Single Dimer Research Articles

Absorption cross-section spectroscopy of a single strong-coupling system between plasmon and molecular exciton resonance using a single silver nanoparticle dimer generating surface-enhanced resonant Raman scattering

This study investigated spectral changes in the absorption cross-sections of single strong coupling systems composed of single silver nanoparticle dimers and a few dye molecules during the quenching of surface-enhanced resonant Raman scattering (SERRS). The absorption cross-section was obtained by subtracting the scattering cross-section from an extinction cross-section. The spectral changes in these cross-sections were evaluated using a classical hybridization model composed of a plasmon and a molecular exciton including a molecular multi-level property. The changes in the scattering and extinction cross-sections exhibit blue-shifts in their peak energy and increased peak intensities, respectively, during SERRS quenching. These properties are effectively reproduced in the model by decreasing the coupling energy. In particular, the peaks in the scattering and extinction cross-sections appear as peaks or dips in the absorption cross-sections depending on the degree of scattering loss, which reflects the dimer sizes. These results are useful for optimizing photophysical and photochemical effects mediated by the electronic excited states of strong coupling systems.

Double-negative acoustic metamaterials

The aim of this paper is to provide a mathematical theory for understanding the mechanism behind the double-negative refractive index phenomenon in bubbly fluids. The design of double-negative metamaterials generally requires the use of two different kinds of subwavelength resonators, which may limits the applicability of double-negative metamaterials. Herein we rely on media that consists of only a single type of resonant element, and show how to turn the acoustic metamaterial with a single negative effective property obtained in [H. Ammari and H. Zhang, Effective medium theory for acoustic waves in bubbly fluids near Minnaert resonant frequency. SIAM J. Math. Anal., 49 (2017), 3252--3276.] into a negative refractive index metamaterial, which refracts waves negatively, hence acting as a superlens. Using bubble dimers made of two identical bubbles, it is proved that both the effective mass density and the bulk modulus of the bubbly fluid can be negative near the anti-resonance of the two hybridized Minnaert resonances for a single constituent bubble dimer. A rigorous justification of the Minnaert resonance hybridization, in the case of a bubble dimer in a homogeneous medium, is established. The acoustic properties of a single bubble dimer are analyzed. Asymptotic formulas for the two hybridized Minnaert resonances are derived. Moreover, it is proved that the bubble dimer can be approximated by a point scatterer with monopole and dipole modes. For an appropriate volume fraction of bubble dimers with certain conditions on their configuration, a double-negative effective medium when the frequency is near the anti-resonance of the hybridized Minnaert resonances can be obtained.

Tunable strong plasmon-exciton coupling between single silver nanocube dimer and J-aggregates

In this paper, single silver nanocube dimer with nanometer-sized gap is designed and numerically simulated. We demonstrate that the electric fields can be highly confined in the gap of nanocube dimer, leading to ultrasmall mode volume of ≈2 × 10-7 μm3. Furthermore, the strong plasmon-exciton coupling in single nanocube dimer coupled with J-aggregate molecules is investigated using coupled oscillator model and we show that the strong plasmon-exciton coupling can be tuned by changing the background refractive index and the concentration of J-aggregate molecules. The tuning of dual strong plasmon-exciton couplings between single rounded silver nanocube dimer and J-aggregate molecules is also investigated, and dual strong couplings can be achieved closely approaching the quantum optics limit benefiting from the ultrasmall mode volume of the proposed system. The proposed systems can be easily prepared and have high experimental feasibility, which has potential applications in integrated nanophotonics such as sensing and all-optical switches.

A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family

TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcriptional silencing of many endogenous retroviral elements and genomic imprinted sites. Silencing is initiated by the recruitment of TRIM28 to a target locus by members of the Krab-ZFP. Subsequently, TRIM28 functions as a scaffold protein to recruit chromatin modifying effectors featuring SETDB1, HP1 and the NuRD complex. Although many protein partners involved in silencing have been identified, the molecular basis of the protein interactions that mediate silencing remains largely unclear. In the present study, we identified the first Bbox domain (T28_B1 135–203) as a molecular interface responsible for the formation of higher-order oligomers of TRIM28. The structure of this domain reveals a new interface on the surface of the Bbox domain. Mutants disrupting the interface disrupt the formation of oligomers but have no observed effect on transcriptional silencing defining a single TRIM28 dimer as the functional unit for silencing. Using assembly-deficient mutants, we employed small-angle X-ray scattering and biophysical techniques to characterize binding to member of the Krab-ZFP family. This allows us to narrow and define the binding interface to the center of the coiled-coil region (residues 294–321) of TRIM28 and define mutants that abolish binding to the Krab-ZFP proteins.

Janus Dimers at Liquid-Liquid Interfaces.

We study the impact of selected parameters on the behavior of Janus-like dimers at liquid-liquid interface. The equilibrium orientation and the adsorption depth of a single Janus dimer are calculated using a simple phenomenological method. We have also performed molecular dynamics simulations for different numbers of Janus dimers trapped at the interface between two partially miscible Lennard-Jones fluids. The particles with different wettabilities of both parts of Janus dimers are considered. Depending on the assumed energy parameters, we observe various structures: orientationally ordered monolayers, fractal-like aggregates, compact clusters, and ordered multilayers containing alternately arranged layers built of Janus particles and molecules of the fluids.

The structure of apoA‐II on HDL reveals novel insights into its regulation of lipoprotein composition and function

High‐density lipoproteins (HDL) are compositionally and functionally diverse. HDL can host at least 95 different proteins and studies suggest many of these interactions are governed by specific conformations of HDL's primary scaffold protein, apolipoprotein (apo)A‐I. Previously, we showed that the presence of HDL's second most abundant scaffold protein, apoA‐II, impacts particle composition and function; presumably through interactions with apoA‐I. The goal of this study was to determine the structural conformation of apoA‐II on HDL to understand how its presence impacts HDL metabolism.We used chemical cross‐linking and mass spectrometry to derive spatial information on homogenous populations of recombinant HDL (rHDL) generated in vitro. The rHDL was created using a mixture of wild‐type and isotopically‐labeled apoA‐I to unambiguously identify the molecular span of the cross‐linked peptides; i.e. within a molecule of apoA‐I (intramolecular) or between two molecules of apoA‐I (intermolecular). Two rHDL populations were studied: (i) rHDL that contained only apoA‐I (LpA‐I) and (ii) rHDL containing both apoA‐I and apoA‐II (LpA‐I/A‐II).Cross‐linking and SDS‐PAGE showed both populations contained two molecules of apoA‐I while the LpA‐I/A‐II rHDL contained a single dimer of apoA‐II. Analysis by negative stain electron microscopy revealed both populations were discoidal in shape with no differences in size. The intermolecular cross‐linking pattern between apoA‐I molecules were consistent with the “double‐belt” model of apoA‐I on HDL and, surprisingly, the presence of apoA‐II didn't appear to perturb the pattern. However, we observed strong cross‐links between apoA‐II and the C‐terminus of apoA‐I.In a parallel approach, native LpA‐I and LpA‐I/A‐II HDL was isolated from human plasma using immunoaffinity and size exclusion chromatography. Shotgun proteomics and cross‐linking revealed accessory proteins were mostly associated with LpA‐I HDL and interactions were primarily localized to the N‐ and C‐termini of apoA‐I. As with the rHDL, we found apoA‐II specifically interacts with the C‐terminus of apoA‐I in the LpA‐I/A‐II particles. Taken together, this suggests that apoA‐II's compositional and functional effects on HDL are exerted via its interaction with the C‐terminus of apoA‐I possibly limiting its availability to interact with the accessory proteins. We have gone on to generate preliminary all‐atoms models of apoA‐II on HDL to illustrate this structural mechanism.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Optimising surface d charge of AuPd nanoalloy catalysts for enhanced catalytic activity

Understanding the catalytic mechanism of bimetallic nanocatalysts remains challenging. Here, we adopt an adsorbate mediated thermal reduction approach to yield monodispersed AuPd catalysts with continuous change of the Pd-Au coordination numbers embedded in a mesoporous carbonaceous matrix. The structure of nanoalloys is well-defined, allowing for a direct determination of the structure-property relationship. The results show that the Pd single atom and dimer are the active sites for the base-free oxidation of primary alcohols. Remarkably, the d-orbital charge on the surface of Pd serves as a descriptor to the adsorbate states and hence the catalytic performance. The maximum d-charge gain occurred in a composition with 33–50 at% Pd corresponds to up to 9 times enhancement in the reaction rate compared to the neat Pd. The findings not only open an avenue towards the rational design of catalysts but also enable the identification of key steps involved in the catalytic reactions.

Activation of MoS2 monolayers by substitutional copper and silver atoms embedded in sulfur vacancies: A theoretical study

Defective molybdenum disulfide monolayers, with up to three copper and silver atoms substituting sulfur atoms, were studied at a dispersion-corrected DFT level. By the first time, changes produced on electronic properties, reactivity, charge distribution and electrostatic potential by trapping these atoms are widely discussed. Embedded species are expected to remain stable and fixed, since large and favorable metal cluster-vacancy defective monolayer binding energies are obtained, higher than – 2.60 eV in all cases. Several defect states are induced in the forbidden region, being the band gap reduced as more substitutional atoms are added. These states mostly come from molybdenum d and p orbitals from embedded metals. Also, defects reduce the gap up to 0.10 and 0.35 eV, for copper and silver trimers, respectively. Substitutional single atoms and dimers donate charge to molybdenum atoms in the middle layer, whereas trimers tend to accumulate it. However, charge transfer is marginal and the most important rearrangements are produced in atoms neighboring defects. Regions with lower electrostatic potential are produced around the defects. Condensed Fukui indices reveal that systems with defects enhanced the chemical reactivity, towards nucleophilic and nucleophilic attacks, in regions around the embedded species. In contrast to the chemically inert pristine MoS2 monolayer, changes on electronic, energetic properties and reactivity of all defective systems indicate that are promising materials for catalytic purposes and to adsorb other molecules.

Enhancement of electric and magnetic dipole transition of rare-earth-doped thin films tailored by high-index dielectric nanostructures.

We propose a simple experimental technique to separately map the emission from electric and magnetic dipole transitions close to single dielectric nanostructures, using a few-nanometer thin film of rare-earth-ion-doped clusters. Rare-earth ions provide electric and magnetic dipole transitions of similar magnitude. By recording the photoluminescence from the deposited layer excited by a focused laser beam, we are able to simultaneously map the electric and magnetic emission enhancement on individual nanostructures. In spite of being a diffraction-limited far-field method with a spatial resolution of a few hundred nanometers, our approach appeals by its simplicity and high signal-to-noise ratio. We demonstrate our technique at the example of single silicon nanorods and dimers, in which we find a significant separation of electric and magnetic near-field contributions. Our method paves the way towards the efficient and rapid characterization of the electric and magnetic optical response of complex photonic nanostructures.

Surface Plasmon Coupling in Dimers of Gold Nanoparticles: Experiment and Theory for Ideal (Spherical) and Nonideal (Faceted) Building Blocks

The surface plasmon (SP) coupling in dimers of spherical and faceted gold nanoparticles was investigated experimentally and computationally at the single-particle level. Individual ideal dimers of two spherical gold nanoparticles with a constant gap, filled by a self-assembled monolayer of 1,8-octanedithiol linker molecules, exhibit highly uniform dark-field (DF) scattering spectra. In contrast, single nonideal dimers of two faceted gold nanoparticles with the same constant gap exhibit a high degree of spectral nonuniformity. We attribute this significant spectral heterogeneity to the many possible gap morphologies, that is, the many possible configurations of the crystal facet orientations at the junction of the two faceted particles in nonideal dimers. This configurational complexity is reduced in so-called hybrid dimers, which comprise an ideal spherical particle and a nonideal faceted particle. Hybrid dimers were therefore investigated theoretically and experimentally for revealing the influence of cr...

Plasmonic Properties of Nano- and Microscale Dielectric Substrates-Supported Nanoshell Dimers: Effects of Type and Propagation Direction of Excitation Light

Herein, we report a finite element method simulated near-field spectra of single nanoshell dimers placed over nano- and microscale dielectric substrates. The simulations have been carried out on an individual basis for the top and bottom illuminated nanodimers with a plane wave and a focused Gaussian beam. Only one peak has been observed in the near-field spectra of free-standing and nano-scale substrate-supported nanodimers, due to the constructive coupling of fundamental modes of nanoshells at the nanogap. The wavelength location of the peak has been slightly red shifted in the presence of the nano-scale dielectric substrate. But, the obtained spectra have been found nearly independent with the type and direction of propagation of excitation light $({\boldsymbol k}_{exc})$ . However, multiple peaks have been noticed in the near-field spectra in the presence of microscale substrates due to the constructive coupling of lower as well as higher order modes (multipolar modes) of nanoshells at the nanogap. In contrast, the near-field spectra have been found sensitive to all dimensions of the substrate, the type of excitation light, and the direction of $({\boldsymbol k}_{exc})$ . Moreover, the far-field scattering spectra of a microscale substrate supported nanodimers have also been found sensitive to the direction of $({\boldsymbol k}_{exc})$ .

Одиночные центры и димеры примесных ионов гольмия в кристаллах синтетического форстерита: спектроскопия высокого разрешения

AbstractHigh-resolution low-temperature absorption spectra in the region of the ^5 I _8 → ^5 I _7, 6, 5, 4, ^5 F _5 transitions in impurity Ho^3+ ions in synthetic forsterite crystals (Mg_2SiO_4) are recorded. Comparison of the observed shape of the spectral lines with the hyperfine structure calculated using crystal-field theory makes it possible to attribute the spectral lines to single centers and dimers for the first time.

Reproduction of surface-enhanced resonant Raman scattering and fluorescence spectra of a strong coupling system composed of a single silver nanoparticle dimer and a few dye molecules.

The spectral changes in surface-enhanced resonant Raman scattering (SERRS) and surface enhanced fluorescence (SEF) of single silver nanoparticle dimers adsorbed by near-single dye molecules are reproduced under strong coupling regimes. For the reproduction, the enhancement and quenching factors in SERRS and SEF are derived from the Purcell factors including both radiative and nonradiative plasmon modes. The Purcell factors are estimated using the coupling energies obtained by analyzing the spectral changes in plasmon resonance during SERRS and SEF decay processes on the basis of a classical hybridization model. The model is composed of a plasmon and a molecular exciton with phonon replicas accurately representing the molecular multi-level system. The reproduced SERRS spectral changes are consistent with the experimental ones. Furthermore, the calculated SEF spectral changes can reproduce the experimental ones by phenomenologically assuming transitions from ultra-fast SEF to conventional SEF with decreasing coupling energies.

Hydrophobic assembly of gold nanoparticles into plasmonic oligomers with Langmuir–Blodgett film

Hydrophobic effect was utilized to self-assemble gold nanoparticles into oligomer structures, or plasmonic dimers, trimers, and so on. Langmuir–Blodgett film of n-octadecanamine was prepared on a glass substrate. Citrate-stabilized gold nanoparticles were adsorbed onto the film, resulting hydrophobic point decoration. The gold nanoparticles with the point decoration were removed from the substrate and self-assembled into plasmonic dimers in ethanol. The products were observed by an atomic force microscope, where not only dimers but also trimers and other aggregates were found. The yield of the plasmonic dimer was ∼13% without any purifications. We measured the scattering spectrum of the single plasmonic dimer, exhibiting the optical anisotropy.

Design of Efficient Catalysts for CO Oxidation on Titanium Carbide-Supported Platinum via Computational Study

The formation, geometries, electronic structures, and catalytic properties of monovacancy and divacancy of the defective TiC(001) with single Pt atom and Pt dimer are systematically studied based on the first-principles calculations. Compared with the diffusion barrier of Pt1 on VC-TiC(001), Pt2 on VC-TiC(001) has a larger diffusion barrier, indicating that the VC-TiC(001) substrate can stabilize the Pt dimer and inhibit its diffusion efficiently. Compared with the Pt1/VC-TiC(001), the DOS plot of Pt2/VC-TiC(001) presents a peak at the Fermi energy caused by variations in the electronic structure of the VC-TiC(001)-modified outermost Pt2, which indicates that the supported Pt2 has a high activity on VC-TiC(001). The steady Pt2/VC-TiC(001) catalyst exhibits outstanding activity for CO oxidation in the Langmuir–Hinshelwood (LH) and termolecular Eley–Rideal (TER) mechanisms for the rate-limiting step of the OOCO and OCOOCO dissociation, having the energy barriers of 0.32 and 0.52 eV, respectively, which are both more preferable than the Eley–Rideal (ER) mechanism. Therefore, the Pt2/VC-TiC(001) is quite efficient for CO oxidation. The existing results are expected to help us to develop efficient catalysts that are highly tolerant to CO poisoning.

Nanomechanical Plasmon Spectroscopy of Single Gold Nanoparticles

We experimentally demonstrate the effect of the localized surface plasmon resonance (LSPR) of a single gold nanoparticle (AuNP) of 100 nm in diameter on the mechanical resonance frequency of a free-standing silicon nitride membrane by means of optomechanical transduction. We discover that a key effect to explain the coupling in these systems is the extinction cross section enhancement due to the excitation of the LSPR at selected wavelengths. In order to validate this coupling, we have developed a fixed wavelength interferometric readout system with an integrated tunable laser source, which allows us to perform the first experimental demonstration of nanomechanical spectroscopy of deposited AuNPs onto the membrane, discerning in between single particles and dimers by the mechanical frequency shift. We have also introduced three-axis mechanical scanners with nanometer-scale resolution in our experimental setup to selectively study single nanoparticles or small clusters. Whereas the single particles are polarization-insensitive, the gold dimers have a clearly defined polarization angle dependency as expected by theory. Finally, we found an unexpected long-distance (∼200 nm) coupling of the LSPR of separated AuNPs coming out from the guided light by the silicon nitride membrane.

Probing the intracellular refractive index and molecular interaction of gold nanoparticles in HeLa cells using single particle spectroscopy.

BackgroundWe have introduced a novel method to quantify the intracellular refractive index (RI) of living cells and determine the molecular interaction of two interacting molecules using single particle spectroscopy. The advantages of this proposed technique over fluorescence-based imaging techniques is that it does not require any contrasting agent and it does not blink and bleach. Instead, our technique provides a non-destructive, non-invasive, high-resolution imaging of live cells.MethodsTo verify our technique, we initially tested our approach for a dielectric medium where gold nanoparticles (AuNPs) were embedded in a polyvinyl alcohol (PVA) matrix, which was then extended to the cellular environment. In the dielectric medium, we identified the single particle and dimer and determined the interparticle distance of AuNPs using confocal laser scattering microscopy. We also determined the single particle RI from dark-field scattering microscopy images, which was confirmed with Mie theory and finite-difference time-domain (FDTD) simulated results. The single particle spectroscopy and microscopy technique was then extended to determine the intracellular RI and biomolecular interaction inside living cells using hyperspectral imaging and dark-field scattering microscopy.ResultsThe novelty of the paper lies in the demonstration of a direct and accurate method to probe the intracellular RI and molecular interaction focused on single particle analysis whereas previous demonstrations were based on AuNP ensembles. Optically acquired single particle and dimer images was verified by correlated SEM images also optical spectrum with analytical models and FDTD simulations for both the dielectric and cellular environment. We reported the interparticle distance of AuNPs inside HeLa cells and intracellular refractive index, which was also confirmed with Mie Theory and extensive FDTD simulations.ConclusionMoreover, we believe that our in-depth plasmonic NP-based alternate imaging technique will provide a new insight in monitoring cellular dynamics and tracking the targeted NPs within live cells, enabling us to use plasmonic NPs as an intracellular biosensor.

Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1.

Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3–H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3–H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3–H4 onto substrate DNA. The CAF-1 trimer binds to a single H3–H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3–H4 complexes co-associate on nucleosome-free DNA depositing (H3–H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.

A single XLF dimer bridges DNA ends during nonhomologous end joining.

Non-homologous end joining (NHEJ) is the primary pathway of DNA double-strand break repair in vertebrate cells, yet it remains unclear how NHEJ factors assemble a synaptic complex that bridges DNA ends. To address the role of XRCC4-like factor (XLF) in synaptic complex assembly, we employed single-molecule fluorescence imaging in Xenopus laevis egg extract, a system that efficiently joins DNA ends. We find that a single XLF dimer binds to DNA substrates just prior to formation of a ligation-competent synaptic complex between DNA ends. The interaction of both globular head domains of the XLF dimer with XRCC4 is required for efficient formation of this synaptic complex. In contrast to a model in which filaments of XLF and XRCC4 bridge DNA ends, our results indicate that binding of a single XLF dimer facilitates the assembly of a stoichiometrically well-defined synaptic complex.

Regulation of UvrD Helicase Activity by MutL

Escherichia coli UvrD is a superfamily 1 helicase/translocase involved in multiple DNA metabolic processes including methyl-directed mismatch DNA repair. Although a UvrD monomer can translocate along single-stranded DNA, a UvrD dimer is needed for processive helicase activity in vitro. E. coli MutL, a regulatory protein involved in methyl-directed mismatch repair, stimulates UvrD helicase activity; however, the mechanism is not well understood. Using single-molecule fluorescence and ensemble approaches, we find that a single MutL dimer can activate latent UvrD monomer helicase activity. However, we also find that MutL stimulates UvrD dimer helicase activity. We further find that MutL enhances the DNA-unwinding processivity of UvrD. Hence, MutL acts as a processivity factor by binding to and presumably moving along with UvrD to facilitate DNA unwinding.