Optical bio sensors application

U10EC055, ODD SEMESTER 2013-2014 Page1

SEMINAR REPORT

Entitled

“OPTICAL FIBER BIO SENSORS APPLICATIONS”

Submitted in partial fulfilment of the requirement

For the Degree of

: 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

((EELLEECCTTRROONNIICCSS &&

CCOOMMMMUUNNIICCAATTIIOONN))

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TTeecchhnnoollooggyy


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


Sardar Vallabhbhai National Institute of Technology

Surat-395 007, Gujarat, INDIA.

DEPARTMENT OF ELECTRONICS AND COMMUNICATION

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 Prof . P.K.Shah

Seminar Guide Head of the Deptt. ECED

Associate Professor Associate Professor

SEMINAR EXAMINERS:

Name Signature with date

1.Prof.____________________ __________________

2.Prof.____________________ __________________

3.Prof.____________________ __________________

EPARTMENT SEAL

December-2013

CCEERRTTIIFFIICCAATTEE


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.


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


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


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 flavin-

containing 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


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 sol-

gel 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


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 bio-

optical 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


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.


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 oxygen-

sensitive 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


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 pmolimg-

amin, 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 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 supplied the gaseous

substances.


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 bio-

sniffer was possible to detect the oxygen consumption induced by FOM3 enzymatic

reaction with DMS application. Evalmfion of optical bio-sniffer for DMS The optical bio-

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 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.


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


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.


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 high-

selective 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


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 UV-

LED (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


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.


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.


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 fiber-

optic bio-sniffer. As the figure indicates, the output signal was sufficiently stable before

alcohol gas exposure.


7yr4\] [` during gas exposure, significant increases of fluorescent intensity and the steady-

state 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.


CHAPTER-4 OPTICAL SENSOR IN THE APPLICATION OF BIO-

DETECTION

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


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


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-Ethyl-

3- [3-dimethylaminopropyl] carbodiimide hydrochloride) and sulfo-NHS (N-

hydroxysulfosuccinimide), then conjugated to affinity purified goat anti human-alpha-

TSH 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


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


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.


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


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.


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

.


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.


CHAPTER-6 A HEMISPHERICAL OMNI-DIRECTIONAL BIO

INSPIRED OPTICAL SENSOR

6.1 Abstract-

Flying insects possess a surprisingly competent vision and navigation system, which

enables them to control various man oeuvres in their flight. The hemispherical Omni-

directional 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


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


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 Omni-

directional 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


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


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 non-

expensive 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


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


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.


CHAPTER-7 OPTICAL TACTILE SENSOR ORIENTED ON BIO-

APPLICATION

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


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


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


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 real-

time 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


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.


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


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


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


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


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 quasi-

TM 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


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


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.


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.


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.


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