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At least 1,351 records · Page 75

The evolution of contact prediction: Evidence that contact selection in statistical contact prediction is changing

Over the last few years, the field of protein structure prediction has been transformed by increasingly-accurate contact prediction software. These methods are based on the detection of coevolutionary relationships between residues from multiple sequence alignments. However, despite speculation, there is little evidence of a link between contact prediction and the physico-chemical interactions which drive amino-acid coevolution. Furthermore, existing protocols predict only a fraction of all protein contacts and it is not clear why some contacts are favoured over others. Using a dataset of 863 protein domains, we assessed the physico-chemical interactions of contacts predicted by CCMpred, MetaPSICOV, and DNCON2, as examples of direct coupling analysis, meta-prediction, and deep learning. We considered correctly-predicted contacts and compared their properties against the protein contacts that were not predicted. Predicted contacts tend to form more bonds than non-predicted contacts, which suggests these contacts may be more important than contacts that were not predicted. Comparing the contacts predicted by each method, we found that metaPSICOV and DNCON2 favour accuracy whereas CCMPred detects contacts with more bonds. This suggests that the push for higher accuracy may lead to a loss of physico-chemically important contacts. These results underscore the connection between protein physico-chemistry and the coevolutionary couplings that can be derived from multiple sequence alignments. This relationship is likely to be relevant to protein structure prediction and functional analysis of protein structure and may be key to understanding their utility for different problems in structural biology. We use publicly-available databases. Our code is available for download at http://opig.stats.ox.ac.uk/.

59 BASIC BIOLOGICAL SCIENCES↗

Generalizable machine learning potentials for quantum-accurate predictions of non-equilibrium behavior in 2D materials

Machine learning interatomic potentials (ML-IAPs) are emerging as transformative tools in materials modeling, promising quantum-level accuracy at a fraction of the computational cost. However, their ability to generalize beyond equilibrium configurations and to reliably capture defect- and temperature-driven behavior remains underexplored. Here, we develop and benchmark two state-of-the-art ML-IAPs, Spectral Neighbor Analysis Potential (SNAP) and Allegro, on a comprehensive dataset for monolayer MoSe₂. Using density functional theory (DFT) as the reference, we evaluate their performance in capturing stress–strain behavior, phase transition energetics, defect evolution, edge stability, and fracture toughness. Allegro, a deep equivariant neural network potential, surpasses both SNAP and the classical Tersoff potential in accuracy, efficiency, and transferability. Importantly, both ML potentials accurately reproduce experimental fracture measurements and ab initio predictions of inversion domain formation—phenomena well beyond their training sets. Our findings establish ML-IAPs as viable replacements for traditional force fields in the study of non-equilibrium mechanical phenomena, enabling large-scale, high-fidelity simulations in 2D materials and beyond. In conclusion, this work provides a broadly applicable framework for data-driven modeling of structural and functional transformations under extreme conditions.

2D materials↗

Physics-constrained deep learning of nonlinear normal modes of spatiotemporal fluid flow dynamics

In this study, we present a physics-constrained deep learning method to discover and visualize from data the invariant nonlinear normal modes (NNMs) which contain the spatiotemporal dynamics of the fluid flow potentially containing strong nonlinearity. Specifically, we develop a NNM-physics-constrained convolutional autoencoder (NNM-CNN-AE) integrated with a multi-temporal-step dynamics prediction block to learn the nonlinear modal transformation, the NNMs containing the spatiotemporal dynamics of the flow, and reduced-order reconstruction and long-time future-state prediction of the flow fields, simultaneously. In test cases, we apply the developed method to analyze different flow regimes past a cylinder, including laminar flows with low Reynolds number in transient and steady states (RD = 100) and high Reynolds number flow (RD = 1000), respectively. The results indicate that the identified NNMs are able to reveal the nonlinear spatiotemporal dynamics of these flows, and the NNMs-based reduced-order modeling consistently achieves better accuracy with orders of magnitudes smaller errors in construction and prediction of the nonlinear velocity and vorticity fields, compared to the linear proper orthogonal decomposition (POD) method and the Koopman-constrained-CNN-AE using the same number or dimension of modes. We perform an analysis of the modal energy distribution of NNMs and find that compared to POD modes, the few fundamental NNMs capture a very high level of total energy of the flow, which is advantageous for reduced-order modeling and representation of the complex flows. Finally, we discuss the potentials and limitations of the presented method.

Mechanics↗

Integration and validation of some modules for modelling of high-speed chemically reactive flows in two-phase gas-droplet mixtures

Three modules are integrated into the built-in OpenFOAM rhoCentralFoam solver towards accurate and efficient modelling of high-speed chemically reactive flows in two-phase gas-droplet mixtures within the OpenFOAM 10.0 framework. The first module is the mixture-averaged diffusion model. The second module is the built-in OpenFOAM Lagrangian solver coupled with optimised droplet drag coefficient and convective heat transfer coefficient sub-models. The last module is a sparse stiff chemistry solver based on dynamic adaptive hybrid integration (AHI-S). The optimised droplet sub-models are first verified in correct implementation for subsequent simulations in this work. Further, they show good accuracy against experimental and analytical data in the modelling of ammonia droplet acceleration and cooling in the flowing and/or low-temperature air. The accuracy and efficiency gains related to the mixture-averaged diffusion model and the AHI-S chemistry solver are examined by simulating 1-D detonation propagation in ammonia droplet-free/laden ammoniaoxygen mixtures. Numerical results of detonation propagation speed, gaseous temperature, density, and species distributions around the induction zone show good agreement with experimental data and analytical solutions. Compared to the built-in OpenFOAM diffusion model, the mixture-averaged diffusion model provides different numerical predictions of pulsating instabilities in detonation propagation. It shows better accuracy in depicting the detonation structure within the droplet-free section attributed to improved multi-component diffusion modelling. Compared to the built-in OpenFOAM solver EulerImplicit (backward Euler), the AHI-S chemistry solver reduces the computational cost by around 50%. It achieves satisfactory accuracy in calculating detonation propagation speed within the droplet-free section with the optimal efficiency when the safety factor, β, equals 0.5.

42 ENGINEERING↗

Yield strength prediction of high-entropy alloys using machine learning

Yield strength at high temperature is an important parameter in the design and application of high entropy alloys (HEAs). However, the experimental measurement of yield strength at high temperature is quite costly, complicated, and time-consuming. Therefore, it is essential to identify and apply a robust method for the accurate prediction of yield strength at high temperature from the available experimental and simulation data. In this study, for the first time, a machine learning (ML) method based on the regression technique of random forest (RF) regressor is used to predict the yield strength of HEAs at the desired temperature. Further, the yield strengths of MoNbTaTiW and HfMoNbTaTiZr at 800 °C and 1200 °C, are predicted using the RF regressor model. We find that the results are consistent with the experimental reports, showing that the RF regressor model predicts the yield strength of HEAs at the desired temperatures with high accuracy.

36 MATERIALS SCIENCE↗

A REDUCED ORDER MODELING APPROACH TO PROBABILISTIC CREEP-DAMAGE PREDICTIONS IN FINITE ELEMENT ANALYSIS

This paper introduces a computationally efficient Reduced Order Modeling (ROM) approach for the probabilistic prediction of creep-damage failure. Component-level probabilistic simulations are needed to assess the reliability and safety of high-temperature components. Full-scale probabilistic creep-damage modeling in finite element (FE) approach is computationally expensive requiring many hundreds of simulations to replicate the uncertainty of component failure. To that end, ROM is proposed to minimize the elevated computational cost while controlling the loss of accuracy. It is proposed that full-scale probabilistic simulations can be completed in 1D at a reduced cost, the extremum conditions extracted, and those conditions applied for lower-cost 2D/3D probabilistic simulations of components that capture the mean and uncertainty of failure. The probabilistic Sine-hyperbolic (Sinh) model is selected which in previous work was calibrated to alloy 304 stainless steel. The Sinh model includes probability density functions (pdfs) for test condition (stress and temperature), initial damage (i.e. microstructure), and material properties uncertainty. The Sinh model is programmed into ANSYS finite element software using the USERCREEP.F material subroutine. First, the Sinh model and FE code are subject to verification and validation to ensure the accuracy of the simulations. Numerous Monte Carlo simulations are executed in a 1D model to generate probabilistic creep deformation, damage, and rupture data. This data is analyzed and the probabilistic parameters corresponding to extreme creep response are extracted. The ROM concept is applied where only the extreme conditions are applied in the 2D probabilistic prediction of a component. The probabilistic predictions between the 1D and 2D geometry is compared to assess ROM for creep. The accuracy of the probabilistic prediction employing the ROM approach will potentially reduce the time and cost of simulating complex engineering systems. Future studies will introduce multi-stage Sinh, stochasticity, and spatial uncertainty for improved prediction.

36 MATERIALS SCIENCE↗

Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states

We report molecular-orbital-based machine learning (MOB-ML) provides a general framework for the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. The application of Nesbet’s theorem makes it possible to recast a typical extrapolation task, training on correlation energies for small molecules and predicting correlation energies for large molecules, into an interpolation task based on the properties of orbital pairs. We demonstrate the importance of preserving physical constraints, including invariance conditions and size consistency, when generating the input for the machine learning model. Numerical improvements are demonstrated for different datasets covering total and relative energies for thermally accessible organic and transition-metal containing molecules, non-covalent interactions, and transition-state energies. MOB-ML requires training data from only 1% of the QM7b-T dataset (i.e., only 70 organic molecules with seven and fewer heavy atoms) to predict the total energy of the remaining 99% of this dataset with sub-kcal/mol accuracy. This MOB-ML model is significantly more accurate than other methods when transferred to a dataset comprising of 13 heavy atom molecules, exhibiting no loss of accuracy on a size intensive (i.e., per-electron) basis. It is shown that MOB-ML also works well for extrapolating to transition-state structures, predicting the barrier region for malonaldehyde intramolecular proton-transfer to within 0.35 kcal/mol when only trained on reactant/product-like structures. Finally, the use of the Gaussian process variance enables an active learning strategy for extending the MOB-ML model to new regions of chemical space with minimal effort. We demonstrate this active learning strategy by extending a QM7b-T model to describe non-covalent interactions in the protein backbone–backbone interaction dataset to an accuracy of 0.28 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning-based predictive models for laser direct drive at the Omega Laser Facility

The rich and complex physics of inertial confinement fusion provides a unique and challenging space for high-fidelity first-principles modeling. Consequently, simulation codes that are used to design experiments are computationally expensive and lack the predictive capability required for extensive parameter exploration in search of a high-performing design for laser direct drive. In this article, we present two deep-learning-based predictive models intended to address these difficulties. The first model (TL DNN) acts as a fast emulator of simulations as well as experiments at the Omega Laser Facility. This model is trained on a simulation database and subsequently calibrated on experimental data using transfer learning. To facilitate the development of this model, an autoencoder is developed to reduce the dimensionality of the input space by compressing the laser pulse input. The model predicts key experimental scalar observables of Omega experiments with high accuracy and minimal computational cost. This deep neural net enables rapid exploration of a high-dimensional input parameter space for an optimal implosion design. The second model (DNN SM+) aims to extend the statistical modeling work of Lees et al. [Phys. Rev. Lett. 127, 105001 (2021)], by increasing the complexity of the model space and allowing for coupling between degradation terms. Since the model capacity of DNN SM+ is higher than the model of Lees et al., DNN SM+ can potentially provide an improvement in predictive capability, and we use this model to provide insight into complicated degradation dependencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Predicting Mössbauer Parameters of Nonheme Diiron Complexes with Density Functional Theory

Mössbauer spectroscopy provides significant insights into the electronic structure and environment of the metal centers. In this work, we investigate the electronic structures of a set of nonheme diiron complexes by evaluating two key parameters pertaining to Mössbauer spectroscopy, namely, the isomer shift (δ) and quadrupole splitting (|ΔE Q |), using different levels of density functional theory (DFT). The diiron systems investigated here span diverse oxidation states, bridging motifs, and spin coupling patterns, which present a challenging case for theoretical predictions. We demonstrate that the combination of B97-D3/def2-TZVP is an efficient approach in modeling both the δ and |ΔEQ| values with high accuracy for the representative nonheme diiron complexes. We also show that δ is accurately predicted irrespective of the choice of approximate density functional while the |ΔE Q | is sensitive to the level of theory employed. Further investigation shows that the present methodology assessed using synthetic nonheme diiron complexes could be extended to nonheme diiron enzyme active sites, featuring both ferromagnetic and antiferromagnetic coupling between the iron centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessment of Cloud Mask Forecasts from the WRF-Solar Ensemble Prediction System: Preprint

Numerical weather prediction (NWP) models are important tools used by government agencies and the renewable energy enterprise to forecast solar radiation. Cloud prediction, a key process of NWP models, has the highest impact on the accuracy of solar forecasting. This study uses satellite observations from the National Solar Radiation Data Base (NSRDB) to evaluate the cloud mask forecast by the WRF-Solar Ensemble Prediction System (WRF-Solar EPS). Preliminary analysis of the data in 2018 demonstrates the need of further improvement in predicting thin and low-level clouds. The information obtained from this work will be used to enhance the WRF-Solar EPS in reproducing the cloud field over the contiguous U.S. and reducing solar forecasting errors.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Predicting Open Quantum Dynamics with Data-Informed Quantum-Classical Dynamics

We introduce a data-informed quantum-classical dynamics (DIQCD) approach for predicting the evolution of an open quantum system. The equation of motion in DIQCD is a Lindblad equation with a flexible, time-dependent Hamiltonian that can be optimized to fit sparse and noisy data from local observations of an extensive open quantum system. We demonstrate the accuracy and efficiency of DIQCD for both experimental and simulated quantum devices. We show that DIQCD can predict entanglement dynamics of ultracold molecules (calcium fluoride) in optical tweezer arrays. DIQCD also successfully predicts carrier mobility in organic semiconductors (rubrene) with accuracy comparable to nearly exact numerical methods.

Lindblad equation↗

Differential cross section measurements for the production of top quark pairs and of additional jets using dilepton events from pp collisions at $\sqrt{s}$ = 13 TeV

Differential cross sections for top quark pair ($\textrm{t}\overline{\textrm{t}}$) production are measured in proton-proton collisions at a center-of-mass energy of 13 TeV using a sample of events containing two oppositely charged leptons. The data were recorded with the CMS detector at the CERN Large Hadron Collider and correspond to an integrated luminosity of 138 fb −1 . The differential cross sections are measured as functions of kinematic observables of the $\textrm{t}\overline{\textrm{t}}$ system, the top quark and antiquark and their decay products, as well as of the number of additional jets in the event. The results are presented as functions of up to three variables and are corrected to the parton and particle levels. When compared to standard model predictions based on quantum chromodynamics at different levels of accuracy, it is found that the calculations do not always describe the observed data. The deviations are found to be largest for the multi-differential cross sections.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurement of the t-channel single top quark cross section in proton-proton collisions at $\sqrt{s}=5.02$ TeV

The single top quark t-channel production cross section is measured in proton-proton collisions at the CERN LHC at $\sqrt{s}=5.02$ TeV, using data recorded with the CMS detector in 2017, corresponding to an integrated luminosity of 302 pb −1 , and resulting in the first CMS measurement of the process at that energy. Events with one electron or muon and two or more jets, among which at least one is identified as originating from a b quark fragmentation, are analyzed. The combined cross section of single top quark (tq) and single top antiquark ($\overline{\mathrm{t}}\mathrm{q}$) production is $\sigma \left(\mathrm{tq}+\overline{\mathrm{t}}\mathrm{q}\right)={25.5}_{-3.5}^{+3.6}{\left(\mathrm{stat}\right)}_{-3.9}^{+4.2}\left(\mathrm{syst}\right)\pm 0.5\left(\mathrm{lumi}\right)$ pb. The individual cross sections are measured to be $\sigma \left(\mathrm{tq}\right)={17.7}_{-2.7}^{+2.9}{\left(\mathrm{stat}\right)}_{-2.4}^{+2.6}\left(\mathrm{syst}\right)\pm 0.3\left(\mathrm{lumi}\right)$ pb and $\sigma \left(\overline{\mathrm{t}}\mathrm{q}\right)={6.7}_{-1.6}^{+2.4}{\left(\mathrm{stat}\right)}_{-2.5}^{+2.1}\left(\mathrm{syst}\right)\pm 0.1\left(\mathrm{lumi}\right)$ pb. Their ratio is measured to be ${\mathcal{R}}_{\mathrm{t}-\mathrm{ch}}={2.7}_{-0.8}^{+1.5}{\left(\mathrm{stat}\right)}_{-0.3}^{+1.2}\left(\mathrm{syst}\right)$. The absolute value of the Cabibbo-Kobayashi-Maskawa matrix element is found to be |f LV V tb | = 0.92 ± 0.09(exp) ± 0.01(theo). The measurements are in good agreement with the standard model predictions at next-to-next-to-leading order accuracy in quantum chromodynamics.

Hadron-Hadron Scattering↗

Binder jetting additive manufacturing of silicon carbide ceramics: Development of bimodal powder feedstocks by modeling and experimental methods

A limitation of binder jetting additive manufacturing is the low density of fabricated parts. Mixing powders with different sizes is a promising approach to increase powder bed packing density and, hence, printed part density. However, in previous studies mixed powder feedstock was prepared by trial and error method. In this research, both modeling and experimental methods were used to prepare the bimodal powder feedstocks. Analytical packing model was introduced for irregular powders. A bimodal powder was prepared by mixing two different-sized silicon carbide powders (i.e. coarse and fine) using ball mill, and their tap densities were measured. Silicon carbide plates were printed using the coarse and bimodal powders by a commercial binder jetting system. Results showed that the modeling method could predict the tap density of bimodal powders with high accuracy. The printed parts from bimodal powder achieved higher green densities than those from the unimodal powder.

36 MATERIALS SCIENCE↗

Developing Science-based fueling protocols for 250-bar hydrogen tanks onboard hydrogen ferries: Experiments and modeling

Combined modeling and experimental studies are reported of the fueling of a large (28 kg capacity) 250-bar Type IV hydrogen tank of the type being deployed on early hydrogen ferries, such as the MV Sea Change. The primary goal was to determine how such tanks can be successfully fueled with hydrogen (state of charge greater than 97%) within 45 minutes without exceeding the 82 °C temperature limit for such tanks. The modeling studies show that a gas injector is needed to avoid thermal stratification during hydrogen fueling which can result in potential hot spots. Empirically, precooling of the hydrogen to 0 °C was found to be needed in some of the cases examined, as ambient conditions greatly affected the need for a precooling to achieve the 45-minute fill time desired by end users. The experimental results afforded a calibration of the engineering model SOFIL for these large 250-bar tanks, which now enables using SOFIL to predict volume-averaged hydrogen fueling temperatures to an accuracy of ±2.7°C for these tanks. The model can therefore be used to evaluate potential scenarios for development of a standardized fueling methodology for ferries utilizing large Type-IV tanks.

08 HYDROGEN↗

Computational design of isotropic and anisotropic ultralow thermal conductivity polymer foams

Current state-of-the-art commercial polymer thermal insulation foam exhibits a thermal conductivity of 24 mW·m -1 ·K -1 (equivalently thermal resistivity of R-6/in.), similar to that of static air. To further optimize building energy efficiency, achieving even lower thermal conductivity is needed, which is, however, highly challenging. This paper presents computational evidence that demonstrates the feasibility of achieving an ultra-low thermal conductivity of less than 14.4 mW·m -1 ·K -1 (equivalently R-10/in.) using isotropic and anisotropic foam cell designs. For the isotropic design, we have identified analytical effective medium approximation (EMA) models within the accuracy of ±5% as finite element analysis (FEA) in predicting the effective thermal conductivity of foams with various porosities and filler gases. For the anisotropic design, we have developed and validated new EMA models against FEA in predicting the effective thermal conductivity of general anisotropic cuboids and Voronoi foams. For both isotropic and anisotropic designs, the design spaces for 18, 16, and 14.4 mW·m -1 ·K -1 (equivalently R-8, R-9 and R-10/in.) using various filler gases are obtained. It is found that polymer foams can be improved to achieve ultralow thermal conductivity by reducing CO 2 concentration, reducing radiation, increasing porosity, and using anisotropic pore geometry. In conclusion, these findings contribute to the development of highly efficient thermal insulation materials, enhancing building energy efficiency and promoting sustainable construction practices.

42 ENGINEERING↗

RSPECT: A PROSPECT-based model incorporating the real structure of rice leaves

Radiative transfer models (RTMs) describe how light is absorbed, scattered, and transmitted within leaves by simulating mechanistic light propagation processes. The PROSPECT model is based on measurable parameters (the leaf biochemical content) and a non-measurable parameter (the leaf anatomical structure represented by the leaf structure parameter (N)). The effect of N on the optical properties of leaves has been investigated through a number of local and global sensitivity analyses. Other studies have directly evaluated the effect of the leaf anatomical structure on spectral reflectance, particularly in the near infrared region. However, the relationship between N and the anatomical structure is unclear. Here, in this study, we leveraged eLeaf, a ray tracing-based 3D rice leaf simulator, to establish relationships between leaf anatomical features and spectral properties, enabling us to replace N in the PROSPECT-4 model with measurable leaf anatomical parameters and develop the RSPECT model. The leaf thickness at minor vein, leaf thickness at bulliform cells, mesophyll thickness at minor vein, and distance between two minor veins could be used to predict N effectively. The RSPECT model achieved spectral simulation accuracy comparable to PROSPECT-4 and was more suitable for parameter inversion of the physical and chemical properties of rice leaves, with relative root mean square errors of 7.4% for chlorophyll content, 5.6% for equivalent water thickness, and 7.5% for dry matter content. In conclusion, RSPECT improves radiative transfer modeling by integrating measurable anatomical features and provides a framework for extending this approach to other vegetation types.

hyperspectral↗

Stochastic Resolution of Identity for Real-Time Second-Order Green’s Function: Ionization Potential and Quasi-Particle Spectrum

Here, we develop a stochastic resolution of identity approach to the real-time second-order Green's function (real-time sRI-GF2) theory, extending our recent work for imaginary-time Matsubara Green's function [ Takeshita et al. J. Chem. Phys. 2019 , 151 , 044114 ]. The approach provides a framework to obtain the quasi-particle spectra across a wide range of frequencies and predicts ionization potentials and electron affinities. To assess the accuracy of the real-time sRI-GF2, we study a series of molecules and compare our results to experiments as well as to a many-body perturbation approach based on the GW approximation, where we find that the real-time sRI-GF2 is as accurate as self-consistent GW. The stochastic formulation reduces the formal computatinal scaling from O(N e 5 ) down to O(N e 3 ) where N e is the number of electrons. Finally, this is illustrated for a chain of hydrogen dimers, where we observe a slightly lower than cubic scaling for systems containing up to N e ≈ 1000 electrons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗