Session B42: Focus Session: BioChip Physics-Detection and Transport

On-chip Metamaterials for Ultra-sensitive Spectroscopy and Identification of Biomolecules

Infrared absorption spectroscopy is a unique tool for identifying and characterizing molecular bonds. For most organic and inorganic molecules (such as proteins, chemical toxins and gases), vibrational and rotational modes are spectroscopically accessible within the mid-infrared (mid-IR; 3-20 $\mu $m) regime of the electromagnetic spectrum. Characteristic vibrational modes are associated with unique IR absorption spectral bands that are bond-specific. Because of that, the IR wavelength range is also known as ``finger print'' region. However, because of the Beer-Lambert law, its sensitivity has been limited to perform analytical/functional studies on small samples often available from biological specimens. In this talk we will describe how we use plasmonic metametrials to overcome these challenges. We will introduce tailoring of the resonances to selectively address fingerprint signatures of proteins. We will also describe novel designs and fabrication methods to exploit extreme near-field enhancements in small gaps for vibrational signal enhancements.\\[4pt] In collaboration with In collaboration with Ronen Adato, Serap Aksu, Alp Artar, Arif Cetin, and Boston University.   

Ultrasensitive Plasmonic Biosensors for Direct Detection of Biomarker Proteins with The Naked Eye

We introduce an ultrasensitive label free biodetection technique based on asymmetric plasmonic Fano resonances. Our sensors bring a number of advantages: (i) ultrasensitive detection limits surpassing gold standard Kretschmann configuration plasmon sensors, (ii) detection of biomarker molecules with ``the naked eye'', (iii) massive multiplexing capabilities. By exploiting extraordinary light transmission phenomena through high quality factor sub-radiant dark modes, we experimentally demonstrate record high figures of merits for intrinsic detection limits surpassing the gold standard BiaCore devices. Our experiments show an order of magnitude improved device performances over the state of art metamaterial and other plasmonic biosensors. Steep dispersion of the plasmonic Fano resonance profiles in engineered plasmonic sensors exhibit dramatic light intensity changes to the slightest perturbations within their local environment. As a spectacular demonstration, we show direct detection of a single monolayer of biomolecules with naked eye using these Fano resonances and the associated Wood's anomalies. The demonstrated sensing platform offers point-of-care diagnostics in resource poor settings by eliminating the need for fluorescent labeling and optical detection instrumentation (such camera, spectrometer, etc.).   

High-Throughput On-Chip Diagnostic System for Circulating Tumor Cells

We have developed a novel, low-cost and high-throughput microfluidic device for detection and molecular analysis of circulating tumor cells (CTCs). The operation is based upon a size-selective cell separation, which was enabled by a weir-style physical barrier with a gap in the fluidic channel. The new system is a versatile CTC analysis platform with many advantages. First, it supports extremely high throughput operation, since the use of weir structure reduces fluidic resistance and enables flow-through separation ($>$ 20,000-fold CTC enrichment from whole blood at the flow rate of 10 mL/h). Second, the CTC-chip facilitates visual verification and enumeration of CTCs during/after operation. By implementing microwell-shaped structures on the physical barrier, CTCs can be individually captured at sites for single-cell resolution analyses. Furthermore, the captured cells could be profiled in situ by introducing antibodies or small molecular probes. The chip thus assumes not only high detection sensitivity but also molecular specificity for CTC identification. Finally, the CTC-chip can retrieve captured CTCs. By reversing the flow direction, the cells can be dislodged from their capture sites and collected for downstream investigation.   

Mass transport to suspended waveguide biosensors

The response of a biosensor is controlled both by the kinetics of analyte adsorption as well as the mass transport to the device. Improving the affinity between a target molecule and the functionalized sensor can pose significant challenges in terms of biochemistry and surface chemistry. The careful design of sample flow systems presents a more convenient route for decreasing the time required for a measurement Using finite element methods, we model mass transport to a novel integrated photonic biosensor suspended within a microfluidic channel in an effort to understand how boundary layer flow patterns may be engineered to improve the transient response of the device. By monitoring the surface concentration of bound analyte over a range of inlet concentrations and vertical positions within the channel, we compare the behavior of suspended devices to that of planar sensors located on the floor of the channel. Thinner boundary layers and increased effective sensing area lead to consistently faster transient responses for the suspended sensor, with optimal performance resulting from the symmetric placement of the sensor with respect to the channel height.   

Weighing single cells in two fluids: measuring mass, volume and density

The Suspended Microchannel Resonator (SMR) is a highly sensitive cantilever-based mass sensor shown to be capable of weighing the buoyant mass of living single cells. We have engineered SMR-based microfluidic systems to achieve consecutive weighing of single cells in two different fluids, with controlled exposure times. By choosing fluids of two different densities, the paired buoyant mass measurements are used to characterize single-cell volume, mass and density. With density precision of 0.001 g.cm$^{-3}$, we explore the application of our techniques to samples ranging from bacterial to mammalian cells and show that cellular density is a tightly regulated biological property within populations, up to 100-fold more so than the other size parameters.   

Label-free screening of niche-to-niche variation in satellite stem cells using functionalized pores

Combinations of surface markers are currently used to identify muscle satellite cells. Using pores functionalized with specific antibodies and measuring the transit time of cells passing through these pores, we discovered remarkable heterogeneity in the expression of these markers in muscle (satellite) stem cells that reside in different single myofibers. Microniche-specific variation in stem cells of the same organ has not been previously described, as bulk analysis does not discriminate between separate myofibers or even separate hind-leg muscle groups. We found a significant population of Sca-1+ satellite cells that form myotubes, thereby demonstrating the myogenic potential of Sca-1+ cells, which are currently excluded in bulk sorting. Finally, using our label-free pore screening technique, we have been able to quantify directly surface expression of Notch1 without activation of the Notch pathway. We show for the first time Notch1-expression heterogeneity in unactivated satellite cells. The discovery of fiber-to-fiber variations prompts new research into the reasons for such diversity in muscle stem cells.   

Demonstration and analysis of the harmonic dithering technique for a high-sensitivity silicon waveguide biosensor

A label-free biosensor readout technique is demonstrated based on a silicon-on-insulator ring resonators and a harmonic dithering technique using a distributed feedback (DFB) laser and a lock-in amplifier. The 400 $\mu$m ring resonator is integrated with a microfluidic sample delivery channel formed with Polydimethylsiloxane (PDMS). Dithering the frequency of the DFB laser across the Lorentzian lineshape of the drop port at high frequency eliminates 1/f noise, and broadband noise is reduced by narrow-band detection with the lock-in amplifier. Biosensor system noise is analyzed and compared with more conventional readout methods, and in our case is dominated by thermal noise of the receiver, shot noise, and relative intensity noise (RIN) of the DFB laser. Because the readout automatically latches onto the drop port and does not require a complex scanning process, this methodology may provide a pathway for high-sensitivity, real-time, and low-cost biosensing.   

Label-free detection of DNA on silicon surfaces using Brewster angle straddle interferometry (BASI)

Label-free sensing of biomolecular interactions is of great importance for drug screening and a variety of clinical assays. Ultrasensitive detection of dsDNA on silicon substrates can be achieved using our new label-free sensing method - Brewster angle straddle interferometry (BASI) which exploits the removal of destructive interference to detect binding of target molecules on a silicon surface functionalized by probe molecules. By exploiting the fact that reflections of p-polarization undergo 180 degree phase shifts above the Brewster angle and none below it, we are able to use unprocessed silicon substrates with native oxide serving as the interference layer. Destructive interference in the geometry we use results in reflectivities $\sim$ 0.01\%. Reflectivity from the chip is a quantitative measure of the amount of bound target molecules and can be imaged in real time in microarray format. We demonstrate detection of DNA intercalation on pyrene modified surfaces. The substrates are shown to exhibit excellent binding toward dsDNAs. This work provides an avenue for understanding the binding specificity of small molecule-DNA interactions that can be potentially helpful in developing anticancer agents.   

Real-time molecular detection using a nanoscale porous silicon waveguide biosensor

A grating-coupled porous silicon waveguide with an integrated PDMS flow cell is demonstrated as a platform for real-time detection of chemical and biological molecules. This sensor platform not only allows for quantification of molecular binding events, but also provides a means to improve understanding of diffusion and binding mechanisms in constricted nanoscale geometries. The large internal surface area of porous silicon enables the capture of molecules inside the waveguide, which causes a large perturbation of the guided mode field and improves detection sensitivity by more than one order of magnitude as compared to evanescent wave-based detection methods. Molecular binding events in the waveguide are monitored by real-time angle-resolved reflectance measurements. Diffusion, adsorption and desorption coefficients of different sized chemical linker and nucleic acid molecules are determined based on the rate of change of the measured resonance angle. Both the magnitude of the waveguide resonance angle shift and kinetic parameters are observed to depend on molecule size. Experimental results are shown to be in good agreement with calculations based on rigorous coupled wave analysis and finite element simulation.   

On-chip Magnetic Separation and Cell Encapsulation in Droplets

The demand for high-throughput single cell assays is gaining importance because of the heterogeneity of many cell suspensions, even after significant initial sorting. These suspensions may display cell-to-cell variability at the gene expression level that could impact single cell functional genomics, cancer, stem-cell research and drug screening. The on-chip monitoring of individual cells in an isolated environment could prevent cross-contamination, provide high recovery yield and ability to study biological traits at a single cell level These advantages of on-chip biological experiments contrast to conventional methods, which require bulk samples that provide only averaged information on cell metabolism. We report on a device that integrates microfluidic technology with a magnetic tweezers array to combine the functionality of separation and encapsulation of objects such as immunomagnetically labeled cells or magnetic beads into pico-liter droplets on the same chip. The ability to control the separation throughput that is independent of the hydrodynamic droplet generation rate allows the encapsulation efficiency to be optimized. The device can potentially be integrated with on-chip labeling and/or bio-detection to become a powerful single-cell analysis device.   

Chip-based magnetic cytometer for high-throughput cellular profiling in unprocessed biological samples

Quantitative, high-throughput measurement of biomarkers in individual cells is a cornerstone of biomedical research, but prohibitive size, cost, and requisite sample processing have kept this technology from being more widely adapted in the clinic. We have developed a miniaturized magnetic cytometer ($\mu $MCM), a hybrid semiconductor / microfluidic chip, to rapidly measure the magnetic moments of individual immunomagnetically tagged cells. The use of magnetic detection enables measurements to be done on native specimens, thus decreasing the loss of rare cells and removing the need for expensive sample processing equipment. Benefiting from the high speed and sensitivity of semiconductor technology, the $\mu $MCM offers high-throughput operation (upwards of 10$^{7}$~cells/sec) with a detection resolution of $\sim $2000 magnetic nanoparticles/cell. The clinical utility of the $\mu $MCM was demonstrated by detecting scant tumor cells (20 cells) in whole blood and by molecularly profiling cells from solid tumor to monitor longitudinal drug efficacy.   

Miniature magnetic resonance system for robust and portable diagnostics

We have recently developed a new diagnostic platform, microNMR($\mu$NMR), specifically designed for clinical applications This new $\mu$NMR system performs rapid, accurate, and robust measurements of cells, proteins and small molecules in point-of-care settings. The system utilizes magnetic nanoparticles (MNPs) to amplify the analytical signals in NMR detection. When molecularly-specific MNPs identify their targets, the particles induce large, amplified changes in the transverse relaxation of water protons by producing local magnetic fields. A major challenge in achieving reliable NMR detection is the fluctuation of NMR frequency ($f$0) with temperature, which originates from the the temperature-dependent drift of the magnetic field. To overcome the challenge, we have implemented a new, automated feedback controller that keeps track of $f$0 and reconfigures measurement settings. The mechanism enables robust $\mu$NMR measurements in realistic clinical environments (4-50 $^{\circ}$C). Moreover, the $\mu$NMR interfaces with mobile devices for its operation, maximizing the portability of $\mu$NMR. The clinical utility of the new $\mu$NMR system is demonstrated by detecting and molecularly profiling cancer cells from patient samples.   

Paper Inside? - New Thinking for Biochip and Other Applications

The drive to improve the performance and reduce the cost of electronic, photonic and fluidic devices is starting to focus on the use of materials that are exotic for these applications but actually readily available in other fields. In this talk the use of paper in biochip and other applications will be reviewed. Paper is a very attractive material for many device applications: very low cost, available in almost any size, versatile surface finishes, portable and flexible. From an environmental point of view, paper is a renewable resource and is readily disposable (incineration, biodegradable). Applications of paper-based electronics currently being considered or investigated include biochips, sensors, communication circuits, batteries, smart packaging, displays. The potential advantages of paper-based devices are in many cases very compelling. For example, biochips fabricated on paper can use the capillary properties of paper to operate without the need of external power sources, greatly simplifying the design and reducing the cost. For e-reader devices, in addition to flexibility, the ideal solution for providing the look-and-feel of ink on paper is to have \textit{e-paper on paper}.