Structural Basis for Clonal Diversity of the Public T Cell Response to Dominant Epitopes from Cytomegalovirus and Influenza

A diverse T cell receptor (TCR) repertoire is a prerequisite for effective viral clearance. However, knowledge of human TCR repertoire to defined viral antigens is limited. Recent advances in high-throughput sequencing (HTS) and single-cell sorting have revolutionized the study of human TCR repertoires to different types of viruses. In collaboration with the laboratory of Dr. Nan-ping Weng (National Institute on Aging, NIH), we applied unique molecular identifier (UMI)-labelled HTS, single-cell paired TCR analysis, surface plasmon resonance, and X-ray crystallography to exhaustively interrogate CD8+ TCR repertoires specific for cytomegalovirus (CMV) and influenza A (Flu) in HLA-A2+ humans. Our two CMV-specific TCR-pMHC structures and two Flu-specific TCR-pMHC structures provide a plausible explanation for the much higher diversity of CMV-specific than Flu-specific TCR repertoires in humans. Our comprehensive biochemical and structural portrait of two different anti-viral T cell responses may contribute to the future development of predictors of immunity or disease at the individual level.

Design and validation of a novel generic platform for the production of tetravalent IgG1-like bispecific antibodies

International audience

Mesoscale Optoelectronic Design of Wire-Based Photovoltaic and Photoelectrochemical Devices

The overarching theme of this thesis is mesoscale optical and optoelectronic design of photovoltaic and photoelectrochemical devices. In a photovoltaic device, light absorption and charge carrier transport are coupled together on the mesoscale, and in a photoelectrochemical device, light absorption, charge carrier transport, catalysis, and solution species transport are all coupled together on the mesoscale. The work discussed herein demonstrates that simulation-based mesoscale optical and optoelectronic modeling can lead to detailed understanding of the operation and performance of these complex mesostructured devices, serve as a powerful tool for device optimization, and efficiently guide device design and experimental fabrication efforts. In-depth studies of two mesoscale wire-based device designs illustrate these principles—(i) an optoelectronic study of a tandem Si|WO3 microwire photoelectrochemical device, and (ii) an optical study of III-V nanowire arrays.

The study of the monolithic, tandem, Si|WO3 microwire photoelectrochemical device begins with development and validation of an optoelectronic model with experiment. This study capitalizes on synergy between experiment and simulation to demonstrate the model’s predictive power for extractable device voltage and light-limited current density. The developed model is then used to understand the limiting factors of the device and optimize its optoelectronic performance. The results of this work reveal that high fidelity modeling can facilitate unequivocal identification of limiting phenomena, such as parasitic absorption via excitation of a surface plasmon-polariton mode, and quick design optimization, achieving over a 300% enhancement in optoelectronic performance over a nominal design for this device architecture, which would be time-consuming and challenging to do via experiment.

The work on III-V nanowire arrays also starts as a collaboration of experiment and simulation aimed at gaining understanding of unprecedented, experimentally observed absorption enhancements in sparse arrays of vertically-oriented GaAs nanowires. To explain this resonant absorption in periodic arrays of high index semiconductor nanowires, a unified framework that combines a leaky waveguide theory perspective and that of photonic crystals supporting Bloch modes is developed in the context of silicon, using both analytic theory and electromagnetic simulations. This detailed theoretical understanding is then applied to a simulation-based optimization of light absorption in sparse arrays of GaAs nanowires. Near-unity absorption in sparse, 5% fill fraction arrays is demonstrated via tapering of nanowires and multiple wire radii in a single array. Finally, experimental efforts are presented towards fabrication of the optimized array geometries. A hybrid self-catalyzed and selective area MOCVD growth method is used to establish morphology control of GaP nanowire arrays. Similarly, morphology and pattern control of nanowires is demonstrated with ICP-RIE of InP. Optical characterization of the InP nanowire arrays gives proof of principle that tapering and multiple wire radii can lead to near-unity absorption in sparse arrays of InP nanowires.

Aluminum nanoholes for optical biosensing

Sub-wavelength diameter holes in thin metal layers can exhibit remarkable optical features that make them highly suitable for (bio)sensing applications. Either as efficient light scattering centers for surface plasmon excitation or metal-clad optical waveguides, they are able to form strongly localized optical fields that can effectively interact with biomolecules and/or nanoparticles on the nanoscale. As the metal of choice, aluminum exhibits good optical and electrical properties, is easy to manufacture and process and, unlike gold and silver, its low cost makes it very promising for commercial applications. However, aluminum has been scarcely used for biosensing purposes due to corrosion and pitting issues. In this short review, we show our recent achievements on aluminum nanohole platforms for (bio)sensing. These include a method to circumvent aluminum degradation—which has been successfully applied to the demonstration of aluminum nanohole array (NHA) immunosensors based on both, glass and polycarbonate compact discs supports—the use of aluminum nanoholes operating as optical waveguides for synthesizing submicron-sized molecularly imprinted polymers by local photopolymerization, and a technique for fabricating transferable aluminum NHAs onto flexible pressure-sensitive adhesive tapes, which could facilitate the development of a wearable technology based on aluminum NHAs.

Plasmon-tuned silver colloids for SERRS analysis of methemoglobin with preserved nativity

Optically tuned silver nanoparticles (AgNP's) functionalized with ω-mercaptoalkanoic acids are synthesized and used as a signal amplifier for the surface-enhanced resonance Raman scattering (SERRS) study of heme cofactor in methemoglobin (metHb). Even though both mercaptopropionic acid (MPA)- and mercaptononanoic acid (MNA)-functionalized AgNP's exemplify vastly enhanced SERRS signal of metHb, MNA-AgNP's amplify the SERRS signal amid preservation of the nativity of the heme pocket, unlike MPA-AgNP's. The electrostatic interaction between MNA-AgNP's and metHb leads to instant signal enhancement with a Raman enhancement factor (EF(SERS)) of 4.2 × 10(3). Additionally, a Langmuir adsorption isotherm has been employed for the adsorption of metHb on the MNA-AgNP surface, which provides the real surface coverage and equilibrium constant (K) of metHb as 139 nM and 3.6 × 10(8) M(-1), respectively. The lowest detection limit of 10 nM for metHb has been demonstrated using MNA-AgNP's besides retaining the nativity of the heme pocket.

Towards improved precision in the quantification of surface-enhanced Raman scattering (SERS) enhancement factors: A renewed approach

This paper demonstrates a renewed procedure for the quantification of surface-enhanced Raman scattering (SERS) enhancement factors with improved precision. The principle of this method relies on deducting the resonance Raman scattering (RRS) contribution from surface-enhanced resonance Raman scattering (SERRS) to end up with the surface enhancement (SERS) effect alone. We employed 1,8,15,22-tetraaminophthalocyanato-cobalt(II) (4α-CoIITAPc), a resonance Raman- and electrochemically redox-active chromophore, as a probe molecule for RRS and SERRS experiments. The number of 4α-CoIITAPc molecules contributing to RRS and SERRS phenomena on plasmon inactive glassy carbon (GC) and plasmon active GC/Au surfaces, respectively, has been precisely estimated by cyclic voltammetry experiments. Furthermore, the SERS substrate enhancement factor (SSEF) quantified by our approach is compared with the traditionally employed methods. We also demonstrate that the present approach of SSEF quantification can be applied for any kind of different SERS substrates by choosing an appropriate laser line and probe molecule.

Mapping bound plasmon propagation on a nanoscale stripe waveguide using quantum dots: Influence of spacer layer thickness

In this paper we image the highly confined long range plasmons of a nanoscale metal stripe waveguide using quantum emitters. Plasmons were excited using a highly focused 633 nm laser beam and a specially designed grating structure to provide stronger incoupling to the desired mode. A homogeneous thin layer of quantum dots was used to image the near field intensity of the propagating plasmons on the waveguide. We observed that the photoluminescence is quenched when the QD to metal surface distance is less than 10 nm. The optimised spacer layer thickness for the stripe waveguides was found to be around 20 nm. Authors believe that the findings of this paper prove beneficial for the development of plasmonic devices utilising stripe waveguides.

Surface oxidation of cadmium, indium, tin and antimony by photoelectron and Auger spectroscopy

Surface oxidation of Cd, In, Sn and Sb has been investigated by employing valence bands, metal 4d levels and plasmon bands in X-ray photoelectron spectra. O(KLL), metal M4N45N45, and plasmon transitions in electron-induced Auger spectra as well as Auger transitions due to the metal (metal oxide) and plasmons in X-ray-induced Auger spectra. The surface oxides are In2O4, CdO and a mixture of SnO and SnO2 in the case of In. Cd and Sn respectively. The facility of surface oxidation is found to vary as In>Cd>Sn>Sb. Inter-atomic Auger transitions involving oxygen valence bands have been identified on oxidized surfaces of Cd and In.

Radiative and non-radiative effects of a substrate on localized plasmon resonance of particles

Experiments have shown strong effects of some substrates on the localized plasmons of metallic nano particles but they are inconclusive on the affecting parameters. Here, we have used discrete dipole approximation in conjunction with Sommerfeld integral relations to explain the effect of the substrates as a function of the parameters of incident radiation. The radiative coupling can both quench and enhance the resonance and its dependence on the angle and polarization of incident radiation with respect to the surface is shown. Non-radiative interaction with the substrate enhances the plasmon resonance of the particles and can shift the resonances from their free-space energies significantly. The non-radiative interaction of the substrate is sensitive to the shape of particles and polarization of incident radiation with respect to substrate. Our results show that the plasmon resonances in coupled and single particles can be significantly altered from their free-space resonances and are quenched or enhanced by the choice of substrate and polarization of incident radiation. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736544]

Surface plasmons and effects of losses in propagating modes in a chain of silver nanoparticles

In this work a chain of 4000 silver nanoparticles embedded in a glass medium is considered, and its leftmost particle is excited by an electric field pulse of Gaussian shape. Considering Drude’s model, losses of the system are taken into account by γ factor, which stands for the Ohmic losses, and different quantities, such as frequencies of excited modes and group velocities are calculated. Besides, these results are compared to those obtained from the dispersion relation of an infinite chain. The increase of losses affects the lifetime and propagation length of the plasmon; besides, although the response dispersion relation for an infinite chain seems to remain invariable, this is not the case for a finite chain. The mismatches are bigger for higher losses. Furthermore, plasmon propagation velocities are analysed, and an explanation for the mismatch of longitudinal modes close to the intersection point with the dispersion of light is suggested. Finally, some concepts to treat this problem from the energy transport point of view are introduced.

The plasmon resonance absorption of Ag/SiO2 nanocomposite films

The plasmon resonance absorption of the Ag/SiO2 nanocomposite film is investigated. The measured absorption spectra are compared with those calculated by the Mie theory. The results indicate that the Mie theory on the basis of classical electrodynamics can only partially explain the optical absorption spectra of the Ag/SiO2 nanocomposite film. We believe that the plasmon resonance absorption is mainly an intrinsic quality of the metal particle, and can be explained only with the electronic structure of the metal particle. In the latter, surface resonance state is introduced to systematically discuss the optical absorption spectra of the Ag/SiO2 nanocomposite film. (C) 2003 Elsevier Science B.V. All rights reserved.

Influence of ambient atmosphere on the plasmon resonance absorption of Ag/SiOx(0 <= x <= 2) nanocomposite film

Nanocomposite films consisting of nanosized Ag particles embedded in partially oxidized amorphous Si-containing matrices were prepared by radio frequency magnetron co-sputtering deposition. We studied the influence of ambient atmosphere during the preparation and heat-treatment of Ag/SiOx (0 less than or equal to x less than or equal to 2) nanocompositefilm on its optical absorption properties. We found that the plasmon resonance absorption peak shifts to shorter wavelengths with the increasing oxygen content in the SiOx matrix. The analysis indicates that the potential barrier between Ag nanoparticles and SiOx matrix increases with the increasing x value, which will induce the surface resonance state to shift to higher energy. The electrons in the vicinity of the Fermi level of Ag nanoparticles must absorb more energy to be transferred to the surface resonance state with the increasing x value. It was also found that the plasmon resonance absorption peaks of the samples annealed in different ambient atmospheres are located at about the same position. This is because the oxidation surface layer is dense enough to prevent the oxygen from penetrating into the sample to oxidize the silicon in the inner layer.

Fine structure of the plasmon resonance absorption peak of Ag nanoparticles embedded in partially oxidized Si matrix

Ag/Si nanocomposite films were prepared by the radio-frequency magnetron cosputtering method. The fine structure of the plasmon resonance absorption peak was found in film samples. X-ray photoelectron spectroscopy analysis indicated that the samples were composed of a two-layer structure, which accounted for the structure of the optical absorption spectra. The peak located near 445 nm is the plasmon resonance absorption peak of Ag nanoparticles embedded in a partially oxidized Si matrix. Its intensity decreases with decreasing film thickness and disappears in a very thin sample. The peak located near 380 nm originates from the plasmon resonance absorption of the thoroughly oxidized surface layer of the sample. Its intensity does not change with increasing thickness, but it cannot be observed in the very thick sample. (C) 2001 American Institute of Physics.

The plasmon resonance absorption of Ag/SiO2 nanocomposite films

The plasmon resonance absorption of the Ag/SiO2 nanocomposite film is investigated. The measured absorption spectra are compared with those calculated by the Mie theory. The results indicate that the Mie theory on the basis of classical electrodynamics can only partially explain the optical absorption spectra of the Ag/SiO2 nanocomposite film. We believe that the plasmon resonance absorption is mainly an intrinsic quality of the metal particle, and can be explained only with the electronic structure of the metal particle. In the latter, surface resonance state is introduced to systematically discuss the optical absorption spectra of the Ag/SiO2 nanocomposite film. (C) 2003 Elsevier Science B.V. All rights reserved.