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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Proteinaceous aggregates containing ?-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson’s disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

Petyuk, Vladislav A.↗
DOE OSTI2022

Transferability of data-driven, many-body models for CO 2 simulations in the vapor and liquid phases

Here, extending on the previous work by Riera et al. [J. Chem. Theory Comput. 16, 2246–2257 (2020)], we introduce a second generation family of data-driven many-body MB-nrg models for CO 2 and systematically assess how the strength and anisotropy of the CO 2 –CO 2 interactions affect the models’ ability to predict vapor, liquid, and vapor–liquid equilibrium properties. Building upon the many-body expansion formalism, we construct a series of MB-nrg models by fitting one-body and two-body reference energies calculated at the coupled cluster level of theory for large monomer and dimer training sets. Advancing from the first generation models, we employ the charge model 5 scheme to determine the atomic charges and systematically scale the two-body energies to obtain more accurate descriptions of vapor, liquid, and vapor–liquid equilibrium properties. Challenges in model construction arise due to the anisotropic nature and small magnitude of the interaction energies in CO 2 , calling for the necessity of highly accurate descriptions of the multidimensional energy landscape of liquid CO 2 . These findings emphasize the key role played by the training set quality in the development of transferable, data-driven models, which, accurately representing high-dimensional many-body effects, can enable predictive computer simulations of molecular fluids across the entire phase diagram.

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

Prenatal exposure to mixtures of persistent endocrine disrupting chemicals and postnatal body size in British girls

Endocrine disrupting chemical (EDC) exposure is ubiquitous. EDC exposure during critical windows of development may interfere with the body's endocrine system, affecting growth. Previous human studies have examined one EDC at a time in relation to infant growth. By studying mixtures, the human experience can be better approximated. We investigated the association of prenatal exposure to persistent EDCs (per- and polyfluoroalkyl substances (PFAS), polychlorinated biphenyls (PCBs), and organochlorine pesticides (OCPs)) as mixtures with postnatal body size among female offspring. We used a sub-sample of the Avon Longitudinal Study of Parents and Children (N = 425), based in the United Kingdom. We quantified 52 EDCs in maternal serum collected during pregnancy. We used Bayesian kernel machine regression with a random intercept to examine the association of prenatal concentrations of EDC mixtures with longitudinal postnatal body size measures for each EDC class separately (PFAS, PCBs, and OCPs) and for all three classes combined. Weight and height measures at 0, 2, 9, and 19 months were obtained by health professionals as part of routine child health surveillance. The mixture representing all three classes combined (31 chemicals) (n = 301) was inversely associated with postnatal body size. Holding all EDCs in the 31-chemical mixture at the 75th percentile compared to the 50th percentile was associated with 0.15 lower weight-for-age z-score (95% credible interval –0.26, –0.03). Weak inverse associations were also seen for height-for-age and body mass index-for-age scores. Furthermore, these results suggest that prenatal exposure to mixtures of persistent EDCs may affect postnatal body size.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Novel Approach for Computing Rigid Body Motion Using Linear Accelerations

Here, a novel approach is presented for computing general rigid body motion based on a few known linear accelerations. This method utilizes linear acceleration data obtained from three distinct points on the body, all within a body-fixed reference frame. The only requirement is that the three chosen points must not be collinear. A system of differential-algebraic equations is derived, combining principles of rigid body kinematics with theory of the rotation group SO(3). These equations provide a framework for numerically computing various motion parameters, including angular velocity, angular acceleration, body orientation, velocity field, acceleration field, and displacement field. By numerically solving this system of equations, we can fully characterize rigid body motion in three-dimensional space. A numerical example is provided to demonstrate the practical implementation and efficacy of the proposed technique, illustrating its potential for accurate motion computation in various applications.

42 ENGINEERING↗
DOE OSTI2023

Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development

Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born–Oppenheimer potential energy surface. In particular, we focus on ab initio–based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through ( a) parameterization of distributed multipoles, ( b) explicit fitting of the MBE, ( c) inclusion of many-atom features in a neural network, and ( d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Initial Conditions of Planet Formation: Time Constraints from Small Bodies and the Lifetime of Reservoirs in the Solar Protoplanetary Disk

This review explores the timescales of the initial phase of planet formation, from nebular dust (CAIs and chondrules) to planetesimal accretion and differentiation, using evidence from meteorite research. Aluminium-Mg systematics of CAIs indicate either an extended period of CAI formation (∼0.3 Ma) or an initial 26 Al heterogeneity, with evidence supporting a homogeneous 26 Al abundance in the protoplanetary disk. Thermal and aqueous alteration on the parent body can disturb the U-Pb and Al-Mg chronometers in chondrules. Focusing on relatively robust isochron data from plagioclase of pristine (types ≤3.05) chondrites indicates a shift in chondrule formation locations, moving from the inner to the outer disk over time. Ages of basaltic achondrites show that silicate differentiation on small bodies was well underway within the first few million years (Ma) of our solar system. Their age record, however, reveals inconsistencies between different chronometers, partly caused by (i) secondary disturbances due to thermal metamorphism, aqueous alteration, or impacts, (ii) the presence of xenolithic minerals, and (iii) potentially variable initial 26 Al abundances due to disturbances at the mineral scale. Nucleosynthetic isotope data indicate that parent bodies of iron and stony meteorites formed in two distinct regions within the protoplanetary disk: the inner, non-carbonaceous (NC) and the outer, carbonaceous (CC) region. Based on Hf-W chronometry it has been demonstrated that NC and CC parent bodies of magmatic iron meteorites segregated their cores within ∼1–3 Ma after CAI formation, implying that parent body accretion occurred within <1 Ma in both reservoirs. Combining accretion ages with nucleosynthetic data further reveals that, at first order, NC and CC reservoirs in the solar protoplanetary disk were established within 1 Ma and existed over several Ma with limited exchange between them. In the CR chondrite accretion region of the disk, planetary bodies formed over at least 3 Ma, while in most other regions, formation spanned at least 1 Ma, with minimal changes in nucleosynthetic isotope compositions. Aerodynamical size sorting of dust likely introduced or amplified some of these variations.

26Al distribution↗
DOE OSTI2021

Chemical characteristics of iron meteorite parent bodies

The projected relative abundances of the highly siderophile elements (HSE; Re, Os, Ir, Ru, Pt, and Pd) for bulk parent bodies of 10 magmatic iron meteorite groups/grouplet (IC, IIAB, IIC, IID, IIF, IIIAB, IIIF, IVA, IVB, and South Byron Trio) are broadly similar and show no resolvable differences between noncarbonaceous (NC) and carbonaceous (CC) genetic heritage. The processes driving genetic isotopic heterogeneity in the early Solar System, therefore, evidently did not leave discernable chemical fingerprints with respect to HSE relative abundances on the bulk planetesimal scale. By contrast, the absolute abundances of HSE projected for parent body cores, which reflect core size, are more variable and, on average, higher in CC bodies compared to NC bodies. Overall, bulk core chemical compositions, as well as core size, are linked to the distribution of Fe within a parent body, which is controlled by its oxidation state. The CC parent bodies are constrained to have formed under heterogeneous oxidizing conditions which were, on average, more oxidizing than those of the NC environment.

Hilton, Connor D.↗
DOE OSTI2023

Accurate calculation of many-body energies in water clusters using a classical geometry-dependent induction model

We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The expansion is carried out up to hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA interaction potentials. The classical induction model with no adjustable parameters reproduces the ab-initio 3- and 4-body terms contained in these teo Databases with a Root-Mean-Square-Error (RMSE) of 0.104/0.058 and a Mean-Absolute-Error (MAE) of 0.054/0.026 kcal/mol, respectively, results that are on a par with those obtained 1 by fitting the same data using tens of thousands of Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy was included in the 3-body energy and was found to be small but not quite negligible. The model represents a practical, efficient and transferable approach for obtaining accurate non-additive interactions for multi-component systems without the need of performing tens of thousands of high level electronic structure calculations and fitting them with tens of thousands of PIPs.

molecular analysis water, aqueous↗
DOE OSTI2024

Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan

Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this “red body,” focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Many-Body Potential for Simulating Self-Assembly of Polymer-Grafted Nanoparticles in a Polymer Matrix

Many-body interactions between polymer-grafted nanoparticles (NPs) play a key role in promoting their assembly into low-dimensional structures within polymer melts, even when the particles are spherical and isotropically grafted. However, capturing such interactions in simulations of NP assembly is very challenging because explicit modeling of the polymer grafts and melt chains is highly computationally expensive, even using coarse-grained models. Here, we develop a many-body potential for describing the effective interactions between spherical polymer-grafted NPs in a polymer matrix through a machine-learning approach. The approach involves using permutationally invariant polynomials to fit two- and three-body interactions derived from the potential of mean force calculations. The potential developed here reduces the computational cost by several orders of magnitude, thereby, allowing us to explore assembly behavior over large length and time scales. We show that the potential not only reproduces previously known assembled phases such as 1D strings and 2D hexagonal sheets, which generally cannot be achieved using isotropic two-body potentials, but can also help discover interesting phases such as networks, clusters, and gels. We demonstrate how each of these assembly morphologies intrinsically arises from a competition between two- and three-body interactions. Our approach for deriving many-body effective potentials can be readily extended to other colloidal systems, enabling researchers to make accurate predictions of their behavior and dissect the role of individual interaction energy terms of the overall potential in the observed behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Probing many-body dynamics in a two-dimensional dipolar spin ensemble

Abstract The most direct approach for characterizing the quantum dynamics of a strongly interacting system is to measure the time evolution of its full many-body state. Despite the conceptual simplicity of this approach, it quickly becomes intractable as the system size grows. An alternate approach is to think of the many-body dynamics as generating noise, which can be measured by the decoherence of a probe qubit. Here we investigate what the decoherence dynamics of such a probe tells us about the many-body system. In particular, we utilize optically addressable probe spins to experimentally characterize both static and dynamical properties of strongly interacting magnetic dipoles. Our experimental platform consists of two types of spin defects in nitrogen delta-doped diamond: nitrogen-vacancy colour centres, which we use as probe spins, and a many-body ensemble of substitutional nitrogen impurities. We demonstrate that the many-body system’s dimensionality, dynamics and disorder are naturally encoded in the probe spins’ decoherence profile. Furthermore, we obtain direct control over the spectral properties of the many-body system, with potential applications in quantum sensing and simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗
DOE OSTI2025

Exactness of the normal-ordered two-body truncation of three-nucleon forces

Reference-state-based many-body methods start from Hamiltonians that are normal ordered with respect to the reference state. In low-energy nuclear physics applications, normal-ordered Hamiltonians consisting of two- and three-nucleon forces are usually truncated at the two-body rank with residual three-nucleon operators being discarded. Benchmark computations have shown that this truncation is accurate, but we lack an understanding about why it works. Here, we show that the normal-ordered two-body truncation is exact for zero-range three-body forces when nuclei are computed using the coupled cluster with singles and doubles method. As the nuclear three-nucleon force is short ranged and a three-body contact is a leading term in effective field theories of quantum chromodynamics, our result provides an analytical basis for the popular normal-ordered two-body approximation.

Rothman, Maxwell [Univ. of Tennessee, Knoxville, T↗
DOE OSTI2024

Spinbox: tools for many-body quantum systems in a Monte Carlo context

Spinbox is a piece of software that facilitates quantum mechanical calculations relevant to Monte Carlo simulation of atomic nuclei. At the front lines of research on the nuclear many-body problem are a large number of supercomputer-scale simulation codes. These codes produce valuable results but can be hard to understand, especially for those without intimate knowledge of the relevant theoretical methods. Thus, tools that fill pedagogical roles are extremely valuable. Spinbox makes it easy for one to replicate and analyze the computational processes relevant to a Quantum Monte Carlo (QMC) simulation that may be difficult to understand/debug/analyze due to the scale of the corresponding simulation software. Spinbox is written in Python using other state-of-the-art Python modules for numerical calculations. While a number of Python libraries exist that are suited to general quantum many-body calculations, the motivation of Spinbox is quite particular. In Diffusion Monte Carlo methods (DMC, GFMC, AFDMC), the central calculation is the imaginary-time propagation of individual samples of the many-body wavefunction. Although quantum wavefunctions generally must be described by a probability distribution over a basis, DMC imbues particles (within one sample) with classical spatial coordinates. This method is unusual, so other Python packages are typically not set up to do this easily. Furthermore, the software has built-in options for nuclear systems assuming isospin symmetry, which can be set up with other libraries but is a nontrivial process to do so. Features: - numerical representation of samples of the many-body wavefunctions, including tensor-product states (used in AFDMC) - numerical representation of many-body operators, including tensor-product operators: general, spin, imaginary-time propagation, etc. - the correct associated arithmetic and algebra, implemented as class methods - classes for representing realistic nuclear two- and three-body Hamiltonians (e.g. Argonne V18, Illinois NNN) - large-scale parallel integration over random variables, crucial for the AFDMC method My goal is to make this package open source so that anyone may use it and contribute to it, particularly other researchers doing AFDMC calculations

Fox, Jordan↗
DOE OSTI2023

A Formulation of the Many-Body Expansion (MBE) for Periodic Systems: Application to Several Ice Phases

A new formulation of the many-body expansion (MBE) for periodic systems, based on their inherent translational symmetry, is introduced and applied to 7 ice polymorphs. This new formulation is built via a hierarchical procedure connecting gas phase unit cells over finite supercells to infinite solids. For finite supercells, it is demonstrated that this method successfully recovers the energetics while reducing the scaling of the calculation of the many-body terms by a factor of ~N, where N is the system size. Furthermore, the proposed framework delineates a straightforward way to obtain properties of macroscopic systems in the limit of an infinite cell. For periodic systems, the success of this approach is demonstrated by showing that the lattice energies computed (up to the 4-th order in the MBE) reproduce the lattice energies obtained using periodic boundary conditions with an Ewald summation for 7 polymorphs of ice (Ih, II, VIII, IX, XIII, XIV, XV). This development makes it possible to quantify, for the first time, the many-body contributions to the lattice energy of various ice polymorphs. The many-body (three-body and higher) interactions were found to vary significantly among the 7 ice phases, amounting between 7-24% of the total lattice energies. So, this development opens the door for obtaining insights into solid-state properties, while leveraging the computational benefits of the MBE.

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

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

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

Three-body Förster resonance of a new type in Rydberg atoms

The three-body Förster resonances 3 × nP{sub 3/2}(|M|) →nS{sub 1/2} + (n + 1)S{sub 1/2} + nP{sub 3/2}(|M*|), controlled by a constant electric field, were realised earlier by the authors in an ensemble of several cold Rydberg Rb atoms. One of the drawbacks of such resonances for potential application in three-qubit quantum gates is the proximity of the two-body Förster resonance 2 × nP{sub 3/2} → nS{sub 1/2} + (n + 1)S{sub 1/2}, as well as the possibility of their implementation only for states with values of the principal quantum numbers n ⩽38. A three-body resonance of a new type, 3 × nP{sub 3/2} → nS{sub 1/2} + (n + 1)S{sub 1/2} + nP{sub 1/2}, which can be realised for arbitrary n, is proposed and analysed. Its specific feature is also that the third atom transits into a state with a different total angular momentum J = 1/2, which has no Stark structure, so that the two-body resonance is completely absent. Numerical calculations showed that for not too strong interaction, it is possible to observe coherent three-body oscillations of the populations of collective states, which is of interest for developing new schemes of three-qubit quantum gates controlled by an electric field. (paper)

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Motif magnetism and quantum many-body scars

In this work, we generally expect quantum systems to thermalize and satisfy the eigenstate thermalization hypothesis (ETH), which states that finite-energy-density eigenstates are thermal. However, some systems, such as many-body localized systems and systems with quantum many-body scars, violate ETH and have high-energy athermal eigenstates. In systems with scars, most eigenstates thermalize, but a few atypical scar states do not. Scar states can give rise to a periodic revival when time-evolving particular initial product states, which can be detected experimentally. Recently, a family of spin Hamiltonians was found with magnetically ordered three-colored eigenstates that are quantum many-body scars [Lee et al., Phys. Rev. B 101, 241111(R) (2020)]. These models can be realized in any lattice that can be tiled by triangles, such as the triangular or kagome lattices, and have been shown to have close connections to the physics of quantum spin liquids in the Heisenberg kagome antiferromagnet. In this paper, we introduce a generalized family of n-colored Hamiltonians with “spiral colored” eigenstates made from n-spin motifs such as polygons or polyhedra. We show how these models can be realized in many different lattice geometries and provide numerical evidence that they can exhibit quantum many-body scars with periodic revivals that can be observed by time-evolving simple product states. The simple structure of these Hamiltonians makes them promising candidates for future experimental studies of quantum many-body scars.

36 MATERIALS SCIENCE↗