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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
DOE OSTI2021

Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning

To expedite new molecular compound development, a long-sought goal within the chemistry community has been to predict molecules’ bulk properties of interest a priori to synthesis from a chemical structure alone. In this work, we demonstrate that machine learning methods can indeed be used to directly learn the relationship between chemical structures and bulk crystalline properties of molecules, even in the absence of any crystal structure information or quantum mechanical calculations. We focus specifically on a class of organic compounds categorized as energetic materials called high explosives (HE) and predicting their crystalline density. An ongoing challenge within the chemistry machine learning community is deciding how best to featurize molecules as inputs into machine learning models—whether expert handcrafted features or learned molecular representations via graph-based neural network models—yield better results and why. We evaluate both types of representations in combination with a number of machine learning models to predict the crystalline densities of HE-like molecules curated from the Cambridge Structural Database, and we report the performance and pros and cons of our methods. Our message passing neural network (MPNN) based models with learned molecular representations generally perform best, outperforming current state-of-the-art methods at predicting crystalline density and performing well even when testing on a data set not representative of the training data. However, these models are traditionally considered black boxes and less easily interpretable. Here, to address this common challenge, we also provide a comparison analysis between our MPNN-based model and models with fixed feature representations that provides insights as to what features are learned by the MPNN to accurately predict density.

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

Boundary-Layer-Coupled and Decoupled Clouds in Global Storm-Resolving Models: Comparisons With the ARM Observations

The accurate representation of interactions between clouds and planetary boundary layer (PBL) is a persistent challenge in climate models, critical for simulating surface energy budget. The emergence of kilometer-grid-scale global storm resolving models (GSRMs) offers the potential for enhanced details of PBL processes in these complex interactions. This study evaluates the representation of PBL-coupled and decoupled clouds in nine GSRM simulations against extensive ground-based observations by the Department of Energy Atmospheric Radiation Measurement (ARM) program, across six sites encompassing diverse regimes such as marine and continental environments in tropics and midlatitude. By differentiating coupling based on the relative positions between cloud bases and PBL tops, our analysis focuses on the simulation of PBL height, cloud frequency, position and vertical extent. The GSRMs generally exhibit commendable agreements with observed cloud structures and PBL diurnal cycles across different ARM sites. In contrast to the relatively consistent representation of decoupled clouds, discrepancies exist between the simulated and the observed coupled clouds, particularly in areas of intense convection, for example, over tropical rainforests and mountainous regions. These biases are probably associated with the models' tendency to underestimate the boundary layer humidity and the frequency of coupled clouds within different ranges of PBL heights. This study underscores the importance for continuous improvements in the representation of boundary layer and convection within these global kilometer-grid-scale models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Augmenting machine learning of energy landscapes with local structural information

We present a machine learning approach for accurately predicting formation energies of binary compounds in the context of crystal structure predictions. The success of any machine learning model depends significantly on the choice of representation used to encode the relevant physical information into machine-learnable data. We test different representation schemes based on partial radial and angular distribution functions (RDF+ADF) on Al–Ni and Cd–Te structures generated using our genetic algorithm for structure prediction. We observe a remarkable improvement in predictive accuracy upon transitioning from global to atom-centered representations, resulting in a threefold decrease in prediction errors. We show that a support vector regression model using a combination of atomic radial and angular distribution functions performs best at the formation energy prediction task, providing small root mean squared errors of 3.9 meV/atom and 10.9 meV/atom for Al–Ni and Cd–Te, respectively. We test the performance of our models against common traditional descriptors and find that RDF- and ADF-based representations significantly outperform many of those in the prediction of formation energies. The high accuracy of predictions makes our machine learning models great candidates for the exploration of energy landscapes.

Honrao, Shreyas J. (ORCID:0000000166155257)↗
DOE OSTI2023

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

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

Overestimated natural biological nitrogen fixation translates to an exaggerated CO 2 fertilization effect in Earth system models

CO 2 fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, in this study, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO 2 enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO 2 that aligns with a meta-analysis of CO 2 enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO 2 (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO 2 . Finally, we find a positive correlation between modeled present-day natural BNF and the CO 2 fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO 2 fertilization effect of approximately 11% in ESMs.

Biological nitrogen fixation↗
DOE OSTI2020

Impact of Radial Reflector Fidelity on Neutronics and Vessel Fluence Simulations

The Consortium for Advanced Simulation of Light Water Reactors is developing the Virtual Environment for Reactor Applications (VERA), and the MPACT code, which is the primary deterministic neutron transport solver in VERA, provides sub-pin level flux and power distributions as part of full-scale cycle depletion and analysis. In such calculations, an important aspect is the radial reflector treatment. To improve the fidelity of the radial reflector treatment, MPACT was extended to approximate the modeling of the reactor’s structural components such as the core shroud, barrel, neutron pads, and vessel. This work explores several modeling configurations with varying levels of fidelity and computational burden and assesses the importance of modeling fidelity on the eigenvalue and pin power distribution. Two two-dimensional (2-D) problems were analyzed to assess the impact on eigenvalue and pin power distributions with low-fidelity, coarse square cell reflector representations: (1) a Watts Bar Nuclear Plant Unit 1 (WBN1) quarter-core slice with depletion and (2) an AP1000 quarter-core slice. In this work, the analyses showed that the effect on eigenvalue is fairly small, but the effect on pin power is more pronounced, especially locally in the assemblies closest to the periphery, where the maximum pin power difference is nearly 3.5% in the AP1000 case. Two additional 2-D problems were used to assess the comparison between the low-fidelity coarse square cell treatment and a high-fidelity geometric representation that uses subpin material specification: (1) the same WBN1 quarter-core slice and (2) a representative model of the NuScale small modular reactor (SMR), which features a solid reflector design with moderator holes. These results demonstrate that even a coarse, low-fidelity representation adequately captures the necessary simulation characteristics. Last, these capabilities were applied to the 2-D WBN1 quarter-core depletion to assess the impact on vessel fluence using VeraShift. From adjoint calculations, pins along the periphery were observed to be of highest importance for fluence calculation, so the impact of the reflector representation in MPACT could theoretically substantially affect the predicted result. However, it was observed that the change in pin powers along the periphery minimally impacts the maximum vessel fluence with a difference within the statistical uncertainty but provides terrific insight on the sensitivity of the peripheral pins.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗
DOE OSTI2025

Learning nuclear cross sections across the chart of nuclides with graph neural networks

We explore the use of deep learning techniques to learn how nuclear cross sections change as we add or remove protons and neutrons. As a proof of principle, we focus on the neutron-induced reactions in the fast energy regime. Our approach follows a two-stage learning framework. First, we apply representation learning to encode cross section data into a latent space using either variational autoencoders (VAEs) or implicit neural representations (INRs). Then, we train graph neural networks (GNNs) on the resulting embeddings to predict missing values across the nuclear chart by leveraging the topological structure of neighboring isotopes. We demonstrate accurate cross section predictions within a 9 × 9 block of missing nuclei. We also find that the optimal GNN training strategy depends on the type of latent representation used, with VAE embeddings performing best under end-to-end optimization in the original space, while INR embeddings achieve better results when the GNN is trained only in the latent space. Furthermore, using clustering algorithms, we map groups of latent vectors into regions of the nuclear chart and show that VAEs and INRs can discover some of the neutron magic numbers. These findings suggest that deep-learning models based on the representation encoding of cross sections combined with graph neural networks hold significant potential in augmenting nuclear theory models, e.g., by providing reliable estimates of covariances of cross sections, including cross-material covariances.

Machine learning↗
DOE OSTI2022

Bosonic field digitization for quantum computers

Quantum simulation of quantum field theory is a flagship application of quantum computers that promises to deliver capabilities beyond classical computing. The realization of quantum advantage will require methods that can accurately predict error scaling as a function of the resolution and parameters of the model and that can be implemented efficiently on quantum hardware. In this paper, we address the representation of lattice bosonic fields in a discretized field amplitude basis, develop methods to predict error scaling, and present efficient qubit implementation strategies. A low-energy subspace of the bosonic Hilbert space, defined by a boson occupation number cutoff, can be represented with exponentially good accuracy by a low-energy subspace of a finite-size Hilbert space. The finite representation construction and the associated errors are directly related to the accuracy of the Nyquist-Shannon sampling and the finite Fourier transforms of the boson number states in the field and the conjugate-field bases. We analyze the relation between the boson mass, the discretization parameters used for wave function sampling, and the finite representation size. Numerical simulations of small size Φ 4 problems demonstrate that the boson mass optimizing the sampling of the ground state wave function is a good approximation to the optimal boson mass yielding the minimum low-energy subspace size. However, we find that accurate sampling of general wave functions does not necessarily result in accurate representation. Finally, we develop methods for validating and adjusting the discretization parameters to achieve more accurate simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Spin-orbit coupling induced demagnetization in Ni: Ab initio nonadiabatic molecular dynamics perspective

Spin-orbit coupling (SOC), which can induce spin flip during the relaxation of photoexcited charge carrier, plays a crucial role in spin dynamics. Here in this work, we have used time-domain ab initio nonadiabatic molecular dynamics (NAMD) method to study the SOC induced ultrafast demagnetization in Ni at 300K. The spin-diabatic representation using spin-polarized Kohn-Sham (KS) basis sets and spin-adiabatic representation using spinor basis sets have been applied, and both of them achieve demagnetization in Ni with a timescale around 100fs. The spin-diabatic representation suggests a picture that the electron-phonon coupling (EPC) provides direct energy relaxation channel among the same-spin states, while the SOC can induce spin flip. After photoexcitation, it is found the spin-minority electrons relax to the same-spin states rather than the opposite-spin states, since EPC is larger than SOC by one order of magnitude. By contrast, for the spin-majority electrons, spin flip occurs since there are no empty same-spin states as electron acceptor above the Fermi level. The different relaxation pathways for spin-majority and spin-minority electrons induce the demagnetization. The spin-adiabatic representation provides an Elliott-Yafet spin-phonon scattering picture. The SOC induced reduction of magnetic moment in Ni may induce magnon to drive further demagnetization. The ab initio NAMD simulation provides a critical angle to understand how the SOC and EPC affect demagnetization process in Ni.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Topology invisible to eigenvalues in obstructed atomic insulators

Here we consider the extent to which symmetry eigenvalues reveal the topological character of bands. Specifically, we compare distinct atomic limit phases (band representations) that share the same irreducible representations (irreps) at all points in the Brillouin zone and, therefore, appear equivalent in a classification based on eigenvalues. We derive examples where such “irrep-equivalent” phases can be distinguished by a quantized Berry phase or generalization thereof. These examples constitute a generalization of the Su-Schrieffer-Heeger chain: neither phase is topological, in the sense that localized Wannier functions exist, yet there is a topological obstruction between them. We refer to two phases as “Berry obstructed atomic limits” if they have the same irreps, but differ by Berry phases. This is a distinct notion from eigenvalue obstructed atomic limits, which differ in their symmetry irreps at some point in the Brillouin zone. We compute exhaustive lists of elementary band representations that are irrep equivalent, in all space groups, with and without time-reversal symmetry and spin-orbit coupling, and use group theory to derive a set of necessary conditions for irrep equivalence. Finally, we conjecture, and in some cases prove, that irrep-equivalent elementary band representations that are not equivalent can be distinguished by a topological invariant.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Euclidean formulation of relativistic quantum mechanics of N particles

A Euclidean formulation of relativistic quantum mechanics for systems of a finite number of degrees of freedom is discussed. Relativistic treatments of quantum theory are needed to study hadronic systems at subhadronic distance scales. While direct interaction approaches to relativistic quantum mechanics have proved to be useful, they have two disadvantages. One is that cluster properties are difficult to realize for systems of more than two particles. The second is that the relation to quantum field theories is indirect. Euclidean formulations of relativistic quantum mechanics provide an alternative representation that does not have these difficulties. More surprising, the theory can be formulated entirely in the Euclidean representation without the need for analytic continuation. In this work a Euclidean representation of a relativistic N-particle system is discussed. Kernels for systems of N free particles of any spin are given and shown to be reflection positive. Explicit formulas for generators of the Poincaré group for any spin are constructed and shown to be self-adjoint on the Euclidean representation of the Hilbert space. The structure of correlations that preserve both the Euclidean covariance and reflection positivity is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Digitization and subduction of S U ( N ) gauge theories

The simulation of lattice gauge theories on quantum computers necessitates digitizing gauge fields. One approach involves substituting the continuous gauge group with a discrete subgroup, but the implications of this approximation still need to be clarified. To gain insights, we investigate the subduction of S U ( 2 ) and S U ( 3 ) to discrete crystal-like subgroups. Using classical lattice calculations, we show that subduction offers valuable information based on subduced direct sums, helping us identify additional terms to incorporate into the lattice action that can mitigate the effects of digitization. Furthermore, we compute the static potentials of all irreducible representations of Σ ( 360 × 3 ) at a fixed lattice spacing. Our results reveal a percent-level agreement with the Casimir scaling of S U ( 3 ) for irreducible representations that subduce to a single Σ ( 360 × 3 ) irreducible representation. This provides a diagnostic measure of approximation quality, as some irreducible representations closely match the expected results while others exhibit significant deviations. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

How to falsify string theory at a collider

The string landscape accommodates a broad range of possible effective field theories. This poses a challenge for extracting verifiable predictions as well as falsifiable signatures of string theory. Motivated by these considerations, in this work we observe that all known stringy standard models support only low-dimensional representations of the gauge group. While it is in principle possible to produce contrived models with higher-dimensional representations, these generically appear in a tower of states with lighter ones in lower-dimensional representations, i.e., not in isolation. With this in mind, we consider the phenomenologically well-motivated scenario given by adding a single Majorana field in a real, 𝑛-dimensional representation of 𝑆⁢𝑈⁢(2) 𝐿 with 𝑛≥5 and nothing else . This scenario is not realized in any known string construction, and we conjecture that this is true of string theory in general. Detection of this scenario would thus amount to falsifying the (known) string landscape. We recast existing LHC searches for new electroweak states to extract updated bounds on this class of scenarios. Improved limits from future colliders and dark matter detection experiments provide additional routes to potentially falsifying string theory.

extensions of fermion sector↗
DOE OSTI2021

Illustrated formalisms for total scattering data: a guide for new practitioners

The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Modeling Multi-View Impedance-Based Cross-Geometry SOH Estimator for Li-ion Batteries

Abstract: Accurately estimating battery’s State of Health (SOH) remains challenging when models must generalize across cell designs and operating conditions. Most Electrochemical Impedance Spectroscopy (EIS)-based approaches either (i) hand-engineer a few Nyquist-plot features for shallow models—fast but does not generalize across geometries—or (ii) learn directly from Nyquist plots with deep networks, which removes manual feature extraction, yet still limited to a single plot type. As a result, cross-geometry robustness and deployability on constrained Internet of Things (IoT) devices remain open problems. We propose a compact Convolutional Neural Network (CNN) (∼ 10k parameters) that takes multi-representation EIS inputs—Nyquist (real/imaginary) and phase–magnitude (|Z|/ϕ) stacked as four channels, so the model can learn complementary degradation signatures while remaining small enough for fast inference. We build a dataset from cyclic aging of two geometries (LG INR18650MJ1 cylindrical cells and LIR2032 coin cells), acquire EIS every ten cycles from 10 kHz to 10 mHz (10 points/decade), and evaluate with leave-one-cell-out testing strategy. We further study fusion vs. single-representation inputs and assess feasibility for on-device deployment (e.g., NVIDIA Jetson device). The results show that training on multiple EIS representations improves SOH estimation accuracy and cross-geometry generalization compared to single-representation models, which uses only Nyquist or phase–magnitude plots. This design targets accurate, generalizable SOH prediction without manual feature engineering while enabling practical real-time use.

Bakr, Ahmed [The University of Alabama (UA)]↗
DOE OSTI2023

Accounting for herbaceous communities in process‐based models will advance our understanding of “grassy” ecosystems

Abstract Grassland and other herbaceous communities cover significant portions of Earth's terrestrial surface and provide many critical services, such as carbon sequestration, wildlife habitat, and food production. Forecasts of global change impacts on these services will require predictive tools, such as process‐based dynamic vegetation models. Yet, model representation of herbaceous communities and ecosystems lags substantially behind that of tree communities and forests. The limited representation of herbaceous communities within models arises from two important knowledge gaps: first, our empirical understanding of the principles governing herbaceous vegetation dynamics is either incomplete or does not provide mechanistic information necessary to drive herbaceous community processes with models; second, current model structure and parameterization of grass and other herbaceous plant functional types limits the ability of models to predict outcomes of competition and growth for herbaceous vegetation. In this review, we provide direction for addressing these gaps by: (1) presenting a brief history of how vegetation dynamics have been developed and incorporated into earth system models, (2) reporting on a model simulation activity to evaluate current model capability to represent herbaceous vegetation dynamics and ecosystem function, and (3) detailing several ecological properties and phenomena that should be a focus for both empiricists and modelers to improve representation of herbaceous vegetation in models. Together, empiricists and modelers can improve representation of herbaceous ecosystem processes within models. In so doing, we will greatly enhance our ability to forecast future states of the earth system, which is of high importance given the rapid rate of environmental change on our planet.

59 BASIC BIOLOGICAL SCIENCES↗