I. Raptis

Integrated optical frequency-resolved Mach-Zehnder interferometers for label-free affinity sensing

Integrated Optical Frequency-Resolved Mach-Zehnder Interferometry (IO FR-MZI) is introduced as an alternative, cost-efficient operation principle for integrated optical label-free affinity sensors that can combine high sensitivity with high versatility in terms of potential applications and experimental configurations. A detailed theoretical analysis of the method is presented followed by a semi-analytical approximation and numerical calculations in order to quantify the sensitivity and limits of detection of the FR-MZI over Single Wavelength MZI. The obtained results substantiate that IO FR-MZI- based sensors constitute a generic technological platform of high sensitivity that can be implemented into a plethora of detection schemes. For an optimized optical design well below 1mm in length the limit of detection can be as low as 0.025A in terms of adlayer effective thickness allowing for truly miniaturized integrated optical sensors fabricated with high yield with standard microfabrication techniques.

Broad-band Mach-Zehnder interferometers as high performance refractive index sensors: Theory and monolithic implementation

Broad-band Mach-Zehnder interferometry is analytically described and experimentally demonstrated as an analytical tool capable of high accuracy refractive index measurements over a wide spectral range. Suitable photonic engineering of the interferometer sensing and reference waveguides result in sinusoidal TE and TM spectra with substantially different eigen-frequencies. This allows for the instantaneous deconvolution of multiplexed polarizations and enables large spectral shifts and noise reduction through filtering in the Fourier Transform domain. Due to enhanced sensitivity, optical systems can be designed that employ portable spectrum analyzers with nm range resolution without compromising the sensor analytical capability. Practical detection limits in the 10(-6)-10(-7) RIU range are achievable, including temperature effects. Finally, a proof of concept device is realized on a silicon microphotonic chip that monolithically integrates broad-band light sources and single mode silicon nitride waveguides. Refractive index detection limits rivaling that of ring resonators with externally coupled laser sources are demonstrated. Sensitivities of 20 μm/RIU and spectral shifts in the tens of a pm are obtained.

Spectroscopic and microscopic characterization of biosensor surfaces with protein/amino-organosilane/silicon structure.

Composition and structure of biorecognition protein layers created on silicon substrates modified with amino-organosilanes determine the sensitivity and specificity of silicon based biosensing devices. In the present work, diverse spectroscopic and microscopic methods were applied to characterize model biosensor surfaces, formed on Si(3)N(4) or SiO(2) by modification with (3-aminopropyl)triethoxysilane, coating with rabbit gamma-globulins (IgGs) through physical adsorption, blocking with bovine serum albumin (BSA) and specific binding of an anti-rabbit IgG antibody. In addition, silanized substrates with directly adsorbed BSA or anti-rabbit IgG antibody were examined as reference surfaces. The protein/amino-organosilane/silicon structure of all surfaces was confirmed by X-ray photoelectron spectroscopy. Homogeneity of protein coverage was verified with near-field scanning optical microscope, working in reflection and fluorescence mode. Surface coverage with proteins was determined with angle-resolved XPS using a previously established bilayer approach. Inner structure of protein layers was examined with atomic force microscopy. Vertical arrangement of carbon functional groups was revealed by high resolution ARXPS. Combined spectroscopic and microscopic data reveal the complex character of interactions with the immobilized IgG molecules during blocking with BSA and immunoreaction with anti-IgG antibody. Within experimental error, neither surface coverage nor lateral structural scales of protein layer (provided by Fourier and auto-correlation analysis of topographic and phase images) increase during blocking procedure. On the other hand, coverage and all structural measures rise considerably after immunoreaction. In addition, it was found that polar functional groups orient towards substrate for all protein layers, independently of coverage, prior to and after both blocking and specific binding.

Protein adsorption and covalent bonding to silicon nitride surfaces modified with organo-silanes: comparison using AFM, angle-resolved XPS and multivariate ToF-SIMS analysis.

Organo-silanes provide a suitable interface between the silicon-based transducers of various biosensing devices and the sensing proteins, immobilized through physical adsorption, as for (3-aminopropyl)triethoxysilane (APTES), or covalent binding, e.g. via protein amine groups to (3-glycidoxypropyl)trimethoxysilane (GOPS) modified surface. Immobilization of rabbit gamma globulins (RgG) to silicon nitride surfaces, modified either with APTES or GOPS, was examined as a function of incubation time using atomic force microscopy (AFM), angle-resolved X-ray photoelectron spectroscopy (ARXPS) and time of flight secondary ion mass spectrometry (ToF-SIMS). Multivariate technique of principal component analysis was applied to ToF-SIMS spectra in order to enhance sensitivity of immobilized RgG detection. Principal component regression shows a linear relationship with surface density determined rigorously from ARXPS following an organic bilayer approach, allowing for protein coverage quantification by ToF-SIMS. Taking it overall the surface immobilized amount of RgG is higher and develops faster on the surfaces silanized with APTES rather than with GOPS. Similar, although less distinct, difference is observed between the two surface types concerning the temporal evolution of average AFM height. The average height of protein overlayer correlates well with ARXPS and ToF-SIMS data expressed in terms of protein surface density. However, determined linear regression coefficients are distinctively higher for the surfaces modified with epoxy- rather than amino-silane, suggesting different surface density and conformation of the proteins immobilized through to covalent binding and physical adsorption.

Ordering domains of spin cast blends of conjugated and dielectric polymers on surfaces patterned by soft- and photo-lithography

Spin casting polymer blends of conjugated and dielectric macromolecules onto chemically patterned metal and oxidized silicon surfaces might provide a simple method to fabricate polymer-based circuitries that can be integrated with conventional electronics. Such solution-processing of the blend components offers simultaneous deposition and pattern-directed alignment of the phase separated polymer domains. The alignment is driven by self-organization guided by preferential surface segregation. Here we demonstrate that the laterally arranged domain structures in spin cast films of the conjugated poly(3-alkylthiophenes) (P3ATs): P3BT, P3DDT and regioregular R-P3HT, blended with dielectric polystyrene (PS), can be ordered by three different surface templates. The templates are formed by a patterned self-assembled monolayer (SAM), micro-contact printed on the surface of interest, i.e. hexadecanethiols on gold (for alignment of P3DDT/PS blend) and octadecyltrichlorosilanes on oxidized silicon (for R-P3HT/PS). Additionally gold lines are micro-patterned on SiO2 with photo-lithography (for P3BT/PS mixture). The forces driving pattern-directed self-organization of the polymers are discussed based on complementary studies of preferential surface segregation, observed for blend films spin cast on homogeneous surfaces that correspond to the different regions of the surface templates.

Surface and line-edge roughness in solution and plasma developed negative tone resists: Experiment and simulation

A methodology is described for the experimental and theoretical study of surface roughness (SR) and line-edge roughness (LER) and their relation for solution and plasma developed resist schemes. Experimental results for a negative-tone nonchemically amplified siloxane bilayer resist scheme are shown. In addition, a molecular-type simulation of SR and LER is presented. The simulator can follow the appearance of SR and LER after each process step and predict the roughness dependence on material properties and process conditions. The simulation results are compared with SR experimental data for a negative-tone chemically amplified epoxy resist.

Evaluation of siloxane and polyhedral silsesquioxane copolymers for 157 nm lithography

Siloxane and silsesquioxane copolymers have been synthesized and first evaluated as potential components of 157 nm resist materials. In block copolymers of dimethylsiloxane and tert-butyl methacrylate negative imaging chemistry dominates at 157 nm, due to the presence of the siloxane component, although positive imaging in aqueous base developers via chemical amplification was obtained at longer wavelengths (248 nm). The same behavior is observed in graft copolymers of dimethylsiloxane and tert-butyl methacrylate. On the other hand, random copolymers of polymerizable polyhedral oligomeric silsesquioxane monomers with various acrylates, including partially fluorinated, can be used as components of resist formulations that provide positive imaging at 157 nm, aqueous base development, and physicochemical properties which resemble those of conventional poly(meth)acrylates. Pattern transfer properties depend on the selection of the silsesquioxane component. Polymers containing 30% or higher w/w ethyl-substitut...

Model immunoassay on silicon surfaces: vertical and lateral nanostructure vs. protein coverage.

To provide complete characterization of immunoassay on silicon biosensor surfaces, atomic force microscopy, (angle-resolved) X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry were applied to examine Si(3)N(4) surfaces modified with (3-aminopropyl)triethoxysilane, coated with gamma globulins (IgG), blocked with bovine serum albumin and then reacted with anti-IgG antibody for two complementary pairs (rabbit and mouse IgG) at various concentrations (from 0.3 nM to 330 nM). Protein coverage, as reflected in (amine to total N1s) XPS signal ratio and determined from ARXPS, decreases slightly due to blocking and then increases monotonically for anti-IgG antibody concentrations higher than 1 nM. AFM images reveal hardly any change of lateral nanostructure due to blocking but response to antibody solutions, based on both the mean size (from autocorrelation) and dominant spacing (from Fourier analysis) of surface features, similar to that given by ARXPS. AFM height histograms provided information about the vertical nanostructure and the parameters of height distribution (average height, spread - roughness and skewness) were distinctly influenced by coating, blocking and immunoreaction. Average protein layer thickness values determined based on protein structure (molecular weight, dimensions) and surface coverage provided from ARXPS were in accord with average height of protein layer determined from AFM. TOF-SIMS analysis indicated that BSA blocks free surface sites and in addition replaces some already adsorbed IgGs.

Surface modification of Si-containing polymers during etching for bilayer lithography

Abstract Surface modification of polydimethylsiloxane (PDMS) under O 2 plasma exposure is studied by XPS and real time ellipsometry. Results show the conversion of the PDMS surface into a SiO x -like material. Total layer thickness and extension of the SiO x layer are controlled by the sample bias. We suggest that surface and line edge roughness defects occurring when using PDMS as top layer in bilayer lithography are intimately related to the rapid kinetics of conversion and to the formation of SiO x hard micromasks on the surface.

Analytical evaluation of the energy deposition function in electron‐beam lithography in the case of a composite substrate

In this article the energy deposition function in the case of e‐beam lithography is calculated analytically. The distribution of electrons as a function of depth and energy is calculated first using a method based on the Boltzmann transport equation which is easily applicable in the case of multilayer substrates. Next the lateral distribution of the electrons is calculated and each contribution (primary, secondary, and backscattered electrons) is considered separately. Energy dissipation results are used as input to a cell removal model for the resist development simulation.