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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Computation of the free energy due to electron density fluctuation of a solute in solution: A QM/MM method with perturbation approach combined with a theory of solutions

We developed a perturbation approach to compute solvation free energy Δμ within the framework of QM (quantum mechanical)/MM (molecular mechanical) method combined with a theory of energy representation (QM/MM-ER). The energy shift η of the whole system due to the electronic polarization of the solute is evaluated using the second-order perturbation theory (PT2), where the electric field formed by surrounding solvent molecules is treated as the perturbation to the electronic Hamiltonian of the isolated solute. The point of our approach is that the energy shift η, thus obtained, is to be adopted for a novel energy coordinate of the distribution functions which serve as fundamental variables in the free energy functional developed in our previous work. The most time-consuming part in the QM/MM-ER simulation can be, thus, avoided without serious loss of accuracy. For our benchmark set of molecules, it is demonstrated that the PT2 approach coupled with QM/MM-ER gives hydration free energies in excellent agreements with those given by the conventional method utilizing the Kohn-Sham SCF procedure except for a few molecules in the benchmark set. A variant of the approach is also proposed to deal with such difficulties associated with the problematic systems. The present approach is also advantageous to parallel implementations. We examined the parallel efficiency of our PT2 code on multi-core processors and found that the speedup increases almost linearly with respect to the number of cores. Thus, it was demonstrated that QM/MM-ER coupled with PT2 deserves practical applications to systems of interest.

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

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron–Sulfur Cubanes

Iron–sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. Here, to provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III) 4 S 4 (SMe) 4 ] -2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Linking Silica Support Morphology to the Dynamics of Aminopolymers in Composites

A combined computational and experimental approach is used to elucidate the effect of silica support morphology on polymer dynamics and CO 2 adsorption capacities in aminopolymer/silica composites. Furthermore, simulations are based on coarse-grained molecular dynamics simulations of aminopolymer composites where a branched aminopolymer, representing poly(ethylenimine) (PEI), is impregnated into different silica mesoporous supports. The morphology of the mesoporous supports varies from hexagonally packed cylindrical pores representing SBA-15, double gyroids representing KIT-6 and MCM-48, and cagelike structures representing SBA-16. In parallel, composites of PEI and the silica supports SBA-15, KIT-6, MCM-48, and SBA-16 are synthesized and characterized, including measuring their CO 2 uptake. Simulations predict that a 3D pore morphology, such as those of KIT-6, MCM-48, and SBA-16, will have faster segmental mobility and have lower probability of primary amine and surface silanol associations, which should translate to higher CO 2 uptake in comparison to a 2D pore morphology such as that of SBA-15. We found that KIT-6 has higher CO 2 uptake than SBA-15 at equivalent PEI loading, even though both supports have similar surface area and pore volume. But, this is not the case for the MCM-48 support, which has smaller pores, and SBA-16, whose pore structure rapidly degrades after PEI impregnation.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Monte Carlo Second- and Third-Order Many-Body Green’s Function Methods with Frequency-Dependent, Nondiagonal Self-Energy

We fully develop the Monte Carlo many-body Green’s function (MC-GF) method with the following enhancements: (1) The truncation order of the perturbation expansion of the Dyson self-energy is raised from the second order (MC-GF2) to the third order (MC-GF3) with the aid of a computerized procedure to enumerate and transform all 84 third-order Goldstone diagrams into Monte Carlo integrable expressions and then into central processing unit (CPU)/graphical processing unit (GPU)-parallel computer codes. (2) An efficient algorithm is proposed that computes all off-diagonal and diagonal elements of the MC-GF2 and MC-GF3 self-energy matrices by common subexpression elimination. (3) The frequency-independent approximation is lifted by introducing a method that computes frequency derivatives of the MC-GF2 and MC-GF3 self-energies up to any arbitrarily high order at nearly no additional computational cost. (4) The imaginary-time integration in the Laplace-transformed expressions of the self-energy is carried out stochastically (instead of using a quadrature in the previous implementations), resulting in a 50- to 200-fold speedup. (5) The efficiency of the redundant-walker convergence acceleration scheme is analyzed numerically, and the guidelines are established to select an optimal number of walkers for maximal efficiency. When such an optimal number is used, the cost per sample is constant of molecular size on either many CPUs or many GPUs. (6) The computational cost to obtain a binding energy within a given statistical uncertainty is observed to increase as (tentatively) O(n 4 ) and O(n 5 ) of molecular size (n is the number of electrons) with and without the diagonal approximation, respectively, as opposed to O(n 5 ) and O(n 6 ) of the corresponding deterministic algorithms. With this method applied to the electron binding energies of C 60 , we show that the third-order corrections to the self-energies are much greater in electron binding energies than in ground-state energies. As a result, they display a sign of oscillatory convergence toward experimental results, not necessarily improving the agreement with increasing perturbation order, justifying MC-GF3 and motivating even higher-order methods.

Algorithms↗
DOE OSTI2019

Kinetic simulation of a low-pressure helium discharge with comparison to experimental measurements

Modern computational validation efforts rely on comparison of known experimental quantities such as current, voltage, particle densities, and other plasma properties with the same values determined through simulation. A discrete photon approach for radiation transport was recently incorporated into a particle-in-cell/direct simulation Monte Carlo code. As a result, spatially and temporally resolved synthetic spectra may be generated even for non-equilibrium plasmas. The generation of this synthetic spectra lends itself to potentially new validation opportunities. In this work, initial comparisons of synthetic spectra are made with experimentally gathered optical emission spectroscopy. A custom test apparatus was constructed that contains a 0.5 cm gap distance parallel plane discharge in ultra high purity helium gas (99.9999%) at a pressure of 75 Torr. Plasma generation is initiated with the application of a fast rise-time, 100 ns full-width half maximum, 2.0 kV voltage pulse. Transient electrical diagnostics are captured along with time-resolved emission spectra. A one-dimensional simulation is run under the same conditions and compared against the experiment to determine if sufficient physics are included to model the discharge. To sync the current measurements from experiment and simulation, significant effort was undertaken to understand the kinetic scheme required to reproduce the observed features. Additionally, the role of the helium molecule excimer emission and atomic helium resonance emission on photocurrent from the cathode are studied to understand which effect dominates photo-feedback processes. Results indicate that during discharge development, atomic helium resonance emission dominates the photo-flux at the cathode even though it is strongly self-absorbed. A comparison between the experiment and simulation demonstrates that the simulation reproduces observed features in the experimental discharge current waveform. Here, the synthesized spectra from the kinetic method produces more favorable agreement with the experimental data than a simple local thermodynamic equilibrium calculation and is a first step towards using spectra generated from a kinetic method in validation procedures. The results of this study produced a detailed compilation of important helium plasma chemistry reactions for simulating transient helium plasma discharges.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Computer simulation of liquid-vapor coexistence of confined quantum fluids

The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential V{sub eff}(r) = V{sub LJ} + V{sub Q}, where V{sub LJ} is the Lennard-Jones 12-6 potential (LJ) and V{sub Q} is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1/kT and de Boer's quantumness parameter Λ=h/σ√(mε), where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ε are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential V{sub eff}(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance L{sub p}, within the range 2σ ⩽ L{sub p} ⩽ 6σ. The critical temperature of the system is reduced by decreasing L{sub p} and increasing Λ, and the liquid-vapor transition is not longer observed for L{sub p}/σ < 2, in contrast to what has been observed for the classical system.

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

Approximate Green’s Function Coupled Cluster A Method Employing Effective Dimension Reduction

The Green’s function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structures of molecular structures and periodic systems, especially when electrons are strongly correlated. However, in order for the GFCC method to become an approach that can be routinely used in the electronic structure calculations, more robust linear algebraic techniques and approximations need to be employed to reduce its extremely high computational overhead. In our recent studies, we showed that the GFCC equation can be numerically solved by seeking solutions of multiple linear systems in the frequency regime of interest, which can be easily distributed in a massively parallel environment, and broaden the avenue for more state-of-the-art numerical linear algebraic tools associated with multiple linear systems to be kicked in to this field. In the present pursuit of this practice, we show a successful application of model order reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires a high resolution of spectral function, instead of solving GFCC linear equation in the original dimension for every single frequency point, an easily-solvable linear system model with reduced dimension can be built upon projecting the original GFCC linear system into a subspace, from which the interpolation and extrapolation can give a reasonable approximation to the results of the original GFCC linear equations. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some select frequencies inside the frequency regime. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The approach is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems including carbon monoxide, 1,3-butadiene, benzene, and adenine molecules. As a byproduct, the high quality linear system model is also found to be able to provide high quality initial guess for the existing linear solver to improve the convergence performance.

Peng, Bo↗
DOE OSTI2020

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

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

Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

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

Speeding up equation of motion coupled cluster theory with the chain of spheres approximation

In the present paper, the chain of spheres exchange (COSX) approximation is applied to the highest scaling terms in the equation of motion (EOM) coupled cluster equations with single and double excitations, in particular, the terms involving integrals with four virtual labels. It is found that even the acceleration of this single term yields significant computational gains without compromising the desired accuracy of the method. For an excitation energy calculation on a cluster of five water molecules using 585 basis functions, the four virtual term is 9.4 times faster using COSX with a loose grid than using the canonical implementation, which yields a 2.6 fold acceleration for the whole of the EOM calculation. For electron attachment calculations, the four virtual term is 15 times and the total EOM calculation is 10 times faster than the canonical calculation for the same system. The accuracy of the new method was tested using Thiel’s test set for excited states using the same settings and the maximum absolute deviation over the whole test set was found to be 12.945 cm{sup −1} (59 μHartree) for excitation energies and 6.799 cm{sup −1} (31 μHartree) for electron attachments. Using MP2 amplitudes for the ground state in combination with the parallel evaluation of the full EOM equations in the manner discussed in this paper enabled us to perform calculations for large systems. Electron affinity values for the two lowest states of a Zn protoporphyrine model compound (224 correlated electrons and 1120 basis functions) were obtained in 3 days 19 h using 4 cores of a Xeon E5-2670 processor allocating 10 GB memory per core. Calculating the lowest two excitation energies for trans-retinal (114 correlated electrons and 539 basis functions) took 1 day 21 h using eight cores of the same processor and identical memory allocation per core.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Reversible Olefin Addition to Extended Lattices of a Nickel–Selenium Framework

We performed density functional theory computations to study the structural and electronic properties as the basis of ethylene addition activity for [Ni(XC)4]n (X = Se, S)-extended lattices. We demonstrated that the mechanism of ethylene cycloaddition to a periodic [Ni(SeC)4]n two-dimensional (2D) network is analogous to that previously described for [Ni(SC)4]n 2D sheets and similar to the metal bis(dithiolene) molecular complexes [M(S2C2R2)2] (M = Ni, Pd, Pt, Co, Cu). These nanosheet materials avoid decomposition upon olefin addition, which is one of the main limitations of the molecular metal bis(dithiolene) complexes, as we find the decomposition processes to be thermodynamically unfavorable. Our calculations also suggest that the preferred conformation of the [Ni(SeC)4]n bilayer lattice is parallel displaced, with the Se atoms positioned above the Ni atoms, which is different from the eclipsed conformation found for [Ni(SC)4]n. We also managed to optimize an adduct of [Ni(SC)4]n in the bilayer form, which exceed the ethylene coverage of molecular complexes. We calculate that the preferred three-dimensional geometry of the stacked sheets is eclipsed because of strong van der Waals interactions. Such an arrangement of the sheets indicates that these materials should be highly porous, pointing to the high capacity for olefin bindings. Indeed, a few moderately stable ethylene adducts have been located. Owing to their unique structures and chemical reactivity, these newly predicted materials can be potentially developed as electrocatalysts for olefin purification. © 2018 American Chemical Society.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Simulation of Coupled Processes of Flow, Transport, and Storage of CO 2 in Saline Aquifers

This report is the final scientific one for the award DE- FE0000988 entitled “Simulation of Coupled Processes of Flow, Transport, and Storage of CO 2 in Saline Aquifers.” The work has been divided into six tasks. In task, “Development of a Three-Phase Non-Isothermal CO 2 Flow Module,” we developed a fluid property module for brine-CO 2 mixtures designed to handle all possible phase combinations of aqueous phase, sub-critical liquid and gaseous CO 2 , supercritical CO 2 , and solid salt. The thermodynamic and thermophysical properties of brine-CO 2 mixtures (density, viscosity, and specific enthalpy of fluid phases; partitioning of mass components among the different phases) use the same correlations as an earlier fluid property module that does not distinguish between gaseous and liquid CO 2 -rich phases. We verified the fluid property module using two leakage scenarios, one that involves CO 2 migration up a blind fault and subsequent accumulation in a secondary “parasitic” reservoir at shallower depth, and another investigating leakage of CO 2 from a deep storage reservoir along a vertical fault zone. In task, “Development of a Rock Mechanical Module,” we developed a massively parallel reservoir simulator for modeling THM processes in porous media brine aquifers. We derived, from the fundamental equations describing deformation of porous elastic media, a momentum conservation equation relating mean stress, pressure, and temperature, and incorporated it alongside the mass and energy conservation equations from the TOUGH2 formulation, the starting point for the simulator. In addition, rock properties, namely permeability and porosity, are functions of effective stress and other variables that are obtained from the literature. We verified the simulator formulation and numerical implementation using analytical solutions and example problems from the literature. For the former, we matched a one-dimensional consolidation problem and a two-dimensional simulation of the Mandel-Cryer effect. For the latter, we obtained a good match of temperature and gas saturation profiles, and surface uplift, after injection of hot fluid into a model of a caldera structure. In task, “Incorporation of Geochemical Reactions of Selected Important Species,” we developed a novel mathematical model of THMC processes in porous and fractured saline aquifers, simulating geo-chemical reactions associated with CO 2 sequestration in saline aquifers. Two computational frameworks, sequentially coupled and fully coupled, were used to simulate the reactions and transport. We verified capabilities of the THMC model to treat complex THMC processes during CO 2 sequestration by analytical solutions and we constructed reactive transport models to analyze the THMC process quantitatively. Three of these are 1D reactive transport under chemical equilibrium, a batch reaction model with equilibrium chemical reactions, and a THMC model with CO 2 dissolution. In task “Study of Instability in CO 2 Dissolution-Diffusion-Convection Processes,” We reviewed literature related to the study of density driven convective flows and on the instability of CO 2 dissolution-diffusion-convection processes. We ran simulations that model the density-driven flow instability that would occur during CO 2 sequestration. CO 2 diffused through the top of the system and dissolved in the aqueous phase there, increasing its density. Density fingers formed along the top boundary, and coalesced into a few prominent ones, causing convective flow that forced the fluid to the system bottom. These simulations were in two and three dimensions. We ran additional simulations of convective mixing with density contrast caused by variable dissolved CO 2 concentration in saline water, modeled after laboratory experiments in which supercritical CO2 was circulated in the headspace above a brine saturated packed sand in a pressure vessel. As CO 2 dissolved into the upper part of the saturated sand, liquid phase density increases causing instability and setting off convective mixing. We obtained good agreement with the laboratory experiments, which were characterized by finger development and associated mixing of dissolved CO 2 into the system. We then varied a wide range of parameters and conceptual models in order to analyze the possibility of convective mixing under different conditions, such as various boundary conditions, and chemical reaction conditions. The CO 2 fingers from different simulations showed great differences as time progressed, caused by permeability heterogeneity. The early time diffusive phenomenon was captured by fine grid resolution, and the permeability heterogeneity affected the pattern of the CO 2 fingers. In addition, the fingers from three-dimensional simulations tended to be larger and flatter than the two-dimensional ones. In task “Implementation of Efficient Parallel Computing Technologies,” we made enhancements and modifications to our code in order to substantially increase the grid size that could be run. We installed and ran it on various platforms, including a multi-core PC and a cluster, and verified the numerical implementation and parallel code using an example problem from the literature. This problem, with a grid size of sixty million, utilized the cluster’s entire memory and all of its processors. In task “Implementation of General Fracture Conceptual Models,” we used the MINC approach, a generalization of the double-porosity concept, to model flow through porous and fractured media. In this approach, flow within the matrix is described by subdividing the matrix into nested volumes, with flow occurring between adjacent nested matrix volumes as well as between the fractures and the outer matrix volume. We generalized Hooke’s law to a thermo-multi- poroelastic medium, and derived from the fundamental equations describing deformation of porous and fractured elastic media a momentum conservation equation for thermo-multi- poroelastic media. This equation is a generalization to multi-poroelastic media of the one derived in Task 3.0 for single porosity media. We describe two simulations to provide model verification and application examples. The first, one-dimensional consolidation of a double-porosity medium, is compared to an analytical solution. The second is a match of published results from the literature, a simulation of CO 2 injection into hypothetical aquifer-caprock systems.

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

Multiple Slater Determinants and Strong Spin-Fluctuations as Key Ingredients of the Electronic Structure of Electron- and Hole-Doped Pb 10− x Cu x (PO 4 ) 6 O

LK-99, with chemical formula Pb 10−x Cu x (PO 4 ) 6 O, was recently reported to be a room-temperature superconductor. While this claim has met with little support in a flurry of ensuing work, a variety of calculations (mostly based on density-functional theory) have demonstrated that the system possesses some unusual characteristics in the electronic structure, in particular flat bands. We have established previously that within DFT, the system is insulating with many characteristics resembling the classic cuprates, provided the structure is not constrained to the P3(143) symmetry nominally assigned to it. Here we describe the basic electronic structure of LK-99 within self-consistent many-body perturbative approach, quasiparticle self-consistent GW (QSGW) approximation and their diagrammatic extensions. QSGW predicts that pristine LK-99 is indeed a Mott/charge transfer insulator, with a bandgap gap in excess of 3 eV, whether or not constrained to the P3(143) symmetry. When Pb 9 Cu(PO 4 ) 6 O is hole-doped, the valence bands modify only slightly, and a hole pocket appears. However, two solutions emerge: a high-moment solution with the Cu local moment aligned parallel to neighbors, and a low-moment solution with Cu aligned antiparallel to its environment. In the electron-doped case the conduction band structure changes significantly: states of mostly Pb character merge with the formerly dispersionless Cu d state, and high-spin and low spin solutions once again appear. Thus we conclude that with suitable doping, the ground state of the system is not adequately described by a band picture, and that strong correlations are likely. Irrespective of whether this system class hosts superconductivity or not, the transition of Pb 10 (PO 4 ) 6 O from being a band insulator to Pb 9 Cu(PO 4 ) 6 O, a Mott insulator, and multi-determinantal nature of doped Mott physics make this an extremely interesting case-study for strongly correlated many-body physics.

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

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A Theoretical Study on Reaction Mechanisms and Kinetics of Thiophene Hydrodesulfurization over MoS 2 Catalysts

In the present work, thiophene hydrodesulphurization (HDS) over the Mo-edge, the S-edge, and the Mo-S connection edge of MoS 2 catalyst with 50% sulfur coverage was studied using first-principles based microkinetic modeling. Two parallel HDS routes, i.e., direct desulfurization (DDS) and hydrogenation (HYD) were taken into account. It has been found that the major reaction route of thiophene HDS on the Mo- and the Mo-S edges is temperature dependent. In the low temperature range of 500~600 K, the HYD route is dominant, leading to the C 4 H 8 formation. As the temperature increases, the DDS route becomes competitive with the HYD route. At the temperature above 650 K, the DDS route will be the dominant HDS reaction route on the Mo- and the Mo-S edges. While the DDS route that leads to the formation of C4H6 is the major thiophene HDS reaction route on the S-edge in the entire temperature range of 500~750 K. The microkinetic modeling results show the overall HDS activity on the S-edge is lower than it on the Mo- and the Mo-S edges. The Mo-S edge also provides a preferential reaction pathway, which facilitates 2-hydrothiophene migration from the Mo-edge to the S-edge, followed by remaining elementary steps with lower activation barriers in the DDS route. The work was financially supported by the National Natural Science Foundation of China (No. 21476012, 21571012, 21407007 and 91534201). The computing time was granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. Part of computing time was provided the National Energy Research Scientific Computing Center (NERSC). D. Mei is supported by the US Department of Energy, Office of Sciences, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences.

Thiophene, hydrodesulphurization, MoS2, DFT, micro↗
DOE OSTI2012

BF{sub 3} PIII modeling: Implantation, amorphisation and diffusion

In the race for highly doped ultra-shallow junctions (USJs) in complementary metal oxide semi-conductor (CMOS) technologies, plasma immersion ion implantation (PIII) is a promising alternative to traditional beamline implantation. Currently, no commercial technology computer aided design (TCAD) process simulator allows modeling the complete USJ fabrication process by PIII, including as-implanted dopant profiles, damage formation, dopant diffusion and activation. In this work, a full simulation of a p-type BF{sub 3} PIII USJ has been carried out. In order to investigate the various physical phenomena mentioned above, process conditions included a high energy/high dose case (10 kV, 5 Multiplication-Sign 10{sup 15} cm{sup -2}), specifically designed to increase damage formation, as well as more technology relevant implant conditions (0.5 kV) for comparison. All implanted samples were annealed at different temperatures and times. As implanted profiles for both boron and fluorine in BF{sub 3} implants were modeled and compared to Secondary Ion Mass Spectrometry (SIMS) measurements. Amorphous/crystalline (a/c) interface depths were measured by transmission electron microscopy (TEM) and successfully simulated. Diffused profiles simulations agreed with SIMS data at low thermal budgets. A boron peak behind the a/c interface was observed in all annealed SIMS profiles for the 10 kV case, indicating boron trapping from EOR defects in this region even after high thermal budgets. TEM measurements on the annealed samples showed an end of range (EOR) defects survival behind the a/c interface, including large dislocation loops (DLs) lying on (001) plane parallel to the surface. In the last part of this work, activation simulations were compared to Hall measurements and confirmed the need to develop a (001) large BICs model.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗