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At least 235 records · Page 13

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DOE OSTI2021

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Evolution of in-medium baryon-baryon scattering cross sections and stiffness of dense nuclear matter from Bayesian analyses of FOPI proton-flow excitation functions

Within a Bayesian statistical framework using a Gaussian process (GP) emulator for an isospin-dependent Boltzmann-Uehling-Uhlenbeck (IBUU) transport model simulator of heavy-ion reactions with momentum-independent Skyrme interactions, we infer from the proton directed and elliptical flow in mid-central Au + Au reactions, measured at beam energies from 150 to 1200 MeV/nucleon by the FOPI Collaboration, the posterior probability distribution functions (PDFs) of the in-medium baryon-baryon scattering cross section (BBSCS) modification factor 𝑋 (with respect to their free-space values) and the stiffness parameter 𝐾 of dense nuclear matter. Here, we find that the most probable value of 𝑋 evolves from around 0.7 to 1.0 as the beam energy 𝐸 beam /𝐴 increases. On the other hand, the posterior PDF⁡(𝐾) may have dual peaks having roughly the same height or extended shoulders at high 𝐾 values. More quantitatively, the posterior PDF⁡(𝐾) changes from having a major peak around 220 MeV, characterizing a soft EOS in the reaction at 𝐸 beam /𝐴 = 150 MeV, to one that peaks around 320 MeV, indicating a stiff EOS in the reactions at 𝐸 beam /𝐴 higher than about 600 MeV. The transition from soft to stiff happens in mid-central Au + Au reactions at beam energies around 250 MeV/nucleon in which 𝐾 = 220 MeV and 𝐾 = 320 MeV are approximately equally probable. Altogether, the FOPI proton-flow excitation function data indicate a gradual hardening of hot and dense nuclear matter as its density and temperature increase in reactions with higher beam energies.

nuclear matter↗

DOE OSTI2024

Superluminal matter waves

The Dirac equation has resided among the greatest successes of modern physics since its emergence as the first quantum mechanical theory fully compatible with special relativity. This compatibility ensures that the expectation value of the velocity is less than the vacuum speed of light. Here, we show that the Dirac equation admits free-particle solutions where the peak amplitude of the wave function can travel at any velocity, including those exceeding the vacuum speed of light, despite having a subluminal velocity expectation value. The solutions are constructed by superposing basis functions with correlations in momentum space. These arbitrary velocity wave functions feature a near-constant profile and may impact quantum mechanical processes that are sensitive to the local value of the probability density as opposed to expectation values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Particle Filter Based Inference Testing

The primary intent of PAR-FIT (Particle Filter based Inference Testing) is to provide hard inductive evidence that a machine learning model is capable and proven for an individual test input. By examining training data used to form the underlying model functional correlation, an estimate of the reliability that a model will make the correct prediction can be made. The Sequential Probability Ratio Test is used to derive a qualitative evaluation for reliability based on hypothesis testing. The PAR-FIT framework achieves this by implementing a particle filter and the sequential probability ratio test algorithms on the machine learning model training data to determine relevancy of new individual test samples to the training dataset. The kernel function evaluates the local proximity and density of training data used to derive a prediction outcome. Particles are used to probabilistically determine which training data to evaluate for proximity. For test samples that are within a close proximity to and surrounded by multiple training data points, the evaluated reliability of the prediction is high. For test samples that are anomalies not represented by the training dataset, in low density data clusters, or are far from existing data points, the evaluated reliability is low as insufficient training evidence exists to suggest the model is capable of making the correct prediction. Sequential Probability Ratio Test is further used to determine when a hypothesis on whether a signal can be rejected or accepted for use. The ratio test collects sequence information from the particle filter to test whether the signal is anomalous or normal via hypothesis testing of the underlying distributions.

Chen, Edward [Idaho National Laboratory (INL), Ida↗

DOE OSTI2024

Disentangling the physics of the attractive Hubbard model as a fully interacting model of fermions via the accessible and symmetry-resolved entanglement entropies

The complicated ways in which electrons interact in many-body systems such as molecules and materials have long been viewed through the lens of local electron correlation and associated correlation functions. However, quantum information science has demonstrated that more global diagnostics of quantum states like the entanglement entropy can provide a complementary and clarifying lens on electronic behavior. One particularly useful measure that can be used to distinguish between quantum and classical sources of entanglement is the accessible entanglement, the entanglement available as a quantum resource for systems subject to conservation laws, such as fixed particle number, due to superselection rules. In this work, we introduce an algorithm and demonstrate how to compute accessible and symmetry-resolved entanglements for interacting fermion systems. This is accomplished by combining an incremental version of the swap algorithm with a recursive auxiliary field quantum Monte Carlo algorithm recently developed by the authors. We apply these tools to study the pairing and charge density waves exhibited in the paradigmatic attractive Hubbard model via entanglement. We find that the particle and spin symmetry-resolved entanglements and their related full probability distribution functions show very clear—and unique—signatures of the underlying electronic behavior even when those features are less pronounced in conventional correlation functions. Altogether, this work provides a systematic means of characterizing the entanglement within quantum systems that can grant a deeper understanding of the complicated electronic behavior that underlies quantum phase transitions and crossovers in many-body systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

ABINIT: Overview and focus on selected capabilities

ABINIT is probably the first electronic-structure package to have been released under an open-source license about 20 years ago. It implements density functional theory, density-functional perturbation theory (DFPT), many-body perturbation theory (GW approximation and Bethe–Salpeter equation), and more specific or advanced formalisms, such as dynamical mean-field theory (DMFT) and the “temperature-dependent effective potential” approach for anharmonic effects. Relying on planewaves for the representation of wavefunctions, density, and other space-dependent quantities, with pseudopotentials or projector-augmented waves (PAWs), it is well suited for the study of periodic materials, although nanostructures and molecules can be treated with the supercell technique. The present article starts with a brief description of the project, a summary of the theories upon which ABINIT relies, and a list of the associated capabilities. It then focuses on selected capabilities that might not be present in the majority of electronic structure packages either among planewave codes or, in general, treatment of strongly correlated materials using DMFT; materials under finite electric fields; properties at nuclei (electric field gradient, Mössbauer shifts, and orbital magnetization); positron annihilation; Raman intensities and electro-optic effect; and DFPT calculations of response to strain perturbation (elastic constants and piezoelectricity), spatial dispersion (flexoelectricity), electronic mobility, temperature dependence of the gap, and spin-magnetic-field perturbation. The ABINIT DFPT implementation is very general, including systems with van der Waals interaction or with noncollinear magnetism. Community projects are also described: generation of pseudopotential and PAW datasets, high-throughput calculations (databases of phonon band structure, second-harmonic generation, and GW computations of bandgaps), and the library libpaw. ABINIT has strong links with many other software projects that are briefly mentioned.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

First simultaneous measurement of the γ-ray and neutron emission probabilities in inverse kinematics at a heavy-ion storage ring

The probabilities for γ-ray and particle emission as a function of the excitation energy of a decaying nucleus are valuable observables for constraining the ingredients of the models that describe the deexcitation of nuclei near the particle emission threshold. These models are essential in nuclear astrophysics and applications. In this paper, we have for the first time simultaneously measured the γ-ray and neutron emission probabilities of 208 Pb. The measurement was performed in inverse kinematics at the Experimental Storage Ring (ESR) of the GSI/FAIR facility, where a 208 Pb beam interacted through the 208 Pb (p,p') reaction with a hydrogen gas jet target. Instead of detecting the γ rays and neutrons emitted by 208 Pb, we detected the heavy beamlike residues produced after γ and neutron emission. These heavy residues were fully separated by a dipole magnet of the ESR and were detected with outstanding efficiencies. The comparison of the measured probabilities with model calculations has allowed us to test and select different descriptions of the γ-ray strength function and the nuclear level density available in the literature.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

DCTRGAN: improving the precision of generative models with reweighting

Significant advances in deep learning have led to more widely used and precise neural network-based generative models such as Generative Adversarial Networks (Gans). We introduce a post-hoc correction to deep generative models to further improve their fidelity, based on the Deep neural networks using the Classification for Tuning and Reweighting (Dctr) protocol. The correction takes the form of a reweighting function that can be applied to generated examples when making predictions from the simulation. We illustrate this approach using Gans trained on standard multimodal probability densities as well as calorimeter simulations from high energy physics. We show that the weighted Gan examples significantly improve the accuracy of the generated samples without a large loss in statistical power. This approach could be applied to any generative model and is a promising refinement method for high energy physics applications and beyond.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Role of quadrupole deformation and continuum effects in the “island of inversion” nuclei 28,29,31 F

The peculiar properties of nuclei in the so-called “island of inversion” around Z = 10 and N = 20 are the focus of current nuclear physics research. Recent studies showed that 28 F has a negative-parity ground state and thus lies within the southern shore of the island of inversion, and 29 F presents a halo structure in its ground state, but it is unclear which effects, such as deformation, shell evolution due to tensor forces, or couplings to the continuum, lead to this situation. Here, we investigate the role of quadrupole deformation and continuum effects on the single-particle structure of 28,29,31 F from a relativistic mean-field approach and show how both phenomena can lead to a negative-parity ground state in 28 F and halo structures in 29,31 F. We solve the Dirac equation in the complex-momentum (Berggren) representation for a potential with quadrupole deformation at the first order obtained from relativistic mean-field calculations using the NL3 interaction and calculate the continuum level densities using the Green’s function method. We extract single-particle energies and widths from the continuum level densities to construct the Nilsson diagrams of 28,29,31 F in the continuum and analyze the evolution of both the widths and occupation probabilities of relevant Nilsson orbitals in 28 F and find that some amount of prolate deformation must be present. In addition, we calculate the density distributions for bound Nilsson orbitals near the Fermi surface in 29,31 F and reveal that, for a quadrupole deformation 0.3 ≤ β 2 ≤ 0.45 (prolate), characteristic halo tails appear at large distances. Using the relativistic mean-field approach in the complex-momentum representation with the Green’s function method, we demonstrate that in neutron-rich fluorine isotopes, while in the spherical case the pf shells are already inverted and close to the neutron emission threshold, a small amount of quadrupole deformation can dramatically reduce the gap between positive- and negative-parity states and increase the role of continuum states, ultimately leading to the negative parity in the ground state of 28 F and the halo structures in 29,31 F.

20 ≤ A ≤ 38↗

DOE OSTI2022

Controlling extrapolations of nuclear properties with feature selection

Predictions of nuclear properties far from measured data are inherently inaccurate because of uncertainties in our knowledge of nuclear forces and in our treatment of quantum many-body effects in strongly-interacting systems. While the model bias can be directly calculated when experimental data is available, only an estimate can be made in the absence of such measurements. Current approaches to compute the estimated bias quickly lose predictive power when their input variables are taken far from the training region, resulting in uncontrolled uncertainties in applications such as nucleosynthesis simulations. In this letter, we present a novel technique to identify the input variables of machine learning algorithms that can provide robust estimates of model bias. Our process is based on selecting input variables, or features, based on their probability distribution functions across the entire nuclear chart. We illustrate our approach on the problem of quantifying the model bias in nuclear binding energies calculated with Density Functional Theory (DFT). We prove that building model biases with only Z and N as features leads to highly unreliable extrapolations. Conversely, we show that proper feature selection can systematically improve theoretical predictions without increasing uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Development of Parameters for the Particle Size Distribution of TATB

Laser light scattering (LLS), manual counting of scanning electron microscopy (SEM) images, and reduction of SEM images using ImageJ (open source program) to determine Feret (caliper) diameters were applied to determine particle size distribution (PSD) of four preparations of 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) and yttria‐stabilized zirconia (YSZ), an SEM certified standard. Mie theory was used to reduce the LLS data. The spherical nature of the YSZ made it a good candidate for LLS. Variations in n , the refractive index, and iκ, the imaginary component, produced very little change in the PSD. However, changing the carrier liquid from H 2 O to a 40% aqueous sucrose solution, thereby changing the carrier refractive index, n 0 , substantially affected the PSD. The Mie complex refractive indices for the YSZ were n = 2.200, iκ = 0.100, with a 40% aqueous sucrose solution, n 0 = 1.400. The triclinic crystal structure of TATB made refractive index determinations more difficult, so a study was conducted varying Mie parameters and comparing them to the same data reduced using the Fraunhofer theory. Changing the n and κ parameters produced PSD with a small concentration of particles less than 1 µm in size or none in this range. SEM images, Feret data, manual counting, and Fraunhofer data reduction indicate particles less than 1 µm are probably < 5% in concentration. The final selection of Mie parameters for TATB was n = 2.283, iκ = 0.1, and suspension medium, n 0 = 1.330. Finally, computations, using density functional theory produced similar parameters.

Feret diameter↗

DOE OSTI2020

Basis light-front quantization for a chiral nucleon-pion Lagrangian

We present the first application of the basis light-front quantization method to a simple chiral model of the nucleon-pion system as a relativistic bound state for the physical proton. In this work, the light-front mass-squared matrix of the nucleon-pion system is obtained within a truncated basis. The mass and the corresponding light-front wave function (LFWF) of the proton are computed by numerical diagonalization of the resulting mass-squared matrix. With the boost-invariant LFWF, we calculate the probability density distribution of the pion's longitudinal momentum fraction and the Dirac form factor of the proton.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Probing the exact form and doping preference of magnesium in ordinary Portland cement clinker phases: A study from experiments and DFT simulations

Highlights: • The doping behaviors of Mg in OPC clinker phases were systematically studied. • About 1.3 wt% MgO enter OPC clinker phases by forming substitutional solid solutions. • In the 4 composed minerals, C{sub 3}S, C{sub 3}A and C{sub 4}AF can host more Mg ions than C{sub 2}S. • Mg ions prefer to replace Ca in C{sub 3}S, C{sub 2}S and C{sub 3}A while replace Fe and Ca in C{sub 4}AF. • Both the large structure distortions and formation energies governs the low solubility. A systematic study was performed to learn the exact existence form and doping behaviors of magnesium in ordinary Portland cement (OPC) clinker. Our results show that about 1.3 wt% MgO incorporates into OPC clinker phases by forming substitutional solid solutions while excess Mg accumulate and exist as periclase. Results from Rietveld refinement present a substitution preference in C{sub 3}S and C{sub 3}A over C{sub 2}S. More in-depth analyses from density function theoretical simulations show that in C{sub 3}S, C{sub 2}S and C{sub 3}A, the substitution occurs by replacing Ca while in C{sub 4}AF, it probably occurs by substituting Fe and Ca ions. The large structure distortions and sharp increase in formation energies with increasing MgO determines its low solubility. This work provides a clear understanding of the existence states and the intrinsic mechanism governing doping behaviors of Mg, thus should be very important in guiding the synthesis of OPC clinker by utilizing high-Mg limestone.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Curing the Divergence in Time-Dependent Density Functional Quadratic Response Theory

While time-dependent density functional theory has emerged as a method of choice for computing electronic spectra and response of molecules and materials, its reliability is hindered by the adiabatic approximation that is commonly made. In this work, we address one problematic aspect that arises from this approximation: an incorrect pole structure in the quadratic response function, leading to unphysical divergences in excited state-to-state transition probabilities and hyperpolarizabilties. We find the form of the exact quadratic response kernel and derive a practical and accurate approximation that cures the divergence. Here, we demonstrate our results on excited state-to-state transition probabilities of a model system and of the LiH molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Microscopic calculation of fission product yields with particle-number projection

Fission fragments' charge and mass distribution is an important input to applications ranging from basic science to energy production or nuclear nonproliferation. In simulations of nucleosynthesis or calculations of superheavy elements, these quantities must be computed from models, as they are needed in nuclei where no experimental information is available. Until now, standard techniques to estimate these distributions were not capable of accounting for fine-structure effects, such as the odd-even staggering of the charge distributions. In this work, we combine a fully microscopic collective model of fission dynamics with a recent extension of the particle number projection formalism to provide the highest-fidelity prediction of the primary fission fragment distributions for the neutron-induced fission of 235 U and 239 Pu. Here, we show that particle-number projection is an essential ingredient to reproduce odd-even staggering in the charge yields and benchmark the performance of various empirical probability laws that could simulate its effect. This new approach also enables for the first time the realistic determination of two-dimensional isotopic yields within nuclear density functional theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Diameter-dependent multiple proton jumps dictate hydronium and hydroxide transport in carbon nanotubes

Nanofluidic channels impose extreme confinement on water, giving rise to unusual transport phenomena of the liquid. However, how the transport of hydroxide and hydronium ions is influenced by such confinement is still not fully understood. This study employs machine learning-accelerated simulations, based on the SCAN density functional, to investigate proton transfer dynamics in CNTs of varying diameters (0.8 nm to 2.8 nm). The extreme confinement of water inside a 0.8 nm CNT not only enhances the probability of multiple consecutive proton jumps, but also reverses the relative diffusion coefficient of hydronium and hydroxide ions in bulk water. In CNTs with diameters larger than 0.8 nm, hydronium diffuses slightly faster than in bulk water, whereas hydroxide diffusion slows because of its localization near CNT walls, hindering multiple proton jumps. This work highlights the significant impact of nanoscale confinement on proton transfer dynamics, with implications for designing nanoscale systems with controlled proton transport.

Chemistry↗

DOE OSTI2020

Play Fairway analysis of geothermal resources across the State of Hawai‘i: 4. Updates with new groundwater chemistry, subsurface stress analysis, and focused geophysical surveys

This paper is the fourth in a series on a play fairway analysis of geothermal resources across the State of Hawai‘i. Here we describe recent exploration activities that include groundwater sampling in ten locations statewide, as well as geophysical surveys on Lana‘i, across the SW rift of Haleakala Volcano (Maui), and surrounding Mauna Kea Volcano (Hawai‘i Island). We derive a first-order method for computing topographic stress using Green’s functions, finding that topography can induce appreciable crustal stress. We develop a new method for incorporating depth information about resistivity, density, and topographic stresses into our previously published equations to calculate resource probability and confidence. We incorporate newly collected and modeled data into our calculations to update statewide maps of probability and confidence. Lana‘i Island and southeast Mauna Kea are identified as the top targets for exploratory drilling. The east rift of Haleakala Volcano, the southern-most region of Mauna Loa’s SW rift (Hawai‘i Island), and central Kauai are identified as targets for geophysical surveying.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Bayesian inference of fine features of the nuclear equation of state from future neutron star radius measurements to 0.1 km accuracy

To more precisely constrain the equation of state (EOS) of supradense neutron-rich nuclear matter, future high-precision x-ray and gravitational wave observatories are proposed to measure the radii of neutron stars (NSs) with an accuracy better than about 0.1 km. However, it remains unclear what particular aspects (other than the stiffness generally spoken of in the literature) of the EOS and to what precision they will be better constrained. In this work, within a Bayesian framework using a metamodel EOS for NSs, we infer the posterior probability distribution functions (PDFs) of incompressibility K 0 and skewness J 0 of symmetric nuclear matter (SNM) as well as the slope L, curvature K sym , and skewness J sym characterizing the density dependence of nuclear symmetry energy E sym ⁡(ρ), respectively, from mean values of NS radii consistent with existing observations and an expected accuracy Δ⁢R ranging from about 1.0 to 0.1 km. Here, we found that (1) the Δ⁢R has little effect on inferring the stiffness of SNM at suprasaturation densities, (2) smaller Δ⁢R reveals more accurately not only the PDFs but also pairwise correlations among parameters characterizing high-density E sym ⁡(ρ), (3) a double-peak feature of the PDF(K sym ) corresponding to the strong K sym – J sym and K sym – L anticorrelations is revealed when Δ⁢R is less than about 0.2 km, and the locations of the two peaks are sensitive to the maximum value of J sym reflecting the stiffness of E sym ⁡(ρ) above about 3 times the saturation density ρ 0 of SNM, and (4) the high-precision radius measurement for canonical NSs is more useful than that for massive ones for constraining the EOS of nucleonic matter around (2–3)⁢ρ 0 .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗