Photo-engineered optoelectronic properties of indium tin oxide via reactive laser annealing.

Transparent conductive oxides are appealing materials for optoelectronic and plasmonic applications as, amongst other advantages, their properties can be modulated by engineering their defects. Optimisation of this adjustment is, however, a complex design problem. This work examined the modification of the carrier transport properties of sputtered tin-doped indium oxide (ITO) via laser annealing in reactive environments. We relate the optical modifications to the structural, compositional, and electronic properties to elucidate the precise mechanisms behind the reactive laser annealing (ReLA) process. For sufficiently high laser fluence, we reveal an ambient-dependent and purely compositional modulation of the carrier concentration of ITO thin films. Hereby, we demonstrate that ReLA utilises the precise energy delivery of photonic processing to enhance the carrier mobility and finely tune the carrier concentration without significantly affecting the crystal structure. Exploitation of this phenomena may enable one to selectively engineer the optoelectronic properties of ITO, promising an alternative to the exploration of new materials for optoelectronic and photonic applications.

Active control of strong plasmon-exciton coupling in biomimetic pigment-polymer antenna complexes grown by surface-initiated polymerisation from gold nanostructures.

Plexcitonic antenna complexes, inspired by photosynthetic light-harvesting complexes, are formed by attachment of chlorophylls (Chl) to poly(cysteine methacrylate) (PCysMA) scaffolds grown by atom-transfer radical polymerisation from gold nanostructure arrays. In these pigment-polymer antenna complexes, localised surface plasmon resonances on gold nanostructures are strongly coupled to Chl excitons, yielding hybrid light-matter states (plexcitons) that are manifested in splitting of the plasmon band. Modelling of the extinction spectra of these systems using a simple coupled oscillator model indicates that their coupling energies are up to twice as large as those measured for LHCs from plants and bacteria. Coupling energies are correlated with the exciton density in the grafted polymer layer, consistent with the collective nature of strong plasmon-exciton coupling. Steric hindrance in fully-dense PCysMA brushes limits binding of bulky chlorophylls, but the chlorophyll concentration can be increased to ∼2 M, exceeding that in biological light-harvesting complexes, by controlling the grafting density and polymerisation time. Moreover, synthetic plexcitonic antenna complexes display pH- and temperature-responsiveness, facilitating active control of plasmon-exciton coupling. Because of the wide range of compatible polymer chemistries and the mild reaction conditions, plexcitonic antenna complexes may offer a versatile route to programmable molecular photonic materials.

Optimization of Apta-Sensing Platform for Detection of Prostate Cancer Marker PCA3.

This work is a continuation of our research into the development of simple, reliable, and cost-effective methods for the early diagnosis of prostate cancer (PCa). The proposed method is based on the electrochemical detection of the PCA3 biomarker of PCa (long non-coded RNA transcript expressed in urine) using a specific aptamer labeled with a redox group (methylene blue). The electrochemical measurements (cyclic voltammograms) obtained from electrodes functionalized with the aptamer were complemented in this work by another biosensing technique: total internal reflection ellipsometry (TIRE). In addition to proving the concept of the detection of PCA3 in low concentrations down to 90 pM, this study improved our understanding of the processes by which PCA3 binds to its specific aptamer. The high specificity of the binding of PCA3 to the aptamer was assessed by studying the binding kinetics, which yielded an affinity constant (KD) of 2.58 × 10-9 M. Additional XPS measurements confirmed the strong covalent binding of aptamers to gold and showed spectral features associated with PCA3 to aptamer binding.

Development of an Immunofluorescence Assay Module for Determination of the Mycotoxin Zearalenone in Water.

Project Aquafluosense is designed to develop prototypes for a fluorescence-based instrumentation setup for in situ measurements of several characteristic parameters of water quality. In the scope of the project an enzyme-linked fluorescent immunoassay (ELFIA) method has been developed for the detection of several environmental xenobiotics, including mycotoxin zearalenone (ZON). ZON, produced by several plant pathogenic Fusarium species, has recently been identified as an emerging pollutant in surface water, presenting a hazard to aquatic ecosystems. Due to its physico-chemical properties, detection of ZON at low concentrations in surface water is a challenging task. The 96-well microplate-based fluorescence instrument is capable of detecting ZON in the concentration range of 0.09-400 ng/mL. The sensitivity and accuracy of the analytical method has been demonstrated by a comparative assessment with detection by high-performance liquid chromatography and by total internal reflection ellipsometry. The limit of detection of the method, 0.09 ng/mL, falls in the low range compared to the other reported immunoassays, but the main advantage of this ELFIA method is its efficacy in combined in situ applications for determination of various important water quality parameters detectable by induced fluorimerty-e.g., total organic carbon content, algal density or the level of other organic micropollutants detectable by immunofluorimetry. In addition, the immunofluorescence module can readily be expanded to other target analytes if proper antibodies are available for detection.

An Optical Planar Waveguide-Based Immunosensors for Determination of Fusarium Mycotoxin Zearalenone.

A planar waveguide (PW) immunosensor working as a polarisation interferometer was developed for the detection of mycotoxin zearalenone (ZON). The main element of the sensor is an optical waveguide consisting of a thin silicon nitride layer between two thicker silicon dioxide layers. A combination of a narrow waveguiding core made by photolithography with an advanced optical set-up providing a coupling of circular polarised light into the PW via its slanted edge allowed the realization of a novel sensing principle by detection of the phase shift between the p- and s-components of polarised light propagating through the PW. As the p-component is sensitive to refractive index changes at the waveguide interface, molecular events between the sensor surface and the contacting sample solution can be detected. To detect ZON concentrations in the sample solution, ZON-specific antibodies were immobilised on the waveguide via an electrostatically deposited polyelectrolyte layer, and protein A was adsorbed on it. Refractive index changes on the surface due to the binding of ZON molecules to the anchored antibodies were detected in a concentration-dependent manner up to 1000 ng/mL of ZON, allowing a limit of detection of 0.01 ng/mL. Structurally unrelated mycotoxins such as aflatoxin B1 or ochratoxin A did not exert observable cross-reactivity.

Highly sensitive label-free in vitro detection of aflatoxin B1 in an aptamer assay using optical planar waveguide operating as a polarization interferometer.

This work reports on further development of an optical biosensor for the in vitro detection of mycotoxins (in particular, aflatoxin B1) using a highly sensitive planar waveguide transducer in combination with a highly specific aptamer bioreceptor. This sensor is built on a SiO2-Si3N4-SiO2 optical planar waveguide (OPW) operating as a polarization interferometer (PI), which detects a phase shift between p- and s-components of polarized light propagating through the waveguide caused by the molecular adsorption. The refractive index sensitivity (RIS) of the recently upgraded PI experimental setup has been improved and reached values of around 9600 rad per refractive index unity (RIU), the highest RIS values reported, which enables the detection of low molecular weight analytes such as mycotoxins in very low concentrations. The biosensing tests yielded remarkable results for the detection of aflatoxin B1 in a wide range of concentrations from 1 pg/mL to 1 µg/mL in direct assay with specific DNA-based aptamers. Graphical abstract Optical planar waveguide polarization interferometry biosensor for detection of aflatoxin B1 using specific aptamer.

Electrochemical inhibition bacterial sensor array for detection of water pollutants: artificial neural network (ANN) approach.

This work reports on further development of an inhibition electrochemical sensor array based on immobilized bacteria for the preliminary detection of a wide range of organic and inorganic pollutants, such as heavy metal salts (HgCl2, PbCl2, CdCl2), pesticides (atrazine, simazine, DDVP), and petrochemicals (hexane, octane, pentane, toluene, pyrene, and ethanol) in water. A series of DC and AC electrochemical measurements, e.g., cyclic voltammograms and impedance spectroscopy, were carried out on screen-printed gold electrodes with three types of bacteria, namely Escherichia coli, Shewanella oneidensis, and Methylococcus capsulatus, immobilized via poly L-lysine. The results obtained showed a possibility of pattern recognition of the above pollutants by their inhibition effect on the three bacteria used. The analysis of a large amount of experimental data was carried out using an artificial neural network (ANN) programme for more accurate identification of pollutants as well as the estimation of their concentration. The results are encouraging for the development of a simple and cost-effective biosensing technology for preliminary in-field analysis (screening) of water samples for the presence of environmental pollutants. Graphical abstract.

Mycotoxin Biosensor Based on Optical Planar Waveguide.

The research aim of this work is to develop a simple and highly sensitive optical biosensor for detection of mycotoxins. This sensor is built on a planar waveguide operating on the polarization interferometry principle, i.e., detecting a phase shift between p- and s-components of polarized light developed during the binding of analyte molecules. The operation of the proposed sensor is similar to that of a Mach⁻Zehnder interferometer, while its design is much simpler and it does not require splitting the waveguide into two arms. The refractive index sensitivity of the polarization interferometer sensor was in the range of 5200 radians per refractive index unit (RIU). Several tests were conducted to detect ochratoxin A (OTA) at different concentrations in direct immunoassay with specific antibodies immobilized in the sensing window. The lowest concentration of OTA of 0.01 ng/mL caused a phase shift of nearly one period. The results obtained prove high sensitivity of the sensors, which are capable of detecting even lower concentrations of mycotoxins at the ppt (part-per-trillion) level.

Label-Free Optical Detection of Mycotoxins Using Specific Aptamers Immobilized on Gold Nanostructures.

This work focuses on the development of the novel label-free optical apta-sensors for detection of mycotoxins. A highly sensitive analytical method of total internal reflection ellipsometry (TIRE) combined with Localized Surface Plasmon Resonance (LSPR) phenomenon in nano-structured gold films was exploited here for the first time for detection of aflatoxin B1 and M1 in direct assay with specific aptamers immobilized on the surface of gold. The achieved detection of low molecular weight molecules, such as aflatoxin B1 and M1, in a wide range of concentrations from 100 ng/mL down to 0.01 ng/mL is remarkable for the LSPR method. The study of binding kinetics of aflatoxin molecules to their respective aptamers using dynamic TIRE measurements yielded the values of affinity constants in the range of 10-8⁻10-7 mol, which is characteristic for highly specific aptamer/target interactions similar to that for monoclonal antibodies. The effect of aptamers' DNA chain length on their binding characteristics was analyzed.

A synthetic biological quantum optical system.

In strong plasmon-exciton coupling, a surface plasmon mode is coupled to an array of localized emitters to yield new hybrid light-matter states (plexcitons), whose properties may in principle be controlled via modification of the arrangement of emitters. We show that plasmon modes are strongly coupled to synthetic light-harvesting maquette proteins, and that the coupling can be controlled via alteration of the protein structure. For maquettes with a single chlorin binding site, the exciton energy (2.06 ± 0.07 eV) is close to the expected energy of the Qy transition. However, for maquettes containing two chlorin binding sites that are collinear in the field direction, an exciton energy of 2.20 ± 0.01 eV is obtained, intermediate between the energies of the Qx and Qy transitions of the chlorin. This observation is attributed to strong coupling of the LSPR to an H-dimer state not observed under weak coupling.

Characterisation of thin films of graphene-surfactant composites produced through a novel semi-automated method.

In this paper we detail a novel semi-automated method for the production of graphene by sonochemical exfoliation of graphite in the presence of ionic surfactants, e.g., sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB). The formation of individual graphene flakes was confirmed by Raman spectroscopy, while the interaction of graphene with surfactants was proven by NMR spectroscopy. The resulting graphene-surfactant composite material formed a stable suspension in water and some organic solvents, such as chloroform. Graphene thin films were then produced using Langmuir-Blodgett (LB) or electrostatic layer-by-layer (LbL) deposition techniques. The composition and morphology of the films produced was studied with SEM/EDX and AFM. The best results in terms of adhesion and surface coverage were achieved using LbL deposition of graphene(-)SDS alternated with polyethyleneimine (PEI). The optical study of graphene thin films deposited on different substrates was carried out using UV-vis absorption spectroscopy and spectroscopic ellipsometry. A particular focus was on studying graphene layers deposited on gold-coated glass using a method of total internal reflection ellipsometry (TIRE) which revealed the enhancement of the surface plasmon resonance in thin gold films by depositing graphene layers.

Fast, simple, combinatorial routes to the fabrication of reusable, plasmonically active gold nanostructures by interferometric lithography of self-assembled monolayers.

We describe a fast, simple method for the fabrication of reusable, robust gold nanostructures over macroscopic (cm(2)) areas. A wide range of nanostructure morphologies is accessible in a combinatorial fashion. Self-assembled monolayers of alkylthiolates on chromium-primed polycrystalline gold films are patterned using a Lloyd's mirror interferometer and etched using mercaptoethylamine in ethanol in a rapid process that does not require access to clean-room facilities. The use of a Cr adhesion layer facilitates the cleaning of specimens by immersion in piranha solution, enabling their repeated reuse without significant change in their absorbance spectra over two years. A library of 200 different nanostructures was prepared and found to exhibit a range of optical behavior. Annealing yielded structures with a uniformly high degree of crystallinity that exhibited strong plasmon bands. Using a combinatorial approach, correlations were established between the preannealing morphologies (determined by the fabrication conditions) and the postannealing optical properties that enabled specimens to be prepared "to order" with a selected localized surface plasmon resonance. The refractive index sensitivity of gold nanostructures formed in this way was found to correlate closely with measurements reported for structures fabricated by other methods. Strong enhancements were observed in the Raman spectra of tetra-tert-butyl-substituted phthalocyanine. The shift in the position of the plasmon band after site-specific attachment of histidine-tagged green fluorescent protein (His-GFP) and bacteriochlorophyll a was measured for a range of nanostructured films, enabling the rapid identification of the one that yielded the largest shift. This approach offers a simple route to the production of durable, reusable, macroscopic arrays of gold nanostructures with precisely controllable morphologies.

Quantification of ligand binding to G-protein coupled receptors on cell membranes by ellipsometry.

G-protein-coupled receptors (GPCRs) are prime drug targets and targeted by approximately 60% of current therapeutic drugs such as ß-blockers, antipsychotics and analgesics. However, no biophysical methods are available to quantify their interactions with ligand binding in a native environment. Here, we use ellipsometry to quantify specific interactions of receptors within native cell membranes. As a model system, the GPCR-ligand CXCL12α and its receptor CXCR4 are used. Human-derived Ishikawa cells were deposited onto gold coated slides via Langmuir-Schaefer film deposition and interactions between the receptor CXCR4 on these cells and its ligand CXCL12α were detected via total internal reflection ellipsometry (TIRE). This interaction could be inhibited by application of the CXCR4-binding drug AMD3100. Advantages of this approach are that it allows measurement of interactions in a lipid environment without the need for labelling, protein purification or reconstitution of membrane proteins. This technique is potentially applicable to a wide variety of cell types and their membrane receptors, providing a novel method to determine ligand or drug interactions targeting GPCRs and other membrane proteins.

Analysis of protein interactions at native chloroplast membranes by ellipsometry.

Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE). We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

Study of receptor-chaperone interactions using the optical technique of spectroscopic ellipsometry.

This work describes a detailed quantitative interaction study between the novel plastidial chaperone receptor OEP61 and isoforms of the chaperone types Hsp70 and Hsp90 using the optical method of total internal reflection ellipsometry (TIRE). The receptor OEP61 was electrostatically immobilized on a gold surface via an intermediate layer of polycations. The TIRE measurements allowed the evaluation of thickness changes in the adsorbed molecular layers as a result of chaperone binding to receptor proteins. Hsp70 chaperone isoforms but not Hsp90 were shown to be capable of binding OEP61. Dynamic TIRE measurements were carried out to evaluate the affinity constants of the above reactions and resulted in clear discrimination between specific and nonspecific binding of chaperones as well as differences in binding properties between the highly similar Hsp70 isoforms.

Hybridization of genomic DNA adsorbed electrostatically onto cationic surfaces.

Our previous study revealed an intriguing phenomenon of partial hybridization of two single strands of genomic DNA, with one of them being electrostatically adsorbed on a solid surface. Although the effect was confirmed with different methods and even recommended for a crude DNA analysis, the exact mechanism of hybridization was not clear. This work presents the results of more detailed study of adsorption and hybridization of two genomic DNA, of salmon and herring, using the experimental techniques of total internal reflection ellipsometry (TIRE), ATR FTIR spectroscopy, and AFM. The in situ TIRE study of the hybridization kinetics allowed the evaluation of the association constant. It appeared to be in the range of 10(5) mol(-1) L for binding complementary ss-DNA in comparison to 10(4) mol(-1) L for binding of noncomplementary ss-DNA. FTIR study directly confirmed the effect of partial binding of complementary ss-DNA by monitoring the 1650 and 1690 cm(-1) spectral bands. AFM showed the transformation from clearly resolved images of separate chains of ss-DNA molecules adsorbed on the surface of mica to an inhomogeneous layer of tangled and overlapping DNA molecules following binding of another complementary ss-DNA.

Specific binding of large aggregates of amphiphilic molecules to the respective antibodies.

The Binding of nonylphenol to respective antibodies immobilized on solid substrates was studied with the methods of total internal reflection ellipsometry (TIRE) and QCM (quartz crystal microbalance) impedance spectroscopy. The binding reaction was proved to be highly specific having an association constant of KA=1.6x10(6) mol(-1) L and resulted in an increase in both the adsorbed layer thickness of 23 nm and the added mass of 18.3 microg/cm2 at saturation. The obtained responses of both TIRE and QCM methods are substantially higher than anticipated for the immune binding of single molecules of nonylphenol. The mechanism of binding of large aggregates of nonylphenol was suggested instead. Modeling of the micelle of amphiphilic nonylphenol molecules in aqueous solutions yielded a micelle size of about 38 nm. The mechanism of binding of large molecular aggregates to respective antibodies can be extended to other hydrophobic low-molecular-weight toxins such as T-2 mycotoxin. The formation of large molecular aggregates of nonylphenol and T-2 mycotoxin molecules on the surface was proved by the AFM study.

The study of genomic DNA adsorption and subsequent interactions using total internal reflection ellipsometry.

The adsorption of genomic DNA and subsequent interactions between adsorbed and solvated DNA was studied using a novel sensitive optical method of total internal reflection ellipsometry (TIRE), which combines spectroscopic ellipsometry with surface plasmon resonance (SPR). Single strands of DNA of two species of fish (herring and salmon) were electrostatically adsorbed on top of polyethylenimine films deposited upon gold coated glass slides. The ellipsometric spectra were recorded and data fitting utilized to extract optical parameters (thickness and refractive index) of adsorbed DNA layers. The further adsorption of single stranded DNA from an identical source, i.e. herring ss-DNA on herring ss-DNA or salmon ss-DNA on salmon ss-DNA, on the surface was observed to give rise to substantial film thickness increases at the surface of about 20-21 nm. Conversely adsorption of DNA from alternate species, i.e. salmon ss-DNA on herring ss-DNA or herring ss-DNA on salmon ss-DNA, yielded much smaller changes in thickness of 3-5 nm. AFM studies of the surface roughness of adsorbed layers were in line with the TIRE data.