Mikhail I. Rudenko

Planar optofluidic chip for single particle detection, manipulation, and analysis.

We present a fully planar integrated optofluidic platform that permits single particle detection, manipulation and analysis on a chip. Liquid-core optical waveguides guide both light and fluids in the same volume. They are integrated with fluidic reservoirs and solid-core optical waveguides to define sub-picoliter excitation volumes and collect the optical signal, resulting in fully planar beam geometries. Single fluorescently labeled liposomes are used to demonstrate the capabilities of the optofluidic chip. Liposome motion is controlled electrically, and fluorescence correlation spectroscopy (FCS) is used to determine concentration and dynamic properties such as diffusion coefficient and velocity. This demonstration of fully planar particle analysis on a semiconductor chip may lead to a new class of planar optofluidics-based instruments.

Ultrasensitive Qβ phage analysis using fluorescence correlation spectroscopy on an optofluidic chip

We demonstrate detection and analysis of the Qbeta bacteriophage on the single virus level using an integrated optofluidic biosensor. Individual Qbeta phages with masses on the order of attograms were sensed and analyzed on a silicon chip in their natural liquid environment without the need for virus immobilization. The diffusion coefficient of the viruses was extracted from the fluorescence signal by means of fluorescence correlation spectroscopy (FCS) and found to be 15.90+/-1.50 microm(2)/s in excellent agreement with previously published values. The aggregation and disintegration of the phage were also observed. Virus flow velocities determined by FCS were in the 60-300 microm/s range. This study suggests considerable potential for an inexpensive and portable sensor capable of discrimination between viruses of different sizes.

Dual-color fluorescence cross-correlation spectroscopy on a planar optofluidic chip.

Fluorescence cross-correlation spectroscopy (FCCS) is a highly sensitive fluorescence technique with distinct advantages in many bioanalytical applications involving interaction and binding of multiple components. Due to the use of multiple beams, bulk optical FCCS setups require delicate and complex alignment procedures. We demonstrate the first implementation of dual-color FCCS on a planar, integrated optofluidic chip based on liquid-core waveguides that can guide liquid and light simultaneously. In this configuration, the excitation beams are delivered in predefined locations and automatically aligned within the excitation waveguides. We implement two canonical applications of FCCS in the optofluidic lab-on-chip environment: particle colocalization and binding/dissociation dynamics. Colocalization is demonstrated in the detection and discrimination of single-color and double-color fluorescently labeled nanobeads. FCCS in combination with fluorescence resonance energy transfer (FRET) is used to detect the denaturation process of double-stranded DNA at nanomolar concentration.

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.

Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip

We describe analysis and control of 50S ribosomal subunits by a solid-state 45nm diameter nanopore incorporated in a microfluidic chip. When used as a resistive pulse sensor, translocation of single 50S subunits through the nanopore produces current blockades that have a linear dependence on applied voltage. Introduction of individual subunits into the fluidic channel shows a threshold behavior that allows controlled entry of individual 50S ribosomal subunits. The incorporation of nanopores into a larger optofluidic chip system opens possibilities for electrical and optical studies of single ribosomes in well-defined and rapidly variable chemical environments.

Integration and characterization of SiN nanopores for single-molecule detection in liquid-core ARROW waveguides

We demonstrate a method for integrating silicon nitride nanopores in liquid core Anti Resonant Reflecting Optical Waveguides (ARROW) for single molecule electrical detection and control. We use a two-step integration process when a micropore is fabricated first, paving the way for subsequent nanopore integration in the first silicon nitride layer of the ARROW structure. Nanopores with dimensions as small as 11 nm were fabricated using a Focused Ion Beam shrinking process commensurate with single particle gating of viruses, proteins, ribosomes and other biomolecules.

Advances in integrated hollow waveguides for on-chip sensors

We have previously produced antiresonant reflecting optical waveguides (ARROWs) with hollow cores that can guide light through liquid or gas media. In order to utilize these structures in sophisticated sensing applications, we have improved our initial designs and fabrication methods to increase yield, lower waveguide transmission loss, and incorporate structural features into the waveguides themselves. Yields have been increased by optimizing PECVD film conformality leading to greater sidewall strength for hollow waveguides. Sensing applications require interfacing hollow waveguides with solid waveguides on the surface of a substrate to direct light on and off a chip and into and out of a test medium. Previous interfaces required light transferring from solid to hollow waveguides to pass through the antiresonant layers, with measured transmission efficiencies of about 30%. By removing the ARROW layers at the interfaces, transmission efficiencies at these interfaces can be improved to greater than 95%. We also demonstrate the fabrication of micropore structures on the hollow waveguides to be used for chemical sensing. A fabrication method has been developed that allows for removal of the thick top oxide and nitride ARROW layers leaving only a thin nitride membrane directly over the hollow core allowing controlled access to test media.

Fluorescence correlation spectroscopy of single molecules on an optofluidic chip

We review our recent progress in bringing fluorescent correlation spectroscopy (FCS) of single molecules on a silicon optofluidic platform. Starting from basic concepts and applications of FCS we move to a description of our integrated optofluidic device, briefly outlining the physics behind its function and relevant geometrical characteristics. We then derive an FCS theoretical model for our sensor geometry, which we subsequently apply to the examination of molecular properties of single fluorophores and bioparticles. The model allows us to extract the diffusion coefficient, translational velocity and local concentration of particles in question. We conclude with future directions of this research.

Liquid-core waveguide based optofluidics

Recent progress in liquid-core waveguide based optofluidic devices for sensing applications will be reviewed.

Optimizing ARROW Transitions by Selective Deposition of Thin Films

Selective deposition of dielectric thin films on an optofluidic sensor provides the means for low loss in hollow-core waveguides and increased solid- to hollow-core interface transmission. This method promises significant throughput improvement over previous devices.