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Polarity governs atomic interaction through two-dimensional materials
The objective of this project is to develop two-dimensional material-based layer transfer (2DLT) for high-efficiency, low-cost III-V solar cells. More specifically, in short term, the team will develop 2DLT for cost-cost, high-throughput GaAs single-junction solar cells. The team will develop ultraclean high yield graphene transfer on GaAs and optimize the remote homoepitaxy process to obtain dislocation-free single-crystalline GaAs on graphene whose crystalline quality is identical to that of the GaAs wafer [1,2]. The team will develop the 2DLT process for a solar cell with highest achievable efficiency. The team will also strive to target GaAs solar cells with efficiency of 25~29% before and after the transfer, and reuse the substrate multiple times without CMP by damage-free transfer process enabled by 2DLT. Our team is partnered with industrial collaborators to obtain World record efficiency of flexible GaAs solar cells. Once the concept is fully realized for the GaAs solar cells, the team will expand the concept for multiple-junction solar cell targeting 35% efficiency with the 2DLT process in other projects.
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions
Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.
Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole–dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation
Aggregation behavior of cyclic polypeptoids bearing zwitterionic end-groups in methanol has been studied using a combination of experimental and simulation techniques. Here, the data from SANS and cryo-TEM indicate that the solution contains small clusters of these cyclic polypeptoids, ranging from a single polypeptoid chain to small oligomers, while the linear counterpart shows no cluster formation. Atomistic molecular dynamics simulations reveal that the driving force for this clustering behavior is due to the interplay between the effective repulsion due to the solvation of the dipoles formed by the charged end-groups in each polypeptoid chain and the attractive forces due to dipole–dipole interactions and the solvophobic effect.
Probing hydrogen and halogen-oxo interactions in uranyl coordination polymers: a combined crystallographic and computational study
Four uranyl compounds containing either benzoic acid ( 1 ), m -chlorobenzoic acid ( 2 ), m -bromobenzoic acid ( 3 ), or m -iodobenzoic acid ( 4 ) are described, and the latter two compounds are used to probe non-covalent interaction strengths via structural, vibrational, and computational means.
Evaluation of Attractive Interactions in the Second Coordination Sphere of Iron Complexes Containing Pendant Amines
The interactions between pendant amines in the second coordination sphere and ligands in the first coordination sphere are important for understanding the structures and reactivity of complexes containing PR2NR'2 ligands, which have been shown to be highly active H2 oxidation/production catalysts. A series of [Fe(PPh2NBn2)2(X)(Y)]n+ complexes have been prepared and structurally characterized. These complexes have two different ligands with which the pendant amines of the diphosphine ligand can interact. The solid state structure of cis-Fe(PPh2NBn2)2Cl2 reveals that the six-membered rings adjacent to the P atoms are in a boat confirmation, resulting in close N•••P distances that suggests the P atoms have a greater affinity for the lone pair of electrons on the N atom than chloride ligands. Similarly, boat conformations are observed for both rings adjacent to the hydride ligands of trans-[HFe(PPh2NBn2)2(CH3CN)]+ and trans-HFe(PPh2NBn2)2Cl, resulting in short N•••H distances. Spectroscopic and computational studies of trans-[HFe(PPh2NBn2)2(CO)]+, trans-[HFe(PPh2NBn2)(PPh2NBn2H)(CO)]2+, and trans-[HFe(PPh2NBn2)2(H2)]+ indicate the complexes are more stable when the pendant amines in boat conformations are adjacent to the hydride ligand. These data suggest an attractor ordering of H- > CO > H2 > PR3 > Cl- ~ CH3CN. This work was supported by the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the U.S. DOE. Computations were performed using the Cascade supercomputer at the Environmental Molecular Sciences Laboratory, a National Scientific User Facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL.
Synthesis of a series of M( ii ) (M = Mn, Fe, Co) chloride complexes with both inter- and intra-ligand hydrogen bonding interactions
Hydrogen bonding networks are vital for metallo-enzymes to function; however, modeling these systems is non-trivial. The development of 1st-row transition metal chloride complexes with intramolecular hydrogen-bonding interactions are detailed herein.
Communication: The origin of many-particle signals in nonlinear optical spectroscopy of non-interacting particles
Nonlinear spectroscopy signals detected by fluorescence from dilute samples of N non-interacting molecules are usually adequately described by simply multiplying the single molecule response by N . Here, we show that signals that scale with higher powers of N are generated by the joint detection of several particles. This can be accomplished by phase sensitive detection such as phase cycling, photo-acoustic modulation, or by Hanbury-Brown Twiss photon coincidence. Such measurements can dissect the ensemble according to the number of excited particles.
On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice
The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water. Published by AIP Publishing.
Study of self-interaction errors in density functional predictions of dipole polarizabilities and ionization energies of water clusters using Perdew-Zunger and locally scaled self-interaction corrected methods
Here, we studied the effects of self-interaction error (SIE) on the static dipole polarizabilities of water clusters modelled with three increasingly sophisticated, non-empirical density functional approximations (DFAs), viz. the local spin density approximation (LDA), the Perdew-Burke-Ernzherof (PBE) generalized-gradient approximation (GGA), and the strongly constrained and appropriately normed (SCAN) meta-GGA, using the Perdew-Zunger self-interaction-correction (PZ-SIC) energy functional in the Fermi-Lowdin orbital SIC (FLO-SIC) framework. Our results show that while all three DFAs overestimate the cluster polarizabilities, the description systematically improves from LDA to PBE to SCAN. The self-correlation free SCAN predicts polarizabilities quite accurately with a mean absolute error (MAE) of 0.58 Bohr 3 with respect to coupled cluster singles and doubles (CCSD) values. Removing SIE using PZ-SIC correctly reduces the DFA polarizabilities, but over-corrects, resulting in underestimated polarizabilities in SIC-LDA, -PBE, and -SCAN. Finally, we applied a recently proposed local-scaling SIC (LSIC) method using a quasi self-consistent scheme and using the kinetic energy density ratio as an iso-orbital indicator. The results show that the LSIC polarizabilities are in excellent agreement with mean absolute error of 0.08 Bohr 3 for LSIC-LDA and 0.06 Bohr 3 for LSIC-PBE with most recent CCSD polarizabilities. Likewise, the ionization energy estimates as an absolute of highest occupied energy eigenvalue predicted by LSIC are also in excellent agreement with CCSD(T) ionization energies with MAE of 0.4 eV for LSIC-LDA and 0.04 eV for LSIC-PBE. The LSIC-LDA predictions of ionization energies are comparable to the reported GW ionization energies while the LSIC-PBE ionization energies are more accurate than reported GW results.
The ion-gas-neutral interactions with surfaces-2 (IGNIS-2) facility for the study of plasma–material interactions
The Ion-Gas-Neutral Interactions with Surfaces-2 (IGNIS-2) surface science facility has been designed at the Pennsylvania State University with the specific purpose of enabling experiments to study plasma–material interactions. This in situ surface modification and characterization facility consists of multiple reconfigurable substations that are connected through a central transfer chamber. This fully connected vacuum system ensures that the physical and chemical properties of samples are not altered between surface modification and analysis. The modification techniques in IGNIS-2 include a low-energy (<300 eV), high-flux (up to 1016 cm−2 s−1) broad-beam ion source, a liquid metal dropper, a lithium injection system, an RF sputter source, and an evaporator. Its characterization techniques include charged particle-based techniques, such as low-energy ion scattering (enabled by two <5 keV ion sources) and x-ray photoelectron spectroscopy, and photon and light-based techniques, such as x-ray fluorescence, multi-beam optical stress sensors, and optical cameras. All of these techniques can be utilized up to mTorr pressures, allowing both in situ and in operando studies to be conducted. Results are presented on lithium wetting experiments of argon-irradiated tungsten-based composites, surface stress measurements of tungsten films during deuterium ion irradiation, and temperature-programmed desorption of deuterium-irradiated graphite to demonstrate the in situ capabilities of this new facility.
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilius strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.
Structural analyses of an RNA stability element interacting with poly(A)
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Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues
Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptor cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.
The interaction of an atmospheric pressure plasma jet with liquid water: dimple dynamics and its impact on crystal violet decomposition
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Interactions between atmospheric pressure plasmas and metallic catalyst particles in packed bed reactors
Atmospheric-pressure plasmas sustained in packed bed reactors (PBRs) are being investigated for chemical conversion of gases and pollution control. Metallic catalysts added to the surfaces of the dielectric beads of PBRs can increase the energy efficiency and selectivity of chemical processes by reducing operating temperature and providing additional reaction pathways. In this paper, results from a computational investigation of plasma surface interactions between micron-scale metallic catalysts and humid-air plasmas in PBRs are discussed. Here we found that high plasma density regions form in the proximity of the metallic catalysts. These higher-density plasma regions were confirmed experimentally using ICCD imaging. The intense plasmas result from geometrical electric field enhancement and redistribution of charges within the conductive particles, leading to further enhancement. The high electric field at the triple points of the catalysts can produce electric field emission of electrons, which provides a pre-ionization source or additional source of electrons. These regions of high electric field and sources of electrons guide discharges towards the catalysts and increases fluxes of excited species, ions, electrons and photons to their surfaces. These fluxes are focused primarily at the triple points between the metal, dielectric and gas. As a result, the catalyst is locally heated, which could lead to further increased rates of thermocatalytic reactions on the surface. Surface roughness of the metal inclusions can lead to additional electric field enhancement, which changes the character of the discharges in the vicinity of the catalysts while reducing breakdown voltage.
The interaction of the ITER first wall with magnetic perturbations
Mitigation of the multiple risks associated with disruptions and runaway electrons in tokamaks involves competing demands. Success requires that each risk be understood sufficiently that appropriate compromises can be made. Here the focus is on the interaction of short timescale magnetic-perturbations with the structure in ITER that is closest to the plasma, blanket modules covered by separated beryllium tiles. The effect of this tiled surface on the perturbations and on the forces on structures is subtle. Indeterminacy can be introduced by tile-to-tile shorting. A determinate subtlety is introduced because electrically separated tiles can act as a conducting surface for magnetic perturbations that have a normal component to the surface. A practical method for including this determinate subtlety into plasma simulations is developed. The shorter the timescales and the greater the localization, particularly in the toroidal direction, the more important the magnetic effects of the tiles become.
Towards efficient density functional theory calculations without self-interaction: The Fermi-Löwdin orbital self-interaction correction
The Fermi-Löwdin orbital (FLO) approach to the Perdew-Zunger self-interaction correction (PZ-SIC) to density functional theory (DFT) is described and an improved approach to the problem of optimizing the Fermi-orbitals in order to minimize the DFT-SIC total energy is introduced. To illustrate the use of the FLO-SIC method, results are given for several applications involving problems where self-interaction errors are pronounced.