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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Correlated particle transport enables biological free energy transduction

Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. Here, we show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near-reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).

bacterial nanowires↗
DOE OSTI2013

Phase stabilities at a glance: Stability diagrams of nickel dipnictides

In the course of the recent advances in chemical structure prediction, a straightforward type of diagram to evaluate phase stabilities is presented based on an expedient example. Crystal structures and energetic stabilities of dipnictides NiPn{sub 2} (Pn = N, P, As, Sb, Bi) are systematically investigated by first principles calculations within the framework of density functional theory using the generalized gradient approximation to treat exchange and correlation. These dipnictides show remarkable polymorphism that is not yet understood systematically and offers room for the discovery of new phases. Relationships between the concerned structures including the marcasite, the pyrite, the arsenopyrite/CoSb{sub 2}, and the NiAs{sub 2} types are highlighted by means of common structural fragments. Electronic stabilities of experimentally known and related AB{sub 2} structure types are presented graphically in so-called stability diagrams. Additionally, competing binary phases are taken into consideration in the diagrams to evaluate the stabilities of the title compounds with respect to decomposition. The main purpose of the stability diagrams is the introduction of an image that enables the estimation of phase stabilities at a single glance. Beyond that, some of the energetically favored structure types can be identified as potential new phases.

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

SU-F-T-78: Minimum Data Set of Measurements for TG 71 Based Electron Monitor-Unit Calculations

Purpose: Building up a TG-71 based electron monitor-unit (MU) calculation protocol usually involves massive measurements. This work investigates a minimum data set of measurements and its calculation accuracy and measurement time. Methods: For 6, 9, 12, 16, and 20 MeV of our Varian Clinac-Series linear accelerators, the complete measurements were performed at different depth using 5 square applicators (6, 10, 15, 20 and 25 cm) with different cutouts (2, 3, 4, 6, 10, 15 and 20 cm up to applicator size) for 5 different SSD’s. For each energy, there were 8 PDD scans and 150 point measurements for applicator factors, cutout factors and effective SSDs that were then converted to air-gap factors for SSD 99–110cm. The dependence of each dosimetric quantity on field size and SSD was examined to determine the minimum data set of measurements as a subset of the complete measurements. The “missing” data excluded in the minimum data set were approximated by linear or polynomial fitting functions based on the included data. The total measurement time and the calculated electron MU using the minimum and the complete data sets were compared. Results: The minimum data set includes 4 or 5 PDD’s and 51 to 66 point measurements for each electron energy, and more PDD’s and fewer point measurements are generally needed as energy increases. Using only <50% of complete measurement time, the minimum data set generates acceptable MU calculation results compared to those with the complete data set. The PDD difference is within 1 mm and the calculated MU difference is less than 1.5%. Conclusion: Data set measurement for TG-71 electron MU calculations can be minimized based on the knowledge of how each dosimetric quantity depends on various setup parameters. The suggested minimum data set allows acceptable MU calculation accuracy and shortens measurement time by a few hours.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2012

Transverse instability of a plane front of fast impact ionization waves

The transverse instability of a plane front of fast impact ionization waves in p{sup +}-n-n{sup +} semiconductor structures with a finite concentration of donors N in the n layer has been theoretically analyzed. It is assumed that the high velocity u of impact ionization waves is ensured owing to the avalanche multiplication of the uniform background of electrons and holes whose concentration {sigma}{sub b} ahead of the front is high enough for the continuum approximation to be applicable. The problem of the calculation of the growth rate s of a small harmonic perturbation with wavenumber k is reduced to the eigenvalue problem for a specific homogeneous Volterra equation of the second kind containing the sum of double and triple integrals of an unknown eigenfunction. This problem has been solved by the method of successive approximations. It has been shown that the function s(k) for small k values increases monotonically in agreement with the analytical theory reported in Thermal Engineering 58 (13), 1119 (2011), reaches a maximum s{sub M} at k = k{sub M}, then decreases, and becomes negative at k > k{sub 01}. This behavior of the function s(k) for short-wavelength perturbations is due to a decrease in the distortion of the field owing to a finite thickness of the space charge region of the front and 'smearing' of perturbation of concentrations owing to the transverse transport of charge carriers. The similarity laws for perturbations with k Greater-Than-Or-Equivalent-To k{sub M} have been established: at fixed {sigma}{sub b} values and the maximum field strength on the front E{sub 0M}, the growth rate s depends only on the ratio k/N and the boundary wavenumber k{sub 01} {proportional_to} N. The parameters s{sub M}, k{sub M}, and k{sub 01}, which determine the perturbation growth dynamics and the upper boundary of the instability region for impact ionization waves, have been presented as functions of E{sub 0M}. These dependences indicate that the model of a plane impact ionization wave is insufficient for describing the operation of avalanche voltage sharpers and that fronts of fast streamers in the continuum approximation should be stable with respect to transverse perturbations in agreement with the previously reported numerical simulation results. The results have been confirmed by the numerical simulation of the evolution of small harmonic perturbations of the steady-state plane impact ionization wave.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Quantum probabilities for inflation from holography

The evolution of the universe is determined by its quantum state. The wave function of the universe obeys the constraints of general relativity and in particular the Wheeler-DeWitt equation (WDWE). For non-zero Λ, we show that solutions of the WDWE at large volume have two domains in which geometries and fields are asymptotically real. In one the histories are Euclidean asymptotically anti-de Sitter, in the other they are Lorentzian asymptotically classical de Sitter. Further, the universal complex semiclassical asymptotic structure of solutions of the WDWE implies that the leading order in h-bar quantum probabilities for classical, asymptotically de Sitter histories can be obtained from the action of asymptotically anti-de Sitter configurations. This leads to a promising, universal connection between quantum cosmology and holography.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Renormalization group evolution of multi-gluon correlators in high energy QCD

Many-body QCD in leading high energy Regge asymptotics is described by the Balitsky-JIMWLK hierarchy of renormalization group equations for the x evolution of multi-point Wilson line correlators. These correlators are universal and ubiquitous in final states in deeply inelastic scattering and hadronic collisions. For instance, recently measured di-hadron correlations at forward rapidity in deuteron-gold collisions at the Relativistic Heavy Ion Collider (RHIC) are sensitive to four and six point correlators of Wilson lines in the small x color fields of the dense nuclear target. We evaluate these correlators numerically by solving the functional Langevin equation that describes the Balitsky-JIMWLK hierarchy. We compare the results to mean-field Gaussian and large Nc approximations used in previous phenomenological studies. We comment on the implications of our results for quantitative studies of multi-gluon final states in high energy QCD.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Connecting relativistic density functional theory to microscopic calculations

The development of systematic effective field theories (EFTs) for nuclear forces and advances in solving the nuclear many-body problem have greatly improved our understanding of dense nuclear matter and the structure of finite nuclei. For global nuclear calculations, density functional theories (DFTs) have been developed to reduce the complexity and computational cost required in describing nuclear systems. However, DFT often makes approximations and assumptions about terms included in the functional, which may introduce systematic uncertainties compared to microscopic calculations using EFTs. In this work, we investigate possible avenues of improving nuclear DFT using nonlinear relativistic mean-field (RMF) theory. We explore the impact of RMF model extensions by fitting the nonlinear RMF model to predictions of nuclear matter and selected closed-shell nuclei using four successful chiral EFT Hamiltonians. We find that these model extensions are impactful and important in capturing the physics present within chiral Hamiltonians, particularly for charge radii and neutron skins of closed-shell nuclei. However, there are additional effects that are not captured within the RMF model, particularly within the isoscalar sector of RMF theory. Additional model extensions and the reliability of the nonlinear RMF model are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Low-frequency Raman spectrum of 2D layered perovskites: Local atomistic motion or superlattice modes?

We report the low-frequency Raman spectrum (ω = 10 cm -1 –150 cm -1 ) of a wide variety of alkylammonium iodide based 2D lead halide perovskites (2D LHPs) as a function of A-site cation (MA = methylammonium and FA = formamidinium), octahedral layer thickness (n = 2–4), organic spacer chain length (butyl-, pentyl-, hexyl-), and sample temperature (T = 77 K–293 K). Using density functional theory calculations under the harmonic approximation for n = 2 BA:MAPbI, we assign several longitudinal/transverse optical phonon modes between 30 cm -1 and 100 cm -1 , the eigen displacements of which are analogous to that observed previously for octahedral twists/distortions in bulk MAPbI. Additionally, we propose an alternative assignment for low-frequency modes below this band (<30 cm -1 ) as zone-folded longitudinal acoustic phonons corresponding to the periodicity of the entire layered structure. Furthermore, we compare measured spectra to predictions of the Rytov elastic continuum model for zone-folded dispersion in layered structures. Our results are consistent across the various 2D LHPs studied herein, with energetic shifts of optical phonons corresponding to microscopic structural differences between materials and energetic shifts of acoustic phonons according to changes in the periodicity and elastic properties of the perovskite/organic subphases. This study highlights the importance of both the local atomic order and the superlattice structure on the vibrational properties of layered 2D materials.

2D materials↗
DOE OSTI2015

Electronic, elastic and dynamic properties of the filled tetrahedral semiconductor LiMgN under pressures

The electronic, elastic and dynamic properties of LiMgN under pressures have been studied using the plane wave pseudopotential method based on density functional theory within the local density approximation (LDA). The calculated lattice constants, bulk modulus and band gap values of the α phase LiMgN at normal conditions are in good agreement with the available experimental and theoretical results. Our GW corrected band gap values 3.190 eV (Γ–Γ) and 3.033 eV (Γ–X) are closer to the experimental data 3.20 eV. The variations of the band gap values, elastic constants, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, elastic anisotropy, microhardness, Debye temperature and melting temperature with pressure for the α phase LiMgN are presented. The calculated phonon dispersion curves and the thermal properties entropy S and heat capacity C{sub V} have also been obtained. - Graphical abstract: The band gaps under pressures using LDA and GW method. - Highlights: • GW corrected band gap values at normal and high pressures are presented. • Mechanical stability, elastic anisotropy of LiMgN under pressures is analyzed. • Microhardness and melting temperatures of LiMgN under pressures is obtained. • Debye temperatures and dynamical stability under pressures are investigated. • Phonon dispersion curve, thermodynamic property under pressures is demonstrated.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Electron-deuteron deep-inelastic scattering with spectator tagging at EIC

We summarize the phenomenological description of electron-deuteron deep-inelastic scattering (DIS) with detection of a nucleon in the nuclear fragmentation region, eD → e' + N + X ("spectator tagging"), at collision energies accessible with an Electron-Ion Collider (EIC), √s eD ~ several 10 GeV. This includes (a) the kinematic variables, differential cross section, conditional structure functions, and phase space elements; (b) a cross section model based on the light-front impulse approximation and an analytic parametrization of the deuteron wave function; (c) counting rate estimates for simulations of cross section measurements and on-shell extrapolation in the recoil nucleon momentum; (d) a FORTRAN 77 code package for computing the cross section and performing counting rate estimates. The document summarizes the definitions and results without derivation and is intended as a reference for programming and simulations.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

On the room-temperature phase diagram of high pressure hydrogen: An ab initio molecular dynamics perspective and a diffusion Monte Carlo study

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

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

First principles studies on the impact of point defects on the phase stability of (Al{sub x}Cr{sub 1−x}){sub 2}O{sub 3} solid solutions

Density Functional Theory applying the generalised gradient approximation is used to study the phase stability of (Al{sub x}Cr{sub 1−x}){sub 2}O{sub 3} solid solutions in the context of physical vapour deposition (PVD). Our results show that the energy of formation for the hexagonal α phase is lower than for the metastable cubic γ and B1-like phases–independent of the Al content x. Even though this suggests higher stability of the α phase, its synthesis by physical vapour deposition is difficult for temperatures below 800 °C. Aluminium oxide and Al-rich oxides typically exhibit a multi-phased, cubic-dominated structure. Using a model system of (Al{sub 0.69}Cr{sub 0.31}){sub 2}O{sub 3} which experimentally yields larger fractions of the desired hexagonal α phase, we show that point defects strongly influence the energetic relationships. Since defects and in particular point defects, are unavoidably present in PVD coatings, they are important factors and can strongly influence the stability regions. We explicitly show that defects with low formation energies (e.g. metal Frenkel pairs) are strongly preferred in the cubic phases, hence a reasonable factor contributing to the observed thermodynamically anomalous phase composition.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Iterative subspace algorithms for finite-temperature solution of Dyson equation

One-particle Green’s functions obtained from the self-consistent solution of the Dyson equation can be employed in the evaluation of spectroscopic and thermodynamic properties for both molecules and solids. However, typical acceleration techniques used in the traditional quantum chemistry self-consistent algorithms cannot be easily deployed for the Green’s function methods because of a non-convex grand potential functional and a non-idempotent density matrix. Moreover, the optimization problem can become more challenging due to the inclusion of correlation effects, changing chemical potential, and fluctuations of the number of particles. In this paper, we study acceleration techniques to target the self-consistent solution of the Dyson equation directly. We use the direct inversion in the iterative subspace (DIIS), the least-squared commutator in the iterative subspace (LCIIS), and the Krylov space accelerated inexact Newton method (KAIN). We observe that the definition of the residual has a significant impact on the convergence of the iterative procedure. Based on the Dyson equation, we generalize the concept of the commutator residual used in DIIS and LCIIS and compare it with the difference residual used in DIIS and KAIN. The commutator residuals outperform the difference residuals for all considered molecular and solid systems within both GW and GF2. For a number of bond-breaking problems, we found that an easily obtained high-temperature solution with effectively suppressed correlations is a very effective starting point for reaching convergence of the problematic low-temperature solutions through a sequential reduction of temperature during calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Improving the efficiency of G 0 W 0 calculations with approximate spectral decompositions of dielectric matrices

Recently, it was shown that the calculation of quasiparticle energies using the G 0 W 0 approximation can be performed without computing explicitly any virtual electronic states, by expanding the Green function and screened Coulomb interaction in terms of the eigenstates of the static dielectric matrix. Avoiding the evaluation of virtual electronic states leads to improved efficiency and ease of convergence of G 0 W 0 calculations. Here, we propose a further improvement of the efficiency of these calculations, based on an approximation of density-density response functions of molecules and solids. The approximation relies on the calculation of a subset of eigenvectors of the dielectric matrix using the kinetic operator instead of the full Hamiltonian, and it does not lead to any substantial loss of accuracy for the quasiparticle energies. The computational savings introduced by this approximation depend on the system, and they become more substantial as the number of electrons increases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Hydrodynamic limit of Wigner-Poisson kinetic theory: Revisited

In this paper, we revisit the hydrodynamic limit of the Langmuir wave dispersion relation based on the Wigner-Poisson model in connection with that obtained directly from the original Lindhard dielectric function based on the random-phase-approximation. It is observed that the (fourth-order) expansion of the exact Lindhard dielectric constant correctly reduces to the hydrodynamic dispersion relation with an additional term of fourth-order, beside that caused by the quantum diffraction effect. It is also revealed that the generalized Lindhard dielectric theory accounts for the recently discovered Shukla-Eliasson attractive potential (SEAP). However, the expansion of the exact Lindhard static dielectric function leads to a k{sup 4} term of different magnitude than that obtained from the linearized quantum hydrodynamics model. It is shown that a correction factor of 1/9 should be included in the term arising from the quantum Bohm potential of the momentum balance equation in fluid model in order for a correct plasma dielectric response treatment. Finally, it is observed that the long-range oscillatory screening potential (Friedel oscillations) of type cos(2k{sub F}r)/r{sup 3}, which is a consequence of the divergence of the dielectric function at point k = 2k{sub F} in a quantum plasma, arises due to the finiteness of the Fermi-wavenumber and is smeared out in the limit of very high electron number-densities, typical of white dwarfs and neutron stars. In the very low electron number-density regime, typical of semiconductors and metals, where the Friedel oscillation wavelength becomes much larger compared to the interparticle distances, the SEAP appears with a much deeper potential valley. It is remarked that the fourth-order approximate Lindhard dielectric constant approaches that of the linearized quantum hydrodynamic in the limit if very high electron number-density. By evaluation of the imaginary part of the Lindhard dielectric function, it is shown that the Landau-damping region in ω-k plane increases dramatically by increase of the electron number-density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

A general ansatz for constructing quasi-diabatic states in electronically excited aggregated systems

We present a general method for analyzing the character of singly excited states in terms of charge transfer (CT) and locally excited (LE) configurations. The analysis is formulated for configuration interaction singles (CIS) singly excited wave functions of aggregate systems. It also approximately works for the second-order approximate coupled cluster singles and doubles and the second-order algebraic-diagrammatic construction methods [CC2 and ADC(2)]. The analysis method not only generates a weight of each character for an excited state, but also allows to define the related quasi-diabatic states and corresponding coupling matrix elements. In the character analysis approach, we divide the target system into domains and use a modified Pipek-Mezey algorithm to localize the canonical MOs on each domain, respectively. The CIS wavefunction is then transformed into the localized basis, which allows us to partition the wavefunction into LE configurations within domains and CT configuration between pairs of different domains. Quasi-diabatic states are then obtained by mixing excited states subject to the condition of maximizing the weight of one single LE or CT configuration (localization in configuration space). Different aims of such a procedure are discussed, either the construction of pure LE and CT states for analysis purposes (by including a large number of excited states) or the construction of effective models for dynamics calculations (by including a restricted number of excited states). Applications are given to LE/CT mixing in π-stacked systems, charge-recombination matrix elements in a hetero-dimer, and excitonic couplings in multi-chromophoric systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Simulation of multi-shell fullerenes using Machine-Learning Gaussian Approximation Potential

Multi-shell fullerenes ”buckyonions ” were simulated, starting from initially random configurations, using a density-functional-theory (DFT)-trained machine-learning carbon potential within the Gaussian Approximation Potential (GAP) Framework [Volker L. Deringer and Gábor Csányi, Phys. Rev. B 95, 094203 (2017)]. Fullerenes formed from seven different system sizes, ranging from 60 ~ 3774 atoms, were considered. The buckyonions are formed by clustering and layering starting from the outermost shell and proceeding inward. Inter-shell cohesion is partly due to interaction between delocalized π electrons protruding into the gallery. The energies of the models were validated ex post facto using density functional codes, VASP and SIESTA , revealing an energy difference within the range of 0.02 - 0.08 eV/atom after conjugate gradient energy convergence of the models was achieved with both methods.

74 ATOMIC AND MOLECULAR PHYSICS↗