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At least 1,117 records · Page 62

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

59 BASIC BIOLOGICAL SCIENCES↗

Probing reaction channels via reinforcement learning

Abstract Chemical reactions are dynamical processes involving the correlated reorganization of atomic configurations, driving the conversion of an initial reactant into a result product. By virtue of the metastability of both the reactants and products, chemical reactions are rare events, proceeding fleetingly. Reaction pathways can be modelled probabilistically by using the notion of reactive density in the phase space of the molecular system. Such density is related to a function known as the committor function, which describes the likelihood of a configuration evolving to one of the nearby metastable regions. In theory, the committor function can be obtained by solving the backward Kolmogorov equation (BKE), which is a partial differential equation (PDE) defined in the full dimensional phase space. However, using traditional methods to solve this problem is not practical for high dimensional systems. In this work, we propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an ensemble of states that concentrate on the transition path ensemble. This configuration ensemble can be effectively employed in a neural network-based PDE solver to obtain an approximation solution of a restricted BKE, even when the dimension of the problem is very high. The resulting solution provides an approximation for the committor function that encodes mechanistic information for the reaction, paving a new way for understanding of complex chemical reactions and evaluation of reaction rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DAmodel: hierarchical Bayesian modelling of DA white dwarfs for spectrophotometric calibration

We use hierarchical Bayesian modelling to calibrate a network of 32 all-sky faint DA white dwarf (DA WD) spectrophotometric standards (⁠16.5 < V , 19.5⁠) alongside three CALSPEC standards, from 912 Å to 32 μm. The framework is the first of its kind to jointly infer photometric zero points and WD parameters (surface gravity log g⁠, effective temperature T eff ⁠, extinction A V ⁠, dust relation parameter R V ) by simultaneously modelling both photometric and spectroscopic data. We model panchromatic Hubble Space Telescope Wide Field Camera 3 (HST/WFC3) UVIS and IR photometry, HST/STIS UV spectroscopy, and ground-based optical spectroscopy to sub-per cent precision. Photometric residuals for the sample are the lowest yet yielding < 0.004 mag RMS on average from the UV to the NIR, achieved by jointly inferring time-dependent changes in system sensitivity and WFC3/IR count-rate nonlinearity. Our GPU-accelerated implementation enables efficient sampling via Hamiltonian Monte Carlo, critical for exploring the high-dimensional posterior space. The hierarchical nature of the model enables population analysis of intrinsic WD and dust parameters. Inferred spectral energy distributions from this model will be essential for calibrating the James Webb Space Telescope as well as next-generation surveys, including Vera Rubin Observatory’s Legacy Survey of Space and Time and the Nancy Grace Roman Space Telescope.

methods: statistical↗

Absence of Off-Diagonal Long-Range Order in hcp 4 He Dislocation Cores

Here, the mass transport properties along dislocation cores in hcp 4 He are revisited by considering two types of edge dislocations as well as a screw dislocation, using a fully correlated quantum simulation approach. Specifically, we employ the zero-temperature path-integral ground state (PIGS) method together with ergodic sampling of the permutation space to investigate the fundamental dislocation core structures and their off-diagonal long-range order properties. It is found that the Bose-Einstein condensate fraction of such defective 4 He systems is practically null (≤ 10 –6 ), just as in the bulk defect-free crystal. These results provide compelling evidence for the absence of intrinsic superfluidity in dislocation cores in hcp 4 He and challenge the superfluid dislocation-network interpretation of the mass-flux-experiment observations, calling for further experimental investigation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A JWST Survey of the Supernova Remnant Cassiopeia A

We present initial results from a James Webb Space Telescope (JWST) survey of the youngest Galactic core-collapse supernova remnant, Cassiopeia A (Cas A), made up of NIRCam and MIRI imaging mosaics that map emission from the main shell, interior, and surrounding circumstellar/interstellar material (CSM/ISM). We also present four exploratory positions of MIRI Medium Resolution Spectrograph integral field unit spectroscopy that sample ejecta, CSM, and associated dust from representative shocked and unshocked regions. Surprising discoveries include (1) a weblike network of unshocked ejecta filaments resolved to ~0.01 pc scales exhibiting an overall morphology consistent with turbulent mixing of cool, low-entropy matter from the progenitor's oxygen layer with hot, high-entropy matter heated by neutrino interactions and radioactivity; (2) a thick sheet of dust-dominated emission from shocked CSM seen in projection toward the remnant's interior pockmarked with small (~1'') round holes formed by ≲0$^"_•$1 knots of high-velocity ejecta that have pierced through the CSM and driven expanding tangential shocks; and (3) dozens of light echoes with angular sizes between ~0$^"_•$1 and 1' reflecting previously unseen fine-scale structure in the ISM. NIRCam observations place new upper limits on infrared emission (≲20 nJy at 3 μm) from the neutron star in Cas A's center and tightly constrain scenarios involving a possible fallback disk. These JWST survey data and initial findings help address unresolved questions about massive star explosions that have broad implications for the formation and evolution of stellar populations, the metal and dust enrichment of galaxies, and the origin of compact remnant objects.

79 ASTRONOMY AND ASTROPHYSICS↗

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

PolyODENet: Deriving mass-action rate equations from incomplete transient kinetics data

Kinetics of a reaction network that follows mass-action rate laws can be described with a system of ordinary differential equations (ODEs) with polynomial right-hand side. However, it is challenging to derive such kinetic differential equations from transient kinetic data without knowing the reaction network, especially when the data are incomplete due to experimental limitations. We introduce a program, PolyODENet, toward this goal. Based on the machine-learning method Neural ODE, PolyODENet defines a generative model and predicts concentrations at arbitrary time. As such, it is possible to include unmeasurable intermediate species in the kinetic equations. Importantly, we have implemented various measures to apply physical constraints and chemical knowledge in the training to regularize the solution space. Here, using simple catalytic reaction models, we demonstrate that PolyODENet can predict reaction profiles of unknown species and doing so even reveal hidden parts of reaction mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Latent Twins

Over the past decade, scientific machine learning has transformed the development of mathematical and computational frameworks for analyzing, modeling, and predicting complex systems. From inverse problems to numerical partial differential equations (PDEs), dynamical systems, and model reduction, these advances have pushed the boundaries of what can be simulated. Yet they have often progressed in parallel, with representation learning and algorithmic solution methods evolving largely as separate pipelines. With Latent Twins, we propose a unifying mathematical framework that creates a hidden surrogate in latent space for the underlying equations. Whereas digital twins mirror physical systems in the digital world, Latent Twins mirror mathematical systems in a learned latent space governed by operators. Through this lens, classical modeling, inversion, model reduction, and operator approximation all emerge as special cases of a single principle. We establish the fundamental approximation properties of Latent Twins for both ordinary differential equations (ODEs) and PDEs and demonstrate the framework across three representative settings: (i) canonical ODEs, capturing diverse dynamical regimes; (ii) a PDE benchmark using the shallow-water equations, contrasting Latent Twin simulations with deep operator network and forecasts with a four-dimensional variational method baseline; and (iii) a challenging real-data geopotential reanalysis dataset, reconstructing and forecasting from sparse, noisy observations. Latent Twins provide a compact, interpretable surrogate for solution operators that evaluate across arbitrary time gaps in a single-shot, while remaining compatible with scientific pipelines such as assimilation, control, and uncertainty quantification. Looking forward, this framework offers scalable, theory-grounded surrogates that bridge data-driven representation learning and classical scientific modeling across disciplines.

Latent Twins↗

Domain Adaptive Graph Neural Networks for Constraining Cosmological Parameters Across Multiple Data Sets

Deep learning models have been shown to outperform methods that rely on summary statistics, like the power spectrum, in extracting information from complex cosmological data sets. However, due to differences in the subgrid physics implementation and numerical approximations across different simulation suites, models trained on data from one cosmological simulation show a drop in performance when tested on another. Similarly, models trained on any of the simulations would also likely experience a drop in performance when applied to observational data. Training on data from two different suites of the CAMELS hydrodynamic cosmological simulations, we examine the generalization capabilities of Domain Adaptive Graph Neural Networks (DA-GNNs). By utilizing GNNs, we capitalize on their capacity to capture structured scale-free cosmological information from galaxy distributions. Moreover, by including unsupervised domain adaptation via Maximum Mean Discrepancy (MMD), we enable our models to extract domain-invariant features. We demonstrate that DA-GNN achieves higher accuracy and robustness on cross-dataset tasks. Using data visualizations, we show the effects of domain adaptation on proper latent space data alignment. This shows that DA-GNNs are a promising method for extracting domain-independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.

79 ASTRONOMY AND ASTROPHYSICS↗

PolyODENet

Kinetics of a reaction network that follows mass-action rate laws can be described with a system of ordinary differential equations (ODEs) with polynomial right-hand side. However, it is challenging to derive such kinetic differential equations from transient kinetic data without knowing the reaction network, especially when the data are incomplete due to experimental limitations. We introduce a program, PolyODENet, toward this goal. Based on the machine-learning method Neural ODE, PolyODENet defines a generative model and predicts concentrations at arbitrary time. As such, it is possible to include unmeasurable intermediate species in the kinetic equations. Importantly, we have implemented various measures to apply physical constraints and chemical knowledge in the training to regularize the solution space.

Wu, Qin [Brookhaven National Lab. (BNL), Upton, NY↗

WISE-PS1-STRM: neural network source classification and photometric redshifts for WISE×PS1

ABSTRACT We cross-match between the WISE All-Sky and PS1 3π DR2 source catalogues. The resulting catalogue has 354 590 570 objects, significantly fewer than the parent PS1 catalogue, but its combination of optical and infrared colours facilitate both better source classification and photometric redshift estimation. We perform a neural network-based classification of the objects into galaxies, quasars, and stars, then run neural network-based photometric redshift estimation for the galaxies. The star sample purity and quasar sample completeness measures improve substantially, and the resulting photo-z’s are significantly more accurate in terms of statistical scatter and bias than those calculated from PS1 properties alone. The catalogue will be a basis for future large-scale structure studies, and will be made available as a high-level science product via the Mikulski Archive for Space Telescopes.

79 ASTRONOMY AND ASTROPHYSICS↗

Entanglement transitions from restricted Boltzmann machines

The search for novel entangled phases of matter has lead to the recent discovery of a new class of “en- tanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Furthermore, our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Maximum respiration rates in hyporheic zone sediments are primarily constrained by organic carbon concentration and secondarily by organic matter chemistry

Abstract. River corridors are fundamental components of the Earth system, and their biogeochemistry can be heavily influenced by processes in subsurface zones immediately below the riverbed, referred to as the hyporheic zone. Within the hyporheic zone, organic matter (OM) fuels microbial respiration, and OM chemistry heavily influences aerobic and anaerobic biogeochemical processes. The link between OM chemistry and respiration has been hypothesized to be mediated by OM molecular diversity, whereby respiration is predicted to decrease with increasing diversity. Here we test the specific prediction that aerobic respiration rates will decrease with increases in the number of unique organic molecules (i.e., OM molecular richness, as a measure of diversity). We use publicly available data across the United States from crowdsourced samples taken by the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS) consortium. Our continental-scale analyses rejected the hypothesis of a direct limitation of respiration by OM molecular richness. In turn, we found that organic carbon (OC) concentration imposes a primary constraint over hyporheic zone respiration, with additional potential influences of OM richness. We specifically observed respiration rates to decrease nonlinearly with the ratio of OM richness to OC concentration. This relationship took the form of a constraint space with respiration rates in most systems falling below the constraint boundary. A similar, but slightly weaker, constraint boundary was observed when relating respiration rate to the inverse of OC concentration. These results indicate that maximum respiration rates may be governed primarily by OC concentration, with secondary influences from OM richness. Our results also show that other variables often suppress respiration rates below the maximum associated with the richness-to-concentration ratio. An important focus of future research will identify physical (e.g., sediment grain size), chemical (e.g., nutrient concentrations), and/or biological (e.g., microbial biomass) factors that suppress hyporheic zone respiration below the constraint boundaries observed here.

58 GEOSCIENCES↗

When van der Waals Met Kagome: A 2D Antimonide with a Vanadium-Kagome Network

2D materials showcase unconventional properties emerging from quantum confinement effects. In this work, a “soft chemical” route allows for the deintercalation of K + from the layered antimonide KV 6 Sb 6 , resulting in the discovery of a new metastable 2D-Kagome antimonide K 0.1(1) V 6 Sb 6 with a van der Waals gap of 3.2 Å. The structure of K 0.1(1) V 6 Sb 6 was determined via the synergistic techniques, including X-ray pair distribution function analysis, advanced transmission electron microscopy, and density functional theory calculations. The K 0.1(1) V 6 Sb 6 compound crystallizes in the monoclinic space group C2/m (a = 9.57(2) Å, b = 5.502(8) Å, c = 10.23(2) Å, β = 97.6(2)°, Z = 2). The [V 6 Sb 6 ] layers in K 0.1(1) V 6 Sb 6 are retained upon deintercalation and closely resemble the layers in the parent compound, yet deintercalation results in a relative shift of the adjacent [V 6 Sb 6 ] layers. The magnetic properties of the K 0.1(1) V 6 Sb 6 phase in the 2–300 K range are comparable to those of KV 6 Sb 6 and another Kagome antimonide KV 3 Sb 5 , consistent with nearly temperature-independent paramagnetism. Electronic band structure calculation suggests a nontrivial band topology with flat bands and opening of band crossing afforded by deintercalation. Transport property measurements reveal a metallic nature for K 0.1(1) V 6 Sb 6 and a low thermal conductivity of 0.6 W K –1 m –1 at 300 K. Additionally, ion exchange in KV 6 Sb 6 via a solvothermal route leads to a successful partial exchange of K + with A + (A = Na, Rb, and Cs). Here, this study highlights the tunability of the layered structure of the KV 6 Sb 6 compound, providing a rich playground for the realization of new 2D materials.

2D↗

First Search for Dark-Trident Processes Using the MicroBooNE Detector

This thesis presents a first search for dark-trident scattering in a neutrino beam using a data set corresponding to $7.2 \times 10^{20}$ protons on target taken with the MicroBooNE detector at Fermilab. Proton interactions in the neutrino target at the Main Injector produce $\pi^0$ and $\eta$ mesons, which could decay into dark matter (DM) particles via a dark photon $A^{\prime}$. A convolutional neural network is trained to identify interactions of the DM particles in the liquid-argon time projection chamber (LArTPC) exploiting its image-like reconstruction capability. In the absence of a DM signal, limits at the $90\%$ confidence level on the squared kinematic mixing parameter $\varepsilon^2$ as a function of the dark-photon mass in the range $10\le M_{A^\prime}\le 400$~MeV are provided. The limits cover previously unconstrained parameter space for the production of fermion or scalar DM particles $\chi$ for two benchmark models with mass ratios $M_{\chi}/M_{A^\prime}=0.6$ and $2$ and for dark fine-structure constants $0.1\le\alpha_D\le 1$.Date of Award1 Aug 2024Original languageEnglishAwarding InstitutionThe University of ManchesterSupervisorStefan Soldner-Rembold (Supervisor) & Justin Evans (Supervisor)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Long–short-term memory encoder–decoder with regularized hidden dynamics for fault detection in industrial processes

The ability of recurrent neural networks (RNN) to model nonlinear dynamics of high dimensional process data has enabled data-driven RNN-based fault detection algorithms. Previous studies have focused on detecting faults by identifying the discrepancies in data distribution between the faulty and normal data, as reflected in prediction errors generated by RNN models. However, in industrial processes, variations in data distribution can also result from changes in normal control setpoints and compensatory control adjustments in response to disturbances, making it hard to differentiate between normal and faulty conditions. This paper proposes a fault detection method utilizing a long short-term memory (LSTM) encoder–decoder structure with regularized hidden dynamics and reversible instance normalization (RevIN) to compactly represent high-dimensional measurements for effective monitoring. During training, the hidden states of the model are regularized to form a low-dimensional latent space representation of the original multivariate time series data. As a result, the prediction errors of the latent states can be used to monitor the abnormal dynamic variations, while the reconstruction errors of the measured variables are used to monitor the abnormal static variations. Furthermore, the proposed indices can reflect operating conditions, even when the distribution of test data changes, which helps distinguish faults from normal adjustments and disturbances that controllers can settle. Here, data from numerical simulation and the Tennessee Eastman process are used to illustrate the effectiveness of the proposed fault detection method.

42 ENGINEERING↗

Improved energies and local energies with weighted variational Monte Carlo

Neural network parametrizations have increasingly been used to represent the ground and excited states in variational Monte Carlo (VMC) with promising results. However, traditional VMC methods only optimize the wave function in regions of peak probability. The wave function is uncontrolled in the tails of the probability distribution, which can limit the accuracy of the trained wave function. To improve the approximation accuracy in the probability tails, this paper interprets VMC as a gradient flow in the space of wave functions, followed by a projection step. From this perspective, arbitrary probability distributions can be used in the projection step, allowing the user to prioritize accuracy in different regions of state space. Motivated by this theoretical perspective, the paper tests a weighted VMC method on the antiferromagnetic Heisenberg model for a periodic spin chain. Compared to traditional VMC, weighted VMC reduces the error in the ground state energy by a factor of 2, and it reduces the errors in the local energies away from the mode by large factors of 10 2 –10 4 .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Autotuning of Double-Dot Devices In Situ with Machine Learning

The current practice of manually tuning quantum dots (QDs) for qubit operation is a relatively time-consuming procedure that is inherently impractical for scaling up and applications. In this work, we report on the in situ implementation of a recently proposed autotuning protocol that combines machine learning (ML) with an optimization routine to navigate the parameter space. In particular, we show that a ML algorithm trained using exclusively simulated data to quantitatively classify the state of a double-QD device can be used to replace human heuristics in the tuning of gate voltages in real devices. Here, we demonstrate active feedback of a functional double-dot device operated at millikelvin temperatures and discuss success rates as a function of the initial conditions and the device performance. Modifications to the training network, fitness function, and optimizer are discussed as a path toward further improvement in the success rate when starting both near and far detuned from the target double-dot range.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗