SEMINAR REPORT
Entitled

“OPTICAL

FIBER BIO SENSORS
APPLICATIONS”

Submitted in partial fulfilment of the requirement
For...
Acknowledgement

It gives me great pleasure to present my seminar report on ―Optical fiber biosensors
applications‖ No wor...
Sardar Vallabhbhai National Institute of Technology
Surat-395 007, Gujarat, INDIA.
DEPARTMENT OF ELECTRONICS AND COMMUNICA...
ABSTRACT:Currently, cancer detection is a difficult, long and invasive process. Many times the
symptoms are unclear or tum...
TABLE OF CONTENTS:TITLE……………………..................................................1
ACKNOWLEDGEMENT…………………………….......2
ABST...
7. Mechanical characterization of totally optical tactile sensor oriented on
bio applications................................
CHAPTER-1 BIO-OPTICAL GAS-SENSOR (SNIFFER DEVICE)
WITH A FIBER OPTIC OXYGEN SENSOR

1.1 Abstract:This bio-optical gas-sens...
for analyzing the enzyme activity or the substrate concentration. Then we have also
developed and reported a bio electroni...
sides of a stainless steel pipe and the inner side edges of the two T-tubes were closed by a
sealing tape. The enzyme memb...
Calibration curve of the bio-optical sniffer with 10.0 mm o vlAsA for
TMA in the gas phase his calibration range of the sn...
CHAPTER-2

OPTICAL BIO-SNIFFER (BIOCHEMICAL
GASSENSOR) FOR DIMETHYL SULFIDE VAPOR

2.1 Abstract:An optical gas-sensor (bio...
for measurement of gaseous DMS .The performance of the sensor is evaluated with a gas
flow measurement system for gas-phas...
Principle of a chemical measurement of DMS using FMO enzyme reaction and substrate
regeneration cycle. A substrate regener...
array. From that point of view, the optical-fiber sensor will be slit able for constructing
the arrayed intelligent nose s...
CHAPTER-3 USING UV-LED LIGHT FOR MONITORING
ETHANOL VAPOR WITH HIGH SENSITIVITY & SELECTIVITY

3.1 Abstract:A fiber optic ...
applications. Particularly, simplified and miniaturized sensing system for portable
application is expected. Alcohol dehyd...
measurement in the liquid phase was constructed and tested. At first, an enzyme
immobilized membrane was prepared by the p...
A 50.0 ppm of ethanol, methyl ethyl ketone (MEK), acetone and n-pentane was exposed
to the bio-sniffer. These gases were a...
7yr4] [` during gas exposure, significant increases of fluorescent intensity and the steadystate values depend on ethanol ...
CHAPTER-4 OPTICAL SENSOR IN THE APPLICATION OF BIODETECTION
4.1 Abstract:This optical sensor was designed and developed fo...
will be addressed by the dye added in. Under the expose of UV light, the addressed
biomarker will emit certain wavelength ...
final result was the averaged value of the particular one hundred readings. The
experiment was repeated four times for eac...
water. The biochips were drained completely by tapping on an absorbent paper. 100
microl of BS buffer was added into each ...
system response was much slower as compared to high cost detection systems, it did not
pose a problem in our protein quant...
CHAPTER-5 OPTICAL BIO-SENSOR FROM DNA AND NANO

STRUCTURES

5.1 Abstract:This type of optical device can be placed inside ...
of quantum wires or quasi 1D system. During the last several years, because of their
carbon based native material having u...
The effective dielectric constant of medium surrounding SWNT can be written as
" =f’eDNA + (1 - f ) "eS

where "DNA and "S...
The pH of certain solution drastically impacts the biomolecules such as DNA, RNA,
proteins etc. Without doubt, this optica...
CHAPTER-6

A HEMISPHERICAL OMNI-DIRECTIONAL BIO
INSPIRED OPTICAL SENSOR

6.1 AbstractFlying insects possess a surprisingly...
trend in biologically inspired vision systems has been to made use of optical flow
information for flight tasks. Numerous ...
converge; nor from the amount of reflective power needed to focus on the objects. They
possess poorer eyesight, with low s...
response of the fly's compound eyes, Reinhardt made the Elementary-Motion-Detector
(EMD) .This method finds the correlatio...
photoreceptors. A total of 256 sensors could be used in this configuration, In order to use
sensors with different field o...
microcontroller has 8 embedded ADC input channels and samples the signals on each
ADC with 10-bit resolution. The

Complet...
systems covering 360 degrees field of view. B. Future work to decrease the dependency
of the response to the tolerances an...
CHAPTER-7 OPTICAL TACTILE SENSOR ORIENTED ON BIOAPPLICATION

7.1 Abstract:A new class of optical pressure sensors in a rob...
sensors, which are capable of detecting contact force, vibration, texture, and temperature,
can be recognized as the next ...
gases. The surface properties of PDMS can easily be changed by exposure of the surface
in oxygen plasma. This way PDMS can...
high refractive index regions. The pressure applied on the GNM introduces a
displacement of the nanoparticles along its in...
viewpoints including those of the basic transduction of tactile data (tactile sensing), the
computer processing of the tra...
CHAPTER :-8

OPTICAL BIO-CHEMICAL SENSORS ON SNOW
RING RESONATORS

8.1 Abstract: The novel ring resonator based bio-chemic...
targeted molecules cannot be controlled. In contrast, in label-free detection the targeted
molecules are detected in their...
possible by simply changing the diameter of the ring in the resonator. Biochemical
sensors based on SOI photonic waveguide...
an effective index waveguide. Fabry-Perot characteristics in the emission demonstrated
guidance of light in the 100 nm pat...
Mode over the bend is appreciably higher compared to the fundamental mode. Also
plotted in the figure, is the radiation lo...
confinement factor for the SNOW is 94 % resulting in the low bend losses as shown in.
The confinement factor for the optic...
200 nm SOI waveguide for the same change in surrounding refractive index. In a ring
resonator the change of the resonance ...
The SNOW ring resonator was simulated for surface attachment of the molecules. A
molecule layer with the test thickness wa...
8.4 Conclusion:-

The SNOW ring resonator consists of a SOI bus waveguide coupled into a ring
waveguide consisting of clos...
REFERENCES: [1] M. Pumera, Mater. Today 14, 7–8 (2011).
[2] C.-H. Lu, H.-H. Yang, C.-L. Zhu, X. Chen, G.-N. Chen, Angew. C...
[20 F. Rufier and N. Franceschini, "Octave, a bioinspiredvisuo-motor control system for
the guidance of Micro-AirVehicles"...
[32] R.R. Reston, and E.S. Kolesar, ―Robotic tactile sensor array fabricated froma
piezoelectric polyvinylidine fluoride f...
[43] R. Tajima, S. Kagami, M. Inaba and H. Inoue, ―Development of soft and distributed
tactile sensors and the application...
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Optical bio sensors application

  1. 1. SEMINAR REPORT Entitled “OPTICAL FIBER BIO SENSORS APPLICATIONS” Submitted in partial fulfilment of the requirement For the Degree of Bachelor of Technology (ELECTRONICS & COMMUNICATION) : Presented & Submitted By: Mr. BHEEMSAIN (Roll No.U10EC055) B. TECH. IV (Electronics & Communication) 7th Semester : Guided By: Prof. Dr.V. MISHRA Associate Professor, ECED. DEPARTMENT OF ELECTRONICS ENGINEERING Sardar Vallabhbhai National Institute of Technology Surat-395 007, Gujarat, INDIA. (DECEMBER – 2013 U10EC055, ODD SEMESTER 2013-2014 Page1
  2. 2. Acknowledgement It gives me great pleasure to present my seminar report on ―Optical fiber biosensors applications‖ No work, big or small, has ever been done without the contributions of others. I would like to express deep gratitude towards Prof. Dr. V. Mishra (Associate Professor at Electronics & Communication Engineering Department, SVNIT) who gave me their valuable suggestions, motivation and the direction to proceed at every stage. He extended towards a kind and valuable guidance, indispensible help and inspiration at times in appreciation I offer them my sincere gratitude. In addition, I would like to thanks Dept. of Electronics and Communication Engineering, SVNIT finally, yet importantly, I would like to express my heartfelt thanks to my beloved parents and my brother for their blessings, my friends/classmates for their help and wishes for the successful completion of this seminar. Bheemsain U10EC055, ODD SEMESTER 2013-2014 Page2
  3. 3. Sardar Vallabhbhai National Institute of Technology Surat-395 007, Gujarat, INDIA. DEPARTMENT OF ELECTRONICS AND COMMUNICATION CERTIFICATE This is to certify that the B.Tech. IV (7th Semester) SEMINAR REPORT entitled “OPTICAL BIO SENSORS APPLICATION” is presented & submitted by Candidate Mr. BHEEMSAIN bearing Roll No. U10EC055,in the partial fulfilment of the requirement for the award of B. Tech. degree in Electronics & Communication Engineering. He/She has successfully and satisfactorily completed his/her Seminar Exam in all respect. We, certify that the work is comprehensive, complete and fit for evaluation. Prof. Dr. V.MISHRA Seminar Guide Associate Professor Prof . P.K.Shah Head of the Deptt. ECED Associate Professor SEMINAR EXAMINERS: Name Signature with date 1.Prof.____________________ __________________ 2.Prof.____________________ __________________ 3.Prof.____________________ __________________ EPARTMENT SEAL December-2013 U10EC055, ODD SEMESTER 2013-2014 Page3
  4. 4. ABSTRACT:Currently, cancer detection is a difficult, long and invasive process. Many times the symptoms are unclear or tumors are detected far into the stages of cancer. Clinical diagnostics aim to recognize abnormal characteristics as efficiently and quickly as possible. The optical biosensor is a faster, cheaper alternative for cancer cell detection. With this new machine for cancer screening integrated into the clinic, a more comprehensive healthcare tool would be more widely available to health care professionals. In other applications HIV, Hepatitis, other viral disease, drug testing, environmental monitoring, genetic monitoring, disease, functional sensors, drug testing, blood, urine, electrolytes, gases, steroids, drugs, hormones, proteins, food industry, medicine, environmental, diabetics, drug testing, detection of environmental pollution and toxicity, agricultural monitoring, ground water screening and Ocean monitoring. So at present the optical bio sensors are play very important role in the biological and Environmental application point of view. U10EC055, ODD SEMESTER 2013-2014 Page4
  5. 5. TABLE OF CONTENTS:TITLE……………………..................................................1 ACKNOWLEDGEMENT…………………………….......2 ABSTRACT………………............................……………4 1. Bio-Optical gas-sensor (sniffer device) With a fiber optic oxygen sensor...............................................................6 1.1 Abstract..............................................................................................................6 1.2 Introduction........................................................................................................6 1.3 Experimental section..........................................................................................8 1.4 Results and discussion........................................................................................9 2. Optical Bio-sniffer (Biochemical gas sensor) For dimethyl sulphide vapour...................................................................11 2.1 Abstract……………………………………………………………………….11 2.2 Introduction......................................................................................................11 2.3 Experimental section........................................................................................12 2.4 Results and discussion......................................................................................13 2.5 Conclusions......................................................................................................14 3. Fiber Optic Bio-sniffer (Biochemical gas sensor) using UV-LED light for monitoring ethanol vapour with high sensitivity & selectivity.....................15 3.1Abstract……………………………………….................................................15 3.2 Introduction……………………………………..............................................15 3.3 Experimental………………………………………........................................16 3.4 Results and discussion………………………………......................................18 4. Optical sensor in the application bio-detection………………................20 4.1 Abstract………………………………………………………........................20 4.2 Introduction………………………………………………..............................20 4.3 Experiments and results……………………………......................................20 4.4 Conclusion……………………………………………...................................23 5. Optical Bio-Sensor from DNA and Nano Structures …………….……25 5.1Abstract……………………………………………………………………….25 5.2 Introduction………………………………......................................................25 5.3 Discussion…....................................................................................................28 6. A hemispherical Omni-directional bio inspired Optical sensor…….................................................................................29 6.1Abstract………………….………....................................................................29 6.2 Introduction …..…...........................................................................................29 6.3 Conclusion…...................................................................................................35 U10EC055, ODD SEMESTER 2013-2014 Page5
  6. 6. 7. Mechanical characterization of totally optical tactile sensor oriented on bio applications..............................................................................................36 7.1Abstract………………………………………………………………………...36 7.2 Introduction…....................................................................................................36 7.3 Tactile sensor description...................................................................................38 7.4 Conclusion…......................................................................................................40 8. Optical Bio-Chemical Sensors on Snow Ring Resonators........................41 8.1 Abstract…………………………………………………..................................41 8.2 Introduction…....................................................................................................41 8.3 Sensor structure…………………………………..............................................44 8.4 Conclusion……………………………………..................................................49 REFERENCES…................................................50-53 U10EC055, ODD SEMESTER 2013-2014 Page6
  7. 7. CHAPTER-1 BIO-OPTICAL GAS-SENSOR (SNIFFER DEVICE) WITH A FIBER OPTIC OXYGEN SENSOR 1.1 Abstract:This bio-optical gas-sensor (sniffer device) was constructed by immobilizing flavincontaining mono-oxygenase 3 (FM03, one of xenobiotic metabolizing enzymes for catalyzing the oxidation of odorous. Substances such as tri methylamine: TMA onto a tip of a fiber optic oxygen sensor with oxygen sensitive ruthenium organic complex, excitation: 470 nm, fluorescent: 600 nm, with a tube-ring. A reaction unit for circulating buffer solution was applied to the tip of the sniffer device. A substrate regeneration cycle was applied to the FM03 immobilized sensor in order to amplify the output signal by coupling the mono oxygenase with a reducing reagent system of ascorbic acid in phosphate buffer. The bio-optical sniffer was possible to detect the oxygen consumption induced by FOM3 enzymatic reaction with TMA application. The sniffer device with 10.0 mmol/l As A could be used to measure TMA Vapor from 0.31 to 125 ppm, this covers the maximum permissible concentration in tube work place 5ppm, and the sensing level-5 of smell in humans, 3.0 ppm. The sniffer device possessed high selectivity for TMA being attributable to the FM03 substrate specificity, continuous measurability. 1.2 Introduction:The sensing and measurement of chemical substances in the gas phase, such as malodor, flammable and harmful gases with higher sensitivity and selectivity than the sense of smell in humans are required in many fields. Tri methylamine is one of volatile nitric compound. The maximum permissible concentration of TMA vapors in the work place are 5.0 ppm (12 mg/m3, TWA Time Weighted Average Concentration) and 15 ppm. Flavin-containing monooxygenase as one of xenobiotic metabolizing enzymes has been reported to catalyze the oxidation of sulfuric and nitric compounds. FM03 is possible to be expressed from human FM03 cDNA using a baculovims expression system and commercialized. Oxygen consumption accompanied the enzyme reaction has been used U10EC055, ODD SEMESTER 2013-2014 Page7
  8. 8. for analyzing the enzyme activity or the substrate concentration. Then we have also developed and reported a bio electronic nose for TMA using FMO. On the other hand, some optical fibers with chemical sensitivity were commercialized, and have been expected to be newly sensing device for biological analysis. The optical fiber is considered to be adaptable device for constructing the arrayed intelligent nose system for multi-analfle in the gas-phase. In this work, we have constructed a bio-optical sniffer using FMO enzyme for measurement of gaseous TMA. The performance of the sensor is evaluated, such as sensitivity, calibration behavior and selectivity. 1.3 Experimental Section:- The bio-optical sniffer consisted of a reaction unit and an oxygen-sensitive optical fiber (FOXY-"-Flat (silicone overcoat), 1/16" outer diameter with an enzyme membrane immobilized with flavin-containing monooxygenase. The optical fiber was coated by solgel process with Ruthenium-organic complex which indicates an optical quenching (excitation wavelength: 470 nm, fluorescent wavelength: 600 nm) to the existence of oxygen molecule in both the liquid and gas phases. For enzyme immobilization, FMO3 was mixed with PVA-SbQ monomer solution in a weight ratio of 1: 2, to the surface of a dialysis membrane (thickness: 15 pm), spread on a glass plate, and then irradiated with a fluorescent lamp for 30 A bio-optical sniffer Min in order to photo crosslink the monomer solution and immobilize the enzyme to the dialysis membrane. The reaction unit was constructed by connecting two T-tubes to both U10EC055, ODD SEMESTER 2013-2014 Page8
  9. 9. sides of a stainless steel pipe and the inner side edges of the two T-tubes were closed by a sealing tape. The enzyme membrane was used to close one of the open edges of the reaction unit and secured with a rubber O-ring. The fiber tip of the optical biosensor was inserted from another open edge to the reaction unit and adjusted so as to directly touch the surface of the enzyme membrane. Then the edge was also closed by the sealing tape. Buffer solution in the obtained reaction unit was flowed into the stainless tube from the middle edge of the root-side T-tube to that of the tip-side one, thus rinsing and cleaning the fiber tip and enzyme membrane. The sensor tip was connected to the side hole of a PTFE tube supplied the gaseous substances. The bio-optical sniffer was used in a batch flow measurement system. In the system, gas and phosphate buffer solution could be flowed individually through the reaction cell, respectively. A standard substance in the gas phase was supplied from a gas generator .Phosphate buffer solution in a carrier reservoir was flowed and circulated to the fiber tip and the enzyme membrane of the optical-sniffer with a flow rate of 0.69mllmin using a peristaltic pump. A computer controlled spectrophotometer with analog-digital converter DAQ700, PCMCIA A/D card with 100 kHz sampling frequency, was optically connected to the biooptical sniffer and monitored the optical quenching by oxygen consumption caused by FMO catalytic reaction with TMA The gas-selectivity of the bio-optical sniffer was evaluated using various odorous substances. 1.4 Results and Discussion:The calibration curve of the bio-optical sniffer for TMA in the gas-phase. The bio-optical sniffer was calibrated against gaseous TMA from 0.31 to 125, deduced from exponential regression analysis of the log-log plot by a method of least squares according to the following equations: Sensor output (counts) = 89.39 x [gaseous TMA (ppm)] 0.45 U10EC055, ODD SEMESTER 2013-2014 Page9
  10. 10. Calibration curve of the bio-optical sniffer with 10.0 mm o vlAsA for TMA in the gas phase his calibration range of the sniffer with FM03 covers the maximum permissible concentration of TMA 215 vapor in the work place, thus allowing to determine the level of intoxication and also encountered the TMA sensing level-S (3.0 ppm) for the human smell as described above. Figure 3 shows the gas selectivity of the bio-optical sniffer for various substances (50 ppm) in the gas-phase. As figure indicates, the sniffer device with FM03 gave negligible to most of gaseous substances, whereas application of dimethyl sulfide (DMS) and methyl mercaptan (MM) induced an increase in the sensor output. The response to DMS and MM was consistently lower than that to TMA because the FM03 from human liver is one of a polymorphic family of FMOs catalyzed in the oxidation of heteroatom-containing compounds for a xenobiotic metabolism. As the previous results, the bioelectronics nose arrayed with 3 kinds (FMO1, 3 and 5) of FMO electrodes was possible to distinguish gaseous substance by applying the patted recognition approach, thus improving gas-selectivity of the nose system. From that point of view, the optical sensor will be suitable for constructing the arrayed intelligent nose system for assaying multi-analyte vapor. U10EC055, ODD SEMESTER 2013-2014 Page10
  11. 11. CHAPTER-2 OPTICAL BIO-SNIFFER (BIOCHEMICAL GASSENSOR) FOR DIMETHYL SULFIDE VAPOR 2.1 Abstract:An optical gas-sensor (bio-sniffer) for dimethyl sulfide (seaweed-odor substance) was constructed by immobilizing flavin-containing mono oxygenase (FMO) to an oxygensensitive optical fiber. The sniffer was calibrated against gaseous DMS over the range of 10 - 100 ppm. Keywords: flavin-containing mono oxygenase, bio sniffer, dimethyl sulfide. 2.2 Introduction:Dimethyl sulfide is the colorless solution in the liquid phase and one of volatile sulfur compounds with characteristic malodor in the gas phase as defined by the International Occupational Safety and Health Information Center, The substance decomposes on burning producing toxic and corrosive fumes, and reacts violently with oxidants causing fire and explosion hazard. Flash point, auto-ignition temperature and explosive limits of DMS are -49"C, 205°C: 2.2 - 19.7 vol% in air, respectively. A harmful contamination of the air can be reached rather quickly on evaporation of DMS at 20°C. The substance irritates the eyes and the skin. In humans, flavin-containing mono oxygenase as one of xenobiotic metabolizing enzymes has been reported to catalyze the oxidation of sulfuric and nitric compounds including DMS. FM03 is possible to be expressed from human FM03 cDNA using a baculovirus expression system, and commercialized. Oxygen consumption accompanied the enzyme reaction has been used for analyzing the enzyme activity or the substrate concentration including DMS. On the other hand, some optical fibers with chemical sensitivity were commercialized. An oxygen-sensitive optical fiber coated with ruthenium-organic complex reacts to the existence of oxygen molecule in both the liquid and gas phases. The optical fiber with biocatalyst has been expected to be newly sensing device for biological analysis including gas analysis for volatile organic compounds (VOC). In this work, we developed an optical bio-sniffer using FMO enzyme U10EC055, ODD SEMESTER 2013-2014 Page11
  12. 12. for measurement of gaseous DMS .The performance of the sensor is evaluated with a gas flow measurement system for gas-phase detection. 2.3 Experimental Section:- Construction of optical bio-sniffer for DMS The optical bio-sniffer consisted of a reaction unit and an oxygen-sensitive optical fiber ([FOXY-WRTV-Flat (silicone overcoat), 1/16’’ outer diameter, Ocean Optics, Inc., FL, USA) with a dialysis membrane immobilized with flavin-containing mono oxygenase type FM03, EC 1.14.13.8, P233, 30200 pmolimgamin, from Adult human liver. The optical fiber was coated by sol-gel process with Ruthenium-organic complex which indicates an optical quenching excitation wavelength: 470 nm, fluorescent wavelength: 600 nm to oxygen molecule in both the liquid and gas phases .For enzyme immobilization, FM03 was mixed with PVA-SbQ monomer solution in a weight ratio of 1 : 2, to the surface of the dialysis membrane (thickness: 15pm) spread on a glass plate, and then irradiated with a fluorescent lamp for 30 min in order to photo crosslink the monomer solution and immobilize the enzyme to the dialysis membrane. The reaction unit was constructed by connecting two T-tubes to both sides of a stainless steel pipe and the inner side edges of the two T-tubes were closed by a sealing tape. The enzyme membrane was used to close one of the open edges of the reaction unit and fixed with a rubber O-ring. The fiber tip of the optical biosensor was inserted from another open edge to the reaction unit and adjusted so as to directly touch the surface of the enzyme membrane. Then the edge was also closed by the sealing tape. Buffer solution in the reaction unit was flowed into the stainless tube from the middle edge of the rootside T-tube to that of the tip-side one, thus rinsing and cleaning the fiber tip and enzyme membrane. The sensor tip was connected to the side hole of a PTFE supplied the gaseous substances. U10EC055, ODD SEMESTER 2013-2014 Page12
  13. 13. Principle of a chemical measurement of DMS using FMO enzyme reaction and substrate regeneration cycle. A substrate regeneration cycle was applied to the FM03 immobilized sensor in order to amplify the output signal by coupling the mono oxygenase with a reducing reagent system of ascorbic acid (AsA) in phosphate buffer. The optical biosniffer was possible to detect the oxygen consumption induced by FOM3 enzymatic reaction with DMS application. Evalmfion of optical bio-sniffer for DMS The optical biosniffer was used in a batch flow measurement system. In the system, gas and phosphate buffer solution could be flowed individually through the reaction cell, respectively. A standard substance in the gas phase was supplied from a gas generate. Phosphate buffer solution (pH8.0,100mm oil) in a carrier reservoir was flowed and circulated to the fiber tip and the enzyme membrane of the optical sniffer with a flow rate of 0.69mlimin using a peristaltic pump. Schematic diagram of gas flow measurement system for gas-phase detection. A computer controlled spectro photo met with analog-digital converter was optically connected to the bio-sniffer and monitored the optical quenching (fluorescent: 600 nm) by oxygen consumption caused by FMO catalytic reaction with DMS. The gas-selectivity of the optical bio-sniffer was evaluated using various odorous substances. 2.4 Results and Discussion:Evaluation of optical bio-sniffer for DMS the optical sniffer was calibrated against gaseous DMS over the range of 10 to 100 ppm, deduced from exponential regression analysis. The calibration range of the optical bio-sniffer for DMS vapor is lower than explosive h I t s of DMS vapor (~01%in air: 2.2 - 19.7) as described above. As the food application, the optical bio-sniffer was used to a gas assessment for seaweed sample. The sample was prepared by immersing Ig of the dried seaweed with 5 ml of the distilled water in 790 ml of the container. The optical sniffer successfully detected gaseous DMS in the sample container. The concentration of DMS in the gas-phase was calculated as 7.0 ppm in the container, which consistent with the result value obtained with a commercial available detection tube. As the previous results, the bioelectronics sniffer devices arrayed with 3 kinds of FMO electrodes was possible to distinguish gaseous substance by applying the 'pattern recognition approach, thus improving gas-selectivity of the sniffer U10EC055, ODD SEMESTER 2013-2014 Page13
  14. 14. array. From that point of view, the optical-fiber sensor will be slit able for constructing the arrayed intelligent nose system for the assessment of multi- analytevapor. 2.5Conclusions:The optical bio-sniffer for DMS was constructed by immobilizing FMO onto a tip of a fiber optic oxygen sensor coated with an oxygen sensitive ruthenium organic complex, together with the reaction unit. The sniffer was used to measure DMS vapor from 2.1 to 126 ppm with gas-selectivity based on the FMO substrate specificity. And the sniffer was also applied to detect gaseous DMS from the seaweed sample as the food application, Potential application of the fiber sensor includes a smart nose system for continuous monitoring of the odorous multi analyte by arraying the optical fiber. We will report about other optical bio-sniffer and the smart nose in the near future. U10EC055, ODD SEMESTER 2013-2014 Page14
  15. 15. CHAPTER-3 USING UV-LED LIGHT FOR MONITORING ETHANOL VAPOR WITH HIGH SENSITIVITY & SELECTIVITY 3.1 Abstract:A fiber optic bio-sniffer (biochemical gas sensor) for alcohol gas monitoring with high sensitivity and high selectivity was fabricated and tested. The bio-sniffer is a gas sensor that uses molecular recognition of enzyme to improve selectivity. Usually, enzyme loses activity in the gas phase. Applying a flow cell with a gas-intake window to the sensing probe, enzyme immobilized at the sensing region was kept in the sufficient wet condition to maintain activity. The bio-sniffer measures ethanol (EtOH) vapor by measuring fluorescence of nicotine amide adenine dinucleotide (NADH), which is produced by enzymatic reaction at the flow-cell. In order to construct a simplified system suitable for on-site applications, a high-intensity ultraviolet light emitting diode (UV-LED) was utilized as an excitation light. Owing to low power consumption comparing with previous light sources, the bio-sniffer was considered to be suitable for laptop applications such as on-site monitoring. According to the characterization, the bio-sniffer for was useful for continuous alcohol monitoring and showed high selectivity. The calibration range was 0.30-300 ppm which is suitable for evaluation of capacity to metabolize alcohol. 3.2 Introduction:Volatile components transpired from patients, which can be associated with disease, is expected as a marker for noninvasive and convenient screening in modern medicine. Since many kinds of chemical components are transpired from human bodies, a highselective and high-sensitive gas sensor is strongly requested for this purpose. Utilization of substrate specificities of biocatalysts such as enzymes is one of the promising approaches to improve selectivity of chemical sensors. In the previous study, we reported a NADH dependent biochemical gas sensor (bio-sniffer) for breath analysis using electrochemical method. Although the electrochemical method is relatively simple and high-selective method, there are several struggle points to be cleared for clinical U10EC055, ODD SEMESTER 2013-2014 Page15
  16. 16. applications. Particularly, simplified and miniaturized sensing system for portable application is expected. Alcohol dehydrogenase (ADH) based biosensors measures alcohol as production of NADH, which yields fluorescence for 340nm excitation light. Recently, high intensity GaN and AlGaN based LEDs with peak emissions in mid- to near-UV (265-360nm) was developed. For its low power consumption, UV-LEDs are suitable for laptop applications such as on-site monitoring. Therefore, we applied a UVLED (λ=340nm) as an excitation source of NADH fluoro metric biosensor in the previous study [9]. Continuous alcohol gas monitoring with simplified measurement system can be expected by applying such a fluoro-metric bio sensing system to the gas phase. Enzyme based biosensors are usually used in the liquid phase because enzyme, which function is determined by its cubic structure, loses activity in the dry circumstance. For this reason, an interface of the gas component and the enzyme in a wet condition with adequate pH and temperature is requested to realize continuous gas monitoring by bio-sniffers. In this study, a fiber optic bio-sniffer for high-selective and continuous alcohol vapor monitoring was developed using the UV-LED excitation system and a flow-cell with a gas-intake window. This paper reports the optical setup, working principle and the characteristics of the bio-sniffer for alcohol gas monitoring in detail. 3.3 Experimental:A. Optical system The UV-LED based portable excitation system was constructed with a UV-LED and a custom-fabricated UV-LED power supply system produced by KLV CO., LTD. A fiber optic spectrometer and the UV-LED excitation system were connected to a Y-shaped optical fiber assembly with optical filters. Band-pass filter with transparent wavelength of 330~350nm was placed in the excitation line. In the detection line, a long- 978 pass filter with cut-on wavelength of 400nm was placed to cut the excitation light coupled into the spectrometer. B. Fiber Optic Biosensor with UV-LED Prior to construct the bio-sniffer, a fiber optic biosensor for ethanol U10EC055, ODD SEMESTER 2013-2014 Page16
  17. 17. measurement in the liquid phase was constructed and tested. At first, an enzyme immobilized membrane was prepared by the previously reported method. A mixture of PMEH solution (1μl cm-2) and ADH (50 unit’s cm- 2) was first spread on the H-PTFE membrane filter and cured in a refrigerator (4 °C, 180min). Afterward, the redundant ADH was rinsed using PB. An ADH immobilized, membrane was thus obtained. The enzyme membrane was cut into 1cm 1 cm and tightly fixed on the optical fiber probe using a silicone O-ring. The biosensor measures the fluorescence of NADH (491nm), which is produced by the enzymatic reaction as follows: EtOH+ NAD+ ⎯A⎯D⎯⎯H→ acet aldehyde + NADH+H+ (1) The fluorescence of NADH was guided into the fiber optic Spectrometer via LPF and recorded using a laptop PC C. Fiber Optic Bio-sniffer after that, a high-selective bio-sniffer for alcohol gas monitoring was constructed. As mentioned above, wet atmosphere with adequate pH and temperature is requested for gas sensing probe to prevent enzyme from deactivation. A flow cell with a gas-intake window was attached on the probe of the fiber-optic biosensor. The flow cell is also used for supplying NAD+ and removing the reaction products from the sensing region. Alcohol gas monitoring with the bio sniffer was then carried out. A PB containing NAD+ (20 moll/l) was circulated in the flow cell with a flow rate of 1.0ml/min. After the fluorescence signal became steady state, ethanol gas (200 ml/min) was exposed to the window of the flow cell using a standard gas generator for 8 minutes. The change of fluorescence intensity (λ=491nm) was recorded for exposure of various concentrations of alcohol gas (0.30 to 300 ppm). Also, the gas selectivity of the bio-sniffer was evaluated. U10EC055, ODD SEMESTER 2013-2014 Page17
  18. 18. A 50.0 ppm of ethanol, methyl ethyl ketone (MEK), acetone and n-pentane was exposed to the bio-sniffer. These gases were also exposed to a commercially available solid-state gas sensor as a comparative experiment. 3.4 Results and Discussion:Characteristics of the Biosensor for Ethanol Solution typical spectral change of the fiber optic biosensor for ethanol solution (1000 moll/l). The background noise was relatively well reduced by the effect of LPF. When ethanol solution was added into the measuring cell, an emission with the peak wavelength of 491nm was generated immediately. This signal is the fluorescence of NADH, produced by the enzymatic reaction as shown in. The value of the fluorescence intensity was related to ethanol concentrations. The biosensor was useful for the ethanol solution with the concentration from 0.10 – 100 mmol/l. The fluorescent intensity reflects the concentration of NADH proximity to the sensor probe. This indicates that the output signal of the biosensor is influenced by the enzyme activity. The activity of ADH used for this biosensor is most active with ethanol and the activity decreases as the size of the alcohol increases. Thus, the biosensor s showed 30 times higher output for ethanol than that of methanol. According to the result, the fiber-optic biosensor for ethanol solution was considered to be useful for gas monitoring use. B. Characteristics of the Bio-sniffer for Alcohol Vapor Change of fluorescent intensity when the standard ethanol gas was exposed to the fiberoptic bio-sniffer. As the figure indicates, the output signal was sufficiently stable before alcohol gas exposure. U10EC055, ODD SEMESTER 2013-2014 Page18
  19. 19. 7yr4] [` during gas exposure, significant increases of fluorescent intensity and the steadystate values depend on ethanol gas concentrations were obtained. Periodical fluctuation of the fluorescent signal indicates the pulsation flow of the buffer flow. This can be eliminated by use of non-pulsation pump or damper device to absorb the pulsation. Reductions of the fluorescence output due to buffer flow were also confirmed when alcohol gas was eliminated from the sensing region (after 10 min). This suggests that the bio-sniffer is useful for continuous monitoring. The output fluorescence was, confirmed from 0.32 - 1000.0 ppm. However, the fluorescent signal was saturated for higher concentration than 300 ppm. The calibration range was suitable for evaluation of human capacity to metabolize alcohol. Also, the calibration range included both the lower limit of the human sense of smell level-1 (0.36 ppm) and the standard for driving under the influence of alcohol (78 ppm). Gas selectivity for various chemical substances of the bio sniffer was also investigated. As a result, the bio-sniffer showed excellent selectivity in compare with a commercially available semiconductor gas sensor. No output signal was confirmed when MEK, acetone and n-pentane were exposed to the bio-sniffer. On the other hand, solid state sensors showed, 102%, 119%, 113% of the output signal for MEK, acetone and n-pentane, respectively. Such a high-selectivity of the bio sniffers due to the specificity of ADH. According to the result, the bio-sniffer is considered to be useful for metabolic capacity for alcohol from expired breath. It is also possible to measure other volatile chemical substances with high selectivity by changing enzyme with similar system. U10EC055, ODD SEMESTER 2013-2014 Page19
  20. 20. CHAPTER-4 OPTICAL SENSOR IN THE APPLICATION OF BIODETECTION 4.1 Abstract:This optical sensor was designed and developed for the application in bio-detection. It consists of excitation module, optical detection module and signal processing module. The sensor has highly sensitive and applied to detect protein concentration in urine arranging from 0.01mg/ml to 0.3 mg/ml. The results show the feasibility of such optical sensor as biomarkers detection in home healthcare 4.2 Introduction:Biomarkers have been of vital importance in diseases diagnosis and monitoring. If patients suffer certain disease, i.e. kidney problem, they can excrete some special biomarkers, albumin, and creatinine, in their urine. By identifying these special biomarkers, the biomarker-related diseases can be diagnosed. The paper is focused to explore the potential of optical sensor for detecting biomarkers in body fluids, i.e. urine. We have designed and developed an optical sensor which consists of excitation module, optical detection module and signal processing module. If there is biomarker in test sample, the sample will emit certain wavelength fluorescence when the sample is mixed with selected dye. The emitted fluorescence intensity is proportional to the biomarker concentration in sample. The detection module will detect the emitting fluorescence from the sample while the excitation module excites the sample. The detected fluorescence intensity will be changed into electrical signal and processed. We did a series of experiments with artificial urine of different protein concentrations using both our optical sensor and a commercial spectrofluorophoto meter by Shimadzu. The experiment results show that our optical sensor fit in with the commercial spectrofluorophoto meter and can be used to quantify biomarkers, i.e. protein in urine effectively. 4.3 Experiments and Results:A System design our optical sensor has three main functions, excitation, detection and signal processing. If there is the disease related biomarker in the sample, the biomarker U10EC055, ODD SEMESTER 2013-2014 Page20
  21. 21. will be addressed by the dye added in. Under the expose of UV light, the addressed biomarker will emit certain wavelength fluorescence. The intensity of fluorescence is proportional to the biomarker concentration. To make the test sample to be exposed uniformly under UV light and emit constant fluorescence, an excitation module was designed and developed. By controlling the bias voltage, the UV light intensity can be adjustable to meet requirement. The UV light will be cast on the sample under test once the sample, i.e. urine, is mixed with dye and is put between excitation module and detection module. Next, the optical detection module will be activated to detect the fluorescence emitted from the sample under test. Following that the detected fluorescence will be converted into electrical signal and be processed. After calculation, the biomarker concentration is displayed. In our design, an excitation light of 390nm was used in the excitation module. In order to block background light, a bandwidth 10nm filter was placed in front of the UV light source. For the same reason, another filter was used in detection module. A photodiode was used to collect the fluorescence signal from sample and converted it into equivalent current. The photodiode was configured in photovoltaic (PV) mode so as not to introduce additional noise current into the system. The detection module deployed a Tran’s impedance amplifier (TIA), an 8th order elliptic low-pass filter and a 16-bit delta-sigma ADC to convert the current from the photodiode into a digitized voltage level with ample amplification to make the result stable and meaningful while providing a high signal-to-noise ratio. The MCU was in charge of all signal controlling and processing. The final result was displayed onto the LCD and saved for future reference. Experimental Procedure:-In experiments, we used artificial urine as test sample. In order to test our optical sensor, we took protein as the biomarker to be detected and added the protein with different concentrations in different samples. According to a standard laboratory procedure, we prepared a batch of thirty samples consisting of artificial urine with difference .Protein concentrations ranging from 0.01mg/ml to 0.3mg/ml in steps of 0.01 we pipette 500ul of artificial urine containing specific protein concentration, borate buffer and dye into a test tube let. The test tube let with sample was excited by UV light and the corresponding fluorescence emitted from the sample were collected by detection module. The detection module was programmed to read in one hundred readings at an interval of 20ms between readings for a single detection from the test tube let and the U10EC055, ODD SEMESTER 2013-2014 Page21
  22. 22. final result was the averaged value of the particular one hundred readings. The experiment was repeated four times for each of the prepared samples. The fluorescence intensity was determined by protein concentration in artificial urine samples. Over the range from 0.01mg/ml to 0.30mg/ml, the measured fluorescence intensity linearly increased with the increasing of protein concentration. The R2 was equal to 0.9906. The minimum detectable protein concentration was 0.01mg/ml. With the linearity between the fluorescence intensity and protein concentration, our optical sensor 0.001 demonstrated the capability to quantify biomarker, protein, another experiment, we used Nano-fluorescent CdSe/ZnS quantum dots (QDs), Carboxy-EviTag as a dye.. They are approximately 10 to 35 nanometers in size. 2 to 20 biotin molecules are covalently bonded to the surface of the modified QDs. While preserving the fluorescent properties, the CdSe/ZnS QD keeps the attached bio markers active and is able to recognize specific biomarkers. The QD Carboxy- EviTag with Em 630nm was activated with DEC (1-Ethyl3- [3-dimethylaminopropyl] carbodiimide hydrochloride) and sulfo-NHS (N- hydroxysulfosuccinimide), then conjugated to affinity purified goat anti human-alphaTSH antibody at 1:10 ratio of EviTag mg to antibody mg. Conjugated antibody was separated by a spinning filter. As a result, alpha-TSH antibody biomolecules were immobilized on the surface of the QD Carboxy-EviTag, forming alpha-TSH antibody-QD conjugate the alpha -TSH antibody has a function of recognizing TSH protein captured by anti-alpha-TSH antibody which is pre-immobilized on the solid surface of the test biochip. In order to capture the biomarker, TSH, mouse anti alpha-TSH Ab was coated onto 96 biochip plate and non-specific binding sites were blocked prior to assay. Biochip coated with non-related mouse Ab serves as system control (Control wells). TSH specimen and conjugates at desirable concentrations were simultaneously added into the coated biochip. During the test, if TSH exists in the specimen, a sandwich complex composed of anti-alpha-TSH Ab-TSH – EviTag conjugate would form in the coated biochip. All the testing materials and reagents were warmed up to room temperature prior to testing. The QD conjugate were diluted to 1:100. 50 microl of TSH at concentration from 2.5 microIU/ml, 10microIU/ml, 20 microIU/ml, and 40 microIU/ml was added into anti alpha-TSH antibody coated biochips, respectively. Next, 50 micro l of diluted QD conjugate were then added into the biochips, respectively. The biochips were sealed to avoid solution evaporation. The samples were incubated at 25°C for two hours. The solution was then removed and unbound reagents were washed away with 4 rinses of DI U10EC055, ODD SEMESTER 2013-2014 Page22
  23. 23. water. The biochips were drained completely by tapping on an absorbent paper. 100 microl of BS buffer was added into each biochip. The amount of the QD conjugated alpha-TSH antibody retained on the biochip was proportional to the amount of the TSH in the specimen. As a control, above process was repeated on the biochips coated with control antibodies. The emission fluorescent signals from each biochip were detected and recorded by our optical sensor. All measurements were made in triplicates. Exhibited the variation of fluorescence intensity of the QD conjugates as a function of TSH concentrations. One can see that the fluorescence intensity of the QD marked TSH was enhanced with increasing TSH concentration. This suggested that the detected QD fluorescence signal was a result of the specific interaction of QD-antibody conjugates and TSH protein. Low levels of target concentration reached to 2.5 microIU/ml which was good enough for normal clinical screening test. In fact, a high signal to noise ratio, or high sensitivity, was crucial for us to discern smaller changes in the fluorescence of the samples with high accuracy. Optical purity was achieved with the selection of excitation and emission wavelengths which led to a very low. 4.4 Discussions:In order to make sensor simple and compact, we used solid state devices for both the excitation source and detector. UV LEDs are available in many different grades and sizes, but none of them gives a clean narrow excitation spectral. When the UV LED is turned on, the detector detects some level of light when there is no sample or the sample contains no biomarker. Therefore we used a narrow band pass filter (D365/10X, Chroma Technology Corp) that allowed light within 365+/-5nm to pass through while blocking the rest. Another filter was used at the detector side which corresponded to the emission maximum of fluorescence from sample. We had successfully eliminates both, the light of other wavelength from the UV LED, the excitation lights itself and the ambient light from entering the detector with the combination of these two filters. Hence, we were able to obtain a high signal-to-noise ratio for the sensor with the used of low cost solid state excitation source and detector simple filters. Our sensor used a low cost PD with gain less than one as the detector, thus a very high gain was required from the TIA circuit in order to output useful readings. One main drawback of operating any op amp with very high gain was its frequency response being greatly reduced as gain and bandwidth of an op amp were inversely proportional to each other (limits by its GBW) Though the overall U10EC055, ODD SEMESTER 2013-2014 Page23
  24. 24. system response was much slower as compared to high cost detection systems, it did not pose a problem in our protein quantification application as our sensor did not require high speed response e.g. in the range of KHz or MHz Additionally, the op amp would go into oscillation due to internal capacitance of the photodiode together with feedback resistor forms a low-pass filter and contributes a negative phase to the feedback loop which caused instability and hence oscillation occurred. The problem was solved by adding a small capacitance to the feedback loop to form a high-pass filter with the feedback resistor. In this way, a positive phase would be introduced to the feedback loop to push to the circuit toward stability but at the same time sacrificing bandwidth. We had shown that high sensitivity was achievable and thus a low cost, compact and portable detection system can be used as effectively and accurately as compared to large, costly detection system. The significant difference between the excitation and emission wavelengths provided high resolution and signal-to-noise ratio, thus making the fluorescence signals easily detectable with simple low-cost photo detector. As a result, the complexity and cost of the entire detection system can be significantly reduced. The application of our optical sensor is not only limited to disease related biomarkers detection. With the use of different fluorescence dye that can react with specific targets of interest, the sensor can be extended to areas like food and beverage industry to test for food safety or the environmental monitoring field for pollution level monitoring. The rapid detection of the sensor can also be used to speed up the process of blood test or urine test done in the police station for drunk-driving as traditional methods usually takes up to a day which is time consuming (samples to be sent to lab for testing) or other drug testing process. 4.5 Conclusion:An optical sensor was designed and developed. The sensor consists of excitation module, optical detection module and signal processing module. The fluorescence properties of biomarkers conjugated with dye had been studied in a systematic way. The fluorescence intensity from sample was a near linear function with the biomarkers concentration. Our sensor can quantify biomarker, protein, in artificial urine and TSH successfully. The sensor was low cost, rapid, compact and highly sensitive. U10EC055, ODD SEMESTER 2013-2014 Page24
  25. 25. CHAPTER-5 OPTICAL BIO-SENSOR FROM DNA AND NANO STRUCTURES 5.1 Abstract:This type of optical device can be placed inside living cells and detect trace amounts of harmful contaminants by means of near infrared light. In this report, we investigate the working principle, design schemes and the role of surrounding environment of this new class of optical biosensor from DNA and carbon Nano structures, such as carbon nanotubes, grapheme ribbons, etc. We also propose some new design models by replacing carbon nanotubes with grapheme ribbon semiconductors. Index Terms—simplicity, beauty, elegance. 5.2 Introduction:New quantum optic method to research the bio-systems was carried out by using physical Nano-systems that have clearly and strongly intensity optical properties such as quantum wire, quantum dot, or Nano particles. By combine bio-systems with Nano physical systems (bio-Nano systems), then analyze the changes of optical properties of new bio physical systems through their optical spectra, we can obtain useful information about the studying bio-systems. At present, the state-of the-art achievements have been made at the frontier of nanotechnology and biotechnology by employing modern nanomaterial’s to manufacture biosensors The paramount role of biosensors has covered a board range of clinical diagnosis, treatment method, and bio- medical studies. Improving qualification of biosensors gives great challenges in terms of technology and requires the increase of understanding of biological world as well as new-found nanomaterial’s.DNA molecule is a very special type of Nano-wires with diameter approximately about 2nm. Not only the separation of double helix structure of DNA into two single strands is an important beginning point in informatics replication process of DNA to reproduce living matter but also its physical properties such as strength, structural phase transition, could be useful in design new type of Nano bio sensorsand robots. Carbon nanotubes (CNs) are a new class U10EC055, ODD SEMESTER 2013-2014 Page25
  26. 26. of quantum wires or quasi 1D system. During the last several years, because of their carbon based native material having useful and promising physical properties, carbon nanotubes have many important application in bio Nano technology in generally and in making biosensor and robots in particularly. Having the same scale, DNA and SWNT can be easily combined together to make a new type of bio-Nano instrument, robot and machine, such as DNA–CN optical biosensor, one can be placed inside living cells and detect trace amounts of harmful contaminants using near infrared light. To make this sensor, the researchers begin by wrapping a piece of double – stranded DNA around the surface of SWNT, in much the same fashion as a telephone cord wraps around a pencil. This discovery could lead to new types of optical sensors and biomarkers at the sub cellular level that exploit the unique properties of nanoparticles in living systems. This combination is due to the Carbon-structure of SWNTs and net negative charge of DNA molecule. And DNA-wrapped carbon nanotubes serve as sensors in living cells. This is the first nanotube-based sensor that can detect analyses at the subcellular level. When the DNA is exposed to ions of certain atoms (e.g., calcium, mercury and sodium) the DNA changes shape, perturbing the electronic structure of single-walled nanotube(SWNT) and shifting the nanotube’s fluorescence to lower energy.II. THEORETICAL MODELS OF THE DNA OPTICAL BIOSENSOR The double stranded DNA coil has a helical configuration. Our optical biosensor models are based on DNA’s ability to wrap around other nanostructures. In this report, this Nano objects are the carbon Nano structures, such carbon nanotube, Nano grapheme ribbon, etc. A. CN-DNA optical biosensor According to the experimental model of the CNNTs wrapped with DNA which serve as bio-sensor in living cell, a simple. In this model, the exciting theory of CNNTs was used to explain the fluorescence of the bio sensor. Here, to approximate the dielectric constant of the B- or Z-DNA wrapped CNNT, the effective medium and effective dielectric constant was introduced. The dielectric constant in the expression of exaction binding energy. The DNA ribbon regularly wraps around surface of cylinder radius of R (nm) with period along the axis of cylinder. U10EC055, ODD SEMESTER 2013-2014 Page26
  27. 27. The effective dielectric constant of medium surrounding SWNT can be written as " =f’eDNA + (1 - f ) "eS where "DNA and "S are dielectric constants of DNA and solution, respectively; f is the ratio of surface area covered by DNA per total cylindrical surface area. When the bio-sensor is in the certain medium where the ionic concentration exceed a critical value, the structure of DNA will be changed over from B to Z form, and the emission energy of SWNT was shifted. The calculated ratio of surface area covered by DNA per total area for two kinds of DNA form vs. radius of SWNT. We see that the ratio covered by DNA in B-form is larger than one in Z-form It well known that the dielectric constant of DNA is much smaller than dielectric constant of water, i.e., the effective dielectric constant in B form must be smaller than that in Form, so the exaction binding energy of SWNT in B-form is larger than Z-form. We note that the bio-sensors is only workable in range of small radius In the case of low concentration, there is no phase transition of DNA and DNA exists in the B-form only. The exaction energy as a function of ionic concentration is presented in . U10EC055, ODD SEMESTER 2013-2014 Page27
  28. 28. The pH of certain solution drastically impacts the biomolecules such as DNA, RNA, proteins etc. Without doubt, this optical bio-sensor based from DNA and CNNTs is effected by pH of solution in some way. When the pH of solution varies, the dielectric constants of DNA and solution around the CNNTs change, it brings about the variation of effective dielectric constant. Therefore, the optical signals of optical biosensor change. We have demonstrated that the sensor is influenced drastically by the protons (H+) in solution, and the pH is strongly dependence. We found that, the workable solution for sensor should has pH range from 6 to 9 where its parameters are nearly constant. 5.3 Discussion:This new combining structure of DNA and CNNTs or AGNR are really interesting and useful for design a new kind of optical sensors, which can be placed inside living cells to detect amounts of harmful contaminants. In the future, this design could be improved by comparing with the new experiment data. Therefore, we can choose the better parameter set for the model. The working condition and properties of this new optical sensors also could be investigation with taking in to account the influence of the surrounding living environmental such as temperature, pKa, pressure, and ionic strength etc. . .CNNTs and are only carbon base type of Nano wires and tubes. At present there are several new quasi one dimensional Nano structures are founded such as Si Nano wire, Al Nano pipe, we will study and develop new design schema of optical bio sensors using them in the future works. U10EC055, ODD SEMESTER 2013-2014 Page28
  29. 29. CHAPTER-6 A HEMISPHERICAL OMNI-DIRECTIONAL BIO INSPIRED OPTICAL SENSOR 6.1 AbstractFlying insects possess a surprisingly competent vision and navigation system, which enables them to control various man oeuvres in their flight. The hemispherical Omnidirectional optical sensor inspired by the compound eye of flying insects. Here, we show the feasibility of a system based on a low complexity optoelectronic system that estimates the optic flow, essentially based on biological findings on the fly Elementary Motion Detectors (EMDs). The valuable properties of our hemispherical compound eye include being lightweight, low power consumption, panoramic field of view and multi resolution. The developed modular system with 128 photoreceptors (up-gradable to 256), with a payload of some hundred grams and power consumption less than 300 mW is light enough to make it suitable to be mounted on VA Vs, MA Vs and mobile robot applications. Keywords-Compound eye; elementary motion detection; moving obstacle detection; Omni-directional camera. 6.2 Introduction:Although modern Unmanned Aerial Vehicles (UAVs) control their position and orientation using systems such as the Global Positioning System (GPS) and the Attitude and Heading Reference System (AHRS), but they are not sufficient to perform vital navigation tasks such as terrain-following, smooth landing, and obstacle avoidance in a complex environment. What's the most important in such tasks is continuously monitoring the surroundings. Active sensing, using laser range finders or Radar, suffer from stealth compromising. Hence, passive sensing such as vision would be of more benefit for UA V s Studies on visual behaviors of flying insects over the decades, has revealed many cues which are used in flight guidance and environment perception. Equipped with neither Radar nor GPS, insects, with their small brains, fly autonomously in unknown environments. Insects like fly, with surprising agility, sense the patterns of image motions to detect their ego-motions and maintain appropriate actions. A recent U10EC055, ODD SEMESTER 2013-2014 Page29
  30. 30. trend in biologically inspired vision systems has been to made use of optical flow information for flight tasks. Numerous designs of self-guided vehicles utilized the knowledge achieved on insects' abilities in various systems such as Micro-Air-Vehicles, and UAVs. Conventional cameras lack wide field of view. This raises the question that is it possible to construct a camera that can simultaneously capture images from all directions. Such an Omni-directional camera would have improved variety of applications, including autonomous navigation, video surveillance, and flight control. For development of a practical Omni-directional camera first of all, its implementation, calibration and maintenance should be easy; secondly, the mapping from actual world coordinates to image coordinates should be simple enough to permit fast computation. Our approach to Omni-directional image sensing includes these properties. We have distributed photo sensors (photo transistors) in a hemispherical surface to construct an imaging system. The distribution of phototransistors in the surface is in a way that, in the main axis the sensor density is more than other directions. In other words, the distances between sensors in that direction are less than other directions. This causes the system to have better resolution in its main direction. This is what we refer to as hemispherical Omni-directional optical sensor. In this paper, we will discuss design and implementation of a wide-angle vision system that has been tailored for the specific needs of model aircraft guidance. The rest of the paper is organized as follows. In section2, we will discuss the flying insects' visual system, Omni-directional vision, and the elementary motion detector (EMD).II. FLYING INSECTS VISUAL SYSTEM There are some differences in vertebrate and insect vision. Simple and complex eyes are two types of insect eyes. The one which is capable of distinguishing lightness from darkness is called simple. Compound eyes compared to simple eyes are larger and more complex, while simple eyes are small and round. Compound eyes are made up of thousands of six-sided compartment, called ommatidia.. An ommatidia cell contains light sensitive cells, a lens, and nerves to brain and able to detect a tiny portion of visual field, combining these tiny portions, makes a complete image. So, the final image is made number of cells are, the better image with higher resolution will be achieved. The eyes of insects are much closer together in comparison with that of vertebrates. The focus of their motionless eyes is fixed. They cannot guess the distances to objects neither from the extent to which the directions of gaze must U10EC055, ODD SEMESTER 2013-2014 Page30
  31. 31. converge; nor from the amount of reflective power needed to focus on the objects. They possess poorer eyesight, with low special precision, and can only estimate very small distances. In spite of these weaknesses, they have an impressive visual system. With limited number of pixels in each compound eye, large field of view and ultra-light processing system, flying insects maintain fast responsibility in tasks such as dynamic speed stabilization, collision avoidance, tracking smooth landing, etc. To deal with visual guidance problems, insects use alternative solutions. They use image motion caused by their own motion and estimate the distances to obstacles and control their flight Compound eye of a fly (Top), beside the built Omni-directional Optical sensor (Bottom) Omni-directional vision Omni-directional sensors for computer vision should have wide field of vision, by definition. For flight, wide field of view sensors are appropriate, and in general useful for mobile robots. Varieties of Omnidirectional sensors include wide FOV dioptric cameras (e.g. fisheye), cat dioptric cameras (e.g. cameras and mirror systems), and poly dioptric cameras. Poly dioptric cameras have high resolution per viewing angle but, bandwidth is a problem for them. They also utilize several cameras instead of several sensors. In comparison with commercial ones, homemade poly dioptric cameras are cheaper, but require calibrating and synchronization. Cata dioptric solutions usually incorporate special shaped mirrors into conventional cameras. This method uses one camera, and therefore produces one image, but low resolution and blind spot are of its weak points. There are a few existing implementations that are based on this approach to image sensing. B. Elementary Motion Detector (EMD) having smart and distributed neural processing, the insects can sense the visual motion of light contrasted obstacles, and generate a safe trajectory. According to the electro physical U10EC055, ODD SEMESTER 2013-2014 Page31
  32. 32. response of the fly's compound eyes, Reinhardt made the Elementary-Motion-Detector (EMD) .This method finds the correlation between two adjacent photo detectors, with their visual axes diverge by an angle called the inter-receptor angle. According to the block diagram shown in fig . Varieties of Omni-directional camera Magnitude and direction of the velocity is calculated by multiplying the signals output from the adjacent detectors by a time delay constant T. The greatest correlation is found when the spatial intensity delay between the photo detectors is equal to the time delay. Differencing the two correlations yields a direction-sensitive representation of the image motion. Using a planar field of EMDs can then create an image motion field. III. OPTICAL SENSOR DESIGN A. Hardware The final system consists of a circular board with a radius of 60mm which is called central board and 32 modular sensor boards with the same radius (900 arches) The central board contains thirty two 10-pin female header connectors and each of the sensor boards has a 10-pin male header connector, connecting them mechanically and electrically to the central board. These connectors are placed on the central board separated by 12S around the axe. On the other hand, the sensor board consists of 8 phototransistors similarly located on 12S arches around a quadrant circle of radius 60mm. This gives a total inter-receptor angle of 12S in both axes, between the two U10EC055, ODD SEMESTER 2013-2014 Page32
  33. 33. photoreceptors. A total of 256 sensors could be used in this configuration, In order to use sensors with different field of view, the sensor boards could be placed on the central board using one of the available connectors. For example, using 30 degrees of sensitivity sensors, the sensor boards could be placed in every other position. This kind of configuration enables us to change the place of sensor boards on the central board easily and reduce the maintenance and assembly time of the whole system structure. Fig. 6 shows the block diagram of the implemented optoelectronic system. Based on the light intensity, the phototransistor produces a signal in one form of voltage or current. Due to limitation in the number of ADC channels, the output of different phototransistors has been multiplexed. Every multiplexer chip has three control signals to determine which of its 8 inputs is to be appeared at output pin. These control signals are produced by the processor located on the central board Central Board (left) with a radius of 60 mm equal size with a Compact Disc. And Sensor Board (right) with eight phototransistors The phototransistor chosen for this application is the L14Nl phototransistor, almost a nonexpensive sensor, available for less than 2$ in quantity. This sensor provides a wide spectral response of 500 to 1000nm as well as 40 degrees of sensitivity. The L14Nl in particular has a saturation current of less than 2mA, allowing low power consumption when used in large numbers. The phototransistors are wired in a common-collector configuration, with a 10 KO resistor between the emitter and ground. Actually this biasing resistor defines the strength of the analogue signal. Each phototransistor is connected via a series of analogue multiplexers to the ADC channels of micro controller. The micro controller used is ATmega64, one of the 8-bit Atmel AVR microcontrollers. Clocked at 16 MHz, it can roughly execute 16 million instructions per second. This U10EC055, ODD SEMESTER 2013-2014 Page33
  34. 34. microcontroller has 8 embedded ADC input channels and samples the signals on each ADC with 10-bit resolution. The Complete optical sensor structure, including one main board With 16 sensor boards (Top View). System Block Diagram including both the sensor board and the central board 6.3 Conclusion:A number of 128 phototransistors (upgradable to 256) are distributed in modular sensor cards to cover a hemispherical surface. The density of the sensors around the main axis of the system is more than other. Direction improving its resolution in that direction. The vision system can produce frame rates of up to 90 fps, a low resolution, but wide angle image. Its low cost, lightweight and low power consumption make it suitable for mobile and UA V applications such as corridor navigation, altitude control, and Terrain Following and auto landing systems. The system can be used as a platform to implement various visual based navigation and flight control algorithms such as optical flow. In conclusion, this sensor can be considered as an alternative for CCD-camera based visual U10EC055, ODD SEMESTER 2013-2014 Page34
  35. 35. systems covering 360 degrees field of view. B. Future work to decrease the dependency of the response to the tolerances and mechanical assembly of the system, we will implement a calibration procedure to have a uniform response of the sensors. This can be done by changing the bias resistors and compensate the tolerances in the software. It seems that, we should improve the implemented AGC, in order to be fast enough in various intensity change of the environment. This can be done by implementing a fuzzy logic in the AGC algorithm. Improvement in Optical Flow calculation is one of the other aspects that we are going to work on. Finally, in order to improve the field of view, we should join two such systems as the left and right eyes of the system. The second system can also be seen as the redundancy system. U10EC055, ODD SEMESTER 2013-2014 Page35
  36. 36. CHAPTER-7 OPTICAL TACTILE SENSOR ORIENTED ON BIOAPPLICATION 7.1 Abstract:A new class of optical pressure sensors in a robot tactile sensing system based on PDMS (Poly-dimethyl-siloxane) is presented. The sensor consists of a tapered optical fiber, where optical signal goes across, embedded into a PDMS-gold Nano composite material. By applying different pressure forces onto the PDMS-based Nano composite, changes of the optical transitivity of the fiber can be detected in real time due to the coupling between the gold Nano composite material and the tapered fiber region. The intensity reduction of the transmitted light is correlated to the pressure force magnitude. A sensitivity in the order of 5 grams is checked. As preliminary results, the sensor is efficiently used for detecting small notches on a beam. The experimental results are very encouraging for foreseeing successful use of this new sensor in medical robotic applications especially for sensing system to measure tactile information such as softness and smoothness of biological tissues. 7.2 Introduction:ENSORY information of human skin for feeling materials and determining their physical properties is Provided by sensors on the skin. Presently, many researchers are attempting to apply the five senses to intelligent robot systems. In particular, many kinds of tactile sensors, combining small force sensors, have been introduced into intelligent robots. These tactile U10EC055, ODD SEMESTER 2013-2014 Page36
  37. 37. sensors, which are capable of detecting contact force, vibration, texture, and temperature, can be recognized as the next generation of information collection system. Future applications of implemented tactile sensors include robotics in medicine for minimally invasive microsurgeries, military uses for dangerous and delicate tasks, and automation in industries. Some tactile sensors and small force sensors using micro electromechanical systems (MEMS) technology have sensors have been realized with bulk and surface micromachining methods. Polymer-based devices that use piezoelectric polymer films such as poly vinylidene fluoride (PVDF) for sensing have also been constructed; but, polymeric piezoelectric materials are not the only ones used for sensing applications. There are a lot of different polymers investigated for this kind of application and oriented on MEMS technology. Although these sensors offer good spatial resolution due to the use of MEMS techniques, they still pick out problems in applications for practical systems. In particular, devices, that incorporate brittle sensing elements such as silicone based diaphragms or piezo resistors, are not reliable for robotic manipulation .Previous efforts have been hindered by rigid substrates, fragile sensing elements, and complex wiring. Moreover, the polymeric solutions found in literature for fabrication of pressure sensor systems. Require complex fabrication processes and post processing analysis. All these drawbacks can be compensated by utilizing flexible optical fiber sensors and transducers. In addition, optical fiber sensors are immune from electromagnetic fields, can be easily multiplexed and integrated with small led sources, thus, providing a good alternative for the implementation of robotic tactile sensors . Moreover, the proposed optical fiber sensor is obtained by means of a simple fabrication process: the used Nano composite material which the fiber is embedded in is achieved simply by chemical reduction that allows to obtain Nano/micro gold particles in the polymeric material (gold Nano composite material, GNM). The use of elastomer such as poly dimethyl-siloxane has many advantages over silicon or glass. PDMS is cheaper than silicon, it is more flexible and it bonds easier to other material than silicon or glass do. PDMS conforms to the surface of the substrate over a large area and can adjust to surfaces that are non-planar. PDMS is a homogenous and optical transparent material down to about 300 nm. PDMS is waterproof and permeable to U10EC055, ODD SEMESTER 2013-2014 Page37
  38. 38. gases. The surface properties of PDMS can easily be changed by exposure of the surface in oxygen plasma. This way PDMS can bond to other materials that have a wide range of free energies. Despite all the advantages the use of PDMS provides, there are some problems with PDMS. Gravity, adhesion and capillary forces stress the features of PDMS leading to collapse which defects the created pattern. The adhesion between the stamp and the substrate can also cause sagging of the structures. PDMS is a shrinking material which can defect the structure of the pattern. It can also swell due to chemical reaction with some kind of nonpolar solvents such as toluene. PDMS polymer film was chosen for the proposed sensor due to its ability to generate gold nanoparticles starting from gold precurson. Additionally, PDMS presents good elastomeric properties which permit to obtain a real time pressure sensor response of 0.6 sec. The use of GNM for the detection process is simpler compared to the approaches presented in literature. The GNM supports the light coupling with a tapered multimodal optical fiber and does not require complex layouts, such as membrane type devices obtained by photolithography processes. The information of the pressure detection is included in the optical transitivity response which decreases by applying pressure forces. The transitivity intensity can be detected and directly converted in an electrical signal by a photodiode, and processed by a proper electronic circuit suitable for robotic implementation. Therefore, we present a newly designed optical fiber, high responsive force sensor based on electromagnetic (EM) coupling effect. Tactile Sensor Description:The sensors is illustrated in, and it is schematized a possible medical implementation including endoscopic approach. An optical ray coming from a broad lamp source is dispersed inside the gold Nano composite material when the sensor is pressed on a surface: this effect is due to the electromagnetic coupling of the tapered fiber with the PDMS-Au material which provides reduction of the transmitted signal. The gold nanoparticles formed in the PDMS material are expected to increase the effective refractive index of the PDMS and support the electromagnetic coupling with the tapered region of the fiber since the transmitted light tends to preferentially propagate into the U10EC055, ODD SEMESTER 2013-2014 Page38
  39. 39. high refractive index regions. The pressure applied on the GNM introduces a displacement of the nanoparticles along its interface with the tapered fiber increasing the light scattering: the nanoparticles thus increase the coupling of light with the GNM, reducing the transmitted light intensity of the optical fiber. Regarding the modifications of the optical properties of the GNM, the effect of the nanoparticle displacements due to the applied pressure is to change the effective refractive index of GNM as a function of gold concentration. In particular the gradual variation of the GNM effective refractive index is higher near the contact interface of the tapered fiber, and, lower towards the pressure contact surface. A sensitivity of few grams is checked. . Biological application The Proposed sensor should be used developed as a robotic indenter to measure soft tissue during surgery (as for abdominal region in laparoscopic). Moreover tactile sensing techniques may distinguish tumor from healthy tissue and have potential for intraoperative tumor diagnosis. The aim of the study is to develop a biocompatible realtime sensing system to measure tactile information such as softness and smoothness of biological tissues. Moreover, by reducing the dimensions, the proposed sensor should be used for minimal access surgery (MAS). Important properties such as tissue compliance, viscosity and surface texture, which give indications regarding the health of the tissue, cannot easily be assessed. The proposed technology can be addressed from different U10EC055, ODD SEMESTER 2013-2014 Page39
  40. 40. viewpoints including those of the basic transduction of tactile data (tactile sensing), the computer processing of the transduced data to obtain useful information (tactile data processing) and the display to the surgeon of this information (tactile display). Applications of tactile sensing in MAS, both to mediate the manipulation of organs and to assess the condition of tissue, are under investigation. 7.3 Conclusion:A PDMS-Au Nano composite optical sensor is analyzed. The high sensitivity of the tactile sensor allows to detect roughness and could be used to detect different tissue anomalies such lesions or tumors. Mechanical improvement and medical implementation are under investigation. U10EC055, ODD SEMESTER 2013-2014 Page40
  41. 41. CHAPTER :-8 OPTICAL BIO-CHEMICAL SENSORS ON SNOW RING RESONATORS 8.1 Abstract: The novel ring resonator based bio-chemical sensors on silicon nanowire optical waveguide (SNOW) and show that the sensitivity of the sensors can be increased by an order of magnitude as compared to silicon-on-insulator based ring resonators while maintaining high index contrast and compact devices. The core of the waveguide is hollow and allows for introduction of biomaterial in the center of the mode, thereby increasing the sensitivity of detection. A sensitivity of 243 nm/refractive index unit (RIU) is achieved for a change in bulk refractive index. For surface attachment, the sensor is able to detect monolayer attachments as small as 1 °A on the surface of the silicon nanowires. 8.2 Introduction:Optical biosensors have attracted considerable attention in the last decade because of their promise to contribute to major advances in medical diagnosis, environmental monitoring, drug development, quality control, and homeland security. Compared to electrical transducers, optical sensors provide significant advantages because of their small size, immunity to electromagnetic interference, ease of multiplexing using wavelength encoding, and capability of remote sensing. Optical sensors can be broadly characterized in two categories: fluorescence based detectors and label-free detectors. In fluorescence based detectors, the target molecules are labeled with fluorescent tags such as dyes and the fluorescence is detected in presence of the targeted molecule. This allows for extremely sensitive detection down to a single molecule. However, the process is laborious and may also affect the function of the biomolecules. Further, precise quantitative measurements are difficult as the number of flourophores attached to the U10EC055, ODD SEMESTER 2013-2014 Page41
  42. 42. targeted molecules cannot be controlled. In contrast, in label-free detection the targeted molecules are detected in their natural form. The targeted molecules are surface attached to the optical sensor using probe molecules and the attachment is detected by measuring the change in optical properties for the sensor. Sensors based on silicon-on-insulator (SOI) photonic wire waveguides have attracted considerable attention because of compatibility with CMOS fabrication and possibility of integrating detection and decision on the same chip leading to ‖laboratories on a chip‖. Further, guided-wave sensors allow for integration of multiple sensors on a single chip. As such, different sensors based on directional couplers, Mach-Zehnder interferometers, Bragg grating based Fabry-Perot resonators, micro disks, microtoroids, photonics crystal cavities, micro ring resonators, and slot waveguides have been demonstrated. In these sensors, the targeted molecule is probed by light guided through a solid medium using the evanescent field. The lower refractive index surrounding medium (typically water with refractive index ∼ 1.3253) is displaced by higher refractive index organic molecules (n ∼ 1.45−1.6) changing the effective index of the propagating mode resulting in a spectral shift of the resonant cavity which can be measured directly. Mach-Zehnder interferometers, Fabry-Perot resonators, micro disks, photonic crystal cavities, and ring resonators have Been demonstrated using silicon photonics .Fabricated SNOW consists of 9 rows of 800nm-long SiNWs with diameter of 40 nm. And the requirement of large interaction length to increase the sensitivity. Bragg-reflectors for Fabry-Perot resonators are difficult to fabricate in high-index contrast materials resulting in high insertion losses. Photonics crystal cavities are also difficult to produce with low propagation losses and it is difficult to couple light in and out of these waveguides reproducibly. Micro disks have higher whispering gallery modes which can overlay on the fundamental characteristics making detection difficult. As such, ring resonators offer most attractive solution as they provide low insertion loss, single mode cavities, and small form factors. Ring resonators offer a compelling solution as multiplexing different sensors on a single chip using wavelength is U10EC055, ODD SEMESTER 2013-2014 Page42
  43. 43. possible by simply changing the diameter of the ring in the resonator. Biochemical sensors based on SOI photonic waveguides have been studied extensively. In, a 70 nm/RIU sensitivity was achieved for bulk changes of refractive index and a 625 pm shift of wavelength was achieved for label-free sensing of proteins. The sensitivity can be further increased by using a slot-waveguide which an optical waveguide is guiding light in a sub wavelength-scale low refractive index region sandwiched between two ridges of high index. This enhances the transverse electric field in the slot thereby increasing the interaction of the optical field with the targeted molecules. An increased sensitivity of 298 nm/RIU was achieved with a foot-print of 13 μm×10 μm. However, the problem with slot waveguides is the difficulty with introduction of fluids within the slot region. Further since the slot waveguide works in the quasi-TE mode, it is lower modal index waveguide compared to SOI waveguides. The proposed and analyzed a new kind of optical waveguide consisting of arrays of silicon nanowires (SiNWs) where the diameter of the SiNW is smaller than 75 nm for 1550 nm wavelength. A fabricated waveguide is shown. For this sample, it consists of 9 rows of 40 nm diameter nanowires with a pitch of 100 nm. The length of the nanowires is 800 nm. If the diameter is less than 75 nm, the diffraction of light through the SiNWs is limited (provided the electric field is polarized along the length of the nanowires) and the medium starts to behave like an effective index medium, thereby guiding light through the structure with very low propagation losses (< 0.2 cm−1). Vertical confinement is provided by the refractive index contrast between the silicon and the insulator. Unlike, photonic band gap structures, the nanowires do not need to be aligned in a crystal and can be randomly arranged with minimal excess losses. Further, the scattering due to side wall roughness results in minimal excess losses. We have also shown that waveguides with bends of radii smaller than 5 μm can be designed on the SNOW structure with low loss (less than 0.06 dB per 360◦ turn). Such geometries have been achieved using electron-beam lithography and BOSCH etching of silicon mainly for solar cells. Further, we have been able to fabricate SNOW structures with nanowire diameters and pitch as small as 15 nm and 75 nm respectively. While we are still in process of measuring optical properties of these waveguides, previous experimental works show that it should be feasible to guide light through these structures. Optical loss as low as 0.023 dB/crossing was achieved with a waveguide which worked as an effective index medium, similar to SNOW .Gain and stimulated emission was observed in Nano patterned silicon. The device consisted of 100 nm thick arrayed sub wavelength structures on a SOI wafer cleaved into 1 mm long devices, again working like U10EC055, ODD SEMESTER 2013-2014 Page43
  44. 44. an effective index waveguide. Fabry-Perot characteristics in the emission demonstrated guidance of light in the 100 nm patterned silicon layer of the device and corresponded well with the effective index calculations. These experiments along with experimental fabrication of SNOW strongly suggest that guidance of light should be possible with the structures. Even over a bend, the effective index approximation works well. This allows for designing and building of ring resonators on the SNOW especially for biochemical sensors. The advantage of SNOW is apparent from the fact that it is a hollow core waveguide and thus it is possible to introduce the bio-chemical agents in the region of highest optical field intensity. In this paper, we propose a ring resonator structure with SNOW in the ring excited by a SOI bus waveguide. We show that the sensitivity is increased by an order of magnitude compared to the SOI waveguides while achieving a compact structure. 8.3 Sensor Structure:In order to be able to fabricate ring resonators, it is important for the SNOW region to support waveguide bends. This shows the radiation loss through a 360◦ turn in the SNOW region as the radius of the bend is changed. For this simulation, the polarization is along the length of SiNWs and the wavelength of operation is 1550 nm. The diameter of the silicon nanowires is 50 nm and the pitch between them is 75 nm, similar to what we had previously proposed. The height of the nanowires is 700 nm. He SNOW region has an effective index of 2.2 when air is surrounding the medium. The width of the SNOW region is 650 nm. At this width, the second order mode in the ring is supported but does not get excited because of the symmetry rules. Further, the radiation loss for the second order U10EC055, ODD SEMESTER 2013-2014 Page44
  45. 45. Mode over the bend is appreciably higher compared to the fundamental mode. Also plotted in the figure, is the radiation loss when the effective-index approximation shown in is used and SNOW is approximated by a rib waveguide. All the simulations are done using the finite-difference time domain (FDTD) method with a grid size of 2 nm for SNOW and a grid size of 10 nm for the effective-index approximation. The simulations were done in 2-dimensions by using effective index method in the vertical direction to decompose a 3-D structure into planar waveguides. The method was tested by comparing results using 3-D simulations with 2-D for few samples. For all the simulations, the electric field was polarized along the length of the nanowires which corresponds to quasiTM polarization for conventional waveguides. At 700 nm waveguide height, the optical mode is highly confined in the vertical direction and the effective index approximation works well. It is clear that the loss through the bend is mainly dominated by the caustic radiation and not by the radiation due to scattering from the individual nanowires. For a radius of 5 μm, the radiation loss over a 360◦ turn is 4.6×10−4dB. These simulations show the appropriateness of using SNOW for bends and allow for fabricating ring resonators on the structure. The proposed structure is shown in. A SOI waveguide is used as a bus waveguide feeding into a ring consisting of SNOW with parameters described above. Use of SOI waveguides allows for conventional input and output optical coupling into the structure resulting in low insertion losses. The bus waveguide has a width of 100 nm and has the same height (700 nm) as the SNOW ring. At this width, the bus waveguide is purely single mode. Separation between the waveguides is adjusted to 100 nm between the end of the bus waveguide and the first nanowire in the SNOW and achieves critical coupling condition for the ring resonator. Figure shows the lateral cut of the FDTD propagation of the electric field through the ring resonator at a wavelength of 1550 nm (not the resonance wavelength) over a few cycles within the ring. One can clearly see that the SNOW ring is guiding the electric field with very little radiation happening in the structure. Figure 5 shows the lateral cut of the electric field through the SNOW structure for the parameters defined above. The lateral cuts for a straight SNOW and over a bend are shown. Lateral cut for the 200 nm wide straight SOI waveguides is also shown. Within the effective-index waveguide, the U10EC055, ODD SEMESTER 2013-2014 Page45
  46. 46. confinement factor for the SNOW is 94 % resulting in the low bend losses as shown in. The confinement factor for the optical mode within silicon in the SNOW region is only 32 % whereas for a 200 nm SOI waveguide, it is 76 %. The optical mode is better guided in the SNOW region as compared to the 200 nm SOI waveguide, and the modal power in the Color online) Lateral cut of the FDTD propagation of electric field through the SNOW ring resonator. Surrounding region is larger in the SNOW as compared to the 200 nm SOI. Thus, it should be possible to increase the sensitivity while still achieving compact devices. Sensor characteristics for bulk refractive index change We first calculated the response of sensor for bulk change in the refractive index of the surrounding medium. The SNOW structure is compared with a SOI waveguide ring resonator where the width of the SOI waveguide is 200 nm, similar to. The geometric parameters for the two compared devices are shown in Table I. For the first set of simulations, the refractive index of the surrounding medium was changed and the effective index of the guided optical mode through SNOW was calculated. Figure 6 shows the change of effective index of the optical mode as a percentage with respect to the value of effective index as the surrounding refractive index is changed from 1.0 to 1.6 for the SNOWand the 200 nm SOI waveguide at a wavelength of 1550 nm. For the SNOW, the effective index changes by a factor of approximately 4 large as compared to a U10EC055, ODD SEMESTER 2013-2014 Page46
  47. 47. 200 nm SOI waveguide for the same change in surrounding refractive index. In a ring resonator the change of the resonance wavelength is approximately given by Δλ =Δne f fλng(1) Where Δne f f is the change of the effective index due to the change of the refractive index of the surrounding medium, λ is the initial resonance wavelength and ng is the group index. This suggests that an improvement in sensitivity of 4 is expected if one uses a SNOW ring resonator as compared to a 200 nm wide SOI waveguide resonator. A wavelength shift of 12.2 nm is achieved for the SNOW ring resonator resulting in a sensitivity of 243 nm/RIU. For the 200 nm SOI waveguide, the wavelength shift for the same refractive index change is 3.14 nm resulting in a sensitivity of 63 nm/RIU. This compares well with the experimental value of 70 nm/RIU for a slightly higher bulk refractive index. An improvement by a factor of 3.9 is seen in the sensitivity for the SNOW ring resonator compared to the 200 nm wide SOI waveguide for bulk change of refractive index. We also studied the effect on sensitivity as the width of the SNOW region is changed. The ring resonator coupling was adjusted individually to achieve critical coupling. The diameter and pitch for the SiNWs are kept the same. An increase of sensitivity is observed when the waveguide width is decreased, reaching a value of 335 nm/RIU for a width of 300 nm. The surrounding index is again changed from 1 to 1.05. An improvement by a factor of 5.3 is observed as compared to the SOI waveguide. The behavior exhibited by the SNOW ring resonator is similar to that of the SOI ring resonators as the width is decreased. This is because of the increased evanescent field as the width is decreased. In optical sensors, surface sensing plays an important role for a wide range of biochemical applications including DNA hybridization, antigen-antibody reactions, protein attachments etc. A layer of receptor molecules is surface attached to optical sensor and selective attachment is done for the targeted molecule. Since the refractive index of the molecules is different from the surrounding medium which is typically water based, a change of index happens at the surface of the sensor which is measured for detecting the presence of the molecule. U10EC055, ODD SEMESTER 2013-2014 Page47
  48. 48. The SNOW ring resonator was simulated for surface attachment of the molecules. A molecule layer with the test thickness was assumed to be attached the surface of the SiNWs. Water was considered as the surrounding medium with a refractive index of 1.325 at a wavelength of 1550 nm. The refractive index of the molecule attached is considered to be 1.6, similar to 3-aminopropyltriethoxysilane (APTES) which we have measured previously and controllably attached different thickness on the surface. Structures summarized in Table I were compared. Wavelength shift of 0.35 nm and 3.1 nm and is achieved with a 0.1 nm and 1 nm attachment of the molecule. For these thin layers, the surface attachment increases linearly with the thickness of the molecule layer. For the SOI waveguides, surface attachment was assumed over all the exposed surfaces of silicon including the sides and the top of the waveguide. Only a 1 nm layer attachment was considered. A wavelength shift of 0.15 nm is achieved for the attachment of 1 nm layer thickness. This shows an improvement by a factor of 20.5 with the SNOW ring resonator. The dependence of the width for the SNOW was also considered. Figure 10 shows the percentage change in the effective index of the SNOW structure as the waveguide width is changed from 300 nm to 1000 nm for a 1 nm thickness of the attached molecule layer. As opposed to the change in bulk refractive index, the behavior is different and the sensitivity increases as the width is increased. This is because the sensor is not working in the evanescent field but within the core of the optical mode. As the width is increased, the optical mode gets more confined within the SNOW region resulting in higher interaction with the surface attached material. 5. U10EC055, ODD SEMESTER 2013-2014 Page48
  49. 49. 8.4 Conclusion:- The SNOW ring resonator consists of a SOI bus waveguide coupled into a ring waveguide consisting of closely etched silicon nanowires acting as an effective index waveguide. We have compared the proposed sensor to the SOI photonic wire based sensors. For bulk refractive index changes, an improvement by a factor of 5.3 is achieved with the SNOW sensor compared to that of the SOI. For surface attachment, an improvement by a factor of 20.5 is achieved for the SNOW sensor. U10EC055, ODD SEMESTER 2013-2014 Page49
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