This PDF file contains the front matter associated with SPIE Proceedings Volume 7188, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and the Conference Committee listing

DNA and protein absorption at 260 and 280 nm can be used to reveal theses species on a biochip UV image. A first study including the design and fabrication of UV reflective multilayer biochips designed for UV contrast enhancement (factor of 4.0) together with spectrally selective AlGaN detectors demonstrated the control of chip biological coating, or Antigen/Antibody complexation with fairly good signals for typical probe density of 4x10¹² molecules/cm². Detection of fractional monolayer molecular binding requires a higher contrast enhancement which can be obtained with structured chips. Grating structures enable, at resonance, a confinement of light at the biochip surface, and thus a large interaction between the biological molecule and the lightwave field. The highest sensitivity obtained with grating-based biochip usually concerns a resonance shift, in wavelength or diffraction angle. Diffraction efficiency is also affected by UV absorption, due to enhanced light-matter interaction, and this mechanism is equally able to produce biochip images in parallel. By adjusting grating parameters, we will see how a biochip that is highly sensitive to UV absorption at its surface can be obtained. Based on the Ewald construction and diffraction diagram, instrumental resolution and smarter experimental configurations are considered. Notably, in conjunction with the 2D UV-sensitive detectors recently developed in-house, we discuss the obtainment of large contrast and good signals in a diffraction order emerging around the sample normal.

Neural microelectrodes are an important component of neural prosthetic systems which assist paralyzed patients by allowing them to operate computers or robots using their neural activity. These microelectrodes are also used in clinical settings to localize the locus of seizure initiation in epilepsy or to stimulate sub-cortical structures in patients with Parkinson's disease. In neural prosthetic systems, implanted microelectrodes record the electrical potential generated by specific thoughts and relay the signals to algorithms trained to interpret these thoughts. In this paper, we describe novel elongated multi-site neural electrodes that can record electrical signals and specific neural biomarkers and that can reach depths greater than 8mm in the sulcus of non-human primates (monkeys). We hypothesize that additional signals recorded by the multimodal probes will increase the information yield when compared to standard probes that record just electropotentials. We describe integration of optical biochemical sensors with neural microelectrodes. The sensors are made using sol-gel derived xerogel thin films that encapsulate specific biomarker responsive luminophores in their nanostructured pores. The desired neural biomarkers are O2, pH, K+, and Na+ ions. As a prototype, we demonstrate direct-write patterning to create oxygen-responsive xerogel waveguide structures on the neural microelectrodes. The recording of neural biomarkers along with electrical activity could help the development of intelligent and more userfriendly neural prosthesis/brain machine interfaces as well as aid in providing answers to complex brain diseases and disorders.

We describe genetic engineering of a novel protein-nanoparticle hybrid system with great potential for patterning of various types of nanoparticles and for biosensing applications. The hybrid system is based on a genetically-modified chaperonin protein from the hyperthermophilic archaeon Sulfolobus shibatae. This chaperonin is an 18-subunit double ring, which self-assembles in the presence of Mg ions and ATP. We describe a chaperonin mutant (His-β- loopless:HBLL), with increased access to the central cavity and His-tags on each subunit extending into the central cavity. This mutant binds water-soluble semiconductor quantum dots, creating a protein-encapsulated fluorescent nanoparticle. By adding selective binding sites to the solvent-exposed regions of the chaperonin, this proteinnanoparticle bioconjugate becomes a sensor for specific targets. Using a combination of biochemical and spectroscopic assays, we characterize the formation, stoichiometry, affinity and stability of these novel sensors.

°The investigation of thermal behaviors and subsequent changes in the conformational order of lipids and liposomes is of importance in understanding various phenomena such as the formation and fusion of vesicles, trans-membrane diffusion and membrane interactions with drugs and proteins. In this work, the thermal behavior of a suite of newly developed self-forming synthetic non-phospholipid (PEGylated) lipids and its nanovesicles in buffer suspensions were investigated by variable-temperature thin-layered Fourier Transform Infrared (FTIR) transmission spectroscopy. The temperature-induced infrared spectra of such lipids composed of 1,2-dimyristoyl-rac-glycerol-3-dodecaethylene glycol (GDM-12) and 1,2-distearoyl-rac-glycerol-3-triicosaethylene glycol (GDS-23) were acquired by using FTIR spectrometer in conjunction with a custom built temperature-controlled demountable liquid cell. In contrast to conventional phospholipids, these novel lipids form liposomes spontaneously upon hydration, without the supply of external activation energy. It was found that the thermal stability of the PEGylated lipids defer greatly depending upon the acyl chain-lengths as well as number of associated head group units. Particularly, GDM-12 (saturated 14 hydrocarbon chains) shows one sharp order-disorder transition with temperature increasing from 3 to 5 °C. Similarly, GDS-23 (saturated 18 hydrocarbon chains) exhibits comparatively broad order-disorder transition profiles between temperature 17 and 22 °C. However, the phase transition temperature becomes significantly higher for lipid nanovesicles formed in aqueous suspensions. The results obtained in this study may find applications in various areas including the development of lipid based substance and drug delivery systems.

Lipids and liposomes have remained an active research topic for several decades due to their significance as membrane model. Several vibrational spectroscopic techniques have been developed and employed to study the properties of lipids and liposomes. In this study, near-infrared (NIR) spectroscopy has been used to analyze a suite of synthesized PEGylated lipids trademarked as QuSomes^TM. The three amphiphiles used in this study, differ in their apolar hydrophobic chain length and contain various units of polar polyethylene glycol (PEG) head groups. In contrast to conventional phospholipids, this new kind of lipids forms liposomes spontaneously upon hydration, without the supply of external activation energy. Whilst the NIR spectra of QuSomes^TM show a common pattern, differences in the spectra are observed which enable the lipids to be distinguished. NIR absorption spectra of these new artificial lipids have been recorded in the spectral range of 4800-9000 cm^-1 (~2100-1100 nm) by using a new miniaturized spectrometer based on micro-optical-electro-mechanical systems (MOEMS) technology. In particular, we have established specific band structures as "molecular fingerprints" corresponding to overtones and combinations vibrational modes involving mainly C-H and O-H functional groups for sample analysis of QuSomes^TM. Moreover, we have demonstrated that the nanovesicles formed by such lipids in polar solvents show high stability and obey Beer's law at low concentration. The results reported in this study may find applications in various field including the development of lipids based drug delivery systems.

A novel optical biosensor using a one-dimensional photonic crystal structure in a total-internal-reflection geometry (PCTIR) is presented and investigated for label-free biosensing applications. This simple configuration forms a micro Fabry- Perot resonator in the top layer which provides a narrow optical resonance to enable label-free, highly sensitive measurements for the presence of analytes on the sensing surface or the refractive index change of the surrounding medium in the enhanced evanescent field; and at the same time it employs an open sensing surface for real-time biomolecular binding detection. The high sensitivity of the sensor was experimentally demonstrated by bulk solvent refractive index changes, ultrathin molecular films adsorbed on the sensing surface, and real-time analytes binding, measuring both the spectral shift of the photonic crystal resonance and the change of the intensity ratio in a differential reflectance measurement. Detection limits of 7×10^-8 RIU for bulk solvent refractive index, 6×10^-5 nm for molecular layer thickness and 24 fg/mm² for mass density were obtained, which represent a significant improvement relative to state-ofthe- art surface-plasmon-resonance (SPR)-based systems. The PC-TIR sensor is thus seen to be a promising technology platform for high sensitivity and accurate biomolecular detection.

The development of intelligent miniaturized biochemical sensors has been an area of active research over the past several years. These microsensors and sensor microarrays are finding niche applications in point-of-care diagnostics, personal care, food safety, and environmental monitoring. Among these sensors, optical (luminescence) sensing holds a great promise towards implementing simple, specific, and highly sensitive biochemical sensors. It is generally understood that biochemical recognition elements that respond specifically to the target analytes play a critical role in the overall sensor operation. Aside from the recognition elements, signal detection and processing components are important to collect the information provided by recognition elements and output an easily understandable response. The signal processing component provides the best opportunity to incorporate intelligence to achieve low-power, adaptive, accurate, and reliable sensors. We deal with sensors that use sol-gel derived xerogels as recognition materials and Complementary Metal-Oxide Semiconductor (CMOS) integrated circuits for signal detection and processing. Xerogels are nano/microporous glasses that can be used to encapsulate luminophores, enzymes, and nanoparticles in their pores. In this Article, we will describe some of the emerging integrated sensor platforms that are based on monitoring the excited-state luminescence intensity and lifetimes of the luminophores housed in the xerogels. Specifically, we describe a CMOS imaging system for simultaneously monitoring xerogels sensor arrays. Next, we describe a non-linear phase luminometric system with enhanced and dynamically tunable sensitivity and improved signal-to-noise performance. Finally, we will describe time-based signal processing that could enable the direct measurement of excited state fluorescence lifetimes. This time-to-digital converter requires simple circuit implementation and can be used to measure lifetimes that are on the order of several hundred nanoseconds. The time based signal processing could ultimately allow the development of low-cost lifetime imaging system wherein one could take the lifetimes' image of an array of recognition elements rather than collecting an image of their fluorescence intensities.

Phosphor/fluorescent molecules/particles have been widely used in various applications for quite some time. Typically, light with longer wavelength(s) is emitted when excited by shorter wavelength light. The opposite effect also exists, where a phosphor particle is excited with an infrared or red light and emits color(s) of shorter wavelengths, a process called up-conversion. Materials with upconverting properties have narrower absorption and line emission spectra than their down-converting counterparts. Because most non-target materials in a complex mixture do not possess such photon up-conversion properties, a dramatically improved S/N ratio is expected in sensing and luminescence reporting applications. This makes photon upconverting materials ideal for identification of trace amounts of target molecules. Here we report the synthesis, characterization and DNA detection application based on NaYF₄:Yb³⁺, Er³⁺ photon upconverting nanoparticles. The design of a nucleotide sensor for the detection of point mutation associated with sickle cell disease is described. The underlying principle for the detection is luminescence resonance energy transfer (LRET), with the photon upconverting nanoparticle as the donor and a dye, N,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA), as the acceptor. The detection scheme is based on a sandwich-type hybridization format. The presence of the target DNA is indicated by the increase of the normalized acceptor's emission. Based on photon upconverting nanoparticles, which display high S/N ratio and no photobleaching, the DNA sensor demonstrates high sensitivity and specificity. The results demonstrate great potential of such nanomaterials as oligonucleotide sensors.

We present a theoretical analysis of the response of whispering gallery modes for biosensing applications, studied numerically in microcylinders and semi-analytically in microspheres. The effect of single and multiple particles is calculated, simulating biological analytes of different sizes and polarizabilities attached to the microresonator surface. Besides whispering-gallery-mode frequency shifts, we find that also broadenings and splittings (from lifted rotational symmetry) appear due to particles attachment and/or the vicinity to a planar coupler. For a single analyte, both particle size and refractive index can be determined from the broadening and shift, opening the perspective to a new biosensing modality.

We have set-up a scanning near-field infrared microscope (SNIM) with widely tunable lasers for label-free molecule identification by infrared spectral fingerprints. The lateral resolution is as low as 30 nm corresponding to the nanotip curvature radius. We obtained infrared spectra from nanoscale sections of self-assembled monolayers (SAM) with volumes as small as 0.01 attoliter corresponding to less than 30000 molecules. Spectroscopy of lipid bilayer stacks on mica revealed nanoscale near-field depth resolution of 80 to 120 nm. We discuss combined systems of membrane proteins and lipids on SAM supports approaching cell like membrane structures. We report on the progress of the set-up of an infrared and terahertz near-field microscope for the new synchrotron beam line at ANKA for full spectral nanoscale information retrieval.

Dynamics of nanoparticles penetrating and accumulating in healthy (skin) and pathologically altered (tumor) tissue was investigated in vivo by the method of optical coherence tomography (OCT). Gold nanoshells having the size of 130/15 nm and titanium dioxide nanoparticles 40-100 nm in size were studied. Nanoparticles accumulation in biotissue was accompanied by the change of optical effects in OCT images. Continuous OCT monitoring of the process of nanoparticles penetration into skin showed that optical effects appeared 30 minutes after application of nanoparticles on the surface; maximal effect of nanoparticles accumulation in the skin was recorded in the observation period of 1.5-5 hours. Nanoparticles accumulation in neoplastic tissue at passive delivery was studied in vivo. Accumulation maximum was 4-6 hours after intravenous introduction. The transmission electron microscopy technique confirmed accumulation of nanoparticles in biotissues.

Researchers employ increasingly complex sub-micron particles for oncological applications to deliver bioactive therapeutic or imaging compounds to known and unknown in vivo tumor targets. In practice, experimental homogeneity using nanoparticles can be difficult to achieve. While several imaging techniques have been previously shown to follow the accumulation of nanoparticles into tumor targets, a more rapid sensor that provides a quantifiable estimate of dose delivery and short-term systemic response could increase the clinical efficacy and greatly reduce the variability of these treatments. We have developed a pulse photometer that when placed on an optically accessible location will estimate the concentration of near-infrared absorbing nanoparticles. The goal is to monitor the accuracy of the delivered dose and the effective circulation time of nanoparticles immediately after intravenous delivery but prior to therapeutic intervention. We present initial tests of our prototype using murine models to assess its ability to quantify circulation half-life and nanoparticle concentration. Four mice were injected with nanoparticles and circulation half-life estimates ranged from 3- 43 minutes. UV-Vis spectrophotometry was used to independently verify these measurements using 5μL blood samples. Linear models relating the two methods produced R² values of 0.91, 0.99, 0.88, and 0.24.

In solid-support immunoassays, the transport of target analyte in sample solution to capture molecules on the sensor surface controls the detected binding signal. Depletion of the target analyte in the sample solution adjacent to the sensor surface leads to deviations from ideal association, and causes inhomogeneity of surface binding as analyte concentration varies spatially across the sensor surface. In the field of label-free optical biosensing, studies of mass-transport-limited reaction kinetics have focused on the average response on the sensor surface, but have not addressed binding inhomogeneities caused by mass-transport limitations. In this paper, we employ Molecular Interferometric Imaging (MI2) to study mass-transport-induced inhomogeneity of analyte binding within a single protein spot. Rabbit IgG binding to immobilized protein A/G was imaged at various concentrations and under different flow rates. In the mass-transport-limited regime, enhanced binding at the edges of the protein spots was caused by depletion of analyte towards the center of the protein spots. The magnitude of the inhomogeneous response was a function of analyte reaction rate and sample flow rate.

Mechanical forces and living cells are closely related, in particular in connections, named Focal Adhesions (FAs), between cells and extracellular matrix. FAs are mechanosensors and regulate physiological processes. The aim of this contribution is to explore the possibility of performing micrometric and submicrometric protein pattern in order to study FAs on different materials. Typical substrates for microelectromechanical systems (MEMS) are tested and the results are reported. A laser is used to produce a pattern of extracellular matrix proteins, like fibronectin. A new use of a Raman microprobe is described. Cells arrange in a regular shape, following the geometry of the pattern. Protein spots last for more than 24 hours. It is very important to have a complete control on FAs and the technique proposed is a suitable solution.

Advanced nanofabrication is capable of producing structures in the vicinity of the size of large biomolecules or their aggregates. Some of these protein aggregates emerge as having deleterious medical effects, e.g., degenerative diseases, or essential for biological processes, e.g., actin, cytoskeleton formation. Therefore it became possible, and important, to think of ways of interacting nanostructured surfaces with biomolecular aggregates in a designed manner. Along this line of thinking, we report on a preliminary atomic force microscopy (AFM) investigation of the behavior of F-actin on unstructured surfaces (mica, silicon) and nanostructured surface (13 nm height nanostructured silicon surface).