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DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Abstract Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.

Bukowski, Brandon C.↗

DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Bukowski, Brandon C.↗

DOE OSTI2022

Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics

We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. Here, we also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Self-assembly and structural relaxation in a model ionomer melt

Molecular dynamics simulations are used to understand the self-assembly and structural relaxation in ionomer melts containing less than 10% degree of ionization on the backbone. We study the self-assembly of charged sites and counterions that show structural ordering and agglomeration with a range of structures that can be achieved by changing the dielectric constant of the medium. The intermediate scattering function shows a decoupling of charge and counterion relaxation at longer length scales for only high dielectric constant and at shorter length scales for all dielectric constants. Finally, the slow structural decay of counterions in the strongly correlated ionomer system closely resembles transport properties of semi-flexible polymers.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Advanced Structured Adsorbent Architectures for Transformative Carbon Dioxide Capture Performance (Final Report)

Svante is a world leader at using solid sorbents for low-cost Carbon Dioxide (CO 2 ) capture, a technology which is recognized as critical in meeting the dual mandates of energy security/reliability and the mitigation of man-made CO 2 emissions. Svante has been developing proprietary adsorbent material compositions, forming them into structured laminates, developing and optimizing process cycles, and system design for efficient capture of CO 2 from post-combustion flue gases of thermal power plants and industrial facilities. The deployment of first-generation CO 2 capture technology has been significantly hampered by high costs and energy penalties, among other barriers. Second generation CO 2 capture technologies (including the Mark I variant of Svante’s Veloxotherm™ adsorption-based technology), utilizing single adsorbent architecture, show promise for reducing the barriers to deploying CO 2 capture plants in commercially meaningful numbers. The objective of this project was to evaluate the Recipient’s transformational (Mark-II) VeloxoTherm™ Technology via the development and bench-scale testing of an advanced structured adsorbent, including novel Bi-layer, laminated adsorbent structures and segmented beds. Svante selected, synthesized, and characterized tailored solid adsorbents for computational modeling, advanced structured adsorbent development, process simulations, and dynamic bench scale (~1-10 kg/day CO 2 captured) testing using an existing single-bed VeloxoTherm™ Station (VTS) coupled with a natural gas-fired boiler. Segmented beds used the in-house, multi-bed Process Demonstration Unit (PDU) to demonstrate key performance indicators (KPIs), such as recovery, product purity, regeneration energy, and the integrated system's productivity in lifetime analysis. Segmented beds were used at a 1 tonne per day (TPD) unit at an industrial site to provide bench-scale validation of performance in an industrial setting. Svante was developing and optimizing the post-combustion CO 2 adsorption technology architectures, including the Bi-layer and segmented laminated adsorbent structure design, integrated rapid cycle temperature swing adsorption (RC-TSA) cycle, flow path architecture, and adsorbent bed construction and packaging (including gas porting) to progress towards achievement of DOE’s Transformational CO 2 Capture goals of 95% CO 2 purity and a cost of electricity at least 30% lower than a supercritical Pulverized Coal (PC) power plant with CO 2 capture, or approximately $30 per tonne of CO 2 captured ready for demonstration by 2030. The main requirements to reach the DOE target cost of carbon capture below $30/MT using Rapid-Cycling Temperature Swing Adsorption (RC-TSA) are as follows: (1) Increased capacity at different CO 2 concentrations, (2) Increased sorbents cycle life, (3) Increased O 2 resistance, and (4) Decreased steam requirement to extract 1 kg of CO 2 .

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Heat- and light-induced transformations of Yb trapping sites in an Ar matrix

The low-lying electronic states of Yb isolated in a solid Ar matrix grown at 4.2 K are characterized through absorption and emission spectroscopy. Yb atoms are found to occupy three distinct thermally stable trapping sites labeled “red,” “blue,” and “violet” according to the relative positions of the absorption features they produce. Classical simulations of the site structure and relative stability broadly reproduced the experimentally observed matrix-induced frequency shifts and thus identified the red, blue, and violet sites as due to respective single substitutional (SS), tetravacancy (TV), and hexavacancy (HV) occupation. Prolonged excitation of the {sup 1}S → {sup 1}P transition was found to transfer the Yb population from HV sites into TV and SS sites. The process showed reversibility in that annealing to 24 K predominantly transferred the TV population back into HV sites. Population kinetics were used to deduce the effective rate parameters for the site transformation processes. Experimental observations indicate that the blue and violet sites lie close in energy, whereas the red one is much less stable. Classical simulations identify the blue site as the most stable one.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Investigation of proton damage in III-V semiconductors by optical spectroscopy

We studied the damage produced by 2 MeV proton radiation on epitaxially grown InGaP/GaAs structure by means of spatially resolved Raman and photoluminescence (PL) spectroscopy. The irradiation was performed parallel to the sample surface in order to determine the proton penetration range in both compounds. An increase in the intensity of longitudinal optical phonons and a decrease in the luminescence were observed. We associate these changes with the creation of defects in the damaged region, also responsible for the observed change of the carrier concentration in the GaAs layer, determined by the shift of the phonon-plasmon coupled mode frequency. From the spatially resolved profile of the PL and phonon intensities, we obtained the proton range in both materials and we compared them with stopping and range of ions in matter simulations. The comparison between the experimentally obtained proton range and simulations shows a very good agreement for GaAs but a discrepancy of 20% for InGaP. This discrepancy can be explained in terms of limitations of the model to simulate the electronic orbitals and bonding structure of the simulated compound. In order to overcome this limitation, we propose an increase in 40% in the electronic stopping power for InGaP.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

Molecular reordering processes on ice (0001) surfaces from long timescale simulations

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 μs at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Half-Metallic and Half-Semiconductor Gaps in Cr-Based Chalcogenides: DFT + U Calculations

Using full-potential linear-augmented plane waves plus local orbitals (FP-LAPW) method, within the generalized gradient approximation (GGA) and GGA + U (Hubbard Coulomb onsite correction) as well as the modified Becke-Johnson approach (mBJ-GGA and mBJ-GGA + U), we have carried out a systematic investigation of the structural, electronic, and magnetic properties of CrS, CrSe, and CrTe compounds in two competing phases: the zinc-blende (ZB) and wurtzite (WZ) structures. We obtained half-metallic (HM) gaps of 1.35 (2.32), 1.65 (2.49), and 1.52 (1.80) for the CrS, CrSe, and CrTe compounds, respectively, in the ZB phase within the GGA + U (mBJ-GGA + U) approach. The HM gaps are 1.78, 2.11, and 1.53 for CrS, CrSe, and CrTe compounds, respectively, in the WZ phase using the GGA + U. Notably, the CrSe and CrTe using the mBJ-GGA + U approach are a half-semiconductor (HSC) in the WZ phase. The HSC gaps are 0.94 and 0.25 eV for CrSe and CrTe compounds, respectively, while CrS has a HM gap of 2.30 eV. We observed a HSC-to-HM transition for the CrSe and CrTe crystal structures on application of strain. The CrS, CrSe, and CrTe compounds have a total magnetic moment of 4.0 µ{sub B} per formula unit with the magnetization predominantly from the Cr ion. The main features observed from the density of states and strain evolution should motivate further experimental exploration on the possible application of the CrS, CrSe, and CrTe compounds for spintronic applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

High-gradient two-beam electron accelerator

The main goal for this project was to design, build, and evaluate a detuned-cavity, collinear, two-beam accelerator structure. Testing was to be at the Yale University Beam Physics Laboratory, under terms of a sub-grant from Omega-P to Yale. Facilities available at Yale for this project include a 6-MeV S-band RF gun and associated beam line for forming and transporting a ~1 A drive beam , a 300 kV beam source for use as a test beam, and a full panoply of laboratory infrastructure and test equipment. During the first year of this project, availability and functionality of the 6-MeV drive beam and 300 kV test beam were confirmed, and the beam line was restored to a layout to be used with the two-beam accelerator project. Major efforts during the first year were also focused on computational design and simulation of the accelerator structure itself, on beam dynamics, and on beam transport. Effort during the second year was focussed on building and preparing to test the structure, including extensive cold testing. Detailed results from work under this project have been published in twelve archival journal articles, listed in Section IV of the technical report.

43 PARTICLE ACCELERATORS↗

DOE OSTI2019

Propagation of Degradation-Induced Defects in Zeolitic Imidazolate Frameworks

Isolated defects induced by water and acid gases have been extensively characterized in ZIF-8, a prototypical metal–organic framework material, yet there is little understanding regarding how these single bond-breaking events lead to the structural amorphization observed after prolonged experimental exposure in acidic environments. We use density functional theory calculations to provide the first analysis of defect propagation in a zeolitic imidazolate framework (ZIF) material. Given a single bond-breaking event (the first step in the formation of any defect state), we exhaustively explore the energetics of subsequent defect states and find strong preference for additional bond-breaking located adjacent to the previous defect in both two-defect and three-defect systems. This series of favorable reaction energies is more exothermic when we replace water with sulfuric acid as a protonating agent, in agreement with experimental observations that ZIF-8 degradation is accelerated in humid acid gas environments. To offer initial insights into experimental signatures of defect propagation, we compare the simulated powder pattern in structures at varying levels of defect concentrations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Simulating a Mesoscale Convective System Using WRF with a New Spectral Bin Microphysics: Part 1: Hail vs Graupel

A modified Fast Spectral Bin Microphysics scheme (FSBM-2) embedded into the Weather Research and Forecasting Model (WRF) is used to simulate a mesoscale deep convective system observed during the Midlatitude Continental Convective Clouds Experiment (MC3E). FSBM-2 uses modified source codes as compared to the current FSBM (FSBM-1). In contrast to FSBM-1, FSBM-2 can simulate hail of several cm in diameter and includes additional processes such as spontaneous breakup of raindrops and aerosol regeneration by drop evaporation. It is shown that allowing large hail particles of diameters exceeding about 1 cm substantially increases the agreement between the simulated and observed squall-line structures both in the convective and stratiform regions. In contrast, if graupel particles are used to represent high-density hydrometeors in convective areas, the ratio of convective-to-stratiform areas diverges from the ratio seen in observations and maximum radar reflectivities are substantially underestimated. Analysis of snow size distributions in the stratiform area shows an important link between the ice crystals formed by homogeneous freezing in the convective area to ice particle number concentration in the stratiform region. Simulated raindrop size distributions in the stratiform area below the melting level from FSBM-2 show a good agreement with observations. The regeneration of CCN by droplet evaporation and detrainment of these CCN to the stratiform region increases the concentration of CCN there up to 8-9 km altitude; the additional CCN penetrate clouds and produce new droplets, leading to some convection intensification. Key words: Mesoscale convective systems (MCS), squall lines, spectral bin microphysics, large hail, in-cloud nucleation, size distributions of hydrometeors in MCS.

Shpund, Kobby↗

DOE OSTI2016

Ab initio X-ray absorption modeling of Cu-SAPO-34: Characterization of Cu exchange sites under different conditions

Copper-exchanged SAPO-34 (Cu-SAPO-34) provides excellent catalytic activity and hydrothermal sta-bility in the selective catalytic reduction (SCR) of NOxby using NH3as a reductant. Here, we find that the6-membered ring (6MR) site is the most energetically favorable for a Cu+ion while the 8-memberedring (8MR) sites are less favorable by about 0.5 eV with respect to the 6MR site in Cu-SAPO-34. Uponadsorption of molecular species (H2O, O, OH, O2), the energy differences between Cu in the 8MR and 6MRsites decreases and almost disappears. Further, a thermodynamic phase diagram study shows that a Cu+ion bound to a single H2O molecule is the most stable species at low oxygen potential values while aCu2+ion bound to 2 OH species is more stable when the oxygen chemical potential is sufficiently high. Bycomparing Cu K-edge XANES between Cu-SSZ-13 and Cu-SAPO-34 with Cu in different oxidation states,we conclude that it is difficult to differentiate the simulated XANES of Cu in these structures at a givenoxidation state. By studying the Cu K-edge XANES of several favorable structures in Cu-SAPO-34 in thepresence of adspecies, the simulated XANES results capture the real trend of the edge shift with oxidationstate and gives new insights into the experimentally determined XANES of Cu-SAPO-34 obtained understandard SCR conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Molecular mechanism of biased signaling at the kappa opioid receptor

The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

A systematic multiscale modeling and experimental approach to protect grain boundaries in magnesium alloys from corrosion

A multiscale modeling Internal State Variable (ISV) constitutive model was developed that captures the fundamental structure-property relationships. The macroscale ISV model used lower length scale simulations (Butler-Volmer and Electronics Structures results) in order to inform the ISVs at the macroscale. The chemomechanical ISV model was calibrated and validated from experiments with magnesium (Mg) alloys that were investigated under corrosive environments coupled with experimental electrochemical studies. Because the ISV chemomechanical model is physically based, it can be used for other material systems to predict corrosion behavior. As such, others can use the chemomechanical model for analyzing corrosion effects on their designs.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The Mira–Titan Universe – IV. High-precision power spectrum emulation

Modern cosmological surveys are delivering data sets characterized by unprecedented quality and statistical completeness; this trend is expected to continue in the future as new ground- and space-based surveys come online. In order to maximally extract cosmological information from these observations, matching theoretical predictions are needed. At low redshifts, the surveys probe the non-linear regime of structure formation where cosmological simulations are the primary means of obtaining the required information. The computational cost of sufficiently resolved large-volume simulations makes it prohibitive to run very large ensembles. Nevertheless, precision emulators built on a tractable number of high-quality simulations can be used to build very fast prediction schemes to enable a variety of cosmological inference studies. We have recently introduced the Mira–Titan Universe simulation suite designed to construct emulators for a range of cosmological probes. This gravity-only set of simulations covers the standard six cosmological parameters {ω m , ω b , σ 8 , $h, n_s, w_0$} and, in addition, includes massive neutrinos and a dynamical dark energy equation of state {ω ν , $w_a$}. In this paper, we present the final emulator for the matter power spectrum based on 111 cosmological simulations, each covering a (2.1 Gpc) 3 volume and evolving 3200 3 particles. In this work, an additional set of 1776 lower resolution simulations and TimeRG perturbation theory results for the power spectrum are used to cover scales straddling the linear to mildly non-linear regimes (maximum wavenumber $\textit{k}$ = 5 Mpc –1 ). The emulator provides predictions at the 2–3 percent level of accuracy over a wide range of cosmological parameters and is publicly released as part of this paper.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Quasi-periodic Oscillations in Flares and Coronal Mass Ejections Associated with Magnetic Reconnection

We propose a mechanism for quasi-periodic oscillations of both coronal mass ejections (CMEs) and flare loops as related to magnetic reconnection in eruptive solar flares. We perform two-dimensional numerical MHD simulations of magnetic flux rope eruption, with three different values of the global Lundquist number. In the low Lundquist number run, no oscillatory behavior is found. In the moderate Lundquist number run, on the other hand, quasi-periodic oscillations are excited both at the bottom of the flux rope and at the flare loop top. In the high Lundquist number run, quasi-periodic oscillations are also excited; in the meanwhile, the dynamics become turbulent owing to the formation of multiple plasmoids in the reconnection current sheet. In high and moderate Lundquist number runs, thin reconnection jets collide with the flux rope bottom or flare loop top and dig them deeply. Steep oblique shocks are formed as termination shocks where reconnection jets are bent (rather than decelerated) in the horizontal direction, resulting in supersonic backflows. The structure becomes unstable, and quasi-periodic oscillations of supersonic backflows appear at locally confined high-beta regions at both the flux rope bottom and flare loop top. We compare the observational characteristics of quasi-periodic oscillations in erupting flux ropes, post-CME current sheets, flare ribbons, and light curves with corresponding dynamical structures found in our simulation.

79 ASTRONOMY AND ASTROPHYSICS↗