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DOE OSTI2020

Nonlinear fluorescence spectroscopy of layered perovskite quantum wells

Interest in layered organohalide perovskites is motivated by their potential for use in optoelectronic devices. In these systems, the smallest and largest quantum wells are primarily concentrated near the glass and air interfaces of a film, thereby establishing a gradient in the average values of the bandgaps. It has been suggested that this layered architecture promotes the funneling of electronic excitations through space in a manner similar to light-harvesting processes in photosynthetic antennae. Whereas energy and charge transfer are difficult to distinguish by conventional transient absorption techniques, it has recently been shown that these competing relaxation mechanisms may be separately targeted with nonlinear fluorescence (NLFL) and photocurrent “action spectroscopies.” Here, we present perturbative rate functions to describe NLFL experiments conducted on layered perovskite systems. The formulas reproduce the patterns of resonances observed in experimental measurements and show how signatures of energy transfer manifest in two-dimensional spectra. Overall, this work suggests that NLFL spectroscopy may be used to fully reveal the trajectories of electronic excitations by correlating ultrafast energy transfer pathways to fluorescence emission from the thickest quantum wells.

Ouyang, Zhenyu↗

DOE OSTI2012

Determinant quantum Monte Carlo study of the enhancement of d -wave pairing by charge inhomogeneity

Striped phases, in which spin, charge, and pairing correlations vary inhomogeneously in the CuO 2 planes, are a known experimental feature of cuprate superconductors, and are also found in a variety of numerical treatments of the two-dimensional Hubbard Hamiltonian. In this paper, we use determinant quantum Monte Carlo to show that if a stripe density pattern is imposed on the model, the d-wave pairing vertex is significantly enhanced. We attribute this enhancement to an increase in antiferromagnetic order which is caused by the appearance of more nearly half-filled regions when the doped holes are confined to the stripes. Here, we also observe a π-phase shift in the magnetic order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology

The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Progress Towards an Investigation of the MiniBooNE Low Energy Excess Using Neutral-Current Delta-Like Single Photons in MicroBooNE with Wire-Cell 3D Reconstruction Algorithms

This note presents progress towards a Neutral-Current (NC) Delta-like single photon search in MicroBooNE using Wire-Cell 3D reconstruction and pattern recognition algorithms. This analysis will help address the question of the MiniBooNE Low Energy Excess (LEE) [1]. The selections are similar to the previously published Pandora-based single photon selections [2] in many ways, but here we use independent reconstruction and selection tools and examine a larger phase space (including charged pions and multiple protons). In the future, we will significantly reduce systematic uncertainties via the use of constraining sideband observations in order to statistically test specific models of the MiniBooNE LEE.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

ASSESMENT OF IMPURITIES IN NP METAL USING DOUBLE-FOCUSING SF-ICP-MS

In the transmutation process, minor actinides such as neptunium, americium and curium obtained from spent nuclear fuel are incorporated into new fuel that can be placed into a fast reactor, where these elements fission into products with shorter half-lives which reduces the health and safety hazards [1]. In order to better understand the all the involved processes, fundamental physical properties of actinides should be investigated, and for that reason, high-purity materials need to be produced. One of the main challenges in characterizing these materials is the lack of pure metal available for study, and lack of analytical methods to determine the purity. Trans-uranic elements are challenging to study because of the need to be handled in specialized facilities, safeguards concerns and they are not easily purchased and/or produced. High-purity Np metal is being produced at the Materials and Fuels Complex (MFC) of Idaho National Laboratory (INL), in a process of direct oxide reduction developed by Squires and Lessing [2], with a target purity of 99.999%. The goal of this research is to develop methods to determine the impurities in the Np metal, with detection limits low enough to achieve this purity level. In this work, we have used several ICP-MS and ICP OES techniques, but the focus was the method development using a recently acquired Double-Focusing Sector Field Inductively Coupled Plasma Mass Spectrometer (SF-ICP-MS). To produce the Np metal, approximately 20 g of the neptunium oxide powder was calcined at 800 oC for 6 h in a magnesium oxide crucible, which is placed inside a stainless steel crucible, that goes into the Hot Uniaxial Press (HUP) furnace insert. After the calcining step, the Np oxide was mixed with approximately 9 g of calcium metal and 100 g of ultra-dry calcium chloride. The HUP furnace was heated in a ramp rate of 50 oC min -1 up to 1000 oC. When the reaction mixture reached 850 oC, a tantalum stirrer was activated at 100 rpm. After the tantalum stirrer was removed and the mixture cooled overnight, the MgO crucible was opened with a hammer and chisel to retrieve the Np metal button at the bottom of the reaction mixture [2]. Prior to the dissolution process, the surface contaminants of the sample were removed. The Np button was washed in 10 mL of ultra-pure water for 1 min, with a faint reaction observed on the surface, indicating the presence of Ca metal. The water-washed sample was placed in a tube with 2 M HCl for only 3 s, as a vigorous reaction in the button surface was observed. The leachates were saved for further analysis. The sample was then rinsed with ultra-pure water and air-dried prior to dissolution. The cleaned sample was placed in a PTFE beaker and 25 mL of 6 M HCl and 150 µL of 24 M HF were added. After 10 minutes of reaction, the beaker was placed on a hot plate for 1 h and 30 min, followed by the addition of 1 mL of 16 M HNO3 and allowed to react for a further 1 h and 20 min. The sample was removed from heat and 10 mL of HNO3 16 M was added to react with the HCl. The beaker was covered and left for overnight reaction, producing a solution with approximately 20 mL of final volume. A Quadrupole Inductively Coupled Plasma Mass Spectrometer (Q-ICP-MS, Perkin Elmer ELAN DRC II Q-ICP-MS) was used to obtain qualitative mass spectra for the dissolution blank, each of the leachates and the dissolved sample. In the water leachate spectrum mainly Ca and Mg were observed, while the acid wash had a similar peak pattern to the one observed for the Np metal sample, indicating that the process not only removed surface contamination, but also reacted with the sample itself. In the Np material spectrum, Ta and actinides were identified as candidates for major contaminants, as the most intense peaks corresponded to the mass-to-charge ratios of these elements. Minor contaminants included Al, Au, Ca, Cr, Fe, I, Na, Nb, Pb, Sn, Ti, Tl, V, Y. The presence of impurities in the material could have originated from several sources, such as the materials used for the casting process, the use of impure NpO2 or contamination of reagents and materials used for the analysis. Some of the isotopes listed as potential contaminants are susceptible to spectral interferences, so Double-Focusing SF-ICP-MS (Nu Instruments Attom ES HR-ICP-MS) was used for the quantitative analysis. For each isotope determined, several items were evaluated: raw signal of a blank solution, sensitivity and determination coefficient of calibration curves, possibility of interferences and comparison of results obtained for at least two resolving powers (RP): 300 and 4000. The evaluation of the signal in a blank solution can indicate if a spectral interference from the plasma gas and/or the solvent was successfully resolved (commonly observed for 52Cr+/40Ar12C+, for example). It is important to highlight that a signal reduction is expected when a higher RP is used, as the ion beam transmission is decreased by the use of na

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Assessment of Impurities in Neptunium Metal Using Double-Focusing SF-ICP-MS

In the transmutation process, minor actinides such as neptunium, americium and curium obtained from spent nuclear fuel are incorporated into new fuel that can be placed into a fast reactor, where these elements fission into products with shorter half-lives which reduces the health and safety hazards. In order to better understand the all the involved processes, fundamental physical properties of actinides should be investigated, and for that reason, high-purity materials need to be produced. One of the main challenges in characterizing these materials is the lack of pure metal available for study, and lack of analytical methods to determine the purity. Trans-uranic elements are challenging to study because of the need to be handled in specialized facilities, safeguards concerns and they are not easily purchased and/or produced. High-purity Np metal is being produced at the Materials and Fuels Complex (MFC) of Idaho National Laboratory (INL), in a process of direct oxide reduction developed by Squires and Lessing, with a target purity of 99.999%. The goal of this research is to develop methods to determine the impurities in the Np metal, with detection limits low enough to achieve this purity level. In this work, we have used several ICP-MS and ICP OES techniques, but the focus was the method development using a recently acquired Double-Focusing Sector Field Inductively Coupled Plasma Mass Spectrometer (SF-ICP-MS). To produce the Np metal, approximately 20 g of the neptunium oxide powder was calcined at 800 oC for 6 h in a magnesium oxide crucible, which is placed inside a stainless steel crucible, that goes into the Hot Uniaxial Press (HUP) furnace insert. After the calcining step, the Np oxide was mixed with approximately 9 g of calcium metal and 100 g of ultra-dry calcium chloride. The HUP furnace was heated in a ramp rate of 50 oC min -1 up to 1000 oC. When the reaction mixture reached 850 oC, a tantalum stirrer was activated at 100 rpm. After the tantalum stirrer was removed and the mixture cooled overnight, the MgO crucible was opened with a hammer and chisel to retrieve the Np metal button at the bottom of the reaction mixture. Prior to the dissolution process, the surface contaminants of the sample were removed. The Np button was washed in 10 mL of ultra-pure water for 1 min, with a faint reaction observed on the surface, indicating the presence of Ca metal. The water-washed sample was placed in a tube with 2 M HCl for only 3 s, as a vigorous reaction in the button surface was observed. The leachates were saved for further analysis. The sample was then rinsed with ultra-pure water and air-dried prior to dissolution. The cleaned sample was placed in a PTFE beaker and 25 mL of 6 M HCl and 150 µL of 24 M HF were added. After 10 minutes of reaction, the beaker was placed on a hot plate for 1 h and 30 min, followed by the addition of 1 mL of 16 M HNO3 and allowed to react for a further 1 h and 20 min. The sample was removed from heat and 10 mL of HNO3 16 M was added to react with the HCl. The beaker was covered and left for overnight reaction, producing a solution with approximately 20 mL of final volume. A Quadrupole Inductively Coupled Plasma Mass Spectrometer (Q-ICP-MS, Perkin Elmer ELAN DRC II Q-ICP-MS) was used to obtain qualitative mass spectra for the dissolution blank, each of the leachates and the dissolved sample. In the water leachate spectrum mainly Ca and Mg were observed, while the acid wash had a similar peak pattern to the one observed for the Np metal sample, indicating that the process not only removed surface contamination, but also reacted with the sample itself. In the Np material spectrum, Ta and actinides were identified as candidates for major contaminants, as the most intense peaks corresponded to the mass-to-charge ratios of these elements. Minor contaminants included Al, Au, Ca, Cr, Fe, I, Na, Nb, Pb, Sn, Ti, Tl, V, Y. The presence of impurities in the material could have originated from several sources, such as the materials used for the casting process, the use of impure NpO2 or contamination of reagents and materials used for the analysis. Some of the isotopes listed as potential contaminants are susceptible to spectral interferences, so Double-Focusing SF-ICP-MS (Nu Instruments Attom ES HR-ICP-MS) was used for the quantitative analysis. For each isotope determined, several items were evaluated: raw signal of a blank solution, sensitivity and determination coefficient of calibration curves, possibility of interferences and comparison of results obtained for at least two resolving powers (RP): 300 and 4000. The evaluation of the signal in a blank solution can indicate if a spectral interference from the plasma gas and/or the solvent was successfully resolved (commonly observed for 52Cr+/40Ar12C+, for example). It is important to highlight that a signal reduction is expected when a higher RP is used, as the ion beam transmission is decreased by the use of narrower slits

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

An LCA model for waste incineration enhanced with new technologies for metal recovery and application to the case of Switzerland

Highlights: • An enhanced process-based LCA model for MSWI is featured and applied in case study. • LCA modeling of recent technological developments for metal recovery from fly ash. • Net release from Swiss MSWI 133 kg CO{sub 2}-eq/tonne waste from attributional LCA perspective. • Net savings from a consequential LCA perspective reach up to 303 kg CO{sub 2}-eq/tonne waste. • Impacts according to ReCiPe and CExD show similar pattern to climate change. - Abstract: A process model of municipal solid waste incinerators (MSWIs) and new technologies for metal recovery from combustion residues was developed. The environmental impact is modeled as a function of waste composition as well as waste treatment and material recovery technologies. The model includes combustion with a grate incinerator, several flue gas treatment technologies, electricity and steam production from waste heat recovery, metal recovery from slag and fly ash, and landfilling of residues and can be tailored to specific plants and sites (software tools can be downloaded free of charge). Application of the model to Switzerland shows that the treatment of one tonne of municipal solid waste results on average in 425 kg CO{sub 2}-eq. generated in the incineration process, and 54 kg CO{sub 2}-eq. accrue in upstream processes such as waste transport and the production of operating materials. Downstream processes, i.e. residue disposal, generates 5 kg CO{sub 2}-eq. Savings from energy recovery are in the range of 67 to 752 kg CO{sub 2}-eq. depending on the assumptions regarding the substituted energy production, while the recovery of metals from slag and fly ash currently results in a net saving of approximately 35 kg CO{sub 2}-eq. A similar impact pattern is observed when assessing the MSWI model for aggregated environmental impacts (ReCiPe) and for non-renewable resource consumption (cumulative exergy demand), except that direct emissions have less and no relevance, respectively, on the total score. The study illustrates that MSWI plants can be an important element of industrial ecology as they provide waste disposal services and can help to close material and energetic cycles.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

An efficient computational framework for charge density estimation in twisted bilayer graphene

Electronic properties such as band structure and Fermi velocity in low-angle twisted bilayer graphene (TBG) are intrinsically dependent on the atomic structure. Rigid rotation between individual graphene layers provides an approximate description of the bilayer symmetry. Upon relaxation, in-plane displacement of the atoms in low angle TBG causes a change in the symmetry through the enlargement of the AB stacking regions and the reduction in size of AA and SP stacking regions. However, the effect of this in-plane relaxation on the charge density remains unexplored, because the necessary electronic structure calculations of such large supercells of low twist angle TBG are computationally infeasible. Therefore, we develop a computationally efficient framework that enables the exploration of the charge density symmetry of the low twist angle TBG. This framework is based on the Fourier representation of the charge density which presents high intensity Bragg peaks. Here we find that with the decrease of twist angle, low intensity satellite peaks also become apparent. Our framework incorporates these satellite peaks which reveals transformation of symmetry in the charge density distribution from high to low twist angle TBG. One striking outcome is the demonstration of the electron localization in the AA region of low twist angle TBG. Our framework helps to explain the effect of the atomistic relaxation on the charge density distribution and thus, it provides information about exotic electronic properties of low twist angle TBG at a low computational expense.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Revisiting Artifacts of Kohn–Sham Density Functionals for Biosimulation

We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn–Sham (KS) density functional theory functionals on simulation of small to medium-sized proteins in a vacuum. Aside from producing unphysical electron densities and total energies, the vanishing of the HOMO–LUMO gap associated with the unphysical charge delocalization leads to an unphysical low-energy spectrum and catastrophic failure of most popular solvers for the KS self-consistent field (SCF) problem. We apply a robust quasi-Newton SCF solver to obtain solutions for some of these difficult cases. The anatomy of the charge delocalization is revealed by the natural deformation orbitals obtained from the density matrix difference between the Hartree–Fock and KS solutions; the charge delocalization not only can occur between charged fragments (such as in zwitterionic polypeptides) but also involves neutral fragments. The vanishing-gap phenomenon and troublesome SCF convergence are both attributed to the unphysical KS Fock operator eigenspectra of molecular fragments (e.g., amino acids or their side chains). Analysis of amino acid pairs suggests that the unphysical charge delocalization can be partially ameliorated by the use of some range-separated hybrid functionals but not by semilocal or standard hybrid functionals. Last, we demonstrate that solutions without the unphysical charge delocalization can be located even for semilocal KS functionals highly prone to such defects, but such solutions have non-Aufbau character and are unstable with respect to mixing of the non-overlapping “frontier” orbitals. Caution should be exercised when unexpectedly small (or vanishing) HOMO–LUMO gaps and atypical SCF convergence patterns (e.g., oscillatory) are observed in KS DFT simulations in any context (bio or otherwise).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Double Quantum Dots with Quenched Charging Energy in PbTe Nanowires

Here, we investigate double quantum dots defined by electrostatic gating in semiconductor PbTe nanowire devices. We perform transport measurements to obtain charge stability diagrams distinguished by negligible separation between paired triple points and by the spin degeneracy of all transport resonances at zero magnetic field. We show a 4-fold splitting of high-bias stability diagram triangles in an applied magnetic field to illustrate the lifting of this spin degeneracy. We also identify patterns of narrow transport resonances in these high-bias triangles and discuss their possible physical origins. Our results represent a step toward the realization of PbTe-based spin qubits.

PbTe nanowire↗

DOE OSTI2016

Chaotic micromixer utilizing electro-osmosis and induced charge electro-osmosis in eccentric annulus

Efficient mixing is of significant importance in numerous chemical and biomedical applications but difficult to realize rapidly in microgeometries due to the lack of turbulence. We propose to enhance mixing by introducing Lagrangian chaos through electro-osmosis (EO) or induced charge electro-osmosis (ICEO) in an eccentric annulus. The analysis reveals that the created Lagrangian chaos can achieve a homogeneous mixing much more rapidly than either the pure EO or the pure ICEO. Our systematic investigations on the key parameters, ranging from the eccentricity, the alternating time period, the number of flow patterns in one time period, to the specific flow patterns utilized for the Lagrangian chaos creation, present that the Lagrangian chaos is considerably robust. The system can obtain a good mixing effect with wide ranges of eccentricity, alternating time period, and specific flow patterns utilized for the Lagrangian chaos creation as long as the number of flow patterns in one time period is two. As the electric field increases, the time consumption for homogenous mixing is reduced more remarkably for the Lagrangian chaos of the ICEO than that of the EO.

42 ENGINEERING↗

DOE OSTI2024

Design & Assembly of Atomically-Precise Quantum Materials & Devices (Final Report)

Atomic-layer honeycomb materials (Xene, where “X” may stand for a number of different elements) are a promising platform for new quantum states. When X is a heavier element such as tin (Sn) or bismuth (Bi), the edges of the honeycomb may conduct electron charge or spin without resistance - an effect that could persist up to room temperature in some cases. The type of edge states, and their robustness at room temperature, depend sensitively on (a) the substrate material that the Xene is sitting on; (b) out-of-plane buckling of the honeycomb structure; (c) the pattern of atoms or molecules sitting atop the honeycomb. This sensitivity suggests that Xene edge states could be tuned and rearranged to construct nanoscale electronic or spintronic devices. We report on theoretical progress in modeling the assembly and structure of Xenes, and their underlying substrates and overlaying atoms. Specifically, we model the stability of Sn atoms forming a single atomic layer (“stanene”), the stability and phase transitions

36 MATERIALS SCIENCE↗

NASA NTRS1976

An investigation of potential applications of OP-SAPS: Operational sampled analog processors

The impact of charge-coupled device (CCD) processors on future instrumentation was investigated. The CCD devices studied process sampled analog data and are referred to as OP-SAPS - operational sampled analog processors. Preliminary studies into various architectural configurations for systems composed of OP-SAPS show that they have potential in such diverse applications as pattern recognition and automatic control. It appears probable that OP-SAPS may be used to construct computing structures which can serve as special peripherals to large-scale computer complexes used in real time flight simulation. The research was limited to the following benchmark programs: (1) face recognition, (2) voice command and control, (3) terrain classification, and (4) terrain identification. A small amount of effort was spent on examining a method by which OP-SAPS may be used to decrease the limiting ground sampling distance encountered in remote sensing from satellites.

Parrish, E. A.↗

DOE OSTI2019

Supramolecular Tessellations by a Rigid Naphthalene Diimide Triangle

Tessellation of organic polygons though [π···π] and charge-transfer (CT) interactions offers a unique opportunity to construct supramolecular organic electronic materials with 2D topologies. Our approach to exploring the 3D topology of 2D tessellations of a naphthalene diimide-based molecular triangle (NDI-Δ) reveals that the 2D molecular arrangement is sensitive to the identity of the solvent and solute concentrations. Utilization of nonhalogenated solvents, combined with careful tailoring of the concentrations, results in NDI-Δ self-assembling though [π···π] interactions into 2D honeycomb triangular and hexagonal tiling patterns. Cocrystallization of NDI-Δ with tetrathiafulvalene (TTF) leads systematically to the formation of 2D tessellations as a result of superstructure-directing CT interactions. Different solvents lead to different packing arrangements. Using MeCN, CHCl 3 , and CH 2 Cl 2 , we identified three sets of cocrystals, namely CT-A, CT-B, and CT-C, respectively. Here, solvent modulation plays a critical role in controlling not only the NDI-Δ:TTF stoichiometric ratios and the molecular arrangements in the crystal superstructures, but also prevents the inclusion of TTF guests inside the cavities of NDI-Δ. Confinement of TTF inside the NDI-Δ cavities in the CT-A superstructure enhances the CT character with the observation of a broad absorption band in the NIR region. In the CT-B superstructure, the CHCl 3 lattice molecules establish a set of [Cl···Cl] and [Cl···S] intermolecular interactions, leading to the formation of a hexagonal grid of solvent in which NDI-Δ forms a triangular grid. In the CT-C superstructure, three TTF molecules self-assemble, forming a supramolecular isosceles triangle TTF-Δ, which tiles in a plane alongside the NDI-Δ, producing a 3 + 3 honeycomb tiling pattern of the two different polygons. Solid-state spectroscopic investigations on CT-C revealed the existence of an absorption band at 2500 nm, which on the basis of TDDFT calculations, was attributed to the mixed-valence character between two TTF • + radical cations and one neutral TTF molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins

A general formalism to compute configurational properties of proteins and other heteropolymers with an arbitrary sequence of charges and non-uniform excluded volume interaction is presented. A variational approach is utilized to predict average distance between any two monomers in the chain. The presented analytical model, for the first time, explicitly incorporates the role of sequence charge distribution to determine relative sizes between two sequences that vary not only in total charge composition but also in charge decoration (even when charge composition is fixed). Furthermore, the formalism is general enough to allow variation in excluded volume interactions between two monomers. Model predictions are benchmarked against the all-atom Monte Carlo studies of Das and Pappu [Proc. Natl. Acad. Sci. U. S. A. 110, 13392 (2013)] for 30 different synthetic sequences of polyampholytes. These sequences possess an equal number of glutamic acid (E) and lysine (K) residues but differ in the patterning within the sequence. Without any fit parameter, the model captures the strong sequence dependence of the simulated values of the radius of gyration with a correlation coefficient of R{sup 2} = 0.9. The model is then applied to real proteins to compare the unfolded state dimensions of 540 orthologous pairs of thermophilic and mesophilic proteins. The excluded volume parameters are assumed similar under denatured conditions, and only electrostatic effects encoded in the sequence are accounted for. With these assumptions, thermophilic proteins are found—with high statistical significance—to have more compact disordered ensemble compared to their mesophilic counterparts. The method presented here, due to its analytical nature, is capable of making such high throughput analysis of multiple proteins and will have broad applications in proteomic studies as well as in other heteropolymeric systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Three-dimensional fabrication and characterisation of core-shell nano-columns using electron beam patterning of Ge-doped SiO{sub 2}

A focused electron beam in a scanning transmission electron microscope (STEM) is used to create arrays of core-shell structures in a specimen of amorphous SiO{sub 2} doped with Ge. The same electron microscope is then used to measure the changes that occurred in the specimen in three dimensions using electron tomography. The results show that transformations in insulators that have been subjected to intense irradiation using charged particles can be studied directly in three dimensions. The fabricated structures include core-shell nano-columns, sputtered regions, voids, and clusters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Photoelectron Spectroscopy and Computational Study on Microsolvated [B 10 H 10 ] 2– Clusters and Comparisons to Their [B 12 H 12 ] 2– Analogues

Microhydrated closo-Boranes have attracted great interests due to their superchaotropic activity related to well-known Hofmeister effect and important applications in biomedical and battery fields. In this work, we report a combined negative ion photoelectron spectroscopy and quantum chemical investigation on hydrated closo-decaborate clusters [B 10 H 10 ] 2- ·nH 2 O (n = 1 – 7) with a direct comparison to their analogues [B 12 H 12 ] 2- ·nH 2 O and free water clusters. A single H 2 O molecule is found sufficient to stabilize the intrinsically unstable [B 10 H 10 ] 2- dianion. The first two water molecules strongly interact with the solute forming B-H···H-O dihydrogen bonds while additional water molecules show substantially reduced binding energies. Unlike [B 12 H 12 ] 2- ·nH 2 O possessing highly structured water network with the attached H 2 O molecules arranged in a unified pattern by maximizing B-H···H-O dihydrogen bonding, distinct structural arrangements of the water clusters within [B 10 H 10 ] 2– ·nH 2 O are achieved with the water cluster networks from trimer to heptamer resembling free water clusters. Such a distinct difference arises from the variations in size, symmetry, and charge distributions between these two dianions. Finally, the present finding again confirms the structural diversity of hydrogen-bonding networks in microhydrated closo-boranes and enrich our understanding of aqueous borate chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Note: Electrochemical cell for in operando X-ray diffraction measurements on a conventional X-ray diffractometer

Electrochemical in operando X-ray diffraction (XRD) is a powerful method to analyze structural changes of energy storage materials while inserting/de-inserting charge carriers, such as Li- or Na-ions, into/from a host structure. The design of an XRD in operando cell is presented, which enables the use of thin (6 μm) aluminum foil as X-ray window as a non-toxic alternative to conventional beryllium windows. Owing to the reduced thickness, diffraction patterns and their changes during cycling can be observed with excellent quality, which was demonstrated for two cathode materials for sodium-ion batteries in a half-cell set-up, P2-Na{sub 0.7}MnO{sub 2} and Na{sub 2.55}V{sub 6}O{sub 16} ⋅ 0.6H{sub 2}O.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗