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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Predicting metal-binding proteins and structures through integration of evolutionary-scale and physics-based modeling

Metals are essential elements in all living organisms, binding to approximately 50% of proteins. They serve to stabilize proteins, catalyze reactions, regulate activities, and fulfill various physiological and pathological functions. While there have been many advancements in determining the structures of protein-metal complexes, numerous metal-binding proteins still need to be identified through computational methods and validated through experiments. Here, to address this need, we have developed the ESMBind workflow, which combines evolutionary scale modeling (ESM) for metal-binding prediction and physics-based protein-metal modeling. Our approach utilizes the ESM-2 and ESM-IF models to predict metal-binding probability at the residue level. In addition, we have designed a metal-placement method and energy minimization technique to generate detailed 3D structures of protein-metal complexes. Our workflow outperforms other models in terms of residue and 3D-level predictions. To demonstrate its effectiveness, we applied the workflow to 142 uncharacterized fungal pathogen proteins and predicted metal-binding proteins involved in fungal infection and virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Recent Improvements to the NWChem COSMO Module

This work presents recent developments in the COSMO solvation model implementation in NWChem. A new cavity construction approach, based on the solvent-excluding surface (SES) and utilizing the well-established GEPOL algorithm, has been introduced. Additionally, a straightforward procedure to merge surface segments that are too close─often a source of numerical artifacts─has been implemented. The available methods for correcting outlying surface charges have also been reviewed and improved. To validate the new implementation, we computed dielectric solvation energies for a chemically diverse set of approximately 100 molecules, including neutral species, small ions, and common ionic liquid components. Results were compared to those from GAMESS using the double-cavity method as a reference. Although the double-cavity approach can be regarded as more accurate, the simpler correction schemes available in NWChem─based on scaling factors or Lagrange multipliers─can achieve excellent agreement if the potential is also properly corrected, with mean unsigned deviations of around 0.15 kcal/mol. Predictions of typical vapor–liquid and liquid–liquid equilibria using a COSMO-SAC variant based on NWChem also showed very promising results.

Cavities↗
DOE OSTI2026

Restricted Partition Function Semiclassical Transition State Theory (RPF-SCTST): Applications to Reactions Involving Hydrogen Cyanide, Hydrogen Peroxide, and Formaldehyde Oxide

We demonstrate the efficiency of the numerical calculation of thermal semiclassical transition state theory (SCTST) rates across several representative chemical reactions using the restricted partition function (RPF)─viz a function that depends only on the imaginary action associated with a reaction. Here, we treat the potential energy surfaces (PESs) through fourth order expansions around the saddle point and integrate the Hamiltonian up to second order in employing vibrational perturbation theory. We apply this formalism to uni- and bimolecular reactions with different─though relatively high─barrier heights to uncover the influence of the barrier properties, minimal energies, and separability of the rotational motion on rate constants and tunneling corrections. Although all modes are coupled within the RPF, we found in our numerical examples that the rotational component in the absence of significant rotational distortions can be separated from the vibrational contributions. Moreover, a classical treatment of the rotational contribution is adequate over the temperature range from approximately 100 to 1000 K. We also found that the choice of DFT basis set can lead to variations in rate constants of up to an order of magnitude. Lastly, different schemes for counting eligible energy levels result in rate constants that differ by no more than a factor of 2, with the remaining discrepancies attributed to the treatment of near-convergent levels in perturbation theory.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Analysis of the Challenges in Developing Sample-Based Multi-fidelity Estimators for Non-deterministic Models

Multifidelity (MF) uncertainty quantification (UQ) seeks to leverage and fuse information from a collection of models to achieve greater statistical accuracy with respect to a single-fidelity counterpart, while maintaining an efficient use of computational resources. Despite many recent advancements in MF UQ, several challenges remain and these often limit its practical impact in certain application areas. In this manuscript, we focus on the challenges introduced by nondeterministic models to sampling MF UQ estimators. Nondeterministic models produce different responses for the same inputs, which means their outputs are effectively noisy. MF UQ is complicated by this noise since many state-of-the-art approaches rely on statistics, e.g., the correlation among models, to optimally fuse information and allocate computational resources. Here, we demonstrate how the statistics of the quantities of interest, which impact the design, effectiveness, and use of existing MF UQ techniques, change as functions of the noise. With this in hand, we extend the unifying approximate control variate framework to account for nondeterminism, providing for the first time a rigorous means of comparing the effect of nondeterminism on different multifidelity estimators and analyzing their performance with respect to one another. Numerical examples are presented throughout the manuscript to illustrate and discuss the consequences of the presented theoretical results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Novel Feature of Valence Quark Distributions in Hadrons

Examining the evolution of the maximum of valence quark distribution, qV, weighted by Bjorken x, h(x,t)≡xqV(x,t), it is observed that h(x,t) at the peak becomes a one-parameter function; h(xp,t)=Φ(xp(t)), where xp is the position of the peak, t=logQ2, and Q2 is the resolution scale. This observation is used to derive a new model-independent relation which connects the partial derivative of the valence parton distribution functions (PDFs) in xp to the quantum chromodynamics (QCD) evolution equation through the xp derivative of the logarithm of the function Φ(xp(t)). A numerical analysis of this relation using empirical PDFs results in an observation of the exponential form of the Φ(xp(t))=h(xp,t)=CeDxp(t) for leading to next-to-next leading order approximations of PDFs for the range of Q2, covering four orders in magnitude. The exponent, D, of the observed “height-position” correlation function converges with the increase in the order of approximation. This result holds for all the PDF sets considered. A similar relation is observed also for the pion valence quark distribution, indicating that the obtained relation may be universal for any non-singlet partonic distribution. The observed “height-position” correlation is used also to indicate that no finite number of exchanges can describe the analytic behavior of the valence quark distribution at the position of the peak at fixed Q2.

Leon, Christopher↗
DOE OSTI2023

Implementation of Chemistry in the Athena++ Code

Chemistry plays a key role in many aspects of astrophysical fluids. Atoms and molecules are agents for heating and cooling, determine the ionization fraction, serve as observational tracers, and build the molecular foundation of life. We present the implementation of a chemistry module in the publicly available magnetohydrodynamic code Athena++ . We implement several chemical networks and heating and cooling processes suitable for simulating the interstellar medium (ISM). A general chemical network framework in the KIDA format is also included, allowing users to easily implement their own chemistry. Radiation transfer and cosmic-ray ionization are coupled with chemistry and solved with the simple six-ray approximation. The chemical and thermal processes are evolved as a system of coupled ordinary differential equations with an implicit solver from the CVODE library. We perform and present a series of tests to ensure the numerical accuracy and convergence of the code. Many tests combine chemistry with gas dynamics, including comparisons with analytic solutions, 1D problems of the photodissociation regions and shocks, and realistic 3D simulations of the turbulent ISM. We release the code with the new public version of Athena++ , aiming to provide a robust and flexible code for the astrochemical simulation community.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

On a simplified solution of climate-carbon dynamics in idealized flat10MIP simulations

Abstract. Idealized experiments with coupled climate-carbon Earth system models (ESMs) provide a basis for understanding the response of the carbon cycle to external forcing and for quantifying climate-carbon feedbacks. Here, we analyze globally-averaged results from idealized esm-flat10 experiments and show that most models exhibit a quasi-linear relationship between cumulative carbon uptake on land and in the ocean during a period of constant fossil fuel emissions of 10 Pg C yr−1. We hypothesize that this relationship does not depend on emission pathways. Further, as a simplification, we quantify the relationship between cumulative ocean carbon uptake and changes in ocean heat content using a linear approximation. In this way, changes in oceanic heat content and atmospheric CO2 concentration become interdependent variables, reducing the coupled temperature-CO2 system to just one differential equation. The equation can be solved analytically or numerically for the atmospheric CO2 concentration as a function of fossil fuel emissions. This approach leads to a simplified description of global carbon and climate dynamics, which could be used for applications beyond existing analytical frameworks.

Brovkin, Victor↗
DOE OSTI2024

Performance of high-order Godunov-type methods in simulations of astrophysical low Mach number flows

High-order Godunov methods for gas dynamics have become a standard tool for simulating different classes of astrophysical flows. Their accuracy is mostly determined by the spatial interpolant used to reconstruct the pair of Riemann states at cell interfaces and by the Riemann solver that computes the interface fluxes. In most Godunov-type methods, these two steps can be treated independently, so that many different schemes can in principle be built from the same numerical framework. Because astrophysical simulations often test out the limits of what is feasible with the computational resources available, it is essential to find the scheme that produces the numerical solution with the desired accuracy at the lowest computational cost. However, establishing the best combination of numerical options in a Godunov-type method to be used for simulating a complex hydrodynamic problem is a nontrivial task. In fact, formally more accurate schemes do not always outperform simpler and more diffusive methods, especially if sharp gradients are present in the flow. For this work, we used our fully compressible Seven-League Hydro (SLH) code to test the accuracy of six reconstruction methods and three approximate Riemann solvers on two- and three-dimensional (2D and 3D) problems involving subsonic flows only. We considered Mach numbers in the range from 10 −3 to 10 −1 , which are characteristic of many stellar and geophysical flows. In particular, we considered a well-posed, 2D, Kelvin–Helmholtz instability problem and a 3D turbulent convection zone that excites internal gravity waves in an overlying stable layer. Although the different combinations of numerical methods converge to the same solution with increasing grid resolution for most of the quantities analyzed here, we find that (i) there is a spread of almost four orders of magnitude in computational cost per fixed accuracy between the methods tested in this study, with the most performant method being a combination of a low-dissipation Riemann solver and a sextic reconstruction scheme; (ii) the low-dissipation solver always outperforms conventional Riemann solvers on a fixed grid when the reconstruction scheme is kept the same; (iii) in simulations of turbulent flows, increasing the order of spatial reconstruction reduces the characteristic dissipation length scale achieved on a given grid even if the overall scheme is only second order accurate; (iv) reconstruction methods based on slope-limiting techniques tend to generate artificial, high-frequency acoustic waves during the evolution of the flow; and (v) unlimited reconstruction methods introduce oscillations in the thermal stratification near the convective boundary, where the entropy gradient is steep.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Bi-fidelity variational auto-encoder for uncertainty quantification

Quantifying the uncertainty of quantities of interest (QoIs) from physical systems is a primary objective in model validation. However, achieving this goal entails balancing the need for computational efficiency with the requirement for numerical accuracy. To address this trade-off, we propose a novel bi-fidelity formulation of variational auto-encoders (BF-VAE) designed to estimate the uncertainty associated with a QoI from low-fidelity (LF) and high-fidelity (HF) samples of the QoI. Here, this model allows for the approximation of the statistics of the HF QoI by leveraging information derived from its LF counterpart. Specifically, we design a bi-fidelity auto-regressive model in the latent space which is integrated within the VAE’s probabilistic encoder–decoder structure. An effective algorithm is proposed to maximize the variational lower bound of the HF log-likelihood in the presence of limited HF data, resulting in the synthesis of HF realizations with a reduced computational cost. Additionally, we introduce the concept of the bi-fidelity information bottleneck (BF-IB) to provide an information-theoretic interpretation of the proposed BF-VAE model. Our numerical results demonstrate that the BF-VAE leads to considerably improved accuracy, as compared to a VAE trained using only HF data, when limited HF data is available.

42 ENGINEERING↗
DOE OSTI2021

A Feynman-Kac based numerical method for the exit time probability of a class of transport problems

The exit time probability, which gives the likelihood that an initial condition leaves a prescribed region of the phase space of a dynamical system at, or before, a given time, is arguably one of the most natural and important transport problems. In this work, we present an accurate and efficient numerical method for computing this probability for systems described by non-autonomous (time-dependent) stochastic differential equations (SDEs) or their equivalent Fokker-Planck partial differential equations. The method is based on the direct approximation of the Feynman-Kac formula that establishes a link between the adjoint Fokker-Planck equation and the forward SDE. The Feynman-Kac formula is approximated using the Gauss-Hermite quadrature rules and piecewise cubic Hermite interpolating polynomials, and a GPU accelerated matrix representation is used to compute the entire time evolution of the exit time probability using a single pass of the algorithm. The method is unconditionally stable, exhibits second order convergence in space, first order convergence in time, and it is straightforward to parallelize. Applications are presented to the advection diffusion of a passive tracer in a fluid flow exhibiting chaotic advection, and to the runaway acceleration of electrons in a plasma in the presence of an electric field, collisions, and radiation damping. Benchmarks against analytical solutions as well as comparisons with explicit and implicit finite difference standard methods for the adjoint Fokker-Planck equation are presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Two-particle correlation functions in cluster perturbation theory: Hubbard spin susceptibilities

Cluster perturbation theory (CPT) is a computationally economic method commonly used to estimate the momentum- and energy-resolved single-particle Green's function. It has been used extensively in direct comparisons with experiments that effectively measure the single-particle Green's function, e.g., angle-resolved photoemission spectroscopy. However, many experimental observables are given by two-particle correlation functions. CPT can be extended to compute two-particle correlation functions by approximately solving the Bethe-Salpeter equation. We implement this method and focus on the transverse spin susceptibility, measurable via inelastic neutron scattering or with optical probes of atomic gases in optical lattices. Finally, we benchmark the method with the one-dimensional Fermi-Hubbard model by comparing with known results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Landscape of nuclear deformation softness with spherical quasiparticle random-phase approximation

We investigate the stability and softness of nuclei against quadrupole, octupole, and hexadecapole deformation. By applying the spherical Skyrme-force Hartree-Fock Bardeen-Cooper-Schrieffer quasiparticle random phase approximation, we diagnose ground-state deformation when imaginary solutions are obtained, i.e., the spherical ground state collapses. We also calculate the multipole polarizability in spherical nuclei with no collapse, as a measure of softness. This numerically light and theoretically sound method is found able to capture deformation patterns across the nuclide chart. As a result, the connection between the intrinsic shape of nuclei and the dynamics of their low-lying collective states is established and the role of shell structure is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Representation Learning via Quantum Neural Tangent Kernels

Variational quantum circuits are used in quantum machine learning and variational quantum simulation tasks. Designing good variational circuits or predicting how well they perform for given learning or optimization tasks is still unclear. Here we discuss these problems, analyzing variational quantum circuits using the theory of neural tangent kernels. We define quantum neural tangent kernels, and derive dynamical equations for their associated loss function in optimization and learning tasks. We analytically solve the dynamics in the frozen limit, or lazy training regime, where variational angles change slowly and a linear perturbation is good enough. We extend the analysis to a dynamical setting, including quadratic corrections in the variational angles. We then consider a hybrid quantum classical architecture and define a large-width limit for hybrid kernels, showing that a hybrid quantum classical neural network can be approximately Gaussian. The results presented here show limits for which analytical understandings of the training dynamics for variational quantum circuits, used for quantum machine learning and optimization problems, are possible. These analytical results are supported by numerical simulations of quantum machine-learning experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Learning to Predict Arbitrary Quantum Processes

We present an efficient machine-learning (ML) algorithm for predicting any unknown quantum process ℰ over 𝑛 qubits. For a wide range of distributions 𝒟 on arbitrary 𝑛-qubit states, we show that this ML algorithm can learn to predict any local property of the output from the unknown process ℰ, with a small average error over input states drawn from 𝒟. The ML algorithm is computationally efficient even when the unknown process is a quantum circuit with exponentially many gates. Our algorithm combines efficient procedures for learning properties of an unknown state and for learning a low-degree approximation to an unknown observable. The analysis hinges on proving new norm inequalities, including a quantum analogue of the classical Bohnenblust-Hille inequality, which we derive by giving an improved algorithm for optimizing local Hamiltonians. Numerical experiments on predicting quantum dynamics with evolution time up to 10 6 and system size up to 50 qubits corroborate our proof. Overall, our results highlight the potential for ML models to predict the output of complex quantum dynamics much faster than the time needed to run the process itself.

quantum computation↗
DOE OSTI2021

Accurate frozen core approximation for all-electron density-functional theory

We implement and benchmark the frozen core approximation, a technique commonly adopted in electronic structure theory to reduce the computational cost by means of mathematically fixing the chemically inactive core electron states. The accuracy and efficiency of this approach are well controlled by a single parameter, the number of frozen orbitals. Explicit corrections for the frozen core orbitals and the unfrozen valence orbitals are introduced, safeguarding against seemingly minor numerical deviations from the assumed orthonormality conditions of the basis functions. A speedup of over twofold can be achieved for the diagonalization step in all-electron density-functional theory simulations containing heavy elements, without any accuracy degradation in terms of the electron density, total energy, and atomic forces. This is demonstrated in a benchmark study covering 103 materials across the Periodic Table and a large-scale simulation of CsPbBr3 with 2560 atoms. Our study provides a rigorous benchmark of the precision of the frozen core approximation (sub-meV per atom for frozen core orbitals below −200 eV) for a wide range of test cases and for chemical elements ranging from Li to Po. The algorithms discussed here are implemented in the open-source Electronic Structure Infrastructure software package.

Yu, Victor Wen-zhe↗
DOE OSTI2025

Regularizing the linearly extrapolated BDF2 scheme for incompressible flows with time relaxation

This paper presents a highly-efficient finite element scheme for the time relaxation model (TRM). The efficiency is achieved through the second-order BDF2 time-stepping scheme with linear extrapolation (BDF2LE). The accuracy of the scheme is also greatly enhanced through the use of the divergence-free Scott-Vogeulis finite elements, and van Cittert approximate deconvolution. A complete finite element analysis is provided, which includes rigorous proofs for the stability, well-possessedness, and convergence of both velocity and pressure solutions. Furthermore, we also demonstrate that the inclusion of the linear time relaxation term preserves the long-time stability of the unregularized BDF2LE scheme. Finally, numerical experiments are presented that demonstrate the added stability and accuracy that time relaxation can provide.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Virtual element approximations of the time-fractional nonlinear convection-diffusion equation on polygonal meshes

We extend the Virtual Element Method to a two-dimensional unsteady nonlinear convection-diffusion equation characterized by a fractional-order derivative with respect to the time variable. Our methodology is based on three fundamental technical components: a fractional version of the Grunwald-Letnikov approximation, discrete maximal regularity, and the regularity theory associated with non-linearity. We prove the method's well-posedness, i.e., the approximate solution's existence and uniqueness to the time-fractional convection-diffusion equation with a Lipschitz nonlinear source term. The fully discrete scheme inherently maintains stability and consistency by leveraging the discrete maximal regularity and the energy projection operator. The convergence in the L 2 -norm and H 1 -norm to various mesh configurations is validated by numerical results, underlining the practical effectiveness of the proposed method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Optimal design of acoustic metamaterial cloaks under uncertainty

In this work, we consider the problem of optimal design of an acoustic cloak under uncertainty and develop scalable approximation and optimization methods to solve this problem. The design variable is taken as an infinite-dimensional spatially-varying field that represents the material property, while an additive infinite-dimensional random field represents the variability of the material property or the manufacturing error. Discretization of this optimal design problem results in high-dimensional design variables and uncertain parameters. To solve this problem, we develop a computational approach based on a Taylor approximation and an approximate Newton method for optimization, which is based on a Hessian derived at the mean of the random field. We show our approach is scalable with respect to the dimension of both the design variables and uncertain parameters, in the sense that the necessary number of acoustic wave propagations is essentially independent of these dimensions, for numerical experiments with up to one million design variables and half a million uncertain parameters. Additionally, we demonstrate that, using our computational approach, an optimal design of the acoustic cloak that is robust to material uncertainty is achieved in a tractable manner. The optimal design under uncertainty problem is posed and solved for the classical circular obstacle surrounded by a ring-shaped cloaking region, subjected to both a single-direction single-frequency incident wave and multiple-direction multiple-frequency incident waves. Finally, we apply the method to a deterministic large-scale optimal cloaking problem with complex geometry, to demonstrate that the approximate Newton method’s Hessian computation is viable for large, complex problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗