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DOE OSTI2019

Modelling electron transfer in photosystem I: limits and perspectives

Uncovering the parameters underlying the electron transfer (ET) in photosynthetic reaction centres is of importance for understanding the molecular mechanisms underpinning their functionality. The reductive nature of most cofactors involved in photosynthetic ET makes the direct estimation of their properties difficult. Photosystem I (PSI) operates in a highly reducing regime, making the assessment of cofactor properties even more difficult. Kinetic modelling coupled to a non-adiabatic description of ET is a useful approach in overcoming this hindrance. Here we review the theory and modelling approaches that have been used in assessing parameters associated with ET reactions in PSI, with particular attention to ET reactions involving the phylloquinones and the iron–sulphur clusters. In most modelling studies, the goal is to estimate the driving force of ET, which is usually associated with the cofactor midpoint potentials. The driving force is sensitive to many factors, which define the ET rate, i.e. the reorganisation energy, the coupling with nuclear modes and the electronic matrix elements, which are explored and discussed here. The importance of an inclusive modelling of both forward and reverse ET processes is discussed and highlighted. It is shown that although estimates are indeed sensitive to the exact parameter sets employed in the modelling, a general consensus is still attained, pointing to a scenario where $ΔG^0_{A_{tA→Fx}}/ΔG^0_{A_{tB→Fx}}$ is weakly endergonic/exergonic, respectively. It is emphasised that to further refine those estimates, it will require a joint effort between computational modelling and more wide-ranging experimental studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Quantum Monte Carlo Approaches to Na Intercalation on Bilayer Graphene

We have performed Quantum Monte Carlo (QMC) simulations on Na-intercalated bilayer graphene to study the evolution of electronic and optical properties upon Na intercalation into hard carbon layers. The objective was to model the optimal configuration of Na intercalation into a hard carbon matrix containing graphene regions. Our study showed that Na intercalation can be energetically stabilized at large interlayer distances (over 6 Å) in both AA- and AB-stacked bilayer graphene. In the QMC results, we found a significant band gap opening at the equilibrium interlayer distance of Na-intercalated bilayer graphene, while corresponding density functional theory (DFT) results showed no gap. This difference between DFT and QMC results indicates that the gap opening induced by Na intercalation into a hard carbon is underestimated within the DFT framework. In addition, a zigzag configuration of Na atoms was found to be energetically stable at interlayer distances up to 10 Å, leading us to predict the existence of a local minimum of Na intercalation at large interlayer distance. These computation and modeling results can provide guidance on how to synthesize and optimize hard carbon with bilayer graphene regions that permit a zigzag intercalation configuration that will maximize and stabilize sodium hosting.

Binding energy↗

DOE OSTI2020

Current and future neutrino oscillation constraints on leptonic unitarity

The unitarity of the lepton mixing matrix is a critical assumption underlying the standard neutrino-mixing paradigm. However, many models seeking to explain the as-yet-unknown origin of neutrino masses predict deviations from unitarity in the mixing of the active neutrino states. Motivated by the prospect that future experiments may provide a precise measurement of the lepton mixing matrix, we revisit current constraints on unitarity violation from oscillation measurements and project how next-generation experiments will improve our current knowledge. With the next-generation data, the normalizations of all rows and columns of the lepton mixing matrix will be constrained to ≲10% precision, with the e-row best measured at ≲1% and the τ-row worst measured at ~10% precision. The measurements of the mixing matrix elements themselves will be improved on average by a factor of 3. We highlight the complementarity of DUNE, T2HK, JUNO, and IceCube Upgrade for these improvements, as well as the importance of ντ appearance measurements and sterile neutrino searches for tests of leptonic unitarity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

Quark and lepton mixing as manifestations of violated mirror symmetry

The existence of heavy mirror analogs of ordinary fermions would provide deeper insight into the gedanken paradox appearing in the Standard Model upon direct parity violation and consisting in a physical distinguishability of left- and right-hand coordinate frames. Arguments are presented in support of the statement that such mirror states may also be involved in the formation of observed properties of the system of Standard Model quarks and leptons—that is, their mass spectra and their weak-mixing matrices: (i) In the case of the involvement of mirror generations, the quark mixing matrix assumes the experimentally observed form. It is determined by the constraints imposed by weak SU(2) symmetry and by the quark-mass hierarchy. (ii) Under the same conditions and upon the involvement of mirror particles, the lepton mixing matrix (neutrino mixing) may become drastically different from its quark analog—the Cabibbo-Kobayashi-Maskawa matrix; that is, it may acquire properties suggested by experimental data. This character of mixing is also indicative of an inverse mass spectrum of Standard Model neutrinos and their Dirac (not Majorana) nature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

Successful N{sub 2} leptogenesis with flavour coupling effects in realistic unified models

In realistic unified models involving so-called SO(10)-inspired patterns of Dirac and heavy right-handed (RH) neutrino masses, the lightest right-handed neutrino N{sub 1} is too light to yield successful thermal leptogenesis, barring highly fine tuned solutions, while the second heaviest right-handed neutrino N{sub 2} is typically in the correct mass range. We show that flavour coupling effects in the Boltzmann equations may be crucial to the success of such N{sub 2} dominated leptogenesis, by helping to ensure that the flavour asymmetries produced at the N{sub 2} scale survive N{sub 1} washout. To illustrate these effects we focus on N{sub 2} dominated leptogenesis in an existing model, the A to Z of flavour with Pati-Salam, where the neutrino Dirac mass matrix may be equal to an up-type quark mass matrix and has a particular constrained structure. The numerical results, supported by analytical insight, show that in order to achieve successful N{sub 2} leptogenesis, consistent with neutrino phenomenology, requires a “flavour swap scenario” together with a less hierarchical pattern of RH neutrino masses than naively expected, at the expense of some mild fine-tuning. In the considered A to Z model neutrino masses are predicted to be normal ordered, with an atmospheric neutrino mixing angle well into the second octant and the Dirac phase δ≃20{sup ∘}, a set of predictions that will be tested in the next years in neutrino oscillation experiments. Flavour coupling effects may be relevant for other SO(10)-inspired unified models where N{sub 2} leptogenesis is necessary.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Absence of Coulomb Blockade in the Anderson Impurity Model at the Symmetric Point

In this study, we investigate the characteristics of the electric current in the so-called symmetric Anderson impurity model. We study the nonequilibrium model using two complementary approximate methods, the perturbative quantum master equation approach to the reduced density matrix and a self-consistent equation of motion approach to the nonequilibrium Green's function. We find that, at a particular symmetry point, an interacting Anderson impurity model recovers the same steady-state current as an equivalent noninteracting model, akin a two-band resonant level model. We show this in the Coulomb blockade regime for both high and low temperatures, where either the approximate master equation approach or the Green's function method provides accurate results for the current. We conclude that the steady-state current in the symmetric Anderson model at this regime does not encode characteristics of a many-body interacting system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Zee and Zee-Babu mechanisms in the minimal 331 model

We show that the minimal 3-3-1 model cannot accommodate the neutrino masses at tree level using present experimental data. Nevertheless, a modified Zee and the Zee-Babu mechanisms for generating neutrino masses at 1-loop and 2-loop, respectively, are automatically implemented in the minimal 3-3-1 model, without introducing new degrees of freedom to the model. We also present a systematic method for finding solutions to the leptonic sector masses and mixing. As a case study, we accommodate the charged and neutral leptons masses and the PMNS matrix in the 1-loop modified Zee mechanism contained in the minimal 3-3-1 model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2013

Study of second phase in bioabsorbable magnesium alloys: Phase stability evaluation via Dmol{sup 3} calculation

Thermodynamical stabilities of four conventional second phases as well as magnesium matrix in bioabsorbable magnesium alloys were investigated theoretically via computer calculation method. Model of individual phase and systems including phase and four water molecular (phase-4H{sub 2}O) were established to simulate the in vitro and in vivo environment. Local orbital density functional theory approach was applied to calculate the total energy for the individual phase and phase-4H{sub 2}O system. The results demonstrated that all the second phases possessed higher phase stability compared with magnesium matrix, but the phase stability was quite different for different types of second phases or second phase-4H{sub 2}O systems. Furthermore, a schematic process of inflammation reaction caused by magnesium alloy implants was proposed for the further evaluation on biocompatibility of different second phases.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Plaquette valence bond state in the spin-$\frac{1}{2}$ J 1 –J 2 XY model on the square lattice

Here, we studied the ground-state phase diagram of spin-1/2 J 1 –J 2 XY model on the square lattice with first-neighbor J 1 and second-neighbor J 2 antiferromagnetic interactions using both infinite density matrix renormalization group (iDMRG) and DMRG approaches. We show that a plaquette valence bond phase is realized in an intermediate region 0.50 ≤ J 2 /J 1 < 0.54 between a Néel magnetic ordered phase at J 2 /J 1 < 0.50 and a stripy magnetic ordered phase at J 2 /J 1 ≥ 0.54 . The plaquette valence bond phase is characterized by finite dimer orders in both the horizontal and vertical directions. Contrary to the spin-1/2 J 1 –J 2 Heisenberg model, we do not find numerical evidence for a quantum spin liquid phase in the J 1 –J 2 XY model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Closures for multicomponent reacting flows based on dispersion analysis

This work presents algebraic closure models associated with advective transport and nonlinear reactions in a Reynolds-averaged Navier-Stokes context for a system of species subject to binary reactions and transport by advection and diffusion. Expanding upon analysis originally developed for non-reactive transport in the context of Taylor dispersion of scalars, this work extends the modified gradient diffusion model explicated by Peters [N. Peters, Turbulent Combustion, Cambridge Monographs on Mechanics (Cambridge University Press, Cambridge, 2000)] and based on work by Corrsin [S. Corrsin, The reactant concentration spectrum in turbulent mixing with a first-order reaction, J. Fluid Mech. 11, 407 (1961)] beyond single-component transport phenomena and involving nonlinear reactions. The presented model forms, from this weakly nonlinear extension of the original dispersion theory, lead to an analytic expression for the eddy diffusivity matrix that explicitly captures the influence of the reaction kinetics on the closure operators. Furthermore, we demonstrate that the derived model form directly translates between flow topologies through a priori and a posteriori testing of a binary species system subject to homogeneous isotropic turbulence. Using two- and three-dimensional direct numerical simulations involving laminar and turbulent flows, it is shown that this framework improves prediction of mean quantities compared to previous results. Lastly, the presented model form, collapses to the earlier gradient diffusion and its modified version derived by Corrsin in the limits of nonreactive species and linear reactions, respectively.

42 ENGINEERING↗

DOE OSTI2019

A fast reconstruction method of the dense point-cloud model for cultural heritage artifacts based on compressed sensing and sparse auto-encoder

Since the point cloud data of cultural heritage artifacts obtained by the laser scanner is enormous and dense, these lead to a large quantity of network resource for storing, processing, and transmission. This paper provided a fast reconstruction method of the dense point cloud model for cultural relics based on sparse auto-encoder and compressed sensing. Firstly, the octree method based on the hash function was utilized to extract local features and remove redundant points. Secondly, the point cloud, which can be seen as the 3D geometric signal, is projected to the discrete Laplacian sparse basis via the point cloud adjacency matrix. Then, aiming at the bottleneck of slow recovery caused by tremendous scale of inverse problem based on compressed sensing theory, the sparse auto-encoder was applied to reduce the dimension and speed up the recovery. Finally, the OMP algorithm was applied to reconstruct 3D point cloud model based on the stochastic Gauss matrix. In order to test the performance of our methods, the 3D point cloud model of terracotta warriors and horses head were used. And the experimental results demonstrated that our approach can obviously accelerate the process of reconstruction of the dense point cloud model for the cultural heritage artifacts and ensure the recovery accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Quantum field theory for the chiral clock transition in one spatial dimension

We describe the quantum phase transition in the N-state chiral clock model in spatial dimension d = 1. With couplings chosen to preserve time-reversal and spatial inversion symmetries, such a model is in the universality class of recent experimental studies of the ordering of pumped Rydberg states in a one-dimensional chain of trapped ultracold alkali atoms. For such couplings and N = 3, the clock model is expected to have a direct phase transition from a gapped phase with a broken global Z N symmetry, to a gapped phase with the Z N symmetry restored. The transition has dynamical critical exponent z ≠ 1, and so cannot be described by a relativistic quantum field theory. We use a lattice duality transformation to map the transition onto that of a Bose gas in d = 1, involving the onset of a single-boson condensate in the background of a higher-dimensional N-boson condensate. Here, we present a renormalization group analysis of the strongly coupled field theory for the Bose gas transition in an expansion in 2 – d, with 4 – N chosen to be of order 2 – d. At two-loop order, we find a regime of parameters with a renormalization group fixed point which can describe a direct phase transition. We also present numerical density-matrix renormalization group studies of lattice chiral clock and Bose gas models for N = 3, finding good evidence for a direct phase transition, and obtain estimates for z and the correlation length exponent ν.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Lattice realizations of topological defects in the critical (1+1)-d three-state Potts model

Topological/perfectly-transmissive defects play a fundamental role in the analysis of the symmetries of two dimensional conformal field theories (CFTs). In the present work, spin chain regularizations for these defects are proposed and analyzed in the case of the three-state Potts CFT. In particular, lattice versions for all the primitive defects are presented, with the remaining defects obtained from the fusion of the primitive ones. The defects are obtained by introducing modified interactions around two given sites of an otherwise homogeneous spin chain with periodic boundary condition. The various primitive defects are topological on the lattice except for one, which is topological only in the scaling limit. The lattice models are analyzed using a combination of exact diagonalization and density matrix renormalization group techniques. Low-lying energy spectra for different defect Hamiltonians as well as entanglement entropy of blocks located symmetrically around the defects are computed. The latter provides a convenient way to compute the g-function which characterizes various defects. Finally, the eigenvalues of the line operators in the “crossed channel” and fusion of different defect lines are also analyzed. The results are all in agreement with expectations from conformal field theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Radionuclide Screening Analysis and Transport Parameters for Pahute Mesa Detonations, Nevada National Security Site

A “screening analysis” is implemented at Pahute Mesa (PM), Nevada National Security Site (NNSS), to determine subsets of the 43 radionuclides listed in the radionuclide inventory of Finnegan et al. (2016) that are of relevance or potential relevance to the hydrologic source term (HST) for assessment of radionuclide transport in groundwater. Consideration is added to how levels of contamination are defined and whether any other radionuclides not in the inventory are relevant to the HST. A model is developed to estimate a range of possible source concentrations in groundwater that account for uncertainty in partitioning into melt glass and sorption into surrounding rock of the exchange zone for the 82 PM underground nuclear tests detonated in vertical shafts. The model also accounts for the varied hydrogeochemical settings. Transport parameters needed for the screening model calculations are developed from databases for hydrogeologic units, chemistry, mineralogy, fracture spacing, fracture aperture, fracture openness, matrix porosity, bulk density, saturation, and alteration. Of key importance is consideration of diagenetic zonation of the mineralogy related to hydrothermal alteration. The screening analysis compares model results with available groundwater radiochemistry data. Consistency between screening model results and available data helps validate the model for application to all 43 radionuclides, most of which have no measurements or only non-detect measurements of concentration in groundwater. The screening analysis determines that ten radionuclides – tritium, Sr-90, I-129, Cs-137, U-232, U-233, U-234, U-238, and the total of Pu-239 and Pu-240 are relevant to the HST. Determination of relevance is primarily based on data and/or model results indicating source concentration exceeding a maximum contaminant level (MCL) out to 100 years since the time of detonation. U-238 is relevant to assessment of contamination relative to MCLs for uranium and gross alpha particle activity. Five other radionuclides – C-14, Cl-36, Tc-99, Np-237, and Pu-238 – are determined potentially relevant to the HST based on a 0.1 MCL threshold. The screening analysis recommends additional attention to the natural daughter radionuclides of the uranium series (U-238) and thorium series (Th-232) decay chains, particularly Ra-226 and Ra-228, that were not included the inventory.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

Spectroscopy of states in 136 Ba using the 138 Ba(p,t) reaction

Background: The 136 Ba isotope is the daughter nucleus in 136 Xe $ββ$ decay. It also lies in a shape transitional region of the nuclear chart, making it a suitable candidate to test a variety of nuclear models. Purpose: To obtain spectroscopic information on states in 136 Ba, which will allow a better understanding of its low-lying structure. These data may prove useful to constrain future 136 Xe → 136 Ba neutrinoless $ββ$ decay matrix element calculations. Methods: Here, a 138 Ba(p, t) reaction was used to populate states in 136 Ba up to approximately 4.6 MeV in excitation energy. The tritons were detected using a high-resolution Q3D magnetic spectrograph. A distorted wave Born approximation analysis was performed for the measured triton angular distributions. Results: 102 excited states in 136 Ba were observed, out of which 52 are reported for the first time. Definite spin-parity assignments are made for 26 newly observed states, while previously ambiguous assignments for ten other states are resolved. Together with other available data, the results are used to determine level densities in 136 Ba. These were compared with theory predictions, obtained using shell model calculations with Hamiltonians previously used for 136 Xe neutrinoless $ββ$ decay matrix element evaluations. Conclusions: The shell model predicted level densities agree reasonably well for the two Hamiltonians. However the results for theory and experiment are found to agree only at lower energies, diverging from one another for the higher lying states, with the discrepancy increasing with energy. This is presumably because of lower production cross sections for a majority of the higher-lying predicted states and the experimental limitations in resolving a large number of nearly degenerate states predicted by the theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Methane Diffusion and Adsorption in Shale Rocks: A Numerical Study Using the Dusty Gas Model in TOUGH2/EOS7C-ECBM

Gas production from shale gas reservoirs plays a significant role in satisfying increasing energy demands. Compared with conventional sandstone and carbonate reservoirs, shale gas reservoirs are characterized by extremely low porosity, ultra-low permeability and high clay content. Slip flow, diffusion, adsorption and desorption are the primary gas transport processes in shale matrix, while Darcy flow is restricted to fractures. Understanding methane diffusion and adsorption, and gas flow and equilibrium in the low-permeability matrix of shale is crucial for shale formation evaluation and for predicting gas production. Modeling of diffusion in low-permeability shale rocks requires use of the Dusty gas model (DGM) rather than Fick’s law. The DGM is incorporated in the TOUGH2 module EOS7C-ECBM, a modified version of EOS7C that simulates multicomponent gas mixture transport in porous media. Also included in EOS7C-ECBM is the extended Langmuir model for adsorption and desorption of gases. In this study, a column shale model was constructed to simulate methane diffusion and adsorption through shale rocks. The process of binary CH 4 - N 2 diffusion and adsorption was analyzed. A sensitivity study was performed to investigate the effects of pressure, temperature and permeability on diffusion and adsorption in shale rocks. The results show that methane gas diffusion and adsorption in shale is a slow process of dynamic equilibrium, which can be illustrated by the slope of a curve in CH4mass variation. The amount of adsorption increases with the pressure increase at the low pressure, and the mass change by gas diffusion will decrease due to the decrease in the compressibility factor of the gas. With the elevated temperature, the gas molecules move faster and then the greater gas diffusion rates make the process duration shorter. The gas diffusion rate decreases with the permeability decrease, and there is a limit of gas diffusion if the permeability is less than 1.0×10 -15 m 2 . In conclusion, the results can provide insights for a better understanding of methane diffusion and adsorption in the shale rocks so as to optimize gas production performance of shale gas reservoirs.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2015

Reassessment of uncertainties for the PU-MET-INTER-002 benchmark - 14432

Uncertainty for the PU-MET-INTER-002 benchmark of ZPR-6/10 was unusually large for a ZPR assembly and was dominated by the uncertainties in matrix tube pitch and composition uncertainties for plutonium, graphite and stainless steel plates. The original uncertainty analysis for PU-MET-INTER-002 was limited by computer resources, software and the nuclear data available in 2002, all of which have been improved since. An as-built Monte Carlo model of ZPR-6/10 was used to quantify components of the transformation from the detailed model to a simplified RZ benchmark in 2002. Compositional uncertainties were estimated based upon TWODANT calculations of the RZ benchmark model (20 group, S{sub 8} - P{sub 1}). MC{sup 2}-2 was used with END/B-V.2 data to generate homogenized cross section data for TWODANT. The MC{sup 2}-2 calculations did not account for lattice cell spatial heterogeneity which was driven by the manual process required to generate ∼80 modifications to the deterministic model and by the software limitations of MC{sup 2}-2. Improvements to DIF3D-VARIANT, development of the MC{sup 2}-3 and BuildZPRModel codes, and better computer resources make accurate 3D transport calculations of reactivity changes practical today. BuildZPRModel imports the as-built geometry and creates a 'drawer' homogenized DIF3D model where each radial DIF3D mesh is the exact size of a single ZPR matrix tube and drawer. A MC{sup 2}-3 input is constructed for each drawer to produce homogenized cross section data where the spatial cell heterogeneity is captured by solving a 1D MOC transport calculation on the ultrafine energy group level. Collapsing 3D drawers into 1D MC{sup 2}-3 drawer models follows conventional procedures and is done by BuildZPRModel. MCNP6 was used to re-compute relevant geometry components of the uncertainty using ENDF/B-VII.0 data with the as-built model. Changes in the geometry components compared with earlier results are insignificant. DIF3D calculations of the compositional uncertainties were performed using 33, 70, 116, 230, 425, and 703 group energy structures and selectively combined with P{sub 3}-P{sub 7} transport approximations and P{sub 1} and P{sub 3} scattering kernels. 3D diffusion theory calculations were also performed for comparison. Many composition uncertainty components were essentially unchanged with the updated methodology. However, the dominant experimental uncertainty for PU-MET-INTER-002 is the composition of stainless steel. The new calculations reduce the stainless steel uncertainty from ∼115 pcm to ∼70 pcm which significantly reduces the total uncertainty for PU-MET-INTER-002. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2017

Predictive modelling of hydration and mechanical performance of low Ca composite cements: Possibilities and limitations from industrial perspective

We quantified hydration and performance development of composites cements containing metakaolin in the rage of 0–40% and investigated applicability of thermodynamic and micromechanical models to predict the evolution of hydrates assemblage and of performance, respectively. The reaction of metakaolin results in a formation of significant amounts of C-S-H phase for lower metakaolin content and of strätlingite for higher contents. This leads to very dense matrix with finer porosity allowing co-existence of thermodynamically incompatible phases, namely portlandite and strätlingite. Hence, thermodynamic modelling cannot be applied to correctly predict the phase assemblage for the systems with high metakaolin content. By introducing constraints into the thermodynamic model in a form of minimum phase content, the XRD-amorphous phases can be quantified. However, such constraints are only valid for the cases studied and limit the general applicability and predictive power of the model. Elastic properties and strength of mortars are influenced by the metakaolin additions in an opposite trend. It indicates that they are sensitive to different microstructural features/mechanisms. Continuum micromechanic-based model is capable to accurately predict the performance evolution based on the volume of hydrates predicted by the thermodynamic modelling. An additional step required for the accurate prediction - porosity is partitioned based on its saturation at 95% RH – is introduced and substantiated.

36 MATERIALS SCIENCE↗