Modeling and simulation of luminescence detection platforms

Challenges in paper-based fluorogenic optical sensing with smartphones

Application of optically superior, tunable fluorescent nanotechnologies have long been demonstrated throughout many chemical and biological sensing applications. Combined with microfluidics technologies, i.e. on lab-on-a-chip platforms, such fluorescent nanotechnologies have often enabled extreme sensitivity, sometimes down to single molecule level. Within recent years there has been a peak interest in translating fluorescent nanotechnology onto paper-based platforms for chemical and biological sensing, as a simple, low-cost, disposable alternative to conventional silicone-based microfluidic substrates. On the other hand, smartphone integration as an optical detection system as well as user interface and data processing component has been widely attempted, serving as a gateway to on-board quantitative processing, enhanced mobility, and interconnectivity with informational networks. Smartphone sensing can be integrated to these paper-based fluorogenic assays towards demonstrating extreme sensitivity as well as ease-of-use and low-cost. However, with these emerging technologies there are always technical limitations that must be addressed; for example, paper's autofluorescence that perturbs fluorogenic sensing; smartphone flash's limitations in fluorescent excitation; smartphone camera's limitations in detecting narrow-band fluorescent emission, etc. In this review, physical optical setups, digital enhancement algorithms, and various fluorescent measurement techniques are discussed and pinpointed as areas of opportunities to further improve paper-based fluorogenic optical sensing with smartphones.

A Bioluminogenic Probe for Monitoring Tyrosinase Activity

A bioluminogenic probe based on luciferin was designed and synthesized to monitor tyrosinase activity. This probe was efficient in assessing tyrosinase activity in a buffered aqueous solution and in measuring endogenous tyrosinase activity in melanoma cells.

APD-Based Detection Module of Single-Photons in Chemiluminescence Immunoassay System

To accurately and rapidly detect single-photons is of the utmost importance for a Chemiluminescence Immunoassay (CLIA) system. An APD-based detection module of single-photons is designed in this paper. By comparison with PMT, APD possesses the advantages of higher detection sensitivity, lower dark current, smaller size, lower power consumption and higher integrity. The designed module can accurately detect single-photons with 22MHz frequency. The experimental results show that the module can be a basis for designing portable CLIA systems.

A computational model of a microfluidic device to measure the dynamics of oxygen-dependent ATP release from erythrocytes

Erythrocytes are proposed to be involved in blood flow regulation through both shear- and oxygen-dependent mechanisms for the release of adenosine triphosphate (ATP), a potent vasodilator. In a recent study, the dynamics of shear-dependent ATP release from erythrocytes was measured using a microfluidic device with a constriction in the channel to increase shear stress. The brief period of increased shear stress resulted in ATP release within 25 to 75 milliseconds downstream of the constriction. The long-term goal of our research is to apply a similar approach to determine the dynamics of oxygen-dependent ATP release. In the place of the constriction, an oxygen permeable membrane would be used to decrease the hemoglobin oxygen saturation of erythrocytes flowing through the channel. This paper describes the first stage in achieving that goal, the development of a computational model of the proposed experimental system to determine the feasibility of altering oxygen saturation rapidly enough to measure ATP release dynamics. The computational model was constructed based on hemodynamics, molecular transport of oxygen and ATP, kinetics of luciferin/luciferase reaction for reporting ATP concentrations, light absorption by hemoglobin, and sensor characteristics. A linear model of oxygen saturation-dependent ATP release with variable time delay was used in this study. The computational results demonstrate that a microfluidic device with a 100 µm deep channel will cause a rapid decrease in oxygen saturation over the oxygen permeable membrane that yields a measurable light intensity profile for a change in rate of ATP release from erythrocytes on a timescale as short as 25 milliseconds. The simulation also demonstrates that the complex dynamics of ATP release from erythrocytes combined with the consumption by luciferin/luciferase in a flowing system results in light intensity values that do not simply correlate with ATP concentrations. A computational model is required for proper interpretation of experimental data.

Contact CMOS imaging of gaseous oxygen sensor array

We describe a compact luminescent gaseous oxygen (O₂) sensor microsystem based on the direct integration of sensor elements with a polymeric optical filter and placed on a low power complementary metal-oxide semiconductor (CMOS) imager integrated circuit (IC). The sensor operates on the measurement of excited-state emission intensity of O₂-sensitive luminophore molecules tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) ([Ru(dpp)₃]²⁺) encapsulated within sol-gel derived xerogel thin films. The polymeric optical filter is made with polydimethylsiloxane (PDMS) that is mixed with a dye (Sudan-II). The PDMS membrane surface is molded to incorporate arrays of trapezoidal microstructures that serve to focus the optical sensor signals on to the imager pixels. The molded PDMS membrane is then attached with the PDMS color filter. The xerogel sensor arrays are contact printed on top of the PDMS trapezoidal lens-like microstructures. The CMOS imager uses a 32 × 32 (1024 elements) array of active pixel sensors and each pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. Correlated double sampling circuit, pixel address, digital control and signal integration circuits are also implemented on-chip. The CMOS imager data is read out as a serial coded signal. The CMOS imager consumes a static power of 320 µW and an average dynamic power of 625 µW when operating at 100 Hz sampling frequency and 1.8 V DC. This CMOS sensor system provides a useful platform for the development of miniaturized optical chemical gas sensors.

CMOS Imaging of Temperature Effects on Pin-Printed Xerogel Sensor Microarrays

In this paper, we study the effect of temperature on the operation and performance of a xerogel-based sensor microarrays coupled to a complementary metal-oxide semiconductor (CMOS) imager integrated circuit (IC) that images the photoluminescence response from the sensor microarray. The CMOS imager uses a 32 × 32 (1024 elements) array of active pixel sensors and each pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. A correlated double sampling circuit and pixel address/digital control/signal integration circuit are also implemented on-chip. The CMOS imager data are read out as a serial coded signal. The sensor system uses a light-emitting diode to excite target analyte responsive organometallic luminophores doped within discrete xerogel-based sensor elements. As a proto type, we developed a 3 × 3 (9 elements) array of oxygen (O2) sensors. Each group of three sensor elements in the array (arranged in a column) is designed to provide a different and specific sensitivity to the target gaseous O2 concentration. This property of multiple sensitivities is achieved by using a mix of two O2 sensitive luminophores in each pin-printed xerogel sensor element. The CMOS imager is designed to be low noise and consumes a static power of 320.4 μW and an average dynamic power of 624.6 μW when operating at 100-Hz sampling frequency and 1.8-V dc power supply.

Optical and Electric Multifunctional CMOS Image Sensors for On-Chip Biosensing Applications

In this review, the concept, design, performance, and a functional demonstration of multifunctional complementary metal-oxide-semiconductor (CMOS) image sensors dedicated to on-chip biosensing applications are described. We developed a sensor architecture that allows flexible configuration of a sensing pixel array consisting of optical and electric sensing pixels, and designed multifunctional CMOS image sensors that can sense light intensity and electric potential or apply a voltage to an on-chip measurement target. We describe the sensors' architecture on the basis of the type of electric measurement or imaging functionalities.

CMOS Imaging of Pin-Printed Xerogel-Based Luminescent Sensor Microarrays

We present the design and implementation of a luminescence-based miniaturized multisensor system using pin-printed xerogel materials which act as host media for chemical recognition elements. We developed a CMOS imager integrated circuit (IC) to image the luminescence response of the xerogel-based sensor array. The imager IC uses a 26 × 20 (520 elements) array of active pixel sensors and each active pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. The imager includes a correlated double sampling circuit and pixel address/digital control circuit; the image data is read-out as coded serial signal. The sensor system uses a light-emitting diode (LED) to excite the target analyte responsive luminophores doped within discrete xerogel-based sensor elements. As a prototype, we developed a 4 × 4 (16 elements) array of oxygen (O2) sensors. Each group of 4 sensor elements in the array (arranged in a row) is designed to provide a different and specific sensitivity to the target gaseous O2 concentration. This property of multiple sensitivities is achieved by using a strategic mix of two oxygen sensitive luminophores ([Ru(dpp)3]2+ and ([Ru(bpy)3]2+) in each pin-printed xerogel sensor element. The CMOS imager consumes an average power of 8 mW operating at 1 kHz sampling frequency driven at 5 V. The developed prototype system demonstrates a low cost and miniaturized luminescence multisensor system.

Low light CMOS contact imager with an integrated poly-acrylic emission filter for fluorescence detection

This study presents the fabrication of a low cost poly-acrylic acid (PAA) based emission filter integrated with a low light CMOS contact imager for fluorescence detection. The process involves the use of PAA as an adhesive for the emission filter. The poly-acrylic solution was chosen due its optical transparent properties, adhesive properties, miscibility with polar protic solvents and most importantly its bio-compatibility with a biological environment. The emission filter, also known as an absorption filter, involves dissolving an absorbing specimen in a polar protic solvent and mixing it with the PAA to uniformly bond the absorbing specimen and harden the filter. The PAA is optically transparent in solid form and therefore does not contribute to the absorbance of light in the visible spectrum. Many combinations of absorbing specimen and polar protic solvents can be derived, yielding different filter characteristics in different parts of the spectrum. We report a specific combination as a first example of implementation of our technology. The filter reported has excitation in the green spectrum and emission in the red spectrum, utilizing the increased quantum efficiency of the photo sensitive sensor array. The thickness of the filter (20 μm) was chosen by calculating the desired SNR using Beer-Lambert’s law for liquids, Quantum Yield of the fluorophore and the Quantum Efficiency of the sensor array. The filters promising characteristics make it suitable for low light fluorescence detection. The filter was integrated with a fully functional low noise, low light CMOS contact imager and experimental results using fluorescence polystyrene micro-spheres are presented.

Stochastic signaling in biochemical cascades and genetic systems in genetically engineered living cells

Living cells, either prokaryote or eukaryote, can be integrated within whole-cell biochips (WCBCs) for various applications. We investigate WCBCs where information is extracted from the cells via a cascade of biochemical reactions that involve gene expression. The overall biological signal is weak due to small sample volume, low intrinsic cell response, and extrinsic signal loss mechanisms. The low signal-to-noise ratio problem is aggravated during initial detection stages and limits the minimum detectable signal or, alternatively, the minimum detection time. Taking into account the stochastic nature of biochemical process, we find that the signal is accompanied by relatively large noise disturbances. In this work, we use genetically engineered microbe sensors as a model to study the biochips output signal stochastic behavior. In our model, the microbes are designed to express detectable reporter proteins under external induction. We present analytical approximated expressions and numerical simulations evaluating the fluctuations of the synthesized reporter proteins population based on a set of equations modeling a cascade of biochemical and genetic reactions. We assume that the reporter proteins decay more slowly than messenger RNA molecules. We calculate the relation between the noise of the input signal (extrinsic noise) and biochemical reaction statistics (intrinsic noise). We discuss in further details two cases: (1) a cascade with large decay rates of all biochemical reactions compared to the protein decay rate. We show that in this case, the noise amplitude has a positive linear correlation with the number of stages in the cascade. (2) A cascade which includes a stable enzymatic-binding reaction with slow decay rate. We show that in this case, the noise strongly depends on the protein decay rate. Finally, a general observation is presented stating that the noise in whole-cell biochip sensors is determined mainly by the first reactions in the genetic system with weak dependence on the number of stages in the cascade.

Development of a quantitative optical biochip based on a double integrating sphere system that determines absolute photon number in bioluminescent solution: application to quantum yield scale realization

We report a new design of an optical biochip based on a double integrating sphere system to quantify the absolute number of the emitted photons or the total photon flux by a whole cell bioluminescent biosensor, for water toxicity detection, based on genetically engineered Escherichia coli bacteria carrying a recA::luxCDABE promoter-reporter fusion. The new design of the double integrating sphere system does not require any external standard light source for calibration of the tested bioluminescent solution and allows a direct determination of the total photon flux of the bioluminescent solution. In our design, we required that the two spheres are symmetric (have the same radius and reflectance) with a surface area larger than the cut cap area between the spheres.

Microfluidic device using chemiluminescence and a DNA-arrayed thin film transistor photosensor for single nucleotide polymorphism genotyping of PCR amplicons from whole blood

This work describes a novel microfluidic device using a thin film transistor (TFT) photosensor integrating a microfluidic channel, a DNA chip platform, and a photodetector for the discrimination of single nucleotide polymorphisms (SNPs). A DNA-arrayed TFT photosensor was used as a DNA chip platform and photo detecting device. Chemiluminescence was used for DNA sensing because chemiluminescence provides higher sensitivity and requires simpler instrumentation than fluorescence methods. The SNP of biotinylated target DNA was detected based on chemiluminescence by using horse radish peroxidase-conjugated streptavidin. The lower detection limit for a model biotinylated oligonucleotide (63-mer) was 0.5 nM, much lower than expected DNA concentrations in a practical application of this device. Furthermore, SNP detection in the aldehyde dehydrogenase 2 gene was successfully achieved using DNA-arrayed TFT photosensor without DNA extraction and DNA purification using PCR products. The assay was completed in less than one hour. Our technology will be a promising approach to developing a miniaturized, disposable DNA chip with high sensitivity.

Single nucleotide polymorphisms: discovery, detection and analysis

Single nucleotide polymorphisms (SNPs) are the most abundant and simple form of DNA variation. Analyses of SNPs in the human population have the potential to greatly improve human health, both by predicting susceptibility to disease and guiding choice of therapy. This review describes new tools for SNP discovery, and current and emerging technologies for large-scale SNP analysis, as well as providing a guide to choosing the best approach for SNP analysis.