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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2020

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used with huge success to model phenomena across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDEs fail to adequately model observed phenomena, or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. Here, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis and of specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modelling and algorithmic extensions, which serve to show the wide applicability of nonlocal modelling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. Here we introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C 7 H 10 O 2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of HartreeFock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

High-Throughput Screening of Metal–Organic Frameworks for CO 2 Capture in the Presence of Water

Competitive co-adsorption of water is a major problem in the deployment of adsorption-based CO 2 capture. Water molecules may compete for adsorption sites, reducing the capacity of the material, and dehumidification prior to separating CO 2 from N 2 increases process complexity and cost. The development of adsorbent materials that can selectively adsorb CO 2 in the presence of water would be a major step forward in the deployment of CO2 capture materials in practice. In this study, large-scale computational screening was carried out to search for metal-organic frameworks (MOFs) with high selectivity toward CO 2 over H 2 O. Calculating framework charges for thousands of MOFs is a significant challenge, so initial screening used a fast, but approximate, charge calculation method. Based on the initial screening, 15 MOFs were selected, and Monte Carlo simulations were carried out to compute the adsorption isotherms for these MOFs using more accurate framework charges calculated by density functional theory. Here, a detailed investigation was performed on the effect of using different methods for calculating partial charges, and it was found that electrostatic interactions contribute the majority of the adsorption energy of H 2 O in the selected MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fully compressible simulations of waves and core convection in main-sequence stars

Context: Recent, nonlinear simulations of wave generation and propagation in full-star models have been carried out in the anelastic approximation using spectral methods. Although it makes long time steps possible, this approach excludes the physics of sound waves completely and requires rather high artificial viscosity and thermal diffusivity for numerical stability. A direct comparison with observations is thus limited. Aims: In this study, we explore the capabilities of our compressible multidimensional Seven-League Hydro (SLH) code to simulate stellar oscillations. Methods: We compare some fundamental properties of internal gravity and pressure waves in 2D SLH simulations to linear wave theory using two test cases: (1) an interval gravity wave packet in the Boussinesq limit and (2) a realistic 3 M ⊙ stellar model with a convective core and a radiative envelope. Oscillation properties of the stellar model are also discussed in the context of observations. Results: Our tests show that specialized low-Mach techniques are necessary when simulating oscillations in stellar interiors. Basic properties of internal gravity and pressure waves in our simulations are in good agreement with linear wave theory. As compared to anelastic simulations of the same stellar model, we can follow internal gravity waves of much lower frequencies. The temporal frequency spectra of velocity and temperature are flat and compatible with the observed spectra of massive stars. Conclusion: The low-Mach compressible approach to hydrodynamical simulations of stellar oscillations is promising. Our simulations are less dissipative and require less luminosity boosting than comparable spectral simulations. The fully-compressible approach allows for the coupling of gravity and pressure waves in the outer convective envelopes of evolved stars to be studied in the future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Protonation effect on the electronic properties of 2-pyridone monomer, dimer and its water clusters: A theoretical study

The CC2 (second order approximate coupled cluster method) has been applied to investigate protonation effect on electronic transition energies of 2-pyridone (2PY), 2-pyridone dimer, and micro-solvated 2-pyridone (0-2 water molecules). The PE profiles of protonated 2-pyridone (2PYH{sup +}) as well as monohydrated 2PYH{sup +} at the different electronic states have been investigated. The {sup 1}πσ* state in protonated species (2PYH{sup +}) is a barrier free and dissociative state along the O-H stretching coordinate. In this reaction coordinate, the lowest lying {sup 1}πσ* predissociates the bound S{sub 1}({sup 1}ππ*) state, connecting the latter to a conical intersection with the S{sub 0} state. These conical intersections lead the {sup 1}ππ* state to proceed as predissociative state and finally direct the excited system to the ground state. Furthermore, in presence of water molecule, the {sup 1}πσ* state still remains dissociative but the conical intersection between {sup 1}πσ* and ground state disappears. In addition, according to the CC2 calculation results, it has been predicted that protonation significantly blue shifts the S{sub 1}-S{sub 0} electronic transition of monomer, dimer, and microhydrated 2-pyridone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

A feedback control strategy for the airfoil system under non-Gaussian colored noise excitation

The stability of a binary airfoil with feedback control under stochastic disturbances, a non-Gaussian colored noise, is studied in this paper. First, based on some approximated theories and methods the non-Gaussian colored noise is simplified to an Ornstein-Uhlenbeck process. Furthermore, via the stochastic averaging method and the logarithmic polar transformation, one dimensional diffusion process can be obtained. At last by applying the boundary conditions, the largest Lyapunov exponent which can determine the almost-sure stability of the system and the effective region of control parameters is calculated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Two-dimensional spatiotemporal focusing of femtosecond pulses and its applications in microscopy

We demonstrate and theoretically analyze the two-dimensional spatiotemporal focusing of femtosecond pulses by utilizing a two-dimensional spectral disperser. Compared with spatiotemporal focusing with a diffraction grating, it can achieve widefield illumination with better sectioning ability for a multiphoton excitation process. By utilizing paraxial approximation, our analytical method improves the axial confinement ability and identifies that the free spectra range (FSR) of the two-dimensional spectral disperser affects the out-of-focus multiphoton excitation intensity due to the temporal self-imaging effect. Based on our numerical simulation, a FSR of 50 GHz is necessary to reduce the out-of-focus two-photon excitation by 2 orders of magnitude compared with that in a grating-based spatiotemporal focusing scheme for a 90-fs excitation laser pulse. We build a two-dimensional spatiotemporal focusing microscope using a virtually imaged phased array and achieve an axial resolution of 1.3 μm, which outperforms the resolution of conventional spatiotemporal focusing using a grating by a factor of 1.7, and demonstrate better image contrast inside a tissue-like phantom.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Ultrarelativistic bound states in the spherical well

We address an eigenvalue problem for the ultrarelativistic (Cauchy) operator (−Δ){sup 1/2}, whose action is restricted to functions that vanish beyond the interior of a unit sphere in three spatial dimensions. We provide high accuracy spectral data for lowest eigenvalues and eigenfunctions of this infinite spherical well problem. Our focus is on radial and orbital shapes of eigenfunctions. The spectrum consists of an ordered set of strictly positive eigenvalues which naturally splits into non-overlapping, orbitally labelled E{sub (k,l)} series. For each orbital label l = 0, 1, 2, …, the label k = 1, 2, … enumerates consecutive lth series eigenvalues. Each of them is 2l + 1-degenerate. The l = 0 eigenvalues series E{sub (k,0)} are identical with the set of even labeled eigenvalues for the d = 1 Cauchy well: E{sub (k,0)}(d = 3) = E{sub 2k}(d = 1). Likewise, the eigenfunctions ψ{sub (k,0)}(d = 3) and ψ{sub 2k}(d = 1) show affinity. We have identified the generic functional form of eigenfunctions of the spherical well which appear to be composed of a product of a solid harmonic and of a suitable purely radial function. The method to evaluate (approximately) the latter has been found to follow the universal pattern which effectively allows to skip all, sometimes involved, intermediate calculations (those were in usage, while computing the eigenvalues for l ≤ 3).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Customizable two-species kinetic equilibria for nonuniform low-beta plasmas

Here, two methods are developed for constructing self-consistent two-species kinetic equilibria for low-beta electrostatic plasmas, in which the magnetic field is uniform and fixed in time. The first method uses Taylor series approximations to construct distribution functions that can be specified analytically. The second method relies on numerically solving a nonlinear ordinary differential equation and produces exact—to numerical precision—equilibria. In both methods, the equilibrium distribution functions for ions and electrons are expressed in terms of constants of motion and satisfy the steady-state Vlasov-Poisson equation system. Provided that the ion drift speed does not exceed the ion thermal speed, the equilibria can be specified with customizable density and electrostatic potential profiles. The methods can thereby be tailored to different applications and are successfully applied to construct kinetic equilibria for cross-field plasmas with sheared flows, large density variations, and different levels of magnetization. The equilibria are used to initialize fourth-order finite-volume Vlasov-Poisson simulations in (x, v x , v y ) coordinates and the associated temporal evolution is used to assess the accuracy of each method. Lastly, the low-amplitude deviations observed in these simulations demonstrate that the kinetic equilibria are robust and that they provide a valuable means of studying the dynamics of nonuniform magnetized plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ~8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation–π and anion–π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion–π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E int ) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent—these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)- based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation–π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E int values, and maximum errors of ±0.2–0.3 kcal/mol (i.e., ~±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Machine learning interatomic potential for silicon-nitride (Si 3 N 4 ) by active learning

Silicon nitride (Si 3 N 4 ) is an extensively used material in the automotive, aerospace, and semiconductor industries. However, its widespread use is in contrast to the scarce availability of reliable interatomic potentials that can be employed to study various aspects of this material on an atomistic scale, particularly its amorphous phase. In this work, we developed a machine learning interatomic potential, using an efficient active learning technique, combined with the Gaussian approximation potential (GAP) method. Our strategy is based on using an inexpensive empirical potential to generate an initial dataset of atomic configurations, for which energies and forces were recalculated with density functional theory (DFT); thereafter, a GAP was trained on these data and an iterative re-training algorithm was used to improve it by learning on-the-fly. When compared to DFT, our potential yielded a mean absolute error of 8 meV/atom in energy calculations for a variety of liquid and amorphous structures and a speed-up of molecular dynamics simulations by 3–4 orders of magnitude, while achieving a first-rate agreement with experimental results. Our potential is publicly available in an open-access repository.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Exciting DeePMD: Learning excited-state energies, forces, and non-adiabatic couplings

We extend the DeePMD neural network architecture to predict electronic structure properties necessary to perform non-adiabatic dynamics simulations. While learning the excited state energies and forces follows a straightforward extension of the DeePMD approach for ground-state energies and forces, how to learn the map between the non-adiabatic coupling vectors (NACV) and the local chemical environment descriptors of DeePMD is less trivial. Most implementations of machine-learning-based non-adiabatic dynamics inherently approximate the NACVs, with an underlying assumption that the energy-difference-scaled NACVs are conservative fields. We overcome this approximation, implementing the method recently introduced by Richardson [J. Chem. Phys. 158, 011102 (2023)], which learns the symmetric dyad of the energy-difference-scaled NACV. Furthermore, the efficiency and accuracy of our neural network architecture are demonstrated through the example of the methaniminium cation CH 2 NH 2 + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Data assimilation in operator algebras

We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by multiplication operators and probability densities by density operators (quantum states). In the algebraic approach, the forecast step of data assimilation is represented by a quantum operation induced by the Koopman operator of the dynamical system. Moreover, the analysis step is described by a quantum effect, which generalizes the Bayesian observational update rule. Projecting this formulation to finite-dimensional matrix algebras leads to computational schemes that are i) automatically positivity-preserving and ii) amenable to consistent data-driven approximation using kernel methods for machine learning. Moreover, these methods are natural candidates for implementation on quantum computers. Applications to the Lorenz 96 multiscale system and the El Niño Southern Oscillation in a climate model show promising results in terms of forecast skill and uncertainty quantification.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Sequential Kalman tuning of the t -preconditioned Crank-Nicolson algorithm: efficient, adaptive and gradient-free inference for Bayesian inverse problems

Ensemble Kalman Inversion (EKI) has been proposed as an efficient method for the approximate solution of Bayesian inverse problems with expensive forward models. However, when applied to the Bayesian inverse problem EKI is only exact in the regime of Gaussian target measures and linear forward models. Here, in this work we propose embedding EKI and Flow Annealed Kalman Inversion, its normalizing flow (NF) preconditioned variant, within a Bayesian annealing scheme as part of an adaptive implementation of the t-preconditioned Crank-Nicolson (tpCN) sampler. The tpCN sampler differs from standard pCN in that its proposal is reversible with respect to the multivariate t-distribution. The more flexible tail behaviour allows for better adaptation to sampling from non-Gaussian targets. Within our Sequential Kalman Tuning (SKT) adaptation scheme, EKI is used to initialize and precondition the tpCN sampler for each annealed target. The subsequent tpCN iterations ensure particles are correctly distributed according to each annealed target, avoiding the accumulation of errors that would otherwise impact EKI. We demonstrate the performance of SKT for tpCN on three challenging numerical benchmarks, showing significant improvements in the rate of convergence compared to adaptation within standard SMC with importance weighted resampling at each temperature level, and compared to similar adaptive implementations of standard pCN. The SKT scheme applied to tpCN offers an efficient, practical solution for solving the Bayesian inverse problem when gradients of the forward model are not available. Code implementing the SKT schemes for tpCN is available at https://github.com/RichardGrumitt/KalmanMC.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Inflation in a two 3-form fields scenario

A setting constituted by N 3-form fields, without any direct interaction between them, minimally coupled to gravity, is introduced in this paper as a framework to study the early evolution of the universe. We focus particularly on the two 3-forms case. An inflationary scenario is found, emerging from the coupling to gravity. More concretely, the fields coupled in this manner exhibit a complex interaction, mediated by the time derivative of the Hubble parameter. Our investigation is supported by means of a suitable choice of potentials, employing numerical methods and analytical approximations. In more detail, the oscillations on the small field limit become correlated, and one field is intertwined with the other. In this type of solution, a varying sound speed is present, together with the generation of isocurvature perturbations. The mentioned features allow to consider an interesting model, to test against observation. It is subsequently shown how our results are consistent with current CMB data (viz.Planck and BICEP2)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

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