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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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At least 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Simulating Heisenberg interactions in the Ising model with strong drive fields

The time evolution of an Ising model with large driving fields over discrete time intervals is shown to be reproduced by an effective XXZ-Heisenberg model at leading order in the inverse field strength. For specific orientations of the drive field, the dynamics of the XXX-Heisenberg model is reproduced. Finally, these approximate equivalences, valid above a critical driving field strength set by dynamical phase transitions in the Ising model, are expected to enable quantum devices that natively evolve qubits according to the Ising model to simulate more complex systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Excited-state vibronic wave-packet dynamics in H 2 probed by XUV transient four-wave mixing

The complex behavior of a molecular wave packet initiated by an extreme ultraviolet (XUV) pulse is investigated with noncollinear wave mixing spectroscopy. A broadband XUV pulse spanning 12-16 eV launches a wave packet in H 2 comprising a coherent superposition of multiple electronic and vibrational levels. The molecular wave packet evolves freely until a delayed few-cycle optical laser pulse arrives to induce nonlinear signals in the XUV via four-wave mixing (FWM). The angularly resolved FWM signals encode rich energy exchange processes between the optical laser field and the XUV-excited molecule. The noncollinear geometry enables spatial separation of ladder and V- or Λ-type transitions induced by the optical field. Ladder transitions, in which the energy exchange with the optical field is around 3 eV, appear off axis from the incident XUV beam. Each vibrationally revolved FWM line probes a different part of the wave packet in energy, serving as a promising tool for energetic tomography of molecular wave packets. V- or Λ-type transitions, in which the energy exchange is well under 1 eV, result in on-axis nonlinear signals. The first-order versus third-order interference of the on-axis signal serves as a mapping tool of the energy flow pathways. Intra- and interelectronic potential energy curve transitions are decisively identified. The current study opens possibilities for accessing complete dynamic information in XUV-excited complex systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Coherent band-edge oscillations and dynamic longitudinal-optical phonon mode splitting as evidence for polarons in perovskites

The coherence of collective modes, such as phonons and polarons, and their modulation of electronic states is long sought in complex systems, which is a crosscutting issue in photovoltaics and quantum electronics. In photovoltaic cells and lasers based on metal halide perovskites, the presence of polarons, i.e., photocarriers dressed by the macroscopic motion of charged lattice, assisted by terahertz (THz) longitudinal-optical (LO) phonons, has been intensely studied yet is still debated. This may be key for explaining the remarkable properties of the perovskite materials, e.g., defect tolerance, long charge lifetimes, and diffusion lengths. In this work we use the intense single-cycle THz pulse with peak electric field up to E THz = 1000 kV/cm to drive coherent polaronic band-edge oscillations at room temperature in CH 3 NH 3 PbI 3 (MAPbI 3 ). We reveal the oscillatory behavior is dominated by a specific quantized lattice vibration mode at $ω$ LO ~ 4 THz, which is both dipole and momentum forbidden. THz-driven coherent polaron dynamics exhibits distinguishing features: room temperature coherent oscillations at ω LO longer than 1 ps in both single crystals and thin films, mode-selective modulation of different band-edge states assisted by electron-phonon interaction, and dynamic mode splitting at low temperature due to entropy and anharmonicity of organic cations. Our results demonstrate intense THz-driven coherent band-edge modulation is a powerful probe of electron-lattice coupling phenomena and polaronic quantum control in perovskites.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unification of nonequilibrium molecular dynamics and the mode-resolved phonon Boltzmann equation for thermal transport simulations

Nano-size confinement induces many intriguing non-Fourier heat conduction phenomena, such as nonlinear temperature gradients, temperature jumps near the contacts, and size-dependent thermal conductivity. Over the past decades, these effects have been studied and interpreted by nonequilibrium molecular dynamics (NEMD) and phonon Boltzmann transport equation (BTE) simulations separately, but no theory that unifies these two methods has ever been established. In this work, we unify these methods using a quantitative mode-level comparison and demonstrate that they are equivalent for various thermostats. We show that different thermostats result in different non-Fourier thermal transport characteristics due to the different mode-level phonon excitations inside the thermostats, which explains the different size-dependent thermal conductivities calculated using different reservoirs, even though they give the same bulk thermal conductivity. Specifically, the Langevin thermostat behaves like a thermalizing boundary in phonon BTE and provides mode-level thermal-equilibrium phonon outlets, while the Nose-Hoover chain thermostat and velocity rescaling method behave like biased reservoirs, which provide a spatially uniform heat generation and mode-level nonequilibrium phonon outlets. These findings explain why different experimental measurement methods can yield different size-dependent thermal conductivity. They also indicate that the thermal conductivity of materials can be tuned for various applications by specifically designing thermostats. Finally, the unification of NEMD and phonon BTE will largely facilitate the study of thermal transport in complex systems in the future by, e.g., replacing computationally unaffordable first-principles NEMD simulations with computationally less expensive spectral BTE simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Ultrafast light-induced shear strain probed by time-resolved x-ray diffraction: Multiferroic BiFeO 3 as a case study

Enabling the light control of complex systems on ultrashort timescales gives rise to rich physics with promising applications. Although crucial, the quantitative determination of both the longitudinal and the shear photoinduced strains still remains challenging. Here, by scrutinizing asymmetric Bragg peaks pairs (±h01) in BiFeO 3 using picosecond time-resolved x-ray diffraction experiments, we simultaneously determine the longitudinal and shear strains. Importantly, we reveal a difference in the dynamical response of the longitudinal strain with respect to the shear one due to an interplay of quasilongitudinal and quasitransverse acoustic modes, well reproduced by our model. Lastly, we show that the relative amplitude of those strains can be explained only if both thermal and nonthermal processes contribute to the acoustic phonon photogeneration process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Systematic approach for simultaneously correcting the band-gap and p - d separation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles method can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.

Wang, Jianwei↗
DOE OSTI2016

Gutzwiller renormalization group

We develop a variational scheme called the “Gutzwiller renormalization group” (GRG), which enables us to calculate the ground state of Anderson impurity models (AIM) with arbitrary numerical precision. Our method exploits the low-entanglement property of the ground state of local Hamiltonians in combination with the framework of the Gutzwiller wave function and indicates that the ground state of the AIM has a very simple structure, which can be represented very accurately in terms of a surprisingly small number of variational parameters. Furthermore, we perform benchmark calculations of the single-band AIM that validate our theory and suggest that the GRG might enable us to study complex systems beyond the reach of the other methods presently available and pave the way to interesting generalizations, e.g., to nonequilibrium transport in nanostructures.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Quantifying correlated truncation errors in effective field theory

Effective field theories (EFTs) organize the description of complex systems into an infinite sequence of decreasing importance. Predictions are made with a finite number of terms, which induces a truncation error that is often left unquantified. Here, we formalize the notion of EFT convergence and propose a Bayesian truncation error model for predictions that are correlated across the independent variables, e.g., energy or scattering angle. Central to our approach are Gaussian processes that encode both the naturalness and correlation structure of EFT coefficients. Our use of Gaussian processes permits efficient and accurate assessment of credible intervals, allows EFT fits to easily include correlated theory errors, and provides analytic posteriors for physical EFT-related quantities such as the expansion parameter. Furthermore, we demonstrate that model-checking diagnostics—applied to the case of multiple curves—are powerful tools for EFT validation. As an example, we assess a set of nucleon-nucleon scattering observables in chiral EFT. In an effort to be self-contained, appendices include thorough derivations of our statistical results. Our methods are packaged in Python code, called gsum, that is available for download on GitHub.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Model emulation and closure tests for (3+1)D relativistic heavy-ion collisions

In nuclear and particle physics, reconciling sophisticated simulations with experimental data is vital for understanding complex systems like the Quark Gluon Plasma (QGP) generated in heavy ion collisions. However, computational demands pose challenges, motivating using Gaussian Process emulators for efficient parameter extraction via Bayesian calibration. We conduct a comparative analysis of Gaussian Process emulators in heavy-ion physics to identify the most adept emulator for parameter extraction with minimal uncertainty. Furthermore, our study contributes to advancing computational techniques in heavy-ion physics, enhancing our ability to interpret experimental data and understand QGP properties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Isospin-invariant Skyrme energy-density-functional approach with axial symmetry

Density functional theory (DFT) is the microscopic tool of choice to describe properties of nuclei over the entire nuclear landscape, with a focus on medium-mass and heavy complex systems. Modern energy density functionals (EDFs) often offer a level of accuracy typical of phenomenological approaches based on parameters locally fitted to the data. It is clear, however, that in order to achieve high quality of predictions to guide spectroscopic studies, current functionals must be improved, especially in the isospin channel. In this respect, experimental studies of short-lived nuclei far from stability offer a unique test of isospin aspects of the many-body theory. In this study, we develop the isospin-invariant Skyrme-EDF method by considering local densities in all possible isospin channels and proton-neutron ($p-n$) mixing terms as mandated by the isospin symmetry. The EDF employed has the most general form that depends quadratically on the isoscalar and isovector densities. We test and benchmark the resulting $p-n$ EDF approach, and study the general properties of the new scheme by means of the cranking in the isospin space. We extend the existing axial DFT solver HFBTHO to the case of isospin-invariant EDF approach with all possible $p-n$ mixing terms. Explicit expressions have been derived for all the densities and potentials that appear in the isospin representation. In practical tests, we consider the Skyrme EDF SkM* and, as a first application, concentrate on Hartree-Fock aspects of the problem, i.e., pairing has been disregarded. Calculations have been performed for the ($A = 78, T ≃ 11), (A = 40, T ≃ 8$), and ($A = 48, T ≃ 4$) isobaric analog chains. Isospin structure of self-consistent $p-n$ mixed solutions has been investigated with and without the Coulomb interaction, which is the sole source of isospin symmetry breaking in our approach. The extended axial HFBTHO solver has been benchmarked against the symmetry-unrestricted HFODD code for deformed and spherical states. We developed and tested a general isospin-invariant Skyrme-EDF framework. The new approach permits spin-isospin densities that may give rise to hitherto unexplored modes in the excitation spectrum. The new formalism has been tested in the Hartree-Fock limit. A systematic comparison between HFODD and HFBTHO results show a maximum deviation of about 10 keV on the total binding energy for deformed nuclei when the Coulomb term is included. Without this term, the results of both solvers agree down to a ~10 eV level.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Strongly resonating bosons in hot nuclei

When two heavy ions near the Fermi energy collide, a warm and low-density region can form in which fragments appear. This region is mainly dominated by proton (p) and alpha (α) particles. In such an environment, the α particles interact with each other and, especially through strong resonances, form complex systems such as 8 Be and 12 C. Our experiments show that 70(64) Zn( 64 Ni) + 70(64) Zn( 64 Ni) reactions at E/A = 35 MeV/nucleon levels of 8Be appear around relative energies E ij = 0.092 MeV, 3.03 MeV as well as above 10 and 100 MeV. We propose a different method to derive the correlation function based on the relative transverse energy distribution to minimize the experimental uncertainties. For the 3α systems, multiresonance processes give rise to excited levels of 12 C. For instance, the Hoyle state at 7.654 MeV excitation energy shows a decay component through the ground state of 8 Be and also components where two different α couples are at relative energies consistent with the ground state of 8 Be at the same time.

6 ≤ A ≤ 19↗
DOE OSTI2019

Multicomponent mutual diffusion in the warm, dense matter regime

In this work, we present the formulation, simulations, and results for multicomponent mutual diffusion coefficients in the warm, dense matter regime. While binary mixtures have received considerable attention for mass transport, far fewer studies have addressed ternary and more complex systems. We therefore explicitly examine ternary systems utilizing the Maxwell-Stefan formulation that relates diffusion to gradients in the chemical potential. Onsager coefficients then connect the macroscopic diffusion to microscopic particle motions, evinced in trajectories characterized by positions and velocities, through various autocorrelation functions (ACFs). These trajectories are generated by molecular dynamics (MD) simulations either through the Born-Oppenheimer approximation, which treats the ions classically and the electrons quantum-mechanically by an orbital-free density-functional theory, or through a classical MD approach with Yukawa pair-potentials, whose effective ionizations and electron screening length derive from quantal considerations. We employ the reference-mean form of the ACFs and determine the center-of-mass coefficients through a simple reference-frame-dependent similarity transformation. The Onsager terms in turn determine the mutual diffusion coefficients. We examine a representative sample of ternary mixtures as a function of density and temperature from those with only light elements (D-Li-C, D-Li-Al) to those with highly asymmetric mass components (D-Li-Cu, D-Li-Ag, H-C-Ag). We also follow trends in the diffusion as a function of number concentration and evaluated the efficacy of various approximations such as the Darken approximation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Damage Spreading in Spatial and Small-world Random Boolean Networks

The study of the response of complex dynamical social, biological, or technological networks to external perturbations has numerous applications. Random Boolean Networks (RBNs) are commonly used a simple generic model for certain dynamics of complex systems. Traditionally, RBNs are interconnected randomly and without considering any spatial extension and arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, power-law, small-world, or other non-random connections. Here we explore the RBN network topology between extreme local connections, random small-world, and pure random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the relevant component at very low connectivities ($\bar{K} \ll 1$) and that the critical connectivity of stability $K_s$ changes compared to random networks. At higher $\bar{K}$, this scaling remains unchanged. We also show that the relevant component of spatially local networks scales with a power-law as the system size N increases, but with a different exponent for local and small-world networks. The scaling behaviors are obtained by finite-size scaling. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key design trade-offs between damage spreading (robustness), the network's wiring cost, and the network's communication characteristics.

Lu, Qiming↗
DOE OSTI2023

Embedding hard physical constraints in neural network coarse-graining of three-dimensional turbulence

In recent years, deep learning approaches have shown much promise in modeling complex systems in the physical sciences. A major challenge in deep learning of partial differential equations is enforcing physical constraints and boundary conditions. In this work, we propose a general framework to directly embed the notion of an incompressible fluid into convolutional neural networks, and apply this to coarse-graining of turbulent flow. These physics-embedded neural networks leverage interpretable strategies from numerical methods and computational fluid dynamics to enforce physical laws and boundary conditions by taking advantage the mathematical properties of the underlying equations. Here, we demonstrate results on three-dimensional fully developed turbulence, showing that this technique drastically improves local conservation of mass, without sacrificing performance according to several other metrics characterizing the fluid flow.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

The de Gennes narrowing phenomenon is frequently observed by neutron or x-ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distance varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. Furthermore, this finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α-relaxation time.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Dynamical Slowing-Down in an Ultrafast Photoinduced Phase Transition

Complex systems, which consist of a large number of interacting constituents, often exhibit universal behavior near a phase transition. A slowdown of certain dynamical observables is one such recurring feature found in a vast array of contexts. This phenomenon, known as critical slowing-down, is well studied mostly in thermodynamic phase transitions. However, it is less understood in highly nonequilibrium settings, where the time it takes to traverse the phase boundary becomes comparable to the timescale of dynamical fluctuations. Using transient optical spectroscopy and femtosecond electron diffraction, we studied a photoinduced transition of a model charge-density-wave (CDW) compound LaTe 3 . We observed that it takes the longest time to suppress the order parameter at the threshold photoexcitation density, where the CDW transiently vanishes. Here, this finding can be captured by generalizing the time-dependent Landau theory to a system far from equilibrium. The experimental observation and theoretical understanding of dynamical slowing-down may offer insight into other general principles behind nonequilibrium phase transitions in many-body systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗