In this paper, we present a new type of guided-mode resonance (GMR)-based sensor that utilizes a planar waveguide structure (PWS). We employed a PWS with an asymmetric three-layer waveguide structure consisting of substrate/Au/photoresist. The ellipsometric characterization of the structure layers, the simulated reflectance spectra, and optical field distributions under GMR conditions showed that multiple waveguide modes can be excited in the PWS. These modes can be used for refractive index sensing, and the theoretical analysis of the designed PWS showed a sensitivity to the refractive index up to 6600 nm per refractive index unit (RIU) and a figure of merit (FOM) up to 224 RIU-1. In response to these promising theoretical results, the PWS was used to measure the relative humidity (RH) of moist air with a sensitivity up to 0.141 nm/%RH and a FOM reaching 3.7 × 10-3%RH-1. The results demonstrate that this highly-sensitive and hysteresis-free sensor based on GMR has the potential to be used in a wide range of applications.

• Klíčová slova
• figure of merit, guided-mode resonance, humidity sensor, planar waveguide structure, resonance wavelength, sensitivity,
• Publikační typ
• dopisy MeSH

The growth of surface-attached single-stranded deoxyribonucleic acid (ssDNA) chains is monitored in situ using an evanescent wave optical biosensor that combines surface plasmon resonance (SPR) and optical waveguide spectroscopy (OWS). The "grafting-from" growth of ssDNA chains is facilitated by rolling circle amplification (RCA), and the gradual prolongation of ssDNA chains anchored to a gold sensor surface is optically tracked in time. At a sufficient density of the polymer chains, the ssDNA takes on a brush architecture with a thickness exceeding 10 μm, supporting a spectrum of guided optical waves traveling along the metallic sensor surface. The simultaneous probing of this interface with the confined optical field of surface plasmons and additional more delocalized dielectric optical waveguide modes enables accurate in situ measurement of the ssDNA brush thickness, polymer volume content, and density gradients. We report for the first time on the utilization of the SPR/OWS technique for the measurement of the RCA speed on a solid surface that can be compared to that in bulk solutions. In addition, the control of ssDNA brush properties by changing the grafting density and ionic strength and post-modification via affinity reaction with complementary short ssDNA staples is discussed. These observations may provide important leads for tailoring RCA toward sensitive and rapid assays in affinity-based biosensors.

• Klíčová slova
• DNA, biointerfaces, optical waveguide spectroscopy, polyelectrolyte brushes, rolling circle amplification, surface plasmon resonance, surface plasmon-enhanced fluorescence,
• MeSH
• biosenzitivní techniky MeSH
• časové faktory MeSH
• jednovláknová DNA genetika   MeSH
• optické jevy * MeSH
• povrchová plasmonová rezonance metody   MeSH
• spektrální analýza * MeSH
• techniky amplifikace nukleových kyselin * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• jednovláknová DNA MeSH

Diamond thin films have remarkable properties comparable with natural diamond. Because of these properties it is a very promising material for many various applications (sensors, heat sink, optical mirrors, chemical and radiation wear, cold cathodes, tissue engineering, etc.) In this paper we report about design, deposition and measurement of properties of optical planar waveguides fabricated from nanocrystalline diamond thin films. The nanocrystalline diamond planar waveguide was deposited by microwave plasma enhanced chemical vapor deposition and the structure of the deposited film was studied by scanning electron microscopy and Raman spectroscopy. The design of the presented planar waveguides was realized on the bases of modified dispersion equation and was schemed for 632.8 nm, 964 nm, 1 310 nm and 1 550 nm wavelengths. Waveguiding properties were examined by prism coupling technique and it was found that the diamond based planar optical element guided one fundamental mode for all measured wavelengths. Values of the refractive indices of our NCD thin film measured at various wavelengths were almost the same as those of natural diamond.

• MeSH
• analýza selhání vybavení MeSH
• design vybavení MeSH
• diamant chemie   MeSH
• krystalizace MeSH
• nanočástice chemie   MeSH
• nanotechnologie přístrojové vybavení   MeSH
• povrchová plasmonová rezonance přístrojové vybavení   MeSH
• refraktometrie přístrojové vybavení   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• diamant MeSH

Membrane-bound pyrophosphatases couple the hydrolysis of inorganic pyrophosphate to the pumping of ions (sodium or protons) across a membrane in order to generate an electrochemical gradient. This class of membrane protein is widely conserved across plants, fungi, archaea, and bacteria, but absent in multicellular animals, making them a viable target for drug design against protozoan parasites such as Plasmodium falciparum. An excellent understanding of many of the catalytic states throughout the enzymatic cycle has already been afforded by crystallography. However, the dynamics and kinetics of the catalytic cycle between these static snapshots remain to be elucidated. Here, we employ single-molecule Förster resonance energy transfer (FRET) measurements to determine the dynamic range and frequency of conformations available to the enzyme in a lipid bilayer during the catalytic cycle. First, we explore issues related to the introduction of fluorescent dyes by cysteine mutagenesis; we discuss the importance of residue selection for dye attachment, and the balance between mutating areas of the protein that will provide useful dynamics while not altering highly conserved residues that could disrupt protein function. To complement and guide the experiments, we used all-atom molecular dynamics simulations and computational methods to estimate FRET efficiency distributions for dye pairs at different sites in different protein conformational states. We present preliminary single-molecule FRET data that points to insights about the binding modes of different membrane-bound pyrophosphatase substrates and inhibitors.

• Klíčová slova
• Conformational change, Cysteine mutagenesis, Ion pumping, Molecular dynamics simulation, mPPase, smALEX, smFRET,
• MeSH
• bakteriální proteiny chemie   genetika   izolace a purifikace   metabolismus   MeSH
• buněčná membrána metabolismus   MeSH
• enzymatické testy přístrojové vybavení   metody   MeSH
• fluorescenční barviva chemie   MeSH
• fluorescenční mikroskopie přístrojové vybavení   metody   MeSH
• mutageneze MeSH
• protozoální proteiny chemie   genetika   izolace a purifikace   metabolismus   MeSH
• pyrofosfatasy chemie   genetika   izolace a purifikace   metabolismus   MeSH
• racionální návrh léčiv MeSH
• rekombinantní proteiny chemie   genetika   izolace a purifikace   metabolismus   MeSH
• rezonanční přenos fluorescenční energie přístrojové vybavení   metody   MeSH
• Saccharomyces cerevisiae MeSH
• sekvenční seřazení MeSH
• simulace molekulární dynamiky * MeSH
• software MeSH
• zobrazení jednotlivé molekuly přístrojové vybavení   metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• fluorescenční barviva MeSH
• protozoální proteiny MeSH
• pyrofosfatasy MeSH
• rekombinantní proteiny MeSH

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. This similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives, as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, L-carnitine, and glycine betaine effectively.The choline-binding protein ChoX exhibits a synergistic dual-site binding mode that allows it to discriminate choline over structural analogues. Here, the authors design a biomimetic triple anion helicate receptor whose selectivity for choline arises from a similar binding mechanism.

• MeSH
• acetylcholin chemie   metabolismus   MeSH
• bakteriální proteiny chemie   metabolismus   MeSH
• cholin chemie   metabolismus   MeSH
• fosfáty chemie   metabolismus   MeSH
• kinetika MeSH
• kompetitivní vazba MeSH
• krystalografie rentgenová MeSH
• membránové transportní proteiny chemie   metabolismus   MeSH
• molekulární modely MeSH
• proteinové domény * MeSH
• protonová magnetická rezonanční spektroskopie MeSH
• Sinorhizobium meliloti metabolismus   MeSH
• transportní proteiny chemie   metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• acetylcholin MeSH
• bakteriální proteiny MeSH
• cholin MeSH
• choline transporter MeSH Prohlížeč
• fosfáty MeSH
• membránové transportní proteiny MeSH
• transportní proteiny MeSH

The Letter suggests treating the infrared reflectivity spectra of single crystal perovskite relaxors as fine-grained ferroelectric ceramics: locally frozen polarization makes the dielectric function strongly anisotropic in the phonon frequency range and the random orientation of the polarization at nanoscopic scale requires taking into account the inhomogeneous depolarization field. Employing a simple effective medium approximation (the Bruggeman symmetrical formula) turns out to be sufficient for reproducing all principal features of room temperature reflectivity of Pb(Mg(1/3)Nb(2/3))O3. One of the reflectivity bands is identified as a geometrical resonance entirely related to the nanoscale polarization inhomogeneity. The approach provides a general guide for systematic determination of the polar mode frequencies split by the inhomogeneous polarization at the nanometer scale.

• Publikační typ
• časopisecké články MeSH

A self-contained formulation for analyzing electromagnetic scattering by a significant class of planar gratings composed of plasmonic nanorods, which were infinite length along their axes, is presented. The procedure for the lattice sums technique was implemented in a cylindrical harmonic expansion method based on the generalized reflection matrix approach for full-wave scattering analysis of plasmonic gratings. The method provided a high computational efficiency and can be considered as one of the best-suited numerical tools for the optimization of plasmonic sensors and plasmonic guiding devices both having a planar geometry. Although the proposed formalism can be applied to analyze a wide class of plasmonic gratings, three configurations were studied in the manuscript. Firstly, a multilayered grating of silver nanocylinders formed analogously to photonic crystals was considered. In the region far from the resonances of a single plasmonic nanocylinder, the structure showed similar properties compared to conventional photonic crystals. When one or a few nanorods were periodically removed from the original crystal, thus forming a crystal with defects, a new band was formed in the spectral responses because of the resonant tunneling through the defect layers. The rigorous formulation of plasmonic gratings with defects was proposed for the first time. Finally, a plasmonic planar grating of metal-coated dielectric nanorods coupled to the dielectric slab was investigated from the viewpoint of design of a refractive index sensor. Dual-absorption bands attributable to the excitation of the localized surface plasmons were studied, and the near field distributions were given in both absorption bands associated with the resonances on the upper and inner surfaces of a single metal-coated nanocylinder. Resonance in the second absorption band was sensitive to the refractive index of the background medium and could be useful for the design of refractive index sensors. Also analyzed was a phase-matching condition between the evanescent space-harmonics of the plasmonic grating and the guided modes inside the slab, leading to a strong coupling.

• Klíčová slova
• bandgap structures, periodic structures, plasmonics, refractive index sensors, scattering,
• Publikační typ
• časopisecké články MeSH

Thin film solar cells are one of the important candidates utilized to reduce the cost of photovoltaic production by minimizing the usage of active materials. However, low light absorption due to low absorption coefficient and/or insufficient active layer thickness can limit the performance of thin film solar cells. Increasing the absorption of light that can be converted into electrical current in thin film solar cells is crucial for enhancing the overall efficiency and in reducing the cost. Therefore, light trapping strategies play a significant role in achieving this goal. The main objectives of light trapping techniques are to decrease incident light reflection, increase the light absorption, and modify the optical response of the device for use in different applications. Nanostructures utilize key sets of approaches to achieve these objectives, including gradual refractive index matching, and coupling incident light into guided modes and localized plasmon resonances, as well as surface plasmon polariton modes. In this review, we discuss some of the recent developments in the design and implementation of nanostructures for light trapping in solar cells. These include the development of solar cells containing photonic and plasmonic nanostructures. The distinct benefits and challenges of these schemes are also explained and discussed.

• Klíčová slova
• light trapping, photonic nanostructures, plasmonic nanostructures, solar cells, thin films,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Photoelectrochemical (PEC) water splitting is a promising approach for producing hydrogen without greenhouse gas emissions. Despite decades of unceasing efforts, the efficiency of PEC devices based on earth-abundant semiconductors is still limited by their low light absorption, low charge mobility, high charge-carrier recombination, and reduced diffusion length. Plasmonics has recently emerged as an effective approach for overcoming these limitations, although a full understanding of the involved physical mechanisms remains elusive. Here, the reported plasmonic effects are outlined, such as resonant energy transfer, scattering, hot electron injection, guided modes, and photonic effects, as well as the less investigated catalytic and thermal effects used in PEC water splitting. In each section, the fundamentals are reviewed and the most representative examples are discussed, illustrating possible future developments for achieving improved efficiency of plasmonic photoelectrodes.

• Klíčová slova
• hydrogen production, photoelectrochemistry, photonic nanostructures, surface plasmons, water splitting,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH