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At least 235 records · Page 13

Interpretable, extensible linear and symbolic regression models for charge density prediction using a hierarchy of many-body correlation descriptors

Here, density functional theory (DFT) is routinely used to make electronic structure predictions for high-throughput screening of materials and molecules for technologically relevant areas, like the identification of better catalysts, electronic materials, and drug discovery. However, the DFT formalism is limited by (a) its poor (quadratic-to-quartic) scaling, and (b) the need to perform repeated eigenvalue computations of the electronic Hamiltonian as part of its self-consistent field (SCF) iteration procedure to obtain the converged ground state electron density, ρ (r). Approaches that directly predict ρ (r) of a structure with high accuracy can accelerate conventional SCF calculations and can also be used in linearly scaling methods such as orbital-free DFT. To this end, we present a procedure to predict the ground state electron density of molecular and periodic three-dimensional systems directly from the atomic structure with a particular emphasis on physical interpretability. In our framework, ρ (r) is modeled using many-body correlation descriptors that accurately capture the effects of local atomic arrangements in the neighborhood of a grid point. Our use of a linear regression scheme to fit to charge density data enables transparent analysis of the relative contributions of various types of local atomic correlations. By systematically including increasingly complex correlations, our model is shown to accurately predict ρ (r) for a variety of chemically and electronically diverse systems — amorphous Ge, Al(001) slab, crystalline Ga 2 O 3 , molecular benzene, and polyethylene. We then demonstrate a symbolic regression-based protocol to construct easily computable, interpretable features from lower-order correlations that significantly improves our electron density predictions with effectively no increase in the computational cost.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗

Linear and Geometrically Nonlinear Structural Shape Sensing from Strain Data

An aircraft’s shape must be measured during flight to implement active shape controls such as active trim shape, divergence, and sonic boom controls. A basis function method for linear as well as geometrically nonlinear structural shape sensing is proposed in this study. Basis functions can be mode shapes, linear static deformation shapes, and/or geometrically nonlinear static deformation shapes. The proposed basis function method is validated using a high-aspect-ratio wing, a swept test plate, and the National Aeronautics and Space Administration X-59 aircraft. A large structural deformation of a high-aspect-ratio wing is successfully captured using the proposed basis function method with less than 0.3%prediction error at the wing-tip section. The basis function method gives excellent deformation prediction, even with stress concentration. Performance of the basis functions is compared using the X-59 stabilator sample case. In most of the sample load cases, static deformations give a better correlation with the target deformation than do mode shapes. Wing shape sensing with sparse strain data are also demonstrated in this study using the X-59 aircraft. Predicted structural deformations match reasonably with the target deformations, even without strain gauges on some structural components. The predicted deformations have a good match with the target deformations.

Static Deformation↗

Structural Dynamic Behavior of Wind Turbines

The structural dynamicist s areas of responsibility require interaction with most other members of the wind turbine project team. These responsibilities are to predict structural loads and deflections that will occur over the lifetime of the machine, ensure favorable dynamic responses through appropriate design and operational procedures, evaluate potential design improvements for their impact on dynamic loads and stability, and correlate load and control test data with design predictions. Load prediction has been a major concern in wind turbine designs to date, and it is perhaps the single most important task faced by the structural dynamics engineer. However, even if we were able to predict all loads perfectly, this in itself would not lead to an economic system. Reduction of dynamic loads, not merely a "design to loads" policy, is required to achieve a cost-effective design. The two processes of load prediction and structural design are highly interactive: loads and deflections must be known before designers and stress analysts can perform structural sizing, which in turn influences the loads through changes in stiffness and mass. Structural design identifies "hot spots" (local areas of high stress) that would benefit most from dynamic load alleviation. Convergence of this cycle leads to a turbine structure that is neither under-designed (which may result in structural failure), nor over-designed (which will lead to excessive weight and cost).

Thresher, Robert W.↗

Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16

ABSTRACT In the CASP16 experiment, our team employed hybrid computational strategies to predict both protein–protein and protein–ligand complex structures. For protein–protein docking, we combined physics‐based sampling—using ClusPro FFT docking and molecular dynamics—with AlphaFold (AF)‐based sampling, followed by AF‐based refinement. Our method produced numerous high‐accuracy complex models, including cases where AF alone failed, underscoring the critical role of physics‐based sampling alongside deep learning‐based refinement. For protein–ligand docking, we integrated the ClusPro LigTBM template‐based approach with a machine learning‐based confidence model for rescoring. The method preserves conserved interaction fragments derived from homologous complexes, followed by local resampling using physics‐based sampling and a diffusion model. Our template‐based strategy achieved a mean lDDT‐PLI of 0.69 across 233 targets, which was highly competitive. These results demonstrate that combining physics‐based modeling with AI‐driven refinement can significantly enhance the accuracy of both protein–protein and protein–ligand structure predictions.

Ashizawa, Ryota [Department of Applied Mathematics↗

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

AI-assisted rapid crystal structure generation towards a target local environment

In material design, traditional crystal structure prediction approaches are expensive as they require extensive structural sampling through expensive energy minimization methods. Emerging artificial intelligence (AI) generative models have shown great promise in rapidly generating realistic crystals, but they typically handle only a few tens of atoms per unit cell. To overcome this limitation, we introduce a symmetry-informed approach, the Local Environment Geometry-Oriented Crystal Generator (LEGO-xtal). Our method generates initial structures using AI models trained on an augmented dataset, and then optimizes them using structure descriptors rather than energy-based optimization. We demonstrate its effectiveness by expanding from 25 known low-energy sp2 carbon allotropes to over 1700, all within 0.5 eV/atom of the ground-state energy of graphite. This framework offers a generalizable strategy for the targeted design of materials with modular building blocks, such as metal-organic frameworks and battery materials.

Ridwan, Osman Goni [University of North Carolina a↗

Liquid state theory of the structure of model polymerized ionic liquids

We employ polymer integral equation theory to study a simplified model of semiflexible polymerized ionic liquids (PolyILs) that interact via hard core repulsions and short range screened Coulomb interactions. The multi-scale structure in real and Fourier space of PolyILs (ions chosen to mimic Li, Na, K, Br, PF 6 , and TFSI) are determined as a function of melt density, Coulomb interaction strength, and ion size. Comparisons with a homopolymer melt, a neutral polymer–solvent-like athermal mixture, and an atomic ionic liquid are carried out to elucidate the distinct manner that ions mediate changes of polymer packing, the role of excluded volume effects, and the influence of chain connectivity, respectively. The effect of Coulomb strength depends in a rich manner on ion size and density, reflecting the interplay of steric packing, ion adsorption, and charge layering. Ion-mediated bridging of monomers is found, which intensifies for larger ions. Intermediate range charge layering correlations are characterized by a many-body screening length that grows with PolyIL density, cooling, and Coulomb strength, in disagreement with Debye–Hückel theory, but in accord with experiments. Qualitative differences in the collective structure, including an ion-size-dependent bifurcation of the polymer structure factor peak and pair correlation function, are predicted. The monomer cage order parameter increases significantly, but its collective ion counterpart decreases, as ions become smaller. Such behaviors allow one to categorize PolyILs into two broad classes of small and large ions. Furthermore, dynamical implications of the predicted structural results are qualitatively discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

LDA + $U_{sc}$ calculations of phase relations in FeO

Using the LDA + $U_{sc}$ method, we present calculation phase relations of iron monoxides involving five polytypes in multiple spin-state configurations. In this work, the Hubbard parameter $\textit{U}$ is determined self-consistently simultaneously with the occupation matrix and structures at arbitrary pressures. The Hubbard parameter strongly depends on pressure, structure, and spin state. Comparison with experimental structural data indicates the LDA + $U_{sc}$ can predict structure, compression curves, phase relations, and transition pressures very well for the insulating $\textit{B}$1 and $\textit{iB}$8 states. However, it requires additional calculations using the Mermin functional that includes the electronic entropic contribution to the free energy to obtain an $\textit{nB}$8 metallic state and a consistent $\textit{iB}$8 to $\textit{nB}$8 insulator to metal transition pressure.

36 MATERIALS SCIENCE↗

Mid-frequency Band Dynamics of Large Space Structures

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

dynamics↗

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Abstract The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-residue distance predictions to enhance EMA, during the 2020 CASP14 experiment, we integrated several new inter-residue distance features with the existing model quality assessment features in several deep learning methods to predict the quality of protein structural models. According to the evaluation of performance in selecting the best model from the models of CASP14 targets, our three multi-model predictors of estimating model accuracy (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) achieve the averaged loss of 0.073, 0.079, and 0.081, respectively, in terms of the global distance test score (GDT-TS). The three methods are ranked first, second, and third out of all 68 CASP14 predictors. MULTICOM-DEEP, the single-model predictor of estimating model accuracy (EMA), is ranked within top 10 among all the single-model EMA methods according to GDT-TS score loss. The results demonstrate that inter-residue distance features are valuable inputs for deep learning to predict the quality of protein structural models. However, larger training datasets and better ways of leveraging inter-residue distance information are needed to fully explore its potentials.

59 BASIC BIOLOGICAL SCIENCES↗

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗

Band gap renormalization, carrier mobilities, and the electron-phonon self-energy in crystalline naphthalene

Organic molecular crystals are expected to feature appreciable electron-phonon interactions that influence their electronic properties at zero and finite temperature. Here, we report first-principles calculations and an analysis of the electron-phonon self-energy in naphthalene crystals. We compute the zero-point renormalization and temperature dependence of the fundamental band gap, and the resulting scattering lifetimes of electronic states near the valence- and conduction-band edges employing density functional theory. Further, our calculated phonon renormalization of the GW-corrected quasiparticle band structure predicts a fundamental band gap of 5 eV for naphthalene at room temperature, in good agreement with experiments. From our calculated phonon-induced electron lifetimes, we obtain the temperature-dependent mobilities of electrons and holes in good agreement with experimental measurements at room temperature. Finally, we show that an approximate energy self-consistent computational scheme for the electron-phonon self-energy leads to the prediction of strong satellite bands in the electronic band structure. We find that a single calculation of the self-energy can reproduce the self-consistent results of the band gap renormalization and electrical mobilities for naphthalene, provided that the on-the-mass-shell approximation is used, i.e., if the self-energy is evaluated at the bare eigenvalues.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural Shape Sensing from Strain Data Using the Basis Function Method

An aircraft shape must be measured during flight to implement an active trim shape control, such as an active dihedral control for a highly flexible aircraft with a high-aspect-ratio wing, and an active sonic boom control for a supersonic transport aircraft. A basis function method for linear as well as geometrically nonlinear structural shape sensing is proposed in this study. Basis functions can be mode shapes, linear static deformation shapes, or geometrically nonlinear static deformation shapes. The proposed basis function method is validated using a high-aspect-ratio wing, a swept test plate, and the National Aeronautics and Space Administration Low Boom Flight Demonstration mission X-59 Quiet Supersonic Technology (QueSST) aircraft (Lockheed Martin, Bethesda, Maryland). A large structural deformation of a high-aspect-ratio wing is successfully captured using the proposed basis function method with less than 0.3-percentprediction error at the wing-tip section. The basis function method gives excellent deformation prediction, even with stress concentration. Performance of the basis functions is compared using the X-59 stabilator sample case. In most of the sample load cases, static deformations give a better correlation with the target deformation than do mode shapes. Wing shape sensing with sparse strain data is also demonstrated in this study using the X-59 QueSST aircraft. Predicted structural deformations match reasonably with the target deformations even without strain gauges on some structural components. The predicted deformations have a good match with the target deformations.

Chan-gi Pak↗

Determining structural performance

An overview of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems is presented. Aeroelasticity, vibration control, dynamic systems, and computational structural methods are four disciplines that make up the structural dynamic effort at LeRC. The aeroelasticity program develops analytical and experimental methods for minimizing flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods were developed for applications on the turbofan, turbopump, and advanced turboprop. In order to improve life and performance, the vibration control program conceives, analyzes, develops, and demonstrates new methods for controlling vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The dynamic systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. Work in this field involves the analysis and parametric identification of large, nonlinear, damped, stochastic systems. The computational structural methods program exploits modern computer science as an aid to the solutions of structural problems.

Ernst, Michael A.↗

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

displacement transfer functions↗

Epitaxial growth, magnetoresistance, and electronic band structure of GdSb magnetic semimetal films

Motivated by observations of extreme magnetoresistance (XMR) in bulk crystals of rare-earth monopnictide (RE-V) compounds and emerging applications in novel spintronic and plasmonic devices based on thin-film semimetals, we have investigated the electronic band structure and transport behavior of epitaxial GdSb thin films grown on III-V semiconductor surfaces. The Gd 3 + ion in GdSb has a high spin S=7/2 and no orbital angular momentum, serving as a model system for studying the effects of antiferromagnetic order and strong exchange coupling on the resulting Fermi surface and magnetotransport properties of RE-Vs. Here, we present a surface and structural characterization study mapping the optimal synthesis window of thin epitaxial GdSb films grown on III-V lattice-matched buffer layers via molecular-beam epitaxy. To determine the factors limiting XMR in RE-V thin films and provide a benchmark for band-structure predictions of topological phases of RE-Vs, the electronic band structure of GdSb thin films is studied, comparing carrier densities extracted from magnetotransport, angle-resolved photoemission spectroscopy (ARPES), and density-functional theory (DFT) calculations. ARPES shows a hole-carrier rich, topologically trivial, semimetallic band structure close to complete electron-hole compensation, with quantum confinement effects in the thin films observed through the presence of quantum-well states. DFT-predicted Fermi wave vectors are in excellent agreement with values obtained from quantum oscillations observed in magnetic field-dependent resistivity measurements. An electron-rich Hall coefficient is measured despite the higher hole-carrier density, attributed to the higher electron Hall mobility. The carrier mobilities are limited by surface and interface scattering, resulting in lower magnetoresistance than that measured for bulk crystals.

36 MATERIALS SCIENCE↗