This PDF file contains the front matter associated with SPIE Proceedings Volume 7040, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and the Conference Committee listing.

Molecular Nonlinear Optics, an otherwise well established domain, is currently revisiting and shaking its foundations, objectives and methods, in the frame of ongoing conceptual as well as methodological revivals. These are based on correlated advances in chemistry and physics, entailing spectacular advances in the new playground of multiphoton bio-imaging. For chemistry, we chose to review and highlight a comprehensive multipolar template approach will helps rationalize and generalize molecular design rules, with current emphasis on multi-functionality and the nano-scale. In consistence with advances in chemistry, we emphasize for physics the domain of nonlinear micro- and nano-photonics, in particular with respect to active nonlinear coupling schemes, based on interference of multi-photon absorption pathways. It permits to encode nonlinear information or guide the displacement of molecular or nano-scale objects by adequate laser illumination. Building-up on these advances and more, advanced bio-imaging methods such as based on phase and polarization resolved nonlinear schemes, are currently opening-up new windows onto cellular structures and mechanisms, with the potential towards unprecedented spatial resolution.

Semiconductor quantum dots are recognized to provide a particularly effective approach to bright nano-objects for bioimaging. However, these inorganic systems suffer from several drawbacks such as toxicity, dispersity, blinking ... and raise a number of questions with respect to environmental issues. With this in mind, we have developed an innovative route towards purely organic nanodots showing exceptional one and two-photon brightness by confining a large number of optimized fluorophores within nano-objects of defined and controlled structure. These novel "soft" nano-objects offer major promises for bio and nanophotonics.

Here we nanoengineered tunable quantum dot and cationic conjugated polymer nanoarrays based on surface plasmon enhanced fluorescence where we achieved a 15-fold and 25-fold increase in their emission intensities, respectively. These peptide mediated hybrid systems were fabricated by horizontally tuning the localized surface plasmon resonance of gold nanoarrays and laterally tuning the distance of the fluorophore from the metal surface. This approach permits a comprehensive control both laterally (i.e., lithographically defined gold nanoarrays) and vertically (i.e., QD/CCP-metal distance) of the collectively behaving QD-NP and CP-NP assemblies by way of biomolecular recognition. The highest photoluminescence was achieved when the quantum dots and cationic conjugated polymers were self-assembled at a distance of 16.00 nm and 18.50 nm from the metal surface, respectively. Specifically, we demonstrated the spectral tuning of plasmon resonant metal nanoarrays and the self-assembly of protein-functionalized QDs/CCPs in a step-wise fashion with a concomitant incremental increase in separation from the metal surface through biotin-streptavidin spacer units. These well-controlled self-assembled patterned arrays provide highly organized architectures for improving optoelectronic devices and/or increasing the sensitivity of bio-chemical sensors.

This paper demonstrates the use of DNA based biopolymers as semiconducting thin films in organic field effect transistors. The "doping" of the DNA molecules with conductive polymers leads to a significant decrease of the overall resistivity in the blend with effective free charge carrier mobilities comparable to other conductive polymers such as Pentacene and P3HT. Baytron P as well as single wall carbon nanotubes (SWCNT) have been explored as "doping" conductive polymers.

Recently, we have proposed a simplified kinetic Monte Carlo model which mimics the inscription/erasure of diffraction gratings in DNA matrix with azodyes. Preliminary results correctly reproduce the observations made for the photochromic system DR1:DNA-CTMA: very short operational times (inscription/erasure), optical stability and reversibility. In this paper we analyze semi-intercalation model of paper analytically and discuss its predictions. Next, we modify this model by taking the DNA model chain directly into account. Local free volume determines the transition probabilities of trans-cis photoisomerization reactin. Using the model we address the open questions: (i), short operational time; (ii), small diffraction efficiency; and (iii), one exponential inscription.

Riboswitches are a type of natural genetic control element that use untranslated sequence in the RNA to recognize and bind to small molecules that regulate expression of that gene. Creation of synthetic riboswitches to novel ligands depends on the ability to screen for analyte binding sensitivity and specificity. In our work, we have coupled a synthetic riboswitch to an optical reporter assay based on fluorescence resonance energy transfer (FRET) between two genetically-coded fluorescent proteins. Specifically, a theophylline-sensitive riboswitch was placed upstream of the Tobacco Etch Virus (TEV) protease coding sequence, and a FRET-based construct, BFP-eGFP or eGFP-REACh, was linked by a peptide encoding the recognition sequence for TEV protease. Cells expressing the riboswitch showed a marked optical difference in fluorescence emission in the presence of theophylline. However, the BFP-eGFP FRET pair posses significant optical background that reduces the sensitivity of a FRET-based assay. To improve the optical assay, we designed a nonfluorescent yellow fluorescent protein (YFP) mutant called REACh (for Resonance Energy-Accepting Chromoprotein) as the FRET acceptor for eGFP. The advantage of using an eGFP-REACh pair is the elimination of acceptor fluorescence which leads to an improved detection of FRET via better signal-to-noise ratio. The EGFP-REACh fusion protein was constructed with the TEV protease cleavage site; thus upon TEV translation, cleavage occurs diminishing REACh quenching and increasing eGFP emission resulting in a 4.5-fold improvement in assay sensitivity.

Photopatterning with 266 nm UV light was accomplished on spin-coated DNA thin films using two different techniques. Lithographic masks were used to create 10-100 micron-sized arrays of enhanced hydrophilicity. Two such masks were used: (1) Polka Dot Filter having opaque squares and a transparent grid and (2) A metal wire-mesh having transparent squares and opaque grid. UV light selectively photodissociates the DNA film where it is exposed into smaller more hydrophilic fragments. UV-exposed films are then coated with a solution of a protein. The protein appears to selectively coat over areas exposed to UV light. We have also used interferometric lithography with UV light to accomplish patterning on the scale of 1 micron on DNA thin films. This technique has the potential to generate micro/nano arrays and vary the array-size. This paper describes the fabrication of these microarrays and a plausible application for fabricating antibody arrays for protein sensing applications.

DNA is one of the best candidates as building blocks for bottom-up approach to nanometer size architecture in nanotechnology. In natural photosynthetic system, the arrangement of porphyrin derivative with regulated distances, orders and orientations provide an efficient photon-energy collecting and transmittion. Sequential arrangement of chromophore (dye molecule) should therefore be a good model of artificial photosynthetic and photo-energy transmission systems. Sequential arrangements of three kinds of chromophores separated by regulated distances equaling approximately one pitch of the DNA duplex (3.4 nm) in non-covalent molecular assembly systems are constructed using chromophore/oligo-DNA conjugates. Vectorial photo-energy transmission along the DNA helix axis by fluorescence resonance energy transfer (FRET) in a sequential chromophore array was observed by fluorescence spectra measurements and analyzed by time-resolved fluorescence spectroscopy measurements using a femtosecond pulse laser system.

Laser-dye-doped-DNA-CTMA-PMMA hybrid films have been studied as a potential material for waveguide type thin-film laser devices. For the purpose of evaluate improving processability, not only optical characteristics of the fluorescence intensity and ASE spectrum but also moisture resistance of the hybrid film have been investigated. It is found that optical characteristics of those films are equally matched to the conventional laser-dye-doped- DNA-CTMA films with better moisture resistivity.

DNA-Ru(bpy)₃²⁺ complex was prepared to study molecular structure and its EL characteristics. Ru(bpy)₃²⁺ was associated with duplex of DNA by not only electrostatic interaction but also intercalation in the aqueous solution. Single-molecular structure of DNA-Ru(bpy)₃²⁺ complex was analyzed with AFM. We found network structure of DNA-Ru(bpy)₃²⁺ complex on the mica substrate, which is similar to naked DNA. The height of DNA-Ru(bpy)₃²⁺ complex on the mica substrate was ranging from 0.8 to 1.6 nm, which was higher than the naked DNA (0.5-1.0 nm). This indicates that single-molecular DNA-Ru(bpy)₃²⁺ complex forms network structure on the mica substrate. DNA-Ru(bpy)₃²⁺ complex was sandwiched with ITO and aluminum electrodes to analyze EL properties. It was revealed that the EL device composed of DNA- Ru(bpy)₃²⁺ complex exhibited extremely faster response than the other Ru(bpy)₃²⁺ based EL devices. The emission mechanism was discussed.

Extensive studies have been carried out on developing the new biopolymer, deoxyribonucleic acid (DNA) derived from salmon, that has been complexed with a surfactant to make it water insoluble for application to bioelectronic and biophotonic devices. One of the key issues associated with the properties and behavior of solid films of this material is the extreme size of the >8 MDa molecular weight of the virgin, as-received material. Reduction of this molecular weight by factors of up to 40 is achieved by high power sonication. To support the various measurements that have been made to confirm that the sonicated material is still double strand DNA and to look for other effects of sonication, Raman studies were carried out to compare the spectra over a wide range of molecular weights and to develop baseline data that can be used in intercolation studies where various dopants are added to change the electrical, mechanical or optical properties. Raman microprobe spectra from solid, dry thin films of DNA with molecular weights ranging from 200 kDa to >8 MDa complexed with cetyltrimethyl-ammonium chloride (CTMA) are reported and compared to the as-received spectrum and to published DNA spectra in aqueous solutions. In addition, microscopy and measurements on macro-molecular structures of DNA-CTMA are reported.

Recent research results on DNA-lipid complexes have shown various attractive features on E/O or O/E devices, optical memories, switches and sensors by intercalating optical dye into DNA double helix. DNA devices absorbed water under high humidity which led to decreases of optical functions. However, it is possible to improve the stability of DNA devices by encapsulating the DNA-lipid complexes into sol-gel materials or synthetic polymers so that water permeation is prevented by glass or synthetic polymers to stabilize and to keep the optical functions for a long time. This research aims at stability improvements of the DNA photon devices by sealing the DNA devices either by sol-gel glass or polymer blending.

DNA has attracted much interest as a material for nano science and technology. We have studied DNA both in natural forms and modified forms M-DNA by insertion of a variety of metal ions. On the ground of basic science, we tried to unveil the intrinsic physical properties, especially magnetic properties of natural DNA and a possibility of charge carrier doping by the metal ion insertion. Diamagnetic nature of natural DNA and a variety of features in M-DNA will be presented.

Blood lactic acid concentration is an important indicator for physiological functions. To develop a rapid and sensitive measurement technique for monitoring blood lactic acid may provide a useful tool in clinical diagnosis. We proposed to develop a microdialysis surface-enhanced Raman spectroscopy (microdialysis-SERS) approach to filter/reduce interference from other large metabolites in blood and enhance the detection sensitivity for blood lactic acid. In this study, a microdialysis probe was constructed using 13 kDa cut-off dialysis membrane. The dialysate was mixed with 50 nm Ag colloidal nanoparticles automatically in a micro-fluid chamber for SERS detection under blood microdialysis of Sprague-Dawley rat. The linear range of SERS-lactic acid measurement is 10^-5~3x10^-4 M with R² value of 0.99. The optimal mixing flow rate of nanoparticles is 18 μl/min under microdialysis at constant flow rate (2 μl/min). Real time lactic acid monitoring in vivo also has been demonstrated using microdialysis-SERS system.