Search NASA⌕ Search

SEARCH · Search NASA

Results for “Capping”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Climate change impact on residual contaminants under sustainable remediation

This study investigates the potential impact of climate change on residual contaminants in vadose zones and groundwater. We assume that the effect of climate changes can be represented by perturbations in the natural recharge through the aquifer system. We perform numerical modeling of unsaturated/saturated flow and transport and consider different performance metrics: contaminant concentrations at observation wells and contaminant export at the site's boundary. We evaluate the effect of increasing and decreasing recharge as well as the impact of potential failure of surface capping structures employed to immobilize vadose zone contaminants. Our approach is demonstrated in a real case study by simulating transport of non-reactive radioactive tritium at the U.S. Department of Energy's Savannah River Site. Results show that recharge changes significantly affect well concentrations: after an initial slight dilution we identify a significant concentration increase at different observation wells some years after the recharge increase and/or the cap failure, as a consequence of contaminants' mobilization. This effect is generally emphasized and occurs earlier as the recharge increases. Under decreased aquifers' recharge the concentration could slightly increase for some years, due to a decrease of dilution, depending on the magnitude of the negative recharge shift. We identify trigger levels of recharge above which the concentration/export breakthrough curves and the time of exceedance of the Maximum Contaminant Level for tritium are remarkably affected. Moreover, we observe that the contaminant export at the control plane, identified as the risk pathway to the downgradient population, may only be minimally affected by shifts in the natural recharge regime, except for some extreme cases. We conclude that more frequent sampling and in-situ monitoring near the source zone should be adopted to better explain concentrations' anomalies under changing climatic conditions. Moreover, the maintenance of the cap is critical not only to sequester residual contaminants in the vadose zone, but also to reduce the uncertainty associated with future precipitation changes. Finally, realistic flow and transport simulations achieved through proper calibration processes, rather than conservative modeling, should be adopted to identify non-trivial trade-offs which enable better allocation of resources towards reducing uncertainty in decision making.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement

Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain. Here we report two new crystal forms of QFR, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles. QFR crystals grown from the lipid cubic phase processed as P1, merged to 7.5 Å resolution, and exhibited crystal packing similar to previous crystal forms. Crystals grown from dodecyl maltoside micelles processed as P21, merged to 3.35 Å resolution, and displayed a unique crystal packing. Furthermore, this latter crystal form provides the first view of the E. coli QFR active site without a dicarboxylate ligand. Instead, an unidentified anion binds at a shifted position. In one of the molecules in the asymmetric unit, this is accompanied by rotation of the capping domain of the catalytic subunit. In the other molecule, this is associated with loss of interpretable electron density for this same capping domain. Analysis of the structure suggests that the ligand adjusts the position of the capping domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Synthesis and catalytic activity of the metastable phase of gold phosphide

Recently, transition metal phosphides have found new applications as catalysts for the hydrogen evolution reaction that has generated an impetus to synthesize these materials at the nanoscale. In this work, Au{sub 2}P{sub 3} was synthesized utilizing the high temperature decomposition of tri-n-octylphosphine as a source of elemental phosphorous. Gold nanorods were used as morphological templates with the aim of controlling the shape and size of the resulting gold phosphide particles. We demonstrate that the surface capping ligand of the gold nanoparticle precursors can influence the purity and extent to which the gold phosphide phase will form. Gold nanorods functionalized with 1-dodecanethiol undergo digestive ripening to produce discrete spherical particles that exhibit reduced reactivity towards phosphorous, resulting in low yields of the gold phosphide. In contrast, gold phosphide was obtained as a phase pure product when cetyltrimethylammonium bromide functionalized gold nanorods are used instead. The Au{sub 2}P{sub 3} nanoparticles exhibited higher activity than polycrystalline gold towards the hydrogen evolution reaction. - Graphical abstract: Au{sub 2}P{sub 3} was synthesized utilizing the high temperature decomposition of tri-n-octylphosphine as a source of elemental phosphorous and gold nanoparticles as reactants. We demonstrate that the surface capping ligand of the gold nanoparticle precursors influence the purity and extent to which the Au{sub 2}P{sub 3} phase will form. Gold nanorods functionalized with 1-dodecanethiol undergo digestive ripening to produce discrete spherical particles that exhibit reduced reactivity towards phosphorous, resulting in low yields of the gold phosphide. In contrast, gold phosphide was obtained as a phase pure product when cetyltrimethylammonium bromide functionalized gold nanoparticles are used instead. The Au{sub 2}P{sub 3} nanoparticles exhibited higher activity than polycrystalline gold towards the hydrogen evolution reaction. - Highlights: • The surface chemistry of gold affects the synthetic yields of Au{sub 2}P{sub 3}. • Imaging of Au{sub 2}P{sub 3} with transmission electron microscopy results in decomposition. • Au{sub 2}P{sub 3} nanoparticles exhibit activity towards the hydrogen evolution reaction.

36 MATERIALS SCIENCE↗
DOE OSTI2017

On the state of Mn in Mn{sub x}Zn{sub 1−x}O nanoparticles and their surface modification with isonipecotic acid

Mn-doped ZnO (Mn{sub x}Zn{sub 1−x}O) nanoparticles were synthesized by the co-precipitation method and coated with isonipecotic acid as capping ligand. The structure, composition and morphology of the resulting nanomaterial were investigated by energy disperse X-ray analysis, X-ray diffraction, and transmission electron microscopy data. Such measurements showed that the solid obtained contains 6 at% of Mn and it is formed by a highly crystalline material with 3–5 nm range of crystallite size, and only a small elongation of its cell parameter with respect to undoped ZnO wurtzite unit cell. Information on the state of manganese atom in the Mn{sub x}Zn{sub 1−x}O nanostructures formed was obtained from X-ray photoelectron (XPS) and electron energy loss (EELS) spectroscopies. XPS and EELS spectra are composed of four peaks, corresponding to two species of Mn(II) and signals from Mn(III) and Mn(IV). Such spectral data on the state of Mn in the material studied is consistent with the mapping of Mn distribution observed in recorded transmission electron microscopy images, which reveal presence of clusters of Mn atoms. Only a fraction of doping Mn atoms were found forming a solid solution with the host ZnO structure. The functionalization of the nanoparticles system with Isonipecotic acid shows that this molecule remains anchored to the nanoparticles surface mainly through its N basic site. The availability of free carboxylate groups in the capping molecule was tested by conjugation to type IV horseradish peroxidase. - Graphical abstract: State of Mn atoms in Mn-doped ZnO nanostructures prepared by the precipitation method, their capping with isonipecotic acid and subsequent conjugation to peroxidase. - Highlights: • State of manganese in manganese-doped zinc oxide nanoparticles. • Isonipecotic acid as surface modifier of ZnO nanoparticles. • Peroxidase conjugation to ZnO nanoparticles modified with isonipecotic acid.

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

Short-Range Structure of Amorphous Calcium Hydrogen Phosphate

Calcium orthophosphates (CaPs) are the hard constituents of bones and teeth, and thus of ultimate importance to humankind, while amorphous CaPs (ACPs) may play crucial roles in CaP biomineralization. Among the various ACPs with Ca/P atomic ratios between 1.0–1.5, an established structural model exists for basic ACP (Ca/P = 1.5), while those of other ACPs remain unclear. In this work, the structure of amorphous calcium hydrogen phosphate (ACHP; Ca/P = 1.0) obtained via aqueous routes at near-neutral pH values, without stabilizers, was studied by experiments (mainly, TEM with ED, XRD, IR, and NMR spectroscopies, as well as XAS) and computer simulation. Our results globally show that ACHP has a distinct short-range structure, and we propose calcium hydrogen phosphate clusters (CHPCs) as its basic unit. This model is consistent with both computer simulations and the experimental results, where CHPCs are arranged together with water molecules to build up ACHP. We demonstrate that Posner’s clusters, which are conventionally accepted to be the building unit of basic ACPs, do not represent the short-range structure of ACHP, as Posner’s clusters and CHPCs are structurally distinct. This finding is important not only for the determination of the structures of diverse ACPs with varying Ca/P atomic ratios but also for fundamental understanding of a major mineral class that is central to biomineralization in vertebrates and, thus, humans, in particular.

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

Building Materials from Colloidal Nanocrystal Assemblies: Molecular Control of Solid/Solid Interfaces in Nanostructured Tetragonal ZrO 2

We describe in this paper a bottom-up approach to control the composition of solid/solid interfaces in nanostructured materials, and we test its effectiveness on tetragonal ZrO 2 , an inorganic phase of great technological significance. Colloidal nanocrystals capped with trioctylphosphine oxide (TOPO) or oleic acid (OA) are deposited, and the organic fraction of the ligands is selectively etched with O 2 plasma. The interfaces in the resulting all-inorganic colloidal nanocrystal assemblies are either nearly bare (for OA-capped nanocrystals) or terminated with phosphate groups (for TOPO-capped nanocrystals) resulting from the reaction of phosphine oxide groups with plasma species. The chemical modification of the interfaces has extensive effects on the thermodynamics and kinetics of the material. Different growth kinetics indicate different rate limiting processes of growth (surface diffusion for the phosphate-terminated surfaces and dissolution for the “bare” surfaces). Phosphate termination led to a higher activation energy of growth, and a 3-fold reduction in interfacial energy, and facilitated significantly the conversion of the tetragonal phase into the monoclinic phase. Finally, films devoid of residual ligands persisted in the tetragonal phase at temperatures as high as 900 °C for 24 h.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electroreduction-Driven Formation and Connectivity of Polyoxometalate Coordination Networks

We present the synthesis of metal oxide coordination networks based on Preyssler-type polyoxoanions ([NaP 5 W 30 O 110 ] 14– and [NaP 5 MoW 29 O 110 ] 14– ) bridged with metal–aquo complexes ([M(H 2 O) n ] m+ , M m+ = Co 2+ , Ni 2+ , Zn 2+ , Y 3+ ), induced by electrochemical reduction. Networks bridged with first-row transition metals are isostructural with a previously reported Co-bridged structure, while the Y 3+ -bridged structure is new. All networks feature an uncommon binding motif of the metal cation to the oxygen atoms at cap positions, which we hypothesize is due to increased electron density at the cap upon reduction. Oxidation of a Zn 2+ -bridged network resulted in a new structure in which Zn 2+ –O cap bonds are lost, indicating the importance of reduction in the connectivity of these polyoxometalate-based coordination networks.

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

Synthesis of Copper–Silica Core–Shell Nanostructures with Sharp and Stable Localized Surface Plasmon Resonance

Copper nanoparticles exhibit intense and sharp localized surface plasmon resonance (LSPR) in the visible region; however, the LSPR peaks become weak and broad when exposed to air due to the oxidation of Cu. In this work, the Cu nanoparticles are successfully encapsulated in SiO 2 by employing trioctyl-n-phosphine (TOP)-capped Cu nanoparticles for the sol–gel reaction, yielding an aqueous Cu–SiO 2 core–shell suspension with stable and well-preserved LSPR properties of the Cu cores. With the TOP capping, the oxidation of the Cu cores in the microemulsion was significantly reduced, thus allowing the Cu cores to sustain the sol–gel process used for coating the SiO 2 protection layer. It was found that the self-assembled TOP-capped Cu nanoparticles were spontaneously disassembled during the sol–gel reaction, thus recovering the LSPR of individual particles. During the disassembling progress, the extinction spectrum of the nanocube agglomerates evolved from a broad extinction profile to a narrow and sharp peak. For a mixture of nanocubes and nanorods, the spectra evolved to two distinct peaks during the dissembling process. The observed spectra match well with the numerical simulations. In conclusion, these Cu–SiO 2 core–shell nanoparticles with sharp and stable LSPR may greatly expand the utilization of Cu nanoparticles in aqueous environments.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Ultrahigh Hot Carrier Transient Photocurrent in Nanocrystal Arrays by Auger Recombination

Here, we show that a new mechanism for carrier transport in solution-processed colloidal semiconductor nanocrystal arrays exists at high excitation intensity on ultrafast time scales and allows for facile intrinsic transport between as-prepared nanocrystals over long distances. By combining a high speed photoconductive switch with an ultrafast laser excitation in a sub-40 ps photoconductor, we observed transient photocurrents with peak densities of 3 × 10 4 – 10 6 mA/ cm 2 in self-assembled PbSe nanocrystals capped with long native oleic acid ligands. The ratio between the transient photocurrent peak and the steady-state dark current is 10 orders of magnitude. The transient mobility at the peak current is estimated to range between 0.5–17.5 cm 2 /(V s) for the various nanocrystal sizes studied, which is 6 to 9 orders of magnitude higher than the dark current steady-state mobility in PbSe, CdSe, and CdTe nanocrystals capped with native ligands. The results are analyzed using a kinetic model which attributes the ultrahigh transient photocurrent to multiple photogenerated excitons undergoing on-particle Auger recombination, followed by rapid tunneling at high energies. This mechanism is demonstrated for a wide range of PbSe nanocrystals sizes (diameters from 2.7 to 7.1 nm) and experimental parameters. Our observations indicate that native ligand-capped nanocrystal arrays are promising for optoelectronics applications wherein multiple carriers are photoinjected to interband states.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Microwave-Assisted Synthesis of Cu@IrO 2 Core-Shell Nanowires for Low-Temperature Methane Conversion

A facile microwave-assisted synthesis was developed for the tunable fabrication of a novel Cu@IrO 2 core@shell nanowire motif. Experimental parameters, such as (i) reaction time, (ii) the method of addition of the Ir precursor, (iii) capping agent, (iv) reducing agent, as well as (v) the capping agent-to-reducing agent ratio, were subsequently optimized. The viability of other methods based on previously reported literature, such as refluxing, stirring, and physical sonication, was studied and compared with our optimized microwave-assisted protocol in creating our as-prepared materials. It should be noted that the magnitude of the IrO 2 shell could be tailored based on varying the Cu: Ir ratio coupled with judicious variations in the amounts of capping agent and reducing agent. Structural characterization techniques, such as XRD, XPS, and HRTEM (including HRTEM-EDS), were used to analyze our Cu@IrO 2 motifs. Specifically, the shell could be reliably tailored from sizes of 10 nm, 8 nm, 6 nm, and 3.5 nm with corresponding Cu: Ir ratios of 10:1, 15:1, 20:1, and 25:1, respectively. Moreover, the structural integrity of the motifs was probed and found to have been maintained after not only heat treatment but also the post-methane conversion process, indicative of an intrinsically high stability. Both components within the CuO-IrO 2 interface were able to activate methane at temperatures between 400 to 500 K with a reduction of the associated metal cations (Cu 2+ → Cu 1+ ; Ir 4+ → Ir 3+ ) and the deposition of CH x fragments on the surface, as clearly observed in the ambient-pressure XPS results. Thus, on the basis of their stability and chemical activity, these core-shell materials could be very useful for the catalytic conversion of methane into 'higher value" chemicals.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Transient Lattice Response upon Photoexcitation in CuInSe 2 Nanocrystals with Organic or Inorganic Surface Passivation

CuInSe 2 nanocrystals offer promise for optoelectronics including thin-film photovoltaics and printed electronics. Additive manufacturing methods such as photonic curing controllably sinter particles into quasi-continuous films and offer improved device performance. To gain understanding of nanocrystal response under such processing conditions, we investigate impacts of photoexcitation on colloidal nanocrystal lattices via time-resolved X-ray diffraction. We probe three sizes of particles and two capping ligands (oleylamine and inorganic S 2- ) to evaluate resultant crystal lattice temperature, phase stability, and thermal dissipation. Elevated fluences produce heating and loss of crystallinity, the onset of which exhibits particle size dependence. We find size-dependent recrystallization and cooling lifetimes ranging from 90 to 200 ps with additional slower cooling on the nanosecond time scale. Sulfide-capped nanocrystals show faster recrystallization and cooling compared to oleylamine-capped nanocrystals. Using these lifetimes, we find interfacial thermal conductivities from 3 to 28 MW/(m 2 K), demonstrating that ligand identity strongly influences thermal dissipation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Oxygen Distribution and Segregation at Grain Boundaries in Nb and Ta-Encapsulated Nb Thin Films for Superconducting Qubits

We report on atomic-scale analyses of oxygen distribution and segregation at grain boundaries (GBs) of Nb and Ta-encapsulated Nb (Ta/Nb) thin films for superconducting qubits using atom probe tomography (APT) and transmission electron microscopy (TEM). We observe oxygen segregation at grain boundaries (GBs) relative to the oxygen concentration within the grains for both Nb and Ta-capped Nb thin films and find that a higher oxygen concentration in the interior of Nb grains leads to greater oxygen segregation levels at GBs. This finding reveals that the formation of a local equilibrium of oxygen concentration between GBs and grain interiors of Nb is the primary driving force of the oxygen segregation behaviors in Nb and Ta-capped Nb. The enrichment factors (CGB/Cgrain) for oxygen segregation at GBs in Nb and Ta-capped Nb range from 2.4 ± 0.3 to 2.7 ± 0.4. The current results also highlight that controlling oxygen impurities in Nb during film deposition and fabrication processing is important to concomitantly reducing the level of oxygen segregation at GBs in Nb. Finally, we find that increases in the oxygen concentration in both Nb grains and GBs correlate with a suppression in the critical temperature for superconductivity (Tc). Together, our comparative chemical and charge transport property analyses provide atomic-scale insights into a potential mechanism, contributing to the decoherence in superconducting qubits.

Lee, Jaeyel [Fermilab] (ORCID:0000000185429612)↗
DOE OSTI2026

Tracking Optical Phonon Dynamics in InP Nanocrystals via Transient Absorption and Femtosecond Stimulated Raman Spectroscopy

Semiconductor nanocrystals (NCs) offer actualized and prospective utility in optoelectronic technologies, yet key aspects of their thermal and vibrational behaviors remain unresolved. Compared with bulk crystals, heat dissipation involving NCs can differ substantially owing to pervasiveness of interfacial scattering, phonon confinement, and relaxed phonon momentum selection rules, as well as influences of ligands. Here, in addition to transient absorption, we use femtosecond stimulated Raman spectroscopy to track nonequilibrium optical-phonon dynamics in InP NCs capped with myristic acid ligands and compare the same particles coated with a ZnS shell. We identify distinct phonon decay pathways in ligand-capped versus ZnS-shelled NCs. Increasing the excitation density and introducing the ZnS shell measurably modify optical-phonon lifetimes, whereas phonon formation times remain largely unchanged. In addition, we observe phonon mode softening in ligand-capped nanocrystals, consistent with lattice expansion. Together, these results demonstrate that core–shell structures can strongly govern nanocrystal thermal dissipation pathways and should be considered a key design parameter for optoelectronic operation.

dissipation↗
DOE OSTI2021

Heterometallic Ce IV / V V Oxo Clusters with Adjustable Catalytic Reactivities

Heterometallic Ce IV /M oxo clusters are underexplored yet and can benefit from synergistic properties from combining cerium and other metal cations to produce efficient redox catalysts. Herein, we designed and synthesized a series of new Ce 12 V 6 oxo clusters with different capping ligands: Ce 12 V 6 -SO 4 , Ce 12 V 6 -OTs (OTs: toluenesulfonic acid), and Ce 12 V 6 -NBSA (NBSA: nitrobenzenesulfonic acid). Single crystal X-ray diffraction (SCXRD) for all three structures reveals a Ce 12 V 6 cubane core formulated [Ce 12 (VO) 6 O 24 ] 18+ with cerium on the edges of the cube, vanadyl capping the faces, and sulfate on the corners. While infrared spectroscopy (IR), ultraviolet–visible spectroscopy (UV–vis), electrospray ionization mass spectrometry (ESI-MS), and proton nuclear magnetic resonance ( 1 H NMR) proved the successful coordination of the organic ligands to the Ce 12 V 6 core, liquid phase 51 V NMR and small-angle X-ray scattering (SAXS) confirmed the integrity of the clusters in the organic solutions. Furthermore, functionalization of the Ce 12 V 6 core with organic ligands both provides increased solubility in term of homogeneous application and introduces porosity to the assemblies of Ce 12 V 6 -OTs and Ce 12 V 6 -NBSA in term of heterogeneous application, thus allowing more catalytic sites to be accessible and improving reactivity as compared to the nonporous and less soluble Ce 12 V 6 -SO 4 . Meanwhile, the coordinated ligands also influenced the electronic environment of the catalytic sites, in turn affecting the reactivity of the cluster, which we probed by the selective oxidation of 2-chloroethyl ethyl sulfide (CEES). Furthermore, this work provides a strategy to make full use of the catalytic sites within a class of inorganic sulfate capped clusters via organic ligand introduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Comprehensive Characterization of Water Group Ion Composition and Distributions in Saturn's Magnetosphere With Cassini Plasma Spectrometer Data

Saturn's magnetosphere is continuously supplied with neutrals from the Enceladus plume and the icy rings, which undergo ionization and charge-exchange to form a complex water-group plasma environment. While the Cassini Plasma Spectrometer (CAPS) instrument has provided extensive compositional information, detailed separation of individual water-group ion species in time-of-flight (TOF) data has not previously been achieved. In this study, we perform forward modeling of CAPS-IMS energy-per-charge (E/Q) and TOF spectra obtained between 2004 and 2012 to resolve O + , OH + , H 2 O + , and H 3 O + and to characterize their plasma properties, including number density, temperature, and thermodynamic κ. Our results demonstrate that O + is the dominant thermal ion species throughout Saturn's magnetosphere, comprising up to ∼70% of the total ion population beyond ∼5 Saturn radii (R S ). In contrast, molecular ions such as OH + , H 2 O + , and H 3 O + dominate closer to Enceladus but rapidly dissociate into atomic ions between ∼5 and 10 R S . This radial region is also characterized by the steepest increase in plasma flow speed, which rises from ∼40% to ∼80% of rigid corotation. Simultaneously, ion velocity distributions approach Maxwell–Boltzmann equilibrium, as indicated by high kappa values. These findings provide new constraints on the ion–neutral chemistry that regulates the balance between molecular and atomic ions in Saturn's magnetosphere. They also emphasize the critical role of the 5–10 R S region as a transition zone for both plasma composition and dynamics. Our results refine previous CAPS-based studies and underscore the need to incorporate seasonal variability and ionospheric coupling into future global models of Saturn's plasma environment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Trapping gases in metal-organic frameworks with a selective surface molecular barrier layer

The main challenge for gas storage and separation in nanoporous materials is that many molecules of interest adsorb too weakly to be effectively retained. Instead of synthetically modifying the internal surface structure of the entire bulk—as is typically done to enhance adsorption—here we show that post exposure of a prototypical porous metal-organic framework to ethylenediamine can effectively retain a variety of weakly adsorbing molecules (for example, CO, CO 2 , SO 2 , C 2 H 4 , NO) inside the materials by forming a monolayer-thick cap at the external surface of microcrystals. Furthermore, this capping mechanism, based on hydrogen bonding as explained by ab initio modelling, opens the door for potential selectivity. For example, water molecules are shown to disrupt the hydrogen-bonded amine network and diffuse through the cap without hindrance and fully displace/release the retained small molecules out of the metal-organic framework at room temperature. Lastly, these findings may provide alternative strategies for gas storage, delivery and separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Topological structure prediction in binary nanoparticle superlattices

Systems of spherical nanoparticles with capping ligands have been shown to self-assemble into beautiful superlattices of fascinating structure and complexity. Here, I show that the spherical geometry of the nanoparticle imposes constraints on the nature of the topological defects associated with the capping ligand and that such topological defects control the structure and stability of the superlattices that can be assembled. Furthermore, all of these considerations form the basis for the orbifold topological model (OTM) described in this paper. Finally, the model quantitatively predicts the structure of super-lattices where capping ligands are hydrocarbon chains in excellent agreement with experimental results, explains the appearance of low packing fraction lattices as equilibrium, why certain similar structures are more stable (bccAB 6 vs. CaB 6 , AuCu vs. CsCl, etc.) and many other experimental observations.

36 MATERIALS SCIENCE↗