative models that share a common ancestor, knowledge transfer, resilience, etc. However, with increasing size of the learning models and popularity of distributed data-parallel training approaches, simple checkpointing techniques used so far face several limitations: low serialization performance, blocking I/O, stragglers due to the fact that only a single process is involved in checkpointing. This paper proposes a checkpointing technique specifically designed to address the aforementioned limitations, introducing efficient asynchronous techniques to hide the overhead of serialization and I/O, and distribute the load over all participating processes. Experiments with two deep learning applications (CANDLE and ResNet) on a pre-Exascale HPC platform (Theta) shows significant improvement over state-of-art, both in terms of checkpointing duration and runtime overhead.

checkpointing↗

Apparent temperatures of neutron-poor and neutron-rich compound nuclei

The possibility of the dependence of the nuclear caloric curve on neutron excess sets a limit on the accuracy of our knowledge of the nuclear equation of state, and thus impacts predictive capabilities of nuclear reaction and nuclear astrophysics models. To date, theoretical models have not reached consensus on the magnitude or sign on the asymmetry dependence. To provide constraints, we have measured evaporated particles and heavy residues for complete and incomplete fusion-evaporation reactions in inverse kinematics. The temperatures extracted from the observed light charged particles tend to favor higher temperatures for the neutron-rich fused systems, though they are near the limits of the systematic uncertainty. The present measurement may be used as an upper limit to constrain the asymmetry dependence of the nuclear caloric curve.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Molecular structure retrieval directly from laboratory-frame photoelectron spectra in laser-induced electron diffraction

Ubiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically exacerbated when imaging larger molecules or for dynamic systems with little a priori knowledge. Here, we employ laser-induced electron diffraction (LIED) which is a powerful means to determine the precise atomic configuration of an isolated gas-phase molecule with picometre spatial and attosecond temporal precision. We introduce a simple molecular retrieval method, which is based only on the identification of critical points in the oscillating molecular interference scattering signal that is extracted directly from the laboratory-frame photoelectron spectrum. The method is compared with a Fourier-based retrieval method, and we show that both methods correctly retrieve the asymmetrically stretched and bent field-dressed configuration of the asymmetric top molecule carbonyl sulfide (OCS), which is confirmed by our quantum-classical calculations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effect of Applied Stress on the Selective Oxidation of Alloy 600 Exposed to PWR Primary Water and Rhines Pack Environments

A mechanistic understanding of corrosion and oxidation processes is crucial to ensure long-term resistance to stress corrosion cracking of Ni-base structural alloys in pressurized water reactor (PWR) primary and secondary systems. Aqueous corrosion of Ni-base alloys under PWR primary water conditions was previously compared to gaseous oxidation with comparable oxygen potentials. However, those studies considered only stress-free conditions, which removes a critical parameter for understanding stress corrosion behaviors. A significant knowledge gap exists for the role of applied stresses on selective internal oxidation in gaseous environments. A micro-4-point-bend jig was designed to facilitate stress in a Rhines Pack set-up. Selective oxidation at different stress and strain conditions was investigated in a series of Rhines Pack experiments for Alloy 600. Focused ion beam milling enabled the extraction of site-specific specimens containing selected high-energy grain boundaries from tensile and compressive stress regions. Analytical transmission electron microscopy was employed to analyze the microstructure and chemical composition of the resulting oxides. Protective surface oxide films and selective intergranular oxides were observed at different conditions. The implications of these fundamental differences are discussed relative to intergranular attack and stress corrosion cracking mechanisms in PWR primary water.

stress, 4-point-bend, selective oxidation, Alloy 6↗

Lithium-Ion Battery Life Model with Electrode Cracking and Early-Life Break-in Processes

This paper develops a physically justified reduced-order capacity fade model from accelerated calendar- and cycle-aging data for 32 lithium-ion (Li-ion) graphite/nickel-manganese-cobalt (NMC) cells. The large data set reveals temperature-, charge C-rate-, depth-of-discharge-, and state of charge (SOC)-dependent degradation patterns that would be unobserved in a smaller test matrix. Model structure is informed by incremental capacity analysis that shows loss of lithium inventory and cathode-material loss as the dominant capacity fade mechanisms. The model includes terms attributable to solid-electrolyte interface (SEI) growth, electrode cracking, cycling-driven acceleration of SEI growth, and "break-in" mechanisms that slightly decrease or increase available Li inventory early in life. The study explores what mathematical couplings of these mechanisms best describe calendar aging, cycle aging, and mixed calendar/cycle aging. Various approaches are discussed for extracting relevant stress factors from complex cycling profiles to predict lifetime during real-world battery loads using models trained on constant-current laboratory test results. The complexity of the present human-driven model identification process motivates future work in machine learning to more widely search and statistically discern the optimal model that correctly extrapolates capacity fade based on physical knowledge.

25 ENERGY STORAGE↗

Simultaneous reweighting of Transverse Momentum Dependent distributions

The Bayesian reweighting procedure is extended to the case of multiple independent extractions of transverse momentum dependent parton distributions (TMDs). By exploiting the data on transverse single spin asymmetries, A N , for inclusive pion production in polarized proton-proton collisions measured at RHIC, we perform a simultaneous reweighting of the quark Sivers, transversity and Collins TMD functions extracted from semi-inclusive deep inelastic scattering (SIDIS) and annihilation into hadron pairs. The impact of the implementation of the Soffer bound, as well as the differences between older and newer e + e - data, are investigated. The agreement with A N data at large-x F values, a kinematical region complementary to those explored in SIDIS measurements, is enhanced, improving the knowledge of the polarized quark TMDs in the large-x region.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Reweighting the Sivers function with jet data from STAR

The reweighting procedure that using Bayesian statistics incorporates the information contained in a new data set, without the need of re-fitting, is applied to the quark Sivers function extracted from Semi-Inclusive Deep Inelastic Scattering (SIDIS) data. We exploit the recently published single spin asymmetry data for the inclusive jet production in polarized pp collisions from the STAR Collaboration at RHIC, which cover a much wider x region compared to SIDIS measurements. The reweighting method is extended to the case of asymmetric errors and the results show a remarkable improvement of the knowledge of the quark Sivers function.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Bayesian inference of nuclear symmetry energy from measured and imagined neutron skin thickness in Sn 116 , 118 , 120 , 122 , 124 , 130 , 132 , Pb 208 , and Ca 48

The neutron skin thickness Δr np in heavy nuclei has been known as one of the most sensitive terrestrial probes of the nuclear symmetry energy E sym (ρ) around $\frac{2}{3}$ of the saturation density ρ 0 of nuclear matter. Existing neutron skin data mostly from hadronic observables suffer from large uncertainties and their extraction from experiments are often strongly model dependent. While waiting eagerly for the promised model-independent and high-precision neutron skin data for 208 Pb and 48 Ca from the parity-violating electron scattering experiments (PREX-II and CREX at JLab as well as MREX at MESA), within the Bayesian statistical framework using the Skyrme-Hartree-Fock model we infer the posterior probability distribution functions (PDFs) of the slope parameter L of the nuclear symmetry energy at ρ 0 from imagined Δr np ( 208 Pb)=0.15, 0.20, and 0.30 fm with a 1σ error bar of 0.02, 0.04, and 0.06 fm, respectively, as well as Δr np ( 48 Ca)=0.12, 0.15, and 0.25 fm, with different 1σ error bar of 0.01 and 0.02 fm, respectively. The results are compared with the PDFs of L inferred using the same approach from the available Δr np data for 116, 118, 120, 122, 124, 130, 132 Sn from hadronic probes. They are also compared with results from a recent Bayesian analysis of the radius and tidal deformability data of canonical neutron stars from GW170817 and NICER. The neutron skin data for Sn isotopes gives L = 45.5 $^{+ 26.5}_{-21.6}$ MeV surrounding its mean value or L = 53 . 4 $^{+ 18.6}_{ -29.5}$ MeV surrounding its maximum a posteriori value, respectively, with the latter smaller than but consistent with the L = 66 $^{+ 12}_{-20}$ MeV from the neutron star data within their 68% confidence intervals. We found that Δr np = 0.17 –0.18 fm in 208 Pb with an error bar of about 0.02 fm leads to a PDF of L compatible with that from analyzing the Sn data. To provide additionally useful information on L extracted from the Δr np of Sn isotopes, the experimental error bar of Δr np in 208 Pb should be at least smaller than 0.06 fm aimed by some current experiments. In addition, the Δr np ( 48 Ca) needs to be larger than 0.15 fm but smaller than 0.25 fm to be compatible with the Sn and/or neutron star results. To further improve our current knowledge about L and distinguish its PDFs in the examples considered, even higher precisions leading to significantly less than ±20 MeV error bars for L at 68% confidence level are necessary.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Snowmass Neutrino Frontier: Neutrino Interaction Cross Sections (NF06) Topical Group Report

A thorough understanding of neutrino cross sections in a wide range of energies is crucial for the successful execution of the entire neutrino physics program. In order to extract neutrino properties, long-baseline experiments need an accurate determination of neutrino cross sections within their detector(s). Since very few of the needed neutrino cross sections across the energy spectrum are directly measured, we emphasize the need for theoretical input and indirect measurements such as electron scattering, which would complement direct measurements. In this report we briefly summarize the current status of our knowledge of the neutrino cross sections and articulate needs of the experiments, ongoing and planned, at energies ranging from CEvNS and supernova neutrino energies to the DUNE and atmospheric neutrino energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Retrieving functional pathways of biomolecules from single-particle snapshots

Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Robotic Understanding of Spatial Relationships Using Neural-Logic Learning

Understanding spatial relations of objects is critical in many robotic applications such as grasping, manipulation, and obstacle avoidance. Humans can simply reason object's spatial relations from a glimpse of a scene based on prior knowledge of spatial constraints. The proposed method enables a robot to comprehend spatial relationships among objects from RGB-D data. This paper proposed a neural-logic learning framework to learn and reason spatial relations from raw data by following logic rules on spatial constraints. The neural-logic network consists of three blocks: grounding block, spatial logic block, and inference block. The grounding block extracts high-level features from the raw sensory data. The spatial logic blocks can predicate fundamental spatial relations by training a neural network with spatial constraints. The inference block can infer complex spatial relations based on the predicated fundamental spatial relations. Simulations and robotic experiments evaluated the performance of the proposed method.

Wang, Dali↗

An Agenda for Multimodal Foundation Models for Earth Observation

Archives of remote sensing (RS) data are increasing swiftly as new sensing modalities with enhanced spatiotemporal resolution become operational. While promising new breakthroughs, the sheer volume of RS archives stretches the limits of human analysts and existing AI tools, as most models are: i) limited to single data modalities; ii) task-specific; iii) heavily reliant on labeled data. The emerging Foundation Models (FMs) have the potential to address these limitations. Trained on vast unlabeled datasets through self-supervised learning, FMs enable generic feature extraction that facilitate specialization to a wide variety of downstream tasks. This paper describes a vision towards an FM for multimodal Earth Observation data (FM4EO), discussing key building blocks and open challenges. We put particular emphasis on multimodal reasoning, a topic underexplored in EO. Our ultimate goal is a practical path toward FM4EO with capacity to unlock breakthroughs in few-shot learning scenarios, multimodal geographic knowledge integration, synthesis, and hypothesis generation.

Ambrozio Dias, Philipe↗

AMIA KDDM Working Group Collaborative Workshop: Enriching Electronic Health Records with Social Determinants of Health to Improve Outcomes and Health Equity

Prior research has demonstrated that social determinants of health (SDoH) are major drivers of health outcomes and contributors to widespread health inequities. It was estimated that, in the United States, SDoH could be responsible for up to 40% of all preventable deaths, significantly higher than the 10-15% for which better medical care is responsible. Public health interventions that target SDoH are instrumental for improving health outcomes and reducing long-standing health inequities. Currently, most mainstream EHR vendors have implemented SDoH screeners in their EHR systems. However, the utility of the screeners is low, rendering patient-level SDoH still widely unavailable in the structured fields. SDoH are sometimes mentioned in free-text clinical notes (e.g., social context section) where natural language processing (NLP) can be applied to extract relevant information. Contextual-level SDoH can be identified from multiple data sources, many of which are publicly available and spatiotemporally linked to EHR data. As such, there is an opportunity for the KDDM research community to create innovative solutions to draw meaningful insights by creating and using rich data with SDoH to improve health outcomes while reducing disparities. In this workshop organized by AMIA Knowledge Discovery and Data Mining Working Group (AMIA KDDM WG), we will invite world-leading experts from academia, national laboratories, and life science industry with varied backgrounds in biomedical informatics, epidemiology, data science, machine learning, natural language processing, and pediatric cardiology to discuss the best practice of capturing, standardizing, and using SDoH information in various applications aiming at improving outcomes and health equity.

He, Zhe↗

Emergence of deep eutectic solvents (DES): chemistry, preparation, properties, and applications in biorefineries and critical materials

The emergence of renewable deep eutectic solvents (DES) as clean and efficient catalysts and solvents has created new opportunities for lignocellulosic biorefineries and critical material sectors, including chemical, energy, pharmaceutical, textile, and hydrometallurgical industries. This review provides an in-depth overview of DES, covering their chemistry, classifications, preparation methods, processing characteristics, and recyclability, while highlighting their unique attributes and industry relevant applications. Emphasis is placed on the integration of DES into advanced biorefinery systems, focusing on their tunable physicochemical and thermodynamic properties for biomass pretreatment and the production of value-added products. The review explores how DES can be tuned for selective dissolution of biomass components and evaluates production and valorization of DES-derived biochemicals, with attention to lignin extraction mechanisms and conversion of biomass into bioproducts and biofuels. Beyond biorefineries, the scope extends to DES applications in electrochemical energy devices, where they serve as electrolytes, synthesis media for electrode materials, and leaching agents in battery recycling. The multifunctional roles of DES in pharmaceutical, hydrometallurgical, and textile sectors are also explored for contributions to sustainable processing. Finally, the review identifies future research directions, outlining benefits, challenges, and knowledge gaps, for continued industrial development.

09 BIOMASS FUELS↗

An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the “feature importance” approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.

Chemistry↗

Neutron Skin Measurement of208Pb Using Parity-Violating Electron Scattering

Nuclear stability requires large nuclei to have more neutrons than protons. While the central core of the nucleus is composed of symmetric nuclear matter, the extra neutrons in heavy nuclei are pushed out to the surface of the nucleus, forming a pure outer neutron skin layer. While the proton distribution inside a nucleus has been accurately measured using electromagnetic probes, previous measurements of neutron distributions in complex nuclei have suffered a lack of systematic precision. PREX-2 and CREX use Parity-Violating electron Scattering (PVeS), as an electroweak interaction probe, to measure the neutron distributions in208Pb and48Ca, respectively. Making use of elastic scattering of longitudinally polarized electrons from unpolarized (isotopically pure) targets, PREX-2 and CREX measure the asymmetry in scattering rates between opposite beam polarization states. Since both experiments share the same exact measurement concept and apparatus, much of this dissertation applies to both PREX-2 and CREX. However, the presented asymmetry analysis and neutron skin extraction are only for PREX-2. PREX-2 measures the parity-violating asymmetry, APV, for 953 MeV electrons scattered elastically from208Pb at?5°in the lab. The final result is APV= 550.00±16.09(stat.)±8.16(syst.)ppb. From this measurement, we report the neutron skin thickness in208Pb nuclei to be, Rskin= 0.278±0.078(exp.)±0.012(model) fm. This measurement has broad implications throughout the physics community, increasing our knowledge in neutron star structure, the equation of state of nuclear matter, nuclear baryon density, nuclear electric dipole polarizability, and more. Key Words: Neutron skin, electroweak interaction, PREX-2, CREX, parity-violating asymmetry, neutron star, quartz detector, weak charge radius, symmetry energy, Hall A, Jefferson Lab

Adhikari, Devi↗