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1.  A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS 
Journal of Applied Crystallography  2013;46(Pt 4):874-881.
Three-dimensional reciprocal space mapping by X-ray and electron diffraction [namely grazing-incidence X-ray diffraction (GIXD), reflection high-energy electron diffraction (RHEED) and grazing-incidence small-angle X-ray scattering (GISAXS)] was used to explore the internal structure and shape of differently oriented epitaxial Co/CaF2 facetted nanoparticles.
In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.
doi:10.1107/S0021889813008777
PMCID: PMC3769055  PMID: 24046491
cobalt-on-fluorite nanoparticles; grazing-incidence X-ray diffraction (GIXD); reflection high-energy electron diffraction (RHEED); grazing-incidence small-angle X-ray scattering (GISAXS); epitaxial growth; three-dimensional reciprocal space mapping
2.  Advanced grazing-incidence techniques for modern soft-matter materials analysis 
IUCrJ  2015;2(Pt 1):106-125.
Advanced grazing-incidence techniques have developed significantly during recent years. With the ongoing progress in instrumentation, novel methods have emerged which allow for an in-depth morphology characterization of modern soft-matter materials. Examples are in situ and in operando grazing-incidence small-angle X-ray scattering (GISAXS), micro- and nanofocused GISAXS, time-of-flight (TOF) grazing-incidence small-angle neutron scattering (GISANS) and surface-sensitive resonant soft X-ray scattering techniques, including the potential to investigate polarization. Progress in software for data analysis is another important aspect.
The complex nano-morphology of modern soft-matter materials is successfully probed with advanced grazing-incidence techniques. Based on grazing-incidence small- and wide-angle X-ray and neutron scattering (GISAXS, GIWAXS, GISANS and GIWANS), new possibilities arise which are discussed with selected examples. Due to instrumental progress, highly interesting possibilities for local structure analysis in this material class arise from the use of micro- and nanometer-sized X-ray beams in micro- or nanofocused GISAXS and GIWAXS experiments. The feasibility of very short data acquisition times down to milliseconds creates exciting possibilities for in situ and in operando GISAXS and GIWAXS studies. Tuning the energy of GISAXS and GIWAXS in the soft X-ray regime and in time-of flight GISANS allows the tailoring of contrast conditions and thereby the probing of more complex morphologies. In addition, recent progress in software packages, useful for data analysis for advanced grazing-incidence techniques, is discussed.
doi:10.1107/S2052252514024178
PMCID: PMC4285885  PMID: 25610632
grazing-incidence techniques; GISAXS; GIWAXS; resonant soft X-ray scattering; GISANS; morphology; soft matter
3.  Depth profiling of polymer films with grazing-incidence small-angle X-ray scattering 
A procedure for obtaining depth-specific scattering profiles of laterally defined nanostructure using grazing-incidence small-angle X-ray scattering is described.
A model-free method of reconstructing depth-specific lateral scattering from incident-angle-resolved grazing-incidence small-angle X-ray scattering (GISAXS) data is proposed. The information on the material which is available through variation of the X-ray penetration depth with incident angle is accessed through reference to the reflected branch of the GISAXS process. Reconstruction of the scattering from lateral density fluctuations is achieved by solving the resulting Fredholm integral equation with minimal a priori information about the experimental system. Results from simulated data generated for hypothetical multilayer polymer systems with constant absorption coefficient are used to verify that the method can be applied to cases with large X-ray penetration depths, as typically seen with polymer materials. Experimental tests on a spin-coated thick film of a blend of diblock copolymers demonstrate that the approach is capable of reconstruction of the scattering from a multilayer structure with the identification of lateral scattering profiles as a function of sample depth.
doi:10.1107/S0108767309007508
PMCID: PMC2724987  PMID: 19349663
depth profiling; grazing-incidence small-angle X-ray scattering; block copolymers
4.  Anisotropic Confinement, Electronic Coupling and Strain Induced Effects Detected by Valence-Band Anisotropy in Self-Assembled Quantum Dots 
A method to determine the effects of the geometry and lateral ordering on the electronic properties of an array of one-dimensional self-assembled quantum dots is discussed. A model that takes into account the valence-band anisotropic effective masses and strain effects must be used to describe the behavior of the photoluminescence emission, proposed as a clean tool for the characterization of dot anisotropy and/or inter-dot coupling. Under special growth conditions, such as substrate temperature and Arsenic background, 1D chains of In0.4Ga0.6 As quantum dots were grown by molecular beam epitaxy. Grazing-incidence X-ray diffraction measurements directly evidence the strong strain anisotropy due to the formation of quantum dot chains, probed by polarization-resolved low-temperature photoluminescence. The results are in fair good agreement with the proposed model.
doi:10.1007/s11671-010-9786-8
PMCID: PMC3212094
Molecular beam epitaxy; Self-assembled quantum dots; Inter-dot coupling; Anisotropic effects; Linear polarized photoluminescence emission; Grazing-incidence X-ray diffraction synchrotron; Optoelectronic
5.  Intracellular distribution of nontargeted quantum dots after natural uptake and microinjection 
Background:
The purpose of this study was to elucidate the mechanism of natural uptake of nonfunctionalized quantum dots in comparison with microinjected quantum dots by focusing on their time-dependent accumulation and intracellular localization in different cell lines.
Methods:
The accumulation dynamics of nontargeted CdSe/ZnS carboxyl-coated quantum dots (emission peak 625 nm) was analyzed in NIH3T3, MCF-7, and HepG2 cells by applying the methods of confocal and steady-state fluorescence spectroscopy. Intracellular colocalization of the quantum dots was investigated by staining with Lysotracker®.
Results:
The uptake of quantum dots into cells was dramatically reduced at a low temperature (4°C), indicating that the process is energy-dependent. The uptake kinetics and imaging of intracellular localization of quantum dots revealed three accumulation stages of carboxyl-coated quantum dots at 37°C, ie, a plateau stage, growth stage, and a saturation stage, which comprised four morphological phases: adherence to the cell membrane; formation of granulated clusters spread throughout the cytoplasm; localization of granulated clusters in the perinuclear region; and formation of multivesicular body-like structures and their redistribution in the cytoplasm. Diverse quantum dots containing intracellular vesicles in the range of approximately 0.5–8 μm in diameter were observed in the cytoplasm, but none were found in the nucleus. Vesicles containing quantum dots formed multivesicular body-like structures in NIH3T3 cells after 24 hours of incubation, which were Lysotracker-negative in serum-free medium and Lysotracker-positive in complete medium. The microinjected quantum dots remained uniformly distributed in the cytosol for at least 24 hours.
Conclusion:
Natural uptake of quantum dots in cells occurs through three accumulation stages via a mechanism requiring energy. The sharp contrast of the intracellular distribution after microinjection of quantum dots in comparison with incubation as well as the limited transfer of quantum dots from vesicles into the cytosol and vice versa support the endocytotic origin of the natural uptake of quantum dots. Quantum dots with proteins adsorbed from the culture medium had a different fate in the final stage of accumulation from that of the protein-free quantum dots, implying different internalization pathways.
doi:10.2147/IJN.S39658
PMCID: PMC3575178  PMID: 23429995
endocytosis; internalization; carboxyl; lysosome; protein corona; multivesicular body-like structures; ring-like vesicles; green fluorescent protein; pathway; saturation
6.  Quantum percolation and transition point of a directed discrete-time quantum walk 
Scientific Reports  2014;4:6583.
Quantum percolation describes the problem of a quantum particle moving through a disordered system. While certain similarities to classical percolation exist, the quantum case has additional complexity due to the possibility of Anderson localisation. Here, we consider a directed discrete-time quantum walk as a model to study quantum percolation of a two-state particle on a two-dimensional lattice. Using numerical analysis we determine the fraction of connected edges required (transition point) in the lattice for the two-state particle to percolate with finite (non-zero) probability for three fundamental lattice geometries, finite square lattice, honeycomb lattice, and nanotube structure and show that it tends towards unity for increasing lattice sizes. To support the numerical results we also use a continuum approximation to analytically derive the expression for the percolation probability for the case of the square lattice and show that it agrees with the numerically obtained results for the discrete case. Beyond the fundamental interest to understand the dynamics of a two-state particle on a lattice (network) with disconnected vertices, our study has the potential to shed light on the transport dynamics in various quantum condensed matter systems and the construction of quantum information processing and communication protocols.
doi:10.1038/srep06583
PMCID: PMC4192638  PMID: 25301394
7.  New approach for structural characterization of planar sets of nanoparticles embedded into a solid matrix 
Scientific Reports  2013;3:3414.
In this work we demonstrate that Medium Energy Ion Scattering (MEIS) measurements in combination with Transmission Electron Microscopy (TEM) or Grazing Incidence Small Angle X-Ray Scattering (GISAXS) can provide a complete characterization of nanoparticle (NP) systems embedded into dielectric films. This includes the determination of the nanoparticle characteristics (location, size distribution and number concentration) as well as the depth distribution and concentration of the NP atomic components dispersed in the matrix. Our studies are performed considering a model case system consisting of planar arrangements of Au NPs (size range from 1 to 10 nm) containing three distinct Au concentrations embedded in a SiO2 film.
doi:10.1038/srep03414
PMCID: PMC3849636  PMID: 24301257
8.  Quantum-dot supercrystals for future nanophotonics 
Scientific Reports  2013;3:1727.
The study of supercrystals made of periodically arranged semiconductor quantum dots is essential for the advancement of emerging nanophotonics technologies. By combining the strong spatial confinement of elementary excitations inside quantum dots and exceptional design flexibility, quantum-dot supercrystals provide broad opportunities for engineering desired optical responses and developing superior light manipulation techniques on the nanoscale. Here we suggest tailoring the energy spectrum and wave functions of the supercrystals' collective excitations through the variation of different structural and material parameters. In particular, by calculating the excitonic spectra of quantum dots assembled in two-dimensional Bravais lattices we demonstrate a wide variety of spectrum transformation scenarios upon alterations in the quantum dot arrangement. This feature offers unprecedented control over the supercrystal's electromagnetic properties and enables the development of new nanophotonics materials and devices.
doi:10.1038/srep01727
PMCID: PMC3635059
9.  Chemical nature and structure of organic coating of quantum dots is crucial for their application in imaging diagnostics 
Background:
One of the most attractive properties of quantum dots is their potential to extend the opportunities for fluorescent and multimodal imaging in vivo. The aim of the present study was to clarify whether the composition and structure of organic coating of nanoparticles are crucial for their application in vivo.
Methods:
We compared quantum dots coated with non-crosslinked amino-functionalized polyamidoamine (PAMAM) dendrimers, quantum dots encapsulated in crosslinked carboxyl-functionalized PAMAM dendrimers, and silica-shelled amino-functionalized quantum dots. A multimodal fluorescent and paramagnetic quantum dot probe was also developed and analyzed. The probes were applied intravenously in anesthetized animals for visualization of brain vasculature using two-photon excited fluorescent microscopy and visualization of tumors using fluorescent IVIS® imaging (Caliper Life Sciences, Hopkinton, MA) and magnetic resonance imaging.
Results:
Quantum dots coated with non-crosslinked dendrimers were cytotoxic. They induced side effects in vivo, including vasodilatation with a decrease in mean arterial blood pressure and heart rate. The quantum dots penetrated the vessels, which caused the quality of fluorescent imaging to deteriorate. Quantum dots encapsulated in crosslinked dendrimers had low cytotoxicity and were biocompatible. In concentrations <0.3 nmol quantum dots/kg bodyweight, these nanoparticles did not affect blood pressure and heart rate, and did not induce vasodilatation or vasoconstriction. PEGylation (PEG [polyethylene glycol]) was an indispensable step in development of a quantum dot probe for in vivo imaging, based on silica-shelled quantum dots. The non-PEGylated silica-shelled quantum dots possessed low colloidal stability in high-salt physiological fluids, accompanied by rapid aggregation in vivo. The conjugation of silica-shelled quantum dots with PEG1100 increased their stability and half-life in the circulation without significant enhancement of their size. In concentrations <2.5 nmol/kg bodyweight, these quantum dots did not affect the main physiological variables. It was possible to visualize capillaries, which makes this quantum dot probe appropriate for investigation of mediators of vasoconstriction, vasodilatation, and brain circulation in intact animals in vivo. The multimodal silica-shelled quantum dots allowed visualization of tumor tissue in an early stage of its development, using magnetic resonance imaging.
Conclusion:
The present study shows that the type and structure of organic/bioorganic shells of quantum dots determine their biocompatibility and are crucial for their application in imaging in vivo, due to the effects of the shell on the following properties: colloidal stability, solubility in physiological fluids, influence of the basic physiological parameters, and cytotoxicity.
doi:10.2147/IJN.S17995
PMCID: PMC3184932  PMID: 21980235
quantum dot; organic shell; biocompatibility; in vivo imaging; two-photon excited fluorescent microscopy; magnetic resonance imaging
10.  Entrapment in phospholipid vesicles quenches photoactivity of quantum dots 
Quantum dots have emerged with great promise for biological applications as fluorescent markers for immunostaining, labels for intracellular trafficking, and photosensitizers for photodynamic therapy. However, upon entry into a cell, quantum dots are trapped and their fluorescence is quenched in endocytic vesicles such as endosomes and lysosomes. In this study, the photophysical properties of quantum dots were investigated in liposomes as an in vitro vesicle model. Entrapment of quantum dots in liposomes decreases their fluorescence lifetime and intensity. Generation of free radicals by liposomal quantum dots is inhibited compared to that of free quantum dots. Nevertheless, quantum dot fluorescence lifetime and intensity increases due to photolysis of liposomes during irradiation. In addition, protein adsorption on the quantum dot surface and the acidic environment of vesicles also lead to quenching of quantum dot fluorescence, which reappears during irradiation. In conclusion, the in vitro model of phospholipid vesicles has demonstrated that those quantum dots that are fated to be entrapped in endocytic vesicles lose their fluorescence and ability to act as photosensitizers.
doi:10.2147/IJN.S22953
PMCID: PMC3173050  PMID: 21931483
fluorescence lifetime; free radicals; liposomes; lipodots; reactive oxygen species
11.  Properties and applications of quantum dot heterostructures grown by molecular beam epitaxy 
Nanoscale Research Letters  2006;1(1):32-45.
One of the main directions of contemporary semiconductor physics is the production and study of structures with a dimension less than two: quantum wires and quantum dots, in order to realize novel devices that make use of low-dimensional confinement effects. One of the promising fabrication methods is to use self-organized three-dimensional (3D) structures, such as 3D coherent islands, which are often formed during the initial stage of heteroepitaxial growth in lattice-mismatched systems. This article is intended to convey the flavour of the subject by focussing on the structural, optical and electronic properties and device applications of self-assembled quantum dots and to give an elementary introduction to some of the essential characteristics.
doi:10.1007/s11671-006-9017-5
PMCID: PMC3246631
Heterostructures; Semiconductors; Self-assembly; Quantum dots; Lasers; Optoelectronics
12.  On the Characterization and Software Implementation of General Protein Lattice Models 
PLoS ONE  2013;8(3):e59504.
Abstract models of proteins have been widely used as a practical means to computationally investigate general properties of the system. In lattice models any sterically feasible conformation is represented as a self-avoiding walk on a lattice, and residue types are limited in number. So far, only two- or three-dimensional lattices have been used. The inspection of the neighborhood of alpha carbons in the core of real proteins reveals that also lattices with higher coordination numbers, possibly in higher dimensional spaces, can be adopted. In this paper, a new general parametric lattice model for simplified protein conformations is proposed and investigated. It is shown how the supporting software can be consistently designed to let algorithms that operate on protein structures be implemented in a lattice-agnostic way. The necessary theoretical foundations are developed and organically presented, pinpointing the role of the concept of main directions in lattice-agnostic model handling. Subsequently, the model features across dimensions and lattice types are explored in tests performed on benchmark protein sequences, using a Python implementation. Simulations give insights on the use of square and triangular lattices in a range of dimensions. The trend of potential minimum for sequences of different lengths, varying the lattice dimension, is uncovered. Moreover, an extensive quantitative characterization of the usage of the so-called “move types” is reported for the first time. The proposed general framework for the development of lattice models is simple yet complete, and an object-oriented architecture can be proficiently employed for the supporting software, by designing ad-hoc classes. The proposed framework represents a new general viewpoint that potentially subsumes a number of solutions previously studied. The adoption of the described model pushes to look at protein structure issues from a more general and essential perspective, making computational investigations over simplified models more straightforward as well.
doi:10.1371/journal.pone.0059504
PMCID: PMC3612044  PMID: 23555684
13.  Self-Assembling Complexes of Quantum Dots and scFv Antibodies for Cancer Cell Targeting and Imaging 
PLoS ONE  2012;7(10):e48248.
Semiconductor quantum dots represent a novel class of fluorophores with unique physical and chemical properties which could enable a remarkable broadening of the current applications of fluorescent imaging and optical diagnostics. Complexes of quantum dots and antibodies are promising visualising agents for fluorescent detection of selective biomarkers overexpressed in tumor tissues. Here we describe the construction of self-assembling fluorescent complexes of quantum dots and anti-HER1 or anti-HER2/neu scFv antibodies and their interactions with cultured tumor cells. A binding strategy based on a very specific non-covalent interaction between two proteins, barnase and barstar, was used to connect quantum dots and the targeting antibodies. Such a strategy allows combining the targeting and visualization functions simply by varying the corresponding modules of the fluorescent complex.
doi:10.1371/journal.pone.0048248
PMCID: PMC3484990  PMID: 23133578
14.  Mapping DNA Quantity into Electrophoretic Mobility through Quantum Dot Nanotethers for High Resolution Genetic and Epigenetic Analysis 
ACS Nano  2011;6(1):858-864.
Newly discovered nanoparticle properties have driven the development of novel applications and uses. We report a new observation where the electrophoretic mobility of a quantum dot-DNA nanoassembly can be precisely modulated by the degree of surface DNA conjugation. By using streptavidin-coated quantum dots (QD) as nanotethers to gather biotin-labeled DNA into electrophoretic nanoassemblies, the QD surface charge is modulated and transformed into electrophoretic mobility shifts using standard agarose gel electrophoresis. Typical fluorescent assays quantify based on relative intensity. However, this phenomenon uses a novel approach that accurately maps DNA quantity into shifts in relative band position. This property was applied in a quantum dot enabled nanoassay called Quantum Dot Electrophoretic Mobility Shift Assay (QEMSA) that enables accurate quantification of DNA targets down to 1.1-fold (9%) changes in quantity, beyond what is achievable in qPCR. In addition to these experimental findings, an analytical model is presented to explain this behavior. Finally, QEMSA was applied to both genetic and epigenetic analysis of cancer. First, it was used to analyze copy number variation (CNV) of the RSF1/HBXAP gene where conventional approaches for CNV analysis based on comparative genomic hybridization (CGH), microarrays, and qPCR are unable to reliably differentiate less than 2-fold changes in copy number. Then, QEMSA was used for DNA methylation analysis of the p16/CDK2A tumor suppressor gene where its ability to detect subtle changes in methylation was shown to be superior to that of qPCR.
doi:10.1021/nn204377k
PMCID: PMC3273333  PMID: 22136600
Quantum dot; Nanother; DNA; Electrophoretic mobility; Copy number variation; methylation
15.  Nuclear magnetization in gallium arsenide quantum dots at zero magnetic field 
Nature Communications  2014;5:3268.
Optical and electrical control of the nuclear spin system allows enhancing the sensitivity of NMR applications and spin-based information storage and processing. Dynamic nuclear polarization in semiconductors is commonly achieved in the presence of a stabilizing external magnetic field. Here we report efficient optical pumping of nuclear spins at zero magnetic field in strain-free GaAs quantum dots. The strong interaction of a single, optically injected electron spin with the nuclear spins acts as a stabilizing, effective magnetic field (Knight field) on the nuclei. We optically tune the Knight field amplitude and direction. In combination with a small transverse magnetic field, we are able to control the longitudinal and transverse components of the nuclear spin polarization in the absence of lattice strain—that is, in dots with strongly reduced static nuclear quadrupole effects, as reproduced by our model calculations.
Optical control of nuclear spin polarization in semiconductor quantum dots is promising for applications in NMR imaging. Sallen et al. report efficient dynamic nuclear polarization at zero magnetic field in strain-free gallium arsenide quantum dots with Knight fields dominating the nuclear quadrupole effects.
doi:10.1038/ncomms4268
PMCID: PMC3926008  PMID: 24500329
16.  Near-infrared quantum dots for HER2 localization and imaging of cancer cells 
Background
Quantum dots are fluorescent nanoparticles with unique photophysical properties that allow them to be used as diagnostic, therapeutic, and theranostic agents, particularly in medical and surgical oncology. Near-infrared-emitting quantum dots can be visualized in deep tissues because the biological window is transparent to these wavelengths. Their small sizes and free surface reactive groups that can be conjugated to biomolecules make them ideal probes for in vivo cancer localization, targeted chemotherapy, and image-guided cancer surgery. The human epidermal growth factor receptor 2 gene (HER2/neu) is overexpressed in 25%–30% of breast cancers. The current methods of detection for HER2 status, including immunohistochemistry and fluorescence in situ hybridization, are used ex vivo and cannot be used in vivo. In this paper, we demonstrate the application of near-infrared-emitting quantum dots for HER2 localization in fixed and live cancer cells as a first step prior to their in vivo application.
Methods
Near-infrared-emitting quantum dots were characterized and their in vitro toxicity was established using three cancer cell lines, ie, HepG2, SK-BR-3 (HER2-overexpressing), and MCF7 (HER2-underexpressing). Mouse antihuman anti-HER2 monoclonal antibody was conjugated to the near-infrared-emitting quantum dots.
Results
In vitro toxicity studies showed biocompatibility of SK-BR-3 and MCF7 cell lines with near-infrared-emitting quantum dots at a concentration of 60 μg/mL after one hour and 24 hours of exposure. Near-infrared-emitting quantum dot antiHER2-antibody bioconjugates successfully localized HER2 receptors on SK-BR-3 cells.
Conclusion
Near-infrared-emitting quantum dot bioconjugates can be used for rapid localization of HER2 receptors and can potentially be used for targeted therapy as well as image-guided surgery.
Video abstract
doi:10.2147/IJN.S51535
PMCID: PMC3956736  PMID: 24648731
anti-HER2 antibody; HER2 localization; quantum dots; in vitro imaging; nanotechnology; cancer
17.  Characterization of Lipid-Templated Silica and Hybrid Thin Film Mesophases by Grazing Incidence Small-Angle X-ray Scattering 
The nanostructure of silica and hybrid thin film mesophases templated by phospholipids via an evaporation-induced self-assembly (EISA) process was investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Diacyl phosphatidylcholines with two tails of 6 or 8 carbons were found to template 2D hexagonal mesophases, with the removal of lipid from these lipid/silica films by thermal or UV/O3 processing resulting in a complete collapse of the pore volume. Monoacyl phosphatidylcholines with single tails of 10–14 carbons formed 3D micellular mesophases; the lipid was found to be extractable from these 3D materials, yielding a porous material. In contrast to pure lipid/silica thin film mesophases, films formed from the hybrid bridged silsesquioxane precursor bis(triethoxysilyl)ethane exhibited greater stability toward (both diacyl and monoacyl) lipid removal. Ellipsometric, FTIR, and NMR studies show that the presence of phospholipid suppresses siloxane network formation, while actually promoting condensation reactions in the hybrid material. 1D X-ray scattering and FTIR data were found to be consistent with strong interactions between lipid headgroups and the silica framework.
doi:10.1021/la900748r
PMCID: PMC2736351  PMID: 19496546
18.  Low-temperature fabrication of layered self-organized Ge clusters by RF-sputtering 
Nanoscale Research Letters  2011;6(1):341.
In this article, we present an investigation of (Ge + SiO2)/SiO2 multilayers deposited by magnetron sputtering and subsequently annealed at different temperatures. The structural properties were investigated by transmission electron microscopy, grazing incidence small angles X-ray scattering, Rutherford backscattering spectrometry, Raman, and X-ray photoelectron spectroscopies. We show a formation of self-assembled Ge clusters during the deposition at 250°C. The clusters are ordered in a three-dimensional lattice, and they have very small sizes (about 3 nm) and narrow size distribution. The crystallization of the clusters was achieved at annealing temperature of 700°C.
doi:10.1186/1556-276X-6-341
PMCID: PMC3211430  PMID: 21711858
19.  Reversible Morphology Control in Block Copolymer Films via Solvent Vapor Processing: An In Situ GISAXS study 
Macromolecules  2010;43(9):4253-4260.
The real time changes occurring within films of cylinder-forming poly(α-methylstyrene-block-4-hydroxystyrene) (PαMS-b-PHOST) were monitored as they were swollen in tetrahydrofuran (THF) and acetone solvent vapors. In situ information was obtained by combining grazing incidence small angle X-ray scattering (GISAXS) with film thickness monitoring of the solvent vapor swollen films. We show that for self assembly to occur, the polymer thin film must surpass a swollen thickness ratio of 212% of its original thickness when swollen in THF vapors and a ratio of 268% for acetone vapor annealing. As the polymer becomes plasticized by solvent vapor uptake, the polymer chains must become sufficiently mobile to self assemble, or reorganize, at room temperature. Using vapors of a solvent selective to one of the blocks, in our case PHOST-selective acetone, an order-order transition occured driven by the shift in volume fraction. The BCC spherical phase assumed in the highly swollen state can be quenched by rapid drying. Upon treatment with vapor of a non-selective solvent, THF, the film maintained the cylindrical morphology suggested by its dry-state volume fraction. In situ studies indicate that self-assembly occurs spontaneously upon attaining the threshold swelling ratios.
doi:10.1021/ma902646t
PMCID: PMC2992440  PMID: 21116459
20.  Self-Assembly and Thermal Stability of Binary Superlattices of Gold and Silicon Nanocrystals 
The journal of physical chemistry letters  2013;4(21):10.1021/jz401964s.
Simple hexagonal (sh) AB2 binary superlattices (BSLs) of organic ligand-capped silicon (A; 5.40(±9.8%) nm diameter) and gold (B; 1.88(±10.1%) nm diameter) nanocrystals were assembled by evaporation of colloidal dispersions and characterized using transmission electron microscopy (TEM) and grazing incidence small-angle X-ray scattering (GISAXS). When deposited on tilted substrates by slow evaporation, the sh-AB2 superlattice contracts slightly towards the substrate with centered orthorhombic structure. Heating the BSL to 200°C in air led to gold coalescence and segregation to the surface of the assembly without disrupting the Si nanocrystal sublattice, thus creating a simple hexagonal superlattice of Si nanocrystals.
doi:10.1021/jz401964s
PMCID: PMC3855828  PMID: 24327828
Si nanocrystal; Monodisperse; Binary superlattice; colloids; self-assembly
21.  Structural rearrangements in a lamellar diblock copolymer thin film during treatment with saturated solvent vapor 
Macromolecules  2010;43(1):418-427.
We have investigated the structural changes in thin films of lamellar poly(styrene-b-butadiene) diblock copolymers during treatment with saturated cyclohexane vapor, a solvent slightly selective for polybutadiene. Using real-time, in-situ grazing-incidence small-angle X-ray scattering (GISAXS), the swelling and the rearrangement of the lamellae were investigated with a time resolution of a few seconds, and the underlying processes on the molecular level were identified. After a few minutes in vapor, a transient state with a more well-defined and more long-range ordered lamellar orientation was encountered. Additional parallel lamellae formed which we attribute to the increased degree of coiling of the polymers in the swollen state. Eventually, the film became disordered. These changes are attributed to the increased mobility of the swollen polymers and the gradually decreasing segment-segment interaction parameter in the film as solvent is absorbed.
doi:10.1021/ma9017795
PMCID: PMC2841441  PMID: 20305742
polymer physics; diblock copolymers; thin films; grazing-incidence small-angle X-ray scattering
22.  Small-Angle X-Ray Scattering for Imaging of Surface Layers on Intact Bacteria in the Native Environment 
Journal of Bacteriology  2013;195(10):2408-2414.
Crystalline cell surface layers (S-layers) represent a natural two-dimensional (2D) protein self-assembly system with nanometer-scale periodicity that decorate many prokaryotic cells. Here, we analyze the S-layer on intact bacterial cells of the Gram-positive organism Geobacillus stearothermophilus ATCC 12980 and the Gram-negative organism Aquaspirillum serpens MW5 by small-angle X-ray scattering (SAXS) and relate it to the structure obtained by transmission electron microscopy (TEM) after platinum/carbon shadowing. By measuring the scattering pattern of X rays obtained from a suspension of bacterial cells, integral information on structural elements such as the thickness and lattice parameters of the S-layers on intact, hydrated cells can be obtained nondestructively. In contrast, TEM of whole mounts is used to analyze the S-layer lattice type and parameters as well as the physical structure in a nonaqueous environment and local information on the structure is delivered. Application of SAXS to S-layer research on intact bacteria is a challenging task, as the scattering volume of the generally thin (3- to 30-nm) bacterial S-layers is low in comparison to the scattering volume of the bacterium itself. For enhancement of the scattering contrast of the S-layer in SAXS measurement, either silicification (treatment with tetraethyl orthosilicate) is used, or the difference between SAXS signals from an S-layer-deficient mutant and the corresponding S-layer-carrying bacterium is used for determination of the scattering signal. The good agreement of the SAXS and TEM data shows that S-layers on the bacterial cell surface are remarkably stable.
doi:10.1128/JB.02164-12
PMCID: PMC3650539  PMID: 23504021
23.  Deterministic and electrically tunable bright single-photon source 
Nature Communications  2014;5:3240.
The scalability of a quantum network based on semiconductor quantum dots lies in the possibility of having an electrical control of the quantum dot state as well as controlling its spontaneous emission. The technological challenge is then to define electrical contacts on photonic microstructures optimally coupled to a single quantum emitter. Here we present a novel photonic structure and a technology allowing the deterministic implementation of electrical control for a quantum dot in a microcavity. The device consists of a micropillar connected to a planar cavity through one-dimensional wires; confined optical modes are evidenced with quality factors as high as 33,000. We develop an advanced in-situ lithography technique and demonstrate the deterministic spatial and spectral coupling of a single quantum dot to the connected pillar cavity. Combining this cavity design and technology with a diode structure, we demonstrate a deterministic and electrically tunable single-photon source with an extraction efficiency of around 53±9%.
Bright and tunable single-photon sources are essential for future quantum technologies. Here, the authors deterministically couple a quantum dot to a pillar structure that enables application of electric fields to provide a tunable single-photon source with a demonstrated extraction efficiency of 53%.
doi:10.1038/ncomms4240
PMCID: PMC3925998  PMID: 24496223
24.  The Development of Quantum Dot Calibration Beads and Quantitative Multicolor Bioassays in Flow Cytometry and Microscopy1 
Analytical biochemistry  2007;364(2):180-192.
The use of fluorescence calibration beads has been the hallmark of quantitative flow cytometry. It has enabled the direct comparison of inter-laboratory data as well as quality control in clinical flow cytometry. In this paper we have described a simple method for producing color-generalizable calibration beads based on streptavidin functionalized quantum dots. Based on their broad absorption spectra and relatively narrow emission, that is tunable on the basis of dot-size, quantum dot calibration beads can be made for any fluorophore that matches their emission color. In an earlier publication(1) we characterized the spectroscopic properties of commercial streptavidin functionalized dots (Invitrogen). Here we describe the molecular assembly of these dots on biotinylated beads. The law of mass action is used to readily define the site densities of the dots on the beads. The applicability of these beads is tested against the industry standard, commercial fluorescein calibration beads. The utility of the calibration beads are also herein extended to the characterization surface densities of dot-labeled epidermal growth factor ligands as well as quantitative indicators of the binding of dot-labeled virus particles to cells.
doi:10.1016/j.ab.2007.02.006
PMCID: PMC2018651  PMID: 17397793
nanotechnology; quantum dots; calibration beads; flow cytometer; quantitation; fluorescence; multiplex; bioassays; virus particles; microscopy; spectroscopy; mass action
25.  Microcavity controlled coupling of excitonic qubits 
Nature Communications  2013;4:1747-.
Controlled non-local energy and coherence transfer enables light harvesting in photosynthesis and non-local logical operations in quantum computing. This process is intuitively pictured by a pair of mechanical oscillators, coupled by a spring, allowing for a reversible exchange of excitation. On a microscopic level, the most relevant mechanism of coherent coupling of distant quantum bits—like trapped ions, superconducting qubits or excitons confined in semiconductor quantum dots—is coupling via the electromagnetic field. Here we demonstrate the controlled coherent coupling of spatially separated quantum dots via the photon mode of a solid state microresonator using the strong exciton–photon coupling regime. This is enabled by two-dimensional spectroscopy of the sample’s coherent response, a sensitive probe of the coherent coupling. The results are quantitatively understood in a rigorous description of the cavity-mediated coupling of the quantum dot excitons. This mechanism can be used, for instance in photonic crystal cavity networks, to enable a long-range, non-local coherent coupling.
Controlling coupling between distant quantum objects is important for implementation of quantum technologies. Providing an important step towards using semiconductor structures for hosting optically controlled qubits, this work shows coherent coupling between three quantum dot excitons via a cavity.
doi:10.1038/ncomms2764
PMCID: PMC3644086  PMID: 23612288

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