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- Front Matter: Volume 7888
- Session I
- Session II
- Microfluidic Devices and Systems for Pathogen Detection: Joint Session with Conference 7929
- Poster Session
Front Matter: Volume 7888
Front Matter: Volume 7888
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This PDF file contains the front matter associated with SPIE
Proceedings Volume 7888, including the Title Page, Copyright
information, Table of Contents, and the Conference Committee listing.
Session I
Silicon photonic microring resonator arrays for scalable and multiplexable bioanalysis
Matthew S. Luchansky,
Adam L. Washburn,
Abraham J. Qavi,
et al.
Show abstract
Silicon photonic devices, such as SOI microring resonators, have optical properties that are incredibly responsive to changes in the local dielectric environment accompanying a biological binding event at or near the ring surface. We have developed a platform in which arrays of uniquely addressable microrings are functionalized with target-specific capture agents so as to create a powerful tool for multiplexed biomolecular detection. We will discuss applications of this technology to the multiplexed detection of DNA, RNA, and proteins in clinically-relevant matrices, and will also describe the rigorous empirical determination of key sensitivity metrics.
Bioconjugation of ultra-high-Q optical microcavities for label-free sensing
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The development of label-free biosensors with high sensitivity and specificity is of significant interest for medical
diagnostics and environmental monitoring, where rapid and real-time detection of antigens, bacteria, viruses, etc., is
necessary. Ultra-high-Q optical microcavities are uniquely suited to sensing applications, but previous research efforts
in this area have focused on the development of the sensor itself. While device sensitivity is crucial to sensor
development, specificity is an equally important feature. Therefore, it is crucial to develop a high density, covalent
surface functionalization process, which also maintains the device's performance. Here, we demonstrate a facile method
to impart specificity to optical microcavities, without adversely impacting their optical performance. In this approach,
we selectively functionalize the surface of the silica microtoroids with amine-terminated silane coupling agents, and
examine the impact of differing reaction schemes on the overall quality of the devices. The chemistries investigated here
result in uniform surface coverage, and no microstructural damage, and do not adversely impact the optical performance
of the devices, as measured by their quality factors before and after functionalization. This work represents one of the
first examples of non-physisorption-based bioconjugation of optical microtoroid resonators, which can be used for the
label-free detection of biomolecules.
Fluorescence enhancement in a polymer-based photonic-crystal biosensor
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Detecting labeled or naturally-fluorescent biomolecules at very low concentrations is of a significant importance for
health sciences, agricultural sciences, and security-related applications. Photonic crystals (PhC) are microfabricated
nano-structures of periodic dielectric permittivity in one, two, or three dimensions that possess unique light manipulation
properties. These include the ability to localize electromagnetic waves at particular PhC lattice locations. Ultra-sensitive
detection using thin-film PhC structures fabricated in semiconductor materials has been demonstrated in both "active"
and "passive" modalities. In the active modality, the adsorption of target molecules to the PhC surface causes a refractive
index change that is translated into reflectance or transmission peak shifts. The passive modality demonstrated by
our group utilizes the PhC structure to observe enhanced fluorescent emission within resonant defect cavities in a 2D
PhC lattice. Integrating these semiconductor-based PhC structures with biocompatible microfluidic channels is a
challenging task that can significantly increase the final cost of the sensor system. We demonstrate here soft lithographic
nanomolding techniques for polymer-based PhC structures that are easily integrated with microfluidic channels to
provide a portable means of biosensing. A TE bandgap of 2.857% for a 2D PhC fabricated in poly(dimethylsiloxane)
(PDMS) will allow these lattices to become core structures in PhC-based biosensors incorporating both active and
passive modalities. Modeling and initial optical characterization results of the Si- and PDMS-based PhC biosensor will
also be presented.
Silicon photonic wire evanescent field sensors: sensor arrays and instrumentation
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We are developing a photonic wire evanescent field (PWEF) sensor chip using 260 nm x 450 nm cross-section silicon
photonic wire waveguides. The waveguide mode is strongly localized near the silicon surface, so that light interacts
strongly with molecules bound to the waveguide surface. The millimeter long sensor waveguides can be folded into tight
spiral structures less than 200 micrometers in diameter, which can be arrayed at densities up to ten or more independent
sensors per square millimeter. The long propagation length in each sensor element gives a response to molecular binding
much better than currently available tools for label-free molecular sensing. Cost of instrumentation, cost per
measurement, ease-of-use, and the number of sensors that can be simultaneously monitored on a sensor array chip are
equally important in determining whether an instrument is practical for the end user and hence commercially viable. The
objective of our recent work on PWEF sensor array chips and the associated instrumentation is to address all of these
issues. This conference paper reviews our ongoing work on the photonic wire sensor chip design and layout, on-chip
integrated fluidics, optical coupling, and chip interrogation using arrays of grating couplers formed using sub-wavelength
patterned structures.
Molecular detection via hybrid peptide-semiconductor photonic devices
E. Estephan,
M.-b. Saab,
M. Martin,
et al.
Show abstract
The aim of this work was to investigate the possibilities to support device functionality that includes strongly confined
and localized light emission and detection processes within nano/micro-structured semiconductors for biosensing
applications. The interface between biological molecules and semiconductor surfaces, yet still under-explored is a key
issue for improving biomolecular recognition in devices.
We report on the use of adhesion peptides, elaborated via combinatorial phage-display libraries for controlled
placement of biomolecules, leading to user-tailored hybrid photonic systems for molecular detection. An M13
bacteriophage library has been used to screen 1010 different peptides against various semiconductors to finally isolate
specific peptides presenting a high binding capacity for the target surfaces. When used to functionalize porous silicon
microcavities (PSiM) and GaAs/AlGaAs photonic crystals, we observe the formation of extremely thin (<1nm) peptide
layers, hereby preserving the nanostructuration of the crystals. This is important to assure the photonic response of these
tiny structures when they are functionalized by a biotinylated peptide layer and then used to capture streptavidin.
Molecular detection was monitored via both linear and nonlinear optical measurements. Our linear reflectance spectra
demonstrate an enhanced detection resolution via PSiM devices, when functionalized with the Si-specific peptide.
Molecular capture at even lower concentrations (femtomols) is possible via the second harmonic generation of
GaAs/AlGaAs photonic crystals when functionalized with GaAs-specific peptides.
Our work demonstrates the outstanding value of adhesion peptides as interface linkers between semiconductors
and biological molecules. They assure an enhanced molecular detection via both linear and nonlinear answers of
photonic crystals.
Application of ring down measurement approach to micro-cavities for bio-sensing applications
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Optical biosensors can detect biomarkers in the blood serum caused by either infections or exposure to toxins.
Until now, most work on the micro-cavity biosensors has been based on measurement of the resonant frequency
shift induced by binding of biomarkers to a cavity. However, frequency domain measurements are not precise for
such high Q micro-cavities. We hypothesize that more accurate measurements and better noise tolerance can be
achieved by the application of the ring down measurement approach to the micro-cavity in a biosensor. To test
our hypothesis, we have developed a full vectorial finite element model of a silica toroidal micro-cavity immersed
in water. Our modeling results show that a toroidal cavity with a major diameter of 70μm and a minor diameter
of 6μm can achieve a sensitivity of 28.6μs/RIU refractive index units (RIU) at 580nm. Therefore, our sensor
would achieve the resolution of 5 x 10-8 RIU by employing a detector with picosecond resolution. Hence we
propose a micro-cavity ring down biosensor with high sensitivity which will find wide applications in real time
and label free bio-sensing.
PMMA-micro goblet resonators for biosensing applications
Torsten Beck,
Mario Hauser,
Tobias Grossmann,
et al.
Show abstract
We report on a new type of whispering gallery mode (WGM) resonator made of out of low-loss polymer poly (methyl
methacrylate) (PMMA). These optical cavities are fabricated using standard semiconductor processing methods in
combination with a specific thermal reflow process. During this subsequent thermal treatment, surface tension leads to
the goblet like geometry of the resonator and to an ultra smooth surface. The Q-factor of these goblet resonators is above
2·106 in the 1310 nm wavelength range. In order to demonstrate the applicability of the goblet resonators for bio sensing,
Bovine Serum Albumin was detected by monitoring the shift of resonator modes due to protein adsorption.
Session II
Confocal Raman microscopy for identification of bacterial species in biofilms
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Implemented through a confocal microscope, Raman spectroscopy has been used to distinguish between biofilm
samples of two common oral bacteria species, Streptococcus sanguinis and mutans, which are associated with
healthy and cariogenic plaque, respectively. Biofilms of these species are studied as a model of dental plaque. A
prediction model has been calibrated and validated using pure biofilms. This model has been used to identify
the species of transferred and dehydrated samples (much like a plaque scraping) as well as hydrated biofilms in
situ. Preliminary results of confocal Raman mapping of species in an intact two-species biofilm will be shown.
Aqueous arrayed imaging reflectometry as a sensitive platform for real-time biomolecular interaction analysis
Show abstract
Arrayed imaging reflectometry (AIR) has been previously demonstrated as a highly sensitive biosensing technique, with
picomolar limits of detection observed for certain cytokines and growth factors. However, the implementation of AIR
has so far been on dry chip surfaces in an end-point sensor format that precludes real-time monitoring of interactions.
The simple substrate format used for dry AIR (a thermally grown oxide film on silicon) is unsuitable for imaging in an
aqueous medium due to near grazing angles of incidence required to achieve total destructive interference of reflected
light, the foundation of AIR. Hence, a new substrate was identified that would allow practically realizable incidence
angles. Here, the substrate proposed for AIR imaging under an aqueous environment has been described, and its ability
to detect Angstrom level thickness differences has been demonstrated. This substrate consisted of a two-layer stack on
silicon: a silicon nitride film followed by a sputtered oxide film, which produced the total destructive interference
condition required for AIR for an operating wavelength of 632.8 nm and an angle of incidence of ~52°. The apparatus
used for imaging substrates in an aqueous environment was essentially the same as that used for dry AIR, modified by
the incorporation of a flow cell. Several chips were patterned with oxide posts such that the background yielded
minimum reflectance while the post heights were varied to test the thickness sensitivity of the new sensor configuration.
Detectable contrast from substrates bearing oxide posts with a 0.2 nm thickness was observed using pure water or
aqueous solutions of sucrose. This substrate can thus be used to monitor biomolecular interactions in real time with a
high sensitivity.
Microfluidic Devices and Systems for Pathogen Detection: Joint Session with Conference 7929
Optical and fluidic design for guaranteed trapping and detection of particles in a silicon microfluidic and photonic crystal system
Show abstract
In recent studies, optical forces have been exploited to guide particles along waveguides and to trap particles near
refractive index sensors. But the ability of photonic devices to bind a freely flowing particle from an adjacent
microfluidic channel has yet to be fully characterized. In order to determine the ability of a given device to trap an
arbitrary particle, we develop a method to numerically calculate the trajectory of a particle flowing near a model system.
We determine the trajectories of 50 nm radius particles in a fluid flowing at an average velocity of 1 cm/s near a
photonic crystal resonator pumped at 1 W. The finite element method is used to calculate the force of the fluid on the
particles and finite-difference time-domain simulations are used to calculate optical forces. The particle equation of
motion is solved using the adaptive Runge-Kutta method.
Towards an optical concentrator for nanoparticles
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Photonic crystal (PC) biosensing platforms have the potential to achieve single-pathogen detection using nanoscale
optical resonant cavities. Real-time sample analysis requires the PC sensor to be interfaced with a fluidic environment,
but current practical fluidic structures typically have dimensions much larger than the PC sensing cavities. To enhance
sensing probability, an on-chip optofluidic structure is being developed to concentrate target material within a narrow
sensing region of the microfluidic channel. The device relies on fluid drag forces to propel material along the
microfluidic channel. Dielectric material is guided transversely within the microfluidic channel by optical gradient forces
due to the evanescent field surrounding a ridge waveguide within the channel. Results of computational modeling are
presented.
All-fiber optofluidic biosensor
Show abstract
Optical fiber provides a unique and versatile platform for developing point-of-care optical sensing systems. Here we first
propose a Fabry-Pérot (FP) based flow-through optofluidic biosensor, and then construct an all-fiber system which fully
utilizes optical fibers to achieve rapid, sensitive, label-free biomolecular detection. This sensor consists of two single
mode fibers (SMFs) with reflecting surfaces and a photonic crystal fiber (PCF) vertically sandwiched by them. Firstly,
the SMFs act as waveguides for delivering light into and out of an optofluidic device (like PCF); secondly, instead of
using the optical properties of the PCF, we take advantage of its inherent multiple fluidic channels and large sensing
surface; thirdly, the two reflective surfaces and the PCF form a Fabry-Pérot microresonator and its resonance mode is
sensitive to the change in the fluidic channels, which can be used to detect the substances flowing through the fluidic
channels or adsorbing on the channel surface. In this paper, we explore the operating principle of the FP-based
optofluidic biosensor, theoretically and experimentally investigate its feasibility and capability. The results show that the
all-fiber optofluidic sensor is a promising technology platform for rapid, sensitive and high-throughput biological and
chemical sensing.
Application of field-modulated birefringence and light scattering to biosensing
Show abstract
Superparamagnetic nanoparticles (NPs) coated with surface ligands are shown to be an effective means to impart magnetic
field modulation to optical signals from targeted receptor complexes. The modulated signals they produce can be used for a
number of important high throughput applications in bio-sensing including: detecting (weaponized) viruses, screening
recombinant libraries of proteins, identifying pathogenic conversions of microbes, and monitoring gene amplification. We
compare the results of two dynamic methods of measuring target binding to NPs: birefringence and field modulated light
scattering (FMLS). These measurements reflect complementary manifestations of NP alignment (orientation) and de-alignment
(relaxation) dynamics. Birefringence originates from the specific crystalline properties of a small subset of
paramagnetic NPs (for example, maghemite) when oriented in a magnetic field. Upon quenching the field, it decays at a rate
exhibiting the Debye-Stokes-Einstein rotational relaxation constant of target-NP complexes. Birefringence relaxation reflects
the particle dynamics of the mixed suspension of NPs, with signal components weighted in proportion to the free and
complexed NP size distributions. FMLS relaxation signals, on the other hand, originate predominately from the inherent
optical anisotropy of the target complexes, show little contribution from non-complexed NPs when the targets are more
optically anisotropic than the NPs, and provide a more direct and accurate method for determining target receptor
concentrations. Several illustrations of the broad range of applications possible using these dynamic measurements and the
kind of information to be derived from each detection modality will be discussed.
An integrated microfluidic biosensor for the rapid screening of foodborne pathogens by surface plasmon resonance imaging
Show abstract
The rapid detection of foodborne pathogens is of vital importance to keep the food supply rid of contamination.
Previously we have demonstrated the design of a hybrid optical device that performs real-time surface plasmon
resonance (SPR) and epi-fluorescence imaging. Additionally we have developed a biosensor array chip that is able
to specifically detect the presence of two known pathogens. This biosensor detects the presence of the pathogen
strains by the selective capture of whole pathogens by peptide ligands functionalized to the spots of the array. We
have incorporated this biosensor array into a self contained PDMS microfluidic chip. The enclosure of the biosensor
array by a PDMS microfluidic chip allows for a sample to be screened for many strains of pathogens simultaneously
in a safe one time use biochip. This disposable optical biochip is inserted into with the hybrid SPR/epi-fluorescence
imaging device to form an integrated system for the detection of foodborne pathogens. Using this integrated system,
we can selectively detect the presence of E. coli 0157:H7 or S. enterica in a simultaneously in real-time.
Additionally, we have modeled the mechanical properties of the microfluidic biochip in order to manipulate the flow
conditions to achieve optimal pathogen capture by the biosensor array. We have developed an integrated system
that is able to screen a sample for multiple foodborne pathogens simultaneously in a safe, rapid and label-free
manner.
Poster Session
The radix 4 base number system for use in theoretical genetics
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The paper will introduce the quaternary, or radix 4, based system for use as a fundamental standard beyond the traditional binary, or radix 2, based system in use today. A greater level compression is noted in the radix 4 based system when compared to the radix 2 base as applied to a model of information theory. The application of this compression algorithm to both DNA and RNA sequences for compression will be reviewed in this paper.