Electrical, Computer and Systems engineering Department

@ Rensselaer

Integrated Biosensors
Arjang Hassibi and Khaled Salama
ISCAS 2007
Background
Traditionally, computation and communication were the driving forces for
advancement in the semiconductor industry

Applications Semiconductor Industry Innovation

Memory Wireline Communications

Feature Size
Speed
Cost
Integration
Power
Consumption
Packaging
Computers Wireless Communications Die Size

ISCAS 2007 2
Background
However, recently new emerging applications such as multimedia,
multimedia imaging,
imaging
biomedical,
biomedical and sensory systems have also become important

Emerging
? Semiconductor Industry ? Innovation
Application
Hybrid Systems Image Sensors
Compatibility
Cost
Architecture
Post-Fabrication
Modifications
Packaging
Integration
Hybrid Systems
Biomedical Sensors Arrays

ISCAS 2007 3
Integrated Sensors
One of the most important emerging applications in the semiconductor
industry is “sensors-on-chip”
chip or “integrated sensors”
sensors

Why is it important to be “on-chip”?

1. High-performance readout circuitry

2. Available and “almost free” computational power

3. Small scaled sensors

4. High yield

5. Realization of “almost” any type of transducer

ISCAS 2007 4
Integrated Sensors
One of the most important emerging applications in the semiconductor
industry is “sensors-on-chip”
chip or “integrated sensors”
sensors

Why is it important to be “on-chip”?

1. High-performance readout circuitry High SNR

2. Available and “almost free” computational power Smart Sensors

3. Small scaled sensors Sensor Arrays

4. High yield Low Cost

5. Realization of “almost” any type of transducer Applications

ISCAS 2007 5
Integrated Biosensors and Biomedical VLSI?
Today, there are many biomedical systems which use VLSI systems
Life Sciences and
Biomedical Applications

Bio-Molecular Biomedical
Detection Medical Devices Networks/Comm Bioinformatics

• Wireless Biomedical • FPGA Accelerated

Telemetry • Supercomputers

• Wireless Biomedical Senor Algorithms:

Networks BLAST
• Lab-on-a-Chip • Pacemaker Smith-Waterman
• Biomedical Wireless HMMs
Implantable Microsystems …
(Bio-WIMS)

• Integrated Microarrays • Cochlear Implant

Semiconductor Industry and IC Design

ISCAS 2007 6
Integrated Biosensors and Biomedical VLSI?
Today, there are many biomedical systems which use VLSI systems
Life Sciences and
Biomedical Applications

Bio-Molecular Biomedical
Detection Medical Devices Networks/Comm Bioinformatics

Analytical Biochemistry • Wireless Biomedical • FPGA Accelerated

Conventional
Telemetry • Supercomputers
Molecular Biology EE/CS
Biophysics • Wireless Biomedical Algorithms:
Problems
Senor Networks BLAST
• Lab-on-a-Chip
(e.g., Implementing a • Pacemaker Smith-Waterman
(e.g., Implementing algorithms)
• Biomedical Wireless HMMs
pathogen detection assay)
Implantable Microsystems …
(Bio-WIMS)

Biosensors
• Integrated Microarrays • Cochlear Implant

Semiconductor Industry and IC Design

ISCAS 2007 7
Overview of Tutorial

Performance metrics of sensors

Bio-molecular detection and biosensors

• Biosensor systems
• Affinity-based biosensors
• Microarrays and bio-chips
• Biosensor SNR and limits of detection

Integrated sensors

Integrated biosensors (biochips)

• General specifications
• Transducer Structure
• Integrated biosensor microarrays
• Examples

Conclusion

ISCAS 2007 8
Overview of Tutorial

Performance metrics of sensors

Bio-molecular detection and biosensors

• Biosensor systems
• Affinity-based biosensors
• Microarrays and bio-chips
• Biosensor SNR and limits of detection

Integrated sensors

Integrated biosensors (biochips)

• General specifications
• Transducer Structure
• Integrated biosensor microarrays
• Examples

Conclusion

ISCAS 2007 9
 Architectures for Sensors
The real-world parameter is translated to an electrical signal using transducer

Detection Circuitry Output Representation

Single tone Analog y A (t )

Output
Real-World

Voltage Interface
Readout
Transducer
Current System
Digital
Parameter A/D Output
Interface y D (t )

ISCAS 2007 10
Example
Thermistor: A resistor made of semiconductors having resistance that
varies rapidly and predictably with temperature.

Transducer

N N
R = ∑ riT i
X ∑ rT i
i
X
i =1
v = AV in i =1 TX
4
10

10kΩ
Low Digital
Lookup
Noise A/D Output
Vin Table
Amp. Interface

Detection Circuitry

ISCAS 2007 11
Performance Metrics of Sensors
Sensor Definitions: Metrics to quantify and occasionally compare the
performance of the sensors, such as:

• Transfer function
• Sensitivity
• Normalized differential nonlinearity (NDNL)
• Uncertainty
• Noise
• Systematic errors
• Signal-to-noise ratio (SNR)
• Resolution
• Dynamic range
• Speed (bandwidth)

ISCAS 2007 12
Sensors Definitions: Transfer Function
Transfer Function: Expected functional relationship between the physical
input phenomenon or signal, x, and the observed output, y
N
1
f ( x ) = lim
N →∞ N
∑ y (x
i =1
i i = x)

f1 ( x ) f3 ( x)
Output (y)

f1 ( x ) : Linear
f 2 ( x) f 2 ( x ) : Non-Linear and Monotonic
f 3 ( x ) : Non-Monotonic

Input ( x )

ISCAS 2007 13
Sensors Definitions: Transfer Function
Sensitivity: Small-signal ratio between the input and the output, for a given
input

∂f ( x )
s( x = X 0 ) =
∂x x = X 0
s( X 2 )
s( X 3 )
f ( x)
Output (y)

s( X 1 )

X1 Input ( x ) X2 X3

ISCAS 2007 14
Sensors Definitions: Nonlinearity
Normalized Differential Nonlinearity (NDNL):
Normalized difference of the output with its best linear fit

f ( x ) − fˆ ( x )
NDNL ( x ) =
fˆ ( x ) fˆ ( x )

f ( x)
Output (y)

f (X0) fˆ ( X 0 )

X min X0 Input ( x ) X max

ISCAS 2007 15
Accuracy of Sensors
Uncertainty and Accuracy:
In practice, the output for a fixed input is not always the same
Output (y)

Upper bound

f ( x)
Lower bound
Y0
gy x ( y x = X0)

g y x ( y x = X 0 ) :Distribution of y , given X0
g x y ( x y = Y0 ) : Distribution of x , given Y0
g x y ( x y = Y0 )

X0 Input ( x )

ISCAS 2007 16
Sensors Definition: Systematic Errors
Systematic Errors: Probabilistic inaccuracies which persists throughout an
entire experiment
Examples:
Gain errors
Random offset
Background interference

Systematic
R (T ) + Δ RT Error
Systematic Error

10kΩ A + ΔA R (T ) + Δ RT
Vout = Vin (A + ΔA )
Low 10 4
Vin Noise
Amp.

ISCAS 2007 17
Sensors Definition: Random Errors
Random Errors: Inevitable statistical fluctuations in the measured data within
experiments
Examples:
Thermal noise
Shot-noise
Quantization noise

R (T ) Vn2
Random Random Error
Error
Vn1
10kΩ A R (T ) + Δ RT
Vout = (Vin + V n1 )A 4
+ Vn 2
Low 10
Vin Noise
Amp.

ISCAS 2007 18
Sensors Definitions: SNR
Signal-to-Noise Ratio (SNR)

SNR (Y ) = 10 log 10
(E [ x y = Y ])2

= 20 log 10
E[ x y = Y ]
y = Y ] − (E [ x y = Y ]) σ x y =Y
2
E[ x 2

f ( x)
Y
Output (y)

g x y(x y = Y ) IMPORTANT:
IMPORTANT SNR in sensors is
always referred to the input

Input ( x )

ISCAS 2007 19
Sensors Definitions: SNR
Signal-to-Noise Ratio (SNR)

SNR (Y ) = 10 log 10
(E [ x y = Y ])2

= 20 log 10
E[ x y = Y ]
y = Y ] − (E [ x y = Y ]) σ x y =Y
2
E[ x 2

SNR max

f (x )
SNR

Input ( x )

ISCAS 2007 20
Sensors Definitions: Dynamic Range
Dynamic Range: The range of input where the SNR is acceptable

X HDL Highest detectable level of X

DR = 20 log 10 = 20 log 10
X MDL Minimum detectable level for X

f ( x)
YHDL
Output (y)

YMDL SNR min

X MDL X HDL Input ( x )

ISCAS 2007 21
Sensors Definitions: Dynamic Range
Dynamic Range: The range of input where the SNR is acceptable

X HDL Highest detectable level of X

DR = 20 log 10 = 20 log 10
X MDL Minimum detectable level for X

SNR max

f (x )
SNR

SNR min

DR

X MDL X HDL Input ( x )

ISCAS 2007 22
Overview of Tutorial

Performance metrics of sensors

Bio-molecular detection and biosensors

• Biosensor systems
• Affinity-based biosensors
• Microarrays and bio-chips
• Biosensor SNR and limits of detection

Integrated sensors

Integrated biosensors (biochips)

• General specifications
• Transducer Structure
• Integrated biosensor microarrays
• Examples

Conclusion

ISCAS 2007 23
Biosensors for Bio-Molecular Detection
Biosensors are essentially sensors which detect the presence and
abundance of bio-molecules

Biosensors
Bio-molecular Detection

Molecules Macromolecules Tissue/Cell Organ

1nm 10nm 10µm 10mm

Indirect Observation Direct Observation

Bio-molecular Detection (Biosensors) Biological Imaging (Microscopy)

ISCAS 2007 24
 Analytes and Bio-molecules in Biosensors
Biochemical Analytes* Copies/ml 1nm

Water 3.3 x 1022

1Å
Molecules

Cholesterol 8 x 1017

Glucose 1018
IgG 2a
Specific antibodies 108 Antibody Glucose

DNA finger printing 106-107

1µm 10nm
Biothreat agents in air <100
Organisms

Food poisoning agents <1

( Salmonella, Listeria, E. coli )

Gram negative bacteria in blood <10

HIV in blood <400

E-Coli Bacteria HIV Virus
* an·a·lyte (ăn'ə-līt') n. A substance or chemical constituent that is undergoing analysis
K. Petersen et al., “The promise of miniaturized clinical diagnostic systems,” IVD Tech. Mag., 1998

ISCAS 2007 25
 Analytes and Bio-molecules in Biosensors
Biochemical Analytes Copies/ml

Water 3.3 x 1022

Molecules

Cholesterol 8 x 1017

Glucose 1018

Specific antibodies 108

DNA finger printing 106-107

Σ
Biothreat agents in air <100
Organisms

Food poisoning agents <1

( Salmonella, Listeria, E. coli )
Most biological samples
Gram negative bacteria in blood <10
are a mixture of many
HIV in blood <400 different species

K. Petersen et al., “The promise of miniaturized clinical diagnostic systems,” IVD Tech. Mag., 1998

ISCAS 2007 26
Bio-Molecular Detection – Size
Region of Interest
Mainly used for
solid-phase objects
Optical Microscopy

SEM1 TEM2
Not suitable

STM3 AFM4 biological systems

Particles

Cells Human
Q-Dots Viruses Hair

Bacteria

Atoms
Molecules Proteins
Color Pollens
Boundary

(A) 1 10 100 1000

(nm) 1 10 100 1000
(µm) 0.1 1 10 100
1 2
Scanning Electron Microscopy Transmission Electron Microscopy
3 4
Scanning Tunneling Microscopy Atomic Force Microscopy

ISCAS 2007 27
Bio-Molecular – Concentration
Region of Interest 1M Concentration

Optical Microscopy

SEM TEM

STM AFM

Proteins Glucose
Solids
Viruses DNA Cholesterol
Liquids

Bacteria Cells in Tissue Gases

H2O in water

(cm2) 1 105 1010 1015 1020 1025 1030

(mm2) 1 103 108 1013 1018 1021 1028
(µm2) 1 102 107 1012 1017 1022

ISCAS 2007 28
Bio-Molecular Detection - Interference
Region of Interest

Optical Microscopy

SEM TEM
Bacterial
Detection Water Testing STM AFM
Process
Cancer Detection Monitoring

Viral detection
High Throughput Screening

Medical Diagnostics

(ppm) 0.001 0.01 0.1 1 10 100 1000

Concentration of the Target Analyte*

Interference Ratio =
Concentration of the Interferer

ISCAS 2007 29
Applications and Opportunities ($$$)

Diagnostics Pharmaceutical Chemical

+ + Analysis
Forensics Life-Sciences +
+ Research Environmental
Applications: Military + Monitoring
Biotechnology

Unproven Market Established Market Established Market

(>$3B) ($6B) ($4B)
Huge Potential Fast Growth (10-15%) Slow Growth (3%)
Growth

PCR Assaying Spectroscopy

Systems Platforms Instruments
+ + +
Technologies: PoC Microarrays Chemical Analysis
Diagnostics + Platforms
Systems High-Throughput
Screening

Unproven Challenging Established

ISCAS 2007 30
Bio-Molecular Detection
Detection of bio-molecules is carried out by biosensor systems

Molecular Biology Fabrication/ Circuit Signal

Biochemistry Synthesis Processes Design Processing

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

1.4203
ADC 01011

DNA Microarrays Photodiode Image Sensor Analog to Digital Conversion

ISCAS 2007 31
Error Sources in Bio-Molecular Detection
Errors in detection can originate from different blocks within the systems
1 2 3
Biochemical Noise Fabrication and Electronic Noise
Interference Process Variation Quantization Noise

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

Uncertainty boundaries
1
Expected behavior 1 +
1 + 2
2 +
Biosensor Output

3
Y0

E[ X ]
Biological Input
(i.e., Analyte Concentration)

Hassibi et al., “On Noise Processes and Limits of Performance in Biosensors” JAP 2007
Hassibi et al., “Biochemical Shot-Noise and Quantum-Limited SNR in Affinity-Based Biosensors.” JAP 2005

ISCAS 2007 32
Limits of Detection in Biosensors
In almost all biosensors, both the minimum detection level (MDL) and
the highest detection level (HDL) are limited by the biological assay
Biochemical Noise Fabrication and Electronic Noise
Interference Process Variation Quantization Noise

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

SNR
Expected behavior

Interference/
Signal-to-Noise Ratio

Assay
Biochemical
Saturation
shot-noise

SNRmin

Dynamic Range Biological

Input

MDL HDL
Hassibi et al., “On Noise Processes and Limits of Performance in Biosensors” JAP 2007
Hassibi et al., “Biochemical Shot-Noise and Quantum-Limited SNR in Affinity-Based Biosensors.” JAP 2005

ISCAS 2007 33
System-Level Design of Biosensors
Biosensor design is essentially a system-level design, and very similar to
many of the conventional systems in EE

Biochemical Noise Fabrication and Electronic Noise

Interference Process Variation Quantization Noise
Biosensor

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

Interference Electronic Noise Electronic Noise

Scattering Process Variation Quantization Noise
Receiver

Transmitted Physical Based

Receiver Detection Data
Signal Layer Band

Physical Layer Integrated Systems

Application Layer

ISCAS 2007 34
Research in the Bio-chip Area

Our goal is the system-level design of bio-molecular detection platforms

Challenges: 1. Interface modeling, protocol design

2. IC implementation in standard CMOS?

Clinical Biotechnology Devices / MEMS IC Design Signal Processing

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

Collaboration Collaboration
Design, Analysis, and Verification
with Bio with EE

Modeling

ISCAS 2007 35
Holy Grail

Our goal is the system-level design of bio-molecular detection platforms

Challenges: 1. Interface modeling, protocol design

2. IC implementation in standard CMOS?

Biological Biological Transducer/ Detection

Detection Data
Sample Assay Interface Circuitry

Biological Application CMOS Implementation of the Detection System

ISCAS 2007 36
Integrated Biosensor Design

Detection
1 Characterize and model Area
the capturing process

Sensor
2 Specify transducer
parameters

3 Design the sensor array

ISCAS 2007 37
Molecular Affinity
When molecules get close to each other, electrostatic interactions, broadly
defined, may create structures with lower energy
Energy

ΔE ≈ 0.1-500kT at room temperature

Attached State Detached State

Because of thermal energy the binding is a reversible stochastic process

ISCAS 2007 38
Molecular Affinity
When molecules get close to each other, electrostatic interactions, broadly
defined, may create structures with lower energy

ACGT
Energy

Hydrogen
TGCA
bonds

ACGT
ΔE ≈ 1-50kT at room temperature
TGCA

CTGA CTGA

GACT
GACT

Because of thermal energy the binding is a reversible stochastic process

ISCAS 2007 39
Stability of Molecular Interactions
Basic energetics specifies the relative stability of the structures
Energy

Not a perfect
bond

ΔE2

ΔE1

ΔE1 > ΔE2

Bond stability > Bond stability

ISCAS 2007 40
Stability of Molecular Interactions
Basic energetics specifies the relative stability of the structures

AC AG
G G
T T
TG TG
CA Not appropriate CA
bond
Energy

AG
G
T
TG
CA

AC ΔE2
G
TG T
CA ΔE1

ΔE1 > ΔE2

Bond stability > Bond stability

ISCAS 2007 41
 Affinity-Based Biosensors
Affinity-based biosensors take advantage of the selectivity and
specificity of molecular interaction to capture and detect analytes

Analyte
Capture probes

Captured
targets

1 Sample exposure 2 Incubation 3 Detection

* There are different transduction methods for “counting” the binding events,
e.g., fluorescence, electrochemical, chemi-luminescence …
ISCAS 2007 42
Parallel Affinity-Based Sensing - Biochips

Affinity-based biosensors can be used in parallel to detect different targets

simultaneously

Biological
sample

Planar solid Capturing

surface probe (A)

Capturing
sites

Capturing
probe (B)

ISCAS 2007 43
DNA Microarrays – DNA Bio-chips
DNA microarrays are massively parallel affinity-based biosensor arrays or
simply bio-chips
10,000 spots

Fluorescent
Tag

Target
DNA (A)

DNA
Probe (A)

A
20-100µm
B
Target
50-300µm DNA (B)

DNA
Probe (B)

ISCAS 2007 44
DNA Microarrays – DNA Bio-Chips
Analyte quantification in biochips is carried out after incubation and in dry-
phase
Fluorescent
Tag

Target
DNA (A)

DNA
Probe (A)

A
20-100µm
B
Target
50-300µm DNA (B)

DNA
Probe (B)

ISCAS 2007 45
 Bio-Chip Detection Process
Detection in bio-chips is a multi-step process
1 Sample Preparation

3 Incubation 4 Detection

2 Array Fabrication

ISCAS 2007 46
Array Fabrication
The goal of array fabrication step is to form densely packed, uniform, and
reproducible capturing probes

Coupling Efficiency

Alignment
Coupling
Histogram
Ideal
Response Different surface probe densities create a
systematic variation in the fluorescent intensity and
the capturing efficiency of the array.

ISCAS 2007 47
Incubation Chambers
Incubation chambers are closed environments where the temperature is
strictly controlled

Solution will be placed on

top of the array

Probes

Typical temperature for

DNA microarrays is from
35°C to 60°C

www/arrayit.com

ISCAS 2007 48
Incubation Chambers
Incubation chambers are closed environments where the temperature is
strictly controlled

1 2 3

www/arrayit.com

Typical temperature for DNA microarrays is from 35°C to 60°C

ISCAS 2007 49
Fluorescence Detection - Scanners
Fluorescence detection is typically carried using scanners

Molecular Devices Axon4000B Scanner The SpotWare™ Colorimetric Microarray Scanner

Almost all commercially available bio-chips use flurescence detection process

ISCAS 2007 50
Fluorescence Detection - Cameras
Fluorescence detection can be carried out using high-resolution digital
cameras
ChromlightTM
Digital Camera

Filter

Excitation
Source

ISCAS 2007 51
Detection Fundamentals in Biosensors
The challenge is to estimate the analyte concentration x 0 , by observing
x ( t1 ) , the captured analytes at time t1

x(t )
Captured Analytes
x (t ) + σ x

x (t )

x (t ) − σ x

Time (hours) x (t )
Captured
t1
Targets at

2σ x x ( t1 )

Distribution of Captured Particles

ISCAS 2007 52
Limitations of Microarrays
Error Sources in microarray platforms
1 Sample Preparation 3 Hybridization
Detection
4 Hardware
Sample Labeling
Purification Variations
Variations Array Image
Washing Acquisition
Hybridization
Artifacts Noise
Noise
2 Array Fabrication +
Cross-
Hybridization
Probe Array
Interference Estimation
Synthesis Printing 5 Software
+
Errors Variations
Saturation

Direct
Synthesis
Variations

ISCAS 2007 53
Limits of Detection in Biosensors
Detection dynamic range currently is limited by the assay performance

Dynamic range of scanners > 80dB

Ideal
Signal-to-Noise Ratio

Response
Typically 30-45dB

SNR
Expected
Interference/ Behavior
Biochemical
Noise Saturation

SNRmin=0dB
Interference
+ Probe Saturatiuon
Biochemical Noise

MDL HDL
Analyte Concentration
0.01-0.1nM 1-10nM

1. Hassibi et al.,“A Probabilistic Model for Inherent Noise and Systematic Errors in Microarray Systems,” Proc. of GENSIPS, 2005.
2. Vikalo et al., “On Limits of Performance of DNA Microarrays,” Proc. of ICASSP, 2006
3. Vikalo et al., “A Statistical Model for Microarrays, Optimal Estimation Algorithms, and Limits of Performance,”
IEEE Tran. on Sig. Proc., (2006).

ISCAS 2007 54
Integrated Bio-Chips
Integrated bio-chips essentially merge detection with incubation

Conventional Bio-Chips Integrated Bio-Chips

ISCAS 2007 55
Integrated Biosensors

Integrated bio-chips essentially merge detection with incubation

Biosensor Microarray Chip

Conventional Bio-Chips Integrated Bio-Chips

ISCAS 2007 56
Basic Specifications for Integrated Bio-Chips

The specifications of the system is defined by the assay (i.e., application)

Spot size: > 25µm x 25µm

Pitch: > 75µm
Array size: > 100
Sampling rate: 0.1Hz
Resolution: >12-14bit
Input-referred
noise: < 1000 analytes
Sensor-to-sensor
isolation: > 120dB
Surface temp.

Captured Analytes
x (t ) + σ x

increase: < +5ºC x (t )

x (t ) − σ x
Sensor life-time > 48 hours
Time (hours)

ISCAS 2007 57
Microarray Signal Characterization
The goal is to evaluate the number of captured analytes and the system
dynamics

Movement of analytes is

Bulk solution
dominated by diffusion

∂X
= DX ∇ 2 X
∂t

Rate Equation

Probes
⎧ X + Y ←⎯ ⎯→ XY
k1 , k −1
⎪
⎨ d [ XY ]
⎪ = k1[ X ][Y ] − k −1[ XY ]
⎩ dt

ISCAS 2007 58
Stochastic Mass Transfer
Instead of Fick’s equation we use a stochastic model for the mass transfer
processes*

Δv
Transition probability:
mi , j = Prob (x ( Δ t ) = vi x ( 0 ) = v j ) Analyte
vi
x ( Δt )
vj
For small Δand
t no drift
or convection (only random walk): x (0)
−2 ẑ
mi +1,i = D Δ tΔ v
ŷ
x̂
*Hassibi et al., “ Biochemical Shot-Noise and Quantum-Limited SNR in Affinity-Based Biosensors,” JAP (2005)
ISCAS 2007 59
Stochastic Binding
Binding also can be statistically modeled*

Δv
Rate equations:
⎧ X + Y ←⎯ ⎯→ XY
k1 , k −1
⎪
⎨ d [ XY ]
⎪ = k1 [ X ][Y ] − k −1[ XY ] Binding
⎩ dt x (t )
[Ym ]
Site

Capturing probabilities:
v0
⎧⎪ m c , 0 = Prob ( x ( Δ t ) = v c x ( 0 ) = v 0 ) = k1[Ym ]Δ t ẑ
⎨
⎪⎩ m 0 ,c = Prob ( x ( Δ t ) = v0 x ( 0 ) = v c ) = k −1Δ t
ŷ
[Ym ] is the saturation concentration in bulk
x̂

*D.T. Gillespie, “A General Method for Numerically Simulating the Stochastic Time Evolution of
Coupled Chemical Reactions,” Journal of Computational Physics (1976)
ISCAS 2007 60
Transition Matrix

ρ ( Δt )

⎛ Prob ( x ( Δ t ) = v1 ) ⎞
⎜ Prob ( x ( Δ t ) = v ) ⎟
⎜ 2 ⎟

⎜ ⎟=
⎜ M ⎟
⎜⎜ ⎟⎟
⎝ Prob ( x ( Δ t ) = v N )⎠

⎛ m1,1 m1, 2 L m1, N ⎞⎛ Prob ( x ( 0 ) = v ) ⎞

⎜ ⎟⎜
m 2 , N ⎟ Prob ( x ( 0 ) = v 2 ) ⎟
1
⎜ m 2 ,1 m2,2 L
⎜ ⎟
⎜ ⎟⎜ ⎟
⎜ ⎟⎜ ⎟
⎜ M M O M ⎟⎜ M ẑ
⎜m ⎟ ⎜ Prob ( x ( 0 ) = v )⎟⎟
⎝ N ,1 m N ,2 L m N , N ⎠⎝ N ⎠

Capturing Area ŷ
M ρ (0) x̂
Transition matrix

ISCAS 2007 61
System Dynamics

I. Analyte distribution evolution after Δt

ρ ( Δ t ) = M ρ (0)

II. Analyte distribution after kΔ t

ρ ( kΔ t ) = M k ρ (0 )
III. Analyte distribution at time t
⎛ [M − I] ⎞ ⎛ ⎞
2
t 1 ⎛ t ⎞
ρ (t ) = exp ⎜ t ⎟ ρ ( 0 ) = ⎜ I + [M − I ] + ⎜ [M − I ] ⎟ + K ⎟ ρ ( 0 )
⎝ Δt ⎠ ⎜ Δt 2 ⎝ Δt ⎠ ⎟
⎝ ⎠
IV. Equilibrium distribution is the eigenvector associated with
eigenvalue of one for M

ρE = MρE ρc : Probability of analytes being captured at equilibrium

ISCAS 2007 62
One-Dimensional Approximations
One dimension Markov model is sufficient
for most biosensors N Δx
N −1
N −2
⎛1 − mc ,0 m 0 ,c 0 0 ⎞
⎜ ⎟
⎜ mc ,0 1 − m 0 ,c − k D kD L 0 ⎟
⎜ 1 − 2k D 0 ⎟
M =⎜ 0 kD
⎟
⎜ O M ⎟ L
⎜
⎜ 0
M
kD ⎟ M
⎝ 0 0 L 1 − k D ⎟⎠

m c , 0 = k1[Ym ]Δ t 2
m 0 ,c = k −1Δ t 1
0, C
k D = D Δ tΔ x −2

ISCAS 2007 63
Settling Time

N Δx
An upper bound for settling time is N −1
N −2
N
Δt
τT = ∑ , whereλ r is the rth eigenvalue of M
r =1 λr

It can be shown that for N >> we

1 have: L
1 1 L
M
τT ≈ + +
k −1 k1 [Ym ] + 4 D [Ym ] 2 / 3 4 D[Ym ]1 / 3
Disassociation Binding and Diffusion
diffusion 2
1
0, C

ISCAS 2007 64
Settling Time

Reaction Rate- Diffusion-Limited N Δx

Settling Time

Limited L
∝
D
N −1
N −2

1 α
+
k −1 k1

Reaction Chamber Size L

M
1 1 L
τT ≈ + + 2
k −1 k1 [Ym ] + 4 D [Ym ] 2 / 3 4 D[Ym ]1 / 3
1
Disassociation Binding and Diffusion
diffusion
0, C

ISCAS 2007 65
Example (Settling Time)

Monte-Carlo simulation of DNA hybridization

Number of capture molecules

Time (second)
ISCAS 2007 66
Inherent Noise and Fluctuations

I. Power spectral density

N Δx
N −1
4nρc (1 − ρc ) N −2
S ( ω) =
( kˆ1 + k −1 )(1 + ω 2 /( kˆ1 + k −1 ) 2 )
Lorentzian Profile

n : Number of particles L
ρc : Capturing probability
kˆ , k : Reaction kinetics
1 −1

2
1
0, C

ISCAS 2007 67
Inherent Noise and Fluctuations

I. Power spectral density N Δx

N −1
4nρc (1 − ρc ) N −2
S ( ω) =
( kˆ1 + k −1 )(1 + ω 2 /( kˆ1 + k −1 ) 2 )
Lorentzian Profile

II. Signal-to-noise ratio (SNR) L

( nρc ) 2 M
SNR =
n ρ c (1 − ρ c ) + σ 2
Inherent binding Detector
fluctuation noise
2
1
III. Quantum-limited SNR
0, C
nρc
SNR QL =
1 − ρc

ISCAS 2007 68
Example (PSD)
Hz Monte-Carlo simulation of DNA hybridization
PSD

30
20
10
0
-10
-20
-30 Time

Frequency (Hz)
ISCAS 2007 69
Example (PSD)

Monte-Carlo simulation of DNA hybridization

PSD (1/ Hz )

Equilibrium
concentration Reaction
kinetics
Noise amplitude

f 3 dB = ( kˆ1 + k −1 ) / 2 π
τ ≈ 1 sec

Frequency (Hz)
ISCAS 2007 70
SNR vs. Speed Tradeoff

SNR (dB)

Target DNA only (QL)

Target and background
Target, background
and detector noise

Settling time (second)

Hassibi at al., “Effects of Scaling on the SNR and Speed of Biosensors,” Proc. of EMBS (2004)

ISCAS 2007 71
SNR vs. Speed Tradeoff
SNR (dB)

Nano-Biosensors

Settling time (second)

Fundamental SNR limitation?

ISCAS 2007 72
Limits of Detection in Microarrays (Revisit)
Scaling reduces the biosensor detection dynamic range

Increase in MDL Decrease in HDL

due to scaling due to scaling
?

Ideal
Signal-to-Noise Ratio

Response
Typically 30-45dB

SNR
Expected
Interference/ Behavior
Biochemical
Noise Saturation

SNRmin=0dB

MDL HDL
Analyte Concentration
0.01-0.1nM 1-10nM

ISCAS 2007 73
Detection Based on Mass Change
Mass change at the surface of the biosensor can be an indication of binding
Cantilever-based Biosensor

Detection based on deflection Detection based on resonance frequency

Savran et al., APL 2003 Voiculescu et al.,2005

Not Compatible with CMOS

ISCAS 2007 74
Surface Acoustic Wave (SAW) Biosensors
Surface acoustic wave (SAW) propagation can be altered by analyte binding

Branch D, and Brozik S., Biosensors and Bioelectronics,

2004

Not Compatible with CMOS

ISCAS 2007 75
Surface Plasmon Resonance (SPR) Methods
At angles and wavelengths near the so-called “surface plasmon resonance”
condition, the optical reflectivity of the gold changes very sensitively with the
presence of biomolecules on the gold surface

The SPR angle mainly depends on:

1. The properties of the metal film

2. The wavelength of the incident light
3. The refractive index of the media on either side of the metal film

Not Compatible with CMOS

ISCAS 2007 76
Fluorescence Detection
Fluorescence detection is typically carried using scanners

Example: Detector Excitation

Source
Filter

0.5nm

Excitation

Fluorescence Detection
Methodology

Detector Compatible with CMOS

ISCAS 2007 77
Using Enzymatic Reporters
We can make reporters using enzymes
Enzymes are proteins that catalyze (i.e. accelerate) chemical reactions.

Example:

Glucose Firefly
Oxidase Luciferase

Can electrochemically be detected Can optically be detected

Detector Compatible with CMOS

ISCAS 2007 78
Using Nano-Particles as Reporters
Nano-particles with distinct physical characteristics can be used as
reporters

Magneto-
Resistive
Sensor

Magnetic
particle
Au Particle

S. Wang et al., J. M&M M, 2005 S. J. Park et al., Science, 2002

Detector Compatible with CMOS

ISCAS 2007 79
Integrated Biosensors
Optical, electrical, and magnetic transducers typically can be integrated in CMOS

Counter
Sensor
CTIA

ADC

ADC

LO
Photodiode Array Electrode Array
Spiral Inductor
Array

Bioluminescence Electrochemical biosensor Magnetic particle detection and

detection chip in 0.18µm CMOS microarray in 0.18µm CMOS manipulation in 0.18µm CMOS
Eltoukhy et al., ISSCC 2004 Hassibi et al., ISSCC 2005 Unpublished

ISCAS 2007 80
Overview of Tutorial

Performance metrics of sensors

Bio-molecular detection and biosensors

• Biosensor systems
• Affinity-based biosensors
• Microarrays and bio-chips
• Biosensor SNR and limits of detection

Integrated sensors

Integrated biosensors (biochips)

• General specifications
• Transducer Structure
• Integrated biosensor microarrays
• Examples

Conclusion

ISCAS 2007 81
Anatomy of Integrated Circuits
Hierarchy

Silicon Wafer Silicon Chip Blocks

0.45m 10mm 10µm

Many Replicates System-on-Chip (SoC) Circuit Block

Many Systems

ISCAS 2007 82
Anatomy of Integrated Circuits
Cross Section

Silicon Wafer

0.45m

0.25µm Technology 90nm Technology

(Motorola, 1996) (TSMC, 2002)

ISCAS 2007 83
Anatomy of Integrated Circuits
Cross Section

Passivation
Silicon Wafer
Metal M5

Via D5
M4

Metal Layers
D4
M3
D3
M2
Dielectric D2
0.45m M1
Silicon

D1

ISCAS 2007 84
Anatomy of Integrated Circuits
Passivation
Opening Si3N4
SiO2
Surface
Al/1%Si
M5
PMOS NMOS
SiO2
Si3N4
M4

Diode M3

M2
Metal
M1 Layers
NPN PNP

Silicon

ISCAS 2007 85
Resistors in Integrated Circuits
Passivation

0.35µm CMOS
Metal
Metal
Via
Via stack
Poly
Metal Layers

N Well
N+
P+
Dielectric
Silicon

ISCAS 2007 86
Inductors in Integrated Circuits

1. Less than 100nH

Passivation

2. Typical 5-10nH
Metal 3. High loss
Via 4. High parasitic
Capacitance
Metal Layers

Dielectric
Silicon

ISCAS 2007 87
Capacitors in Integrated Circuits
MIM (Metal-Insulator-Metal) cap.
Passivation

Metal

Via
Metal Layers

MOS cap. Poly-Poly cap.

Dielectric
Silicon

ISCAS 2007 88
Error Sources in Integrated Sensors?

Relevant to Sensors
Passive components

Resistor
Systematic errors
Capacitor Process variations

Inductor Random errors

Thermal noise
Shot noise
CMOS Substrate noise
BJT
Devices

Diode

ISCAS 2007 89
Error Sources in Integrated Sensors?

Relevant to Sensors
Passive components

Resistor
Systematic errors
Capacitor Process variations

Inductor Random errors

Thermal noise
Shot noise
CMOS Substrate noise
BJT
Devices

Diode

ISCAS 2007 90
Typical Specification Sheet
Passivation

0 .4 Thickness Resistance
1 .6 (nm) (mΩ/ or Ω/square via )

Metal M5 860 ± 50 36 ± 4

Via D5 ≈ 600 4±2

M4 470 ± 50 72 ± 7
D4 ≈ 600 4±2
Metal Layers

M3 470 ± 50 72 ± 7
D3 ≈ 600 4±2
M2 470 ± 50 72 ± 7
Dielectric D2 ≈ 600 4±2
M1 421 ± 40 89 ± 9
D1
Silicon

± X corresponds to ± 3σ of
X X

ISCAS 2007 91
Six Sigma
Six Sigma in semiconductor industry is measure of quality that strives for near perfection.
Six Sigma is a disciplined, data-driven approach and methodology for eliminating defects
(driving towards six standard deviations between the mean and the nearest specification
limit) in any process

Acceptable

Not acceptable
Specification
Not acceptable

ISCAS 2007 92
Example
Typical datasheet from a CMOS fabrication Process

TABLE 1. CMOS/5LM layer thickness

(±3 sigma variation of dielectric and metal layer thickness)
Thickness
Type Layer Unit
Minimum Typical Maximum
Dielectric(pox) Passivation Oxide over M5 9000 10000 11000 A
Dielectric(pnit) Passivation Nitride over M5 3600 4000 4400 A

ISCAS 2007 93
 Circuit Architectures for Sensors
There are four general signals which the transducers generate:
• Detecting sinusoidal tones
• Voltage detection
• Current detection
• Parametric measurements

Circuit Architectures Output Representation

Single tone Analog y A (t )

Output
Real-World

Voltage Interface
Readout
Transducer
Current System
Digital
Parameter A/D Output
Interface y D (t )

ISCAS 2007 94
 Single Tone Sensors
We are required to measure amplitude and/or frequency and/or phase
ZS Interference

Signal
Transducer Noise
Interference

Signal Frequency

Analog y A (t )
Output
Real-World

Interface
Single tone Readout
Transducer
System
Digital
A/D Output
Interface y D (t )

ISCAS 2007 95
Example
NMR: Nuclear magnetic resonance
Excitation Signal
Permanent B1
magnet
Excitation
coil
0 t

Output Signal
S (t ) ω H = γ H B0
0 t

1H Transducer
Detection coil 23Na Noise
31P

Signal ωH Frequency

ISCAS 2007 96
 Method (1)
Do everything in the digital signal processing (DSP) block
Real-World

y D (t )
Signal
Transducer Single tone A/D FFT Processing

Challenges:
Signal Frequency
1. A/D needs to be very fast
2. The resolution of the A/D needs to be high with a MDL
smaller than the transducer noise standard deviation
3. Requires a lot of signal processing power and silicon area

ISCAS 2007 97
 Method (2)
Superhetrodyne architecture

1 2 3

Single tone
Real-World

MIXER BPF MIXER LPF

Transducer LNA A

LO1 Tunable LO2

1 2 3

LO1 Frequency LO2 Frequency Frequency

ISCAS 2007 98
 Method (3)
Direct-conversion architecture

1 2

Single tone
Real-World

MIXER LPF y D (t )
Transducer LNA A A/D

Tunable LO

1 2

LO1 Frequency Frequency

ISCAS 2007 99
Coherent Detection
If the phase and amplitude of the input signal is unknown we need to
recover both of them
MIXER LPF
AB Cannot find both
A cos( ω S t + θ ) cos( θ ) phase and
2
amplitude
B cos( ω S t ) LO

LPF
AB
cos( θ )
2

A cos( ω S t + θ )
LO B cos( ω S t ) Solvable
90° LPF
AB
sin( θ )
2

ISCAS 2007 10
0
 Voltage Detection Sensors
Acquire a voltage signal which has DC or low frequency component
ZS
Interference

Signal
Interference Signal Transducer Noise

Frequency

Analog y A (t )
Output
Real-World

Interface
Voltage Readout
Transducer
System
Digital
A/D Output
Interface y D (t )

ISCAS 2007 10
1
Example
Thermocouple: Measures temperatures which consists of two dissimilar
metals joined so that a potential difference generated between the points
of contact is a measure of the temperature

Metal 1
Metal 3 LNA A/D
Metal 2

LNA Interference

Unknown T X Reference Tref

Signal Noise

Frequency

ISCAS 2007 10
2
Challenges
Low frequency fluctuation and 1/f noise of the amplifier is an issue

LNA Noisy

LNA
Signal Noise
1 2
Frequency Frequency Frequency

1 2
Real-World

Transducer Voltage LNA A/D

ISCAS 2007 10
3
Method (1)
Chopper stabilization (CHS) fc fc

1 2 3 4
Real-World

Transducer Voltage LNA A/D

MIXER MIXER

1 2

0 0
fc fc
LNA
LNA Noise
3 4 LNA Noise

fc 0
fc fc 0 fc

ISCAS 2007 10
4
Method (1): Implementation

AMPLIFIER
MIXER
R2 R3
Φ
R1 R3 Φ

Φ Φ
Vin Vout
Φ

R3
Φ MIXER

C. C. Enz and G. C. Gabor, “Circuit Techniques for Reducing the Effects of Op-Amp Imperfections:
Autozeroing, Correlated Double Sampling, and Chopper Stabilization,” Proc. of IEEE, 1996.

ISCAS 2007 10
5
Method (1): Implementation

1/f
suppression

Enz et al. 1996

Φ Φ

Φ
Vin Φ Φ A1
A2 Vout

ISCAS 2007 10
6
Method (2)
Autozeroing method (AZ)
If we have an additive spontaneous fluctuating which is slow (e.g., 1/f), we can use
certain switched capacitor circuits to suppress noise
Signal Vn
Vin A Vout
time
Signal + Noise

Amplifier Noise

time

Output
Noise time

In this system can we subtract the noise from

time the signal?

ISCAS 2007 10
7
Method (2): Implementation
Output series cancellation – Open-loop offset cancellation
(I) (II)
S1
S1
Vin C
A Vout S2
S2
S3 S3

Phase (I) Phase (II)

Vn AVn Vn
AVn
Vin
A A Vout

Vout = A(Vin+ Vn) – AVin = AVin

ISCAS 2007 10
8
Method (2): Implementation
Input series cancellation – Closed-loop offset cancellation
S3 (I) (II)
S1 C
S1
Vin
A Vout S2
S2
S3

Phase (I) Phase (II)

C Vn
-VnA/(1+A) Vn Vin
A Vout
A

Vout = - AVin- A/(A+1)Vn

ISCAS 2007 10
9
 Current Detection Sensors
Acquire a current signal which has DC or low frequency component

Interference

Signal
ZS
Interference Signal Transducer Noise

Frequency

Analog y A (t )
Output
Real-World

Interface
Current Readout
Transducer
System
Digital
A/D Output
Interface y D (t )

ISCAS 2007 11
0
Difference in Current and Voltage Sensing
No difference in intrinsic SNR

Transducer Transducer

I2 R V2
I R SNR = V SNR =
4 kTG Δ f 4 kTR Δ f

Transducer Transducer

R2I 2 R V 2G 2
I R SNR = V SNR =
4 kTR Δ f 4 kTG Δ f

ISCAS 2007 11
1
Example (1)
Photodiodes: Current sensing is a better choice because of the linearity of
the transfer function

hυ We need to solve the following to find V (t ) :

V (t ) ⎛ VV( t ) ⎞ t
I D (τ )
I ph Cj I D (t ) = I 0 ⎜ e T − 1 ⎟ − I ph (t ), V (t ) = − ∫ dτ
⎜
⎝
⎟
⎠ 0
C j (V (τ ) )

Absorption
I ph (t ) = α ⋅ QE ⋅ I (t ) Photon Flux
Quantum Efficiency
hυ
The transfer function is very simple:
I (t )
I ph C j I (t ) = I ph (t )

ISCAS 2007 11
2
Challenges
Low frequency fluctuation and 1/f noise of the amplifier is an issue in
addition to creating a low impedance node

LNA Noisy

LNA
Signal Noise
1 2
Frequency Frequency Frequency

Current
1 2
Real-World

Transducer ZS LNA A/D

I (t )

Z in << Z s

Interference
ISCAS 2007 11
3
 Current Amplifier
Common-gate amplifier

Vdd Vdd Vdd

Vout R Vout Vout R

-A
VG VG
Iin Iin Iin
IS VB IS

Z in ≈ 1 / g m Z in ≈ 1 / g m Z in ≈ 1 / g m A

ISCAS 2007 11
4
Method (1): Implementation
Chopper stabilization (CHS)

MIXER Vdd Vdd MIXER

Φ R R Φ

Vout
I R Φ Φ Φ Φ A
VG
Φ Φ
VB IS IS

AMPLIFIER

ISCAS 2007 11
5
Method (1): Implementation
Chopper stabilization (CHS) Vdd
VB MIXER

Φ Φ Vout
VG
AMPLIFIER Φ
I /2 I
Φ Φ
MIXER 1/ 2gm Φ Φ 1/ gm

ISCAS 2007 11
6
Method (2) and (3)
Autozeroing method (AZ)
Not very practical at the current level since it needs inductors

S1 Dual S1
Vin Circuits Iin
S2 C S2 L

ISCAS 2007 11
7
Transimpedance Amplifiers (TIA)
Transimpedance amplifiers (TIA): They are the most popular current
sensing topologies
Low-pass filter

R 4 kTR
Z in << Z s 10dB/dec

20dB/dec

I Zs Vout = RI 1/ f ω1 ω2 40dB/dec

Amplifier common
VB1 VB2 mode and
transducer bias
are independent Frequency (Log)

ISCAS 2007 11
8
Capacitive Transimpedance Amplifiers (CTIA)

Capacitive Transimpedance amplifiers (CTIA): They have the lowest noise

and highest gain in ICs
Noise-less
Integrator

Reset Weird noise

behavior
C
Z in << Z s Vn2 ( jω )
Op-amp
Vn poles

I Zs ω1 ω2
I (τ )
t
Vout (t ) = − ∫ dτ
0
C
Frequency (Log)

ISCAS 2007 11
9
Capacitive Transimpedance Amplifiers (CTIA)

Capacitive Transimpedance amplifiers (TIA): They have the lowest noise

and highest gain in ICs
Noise-less
Integrator

Reset
I (τ )
t

C Vout (t ) = − ∫ d τ − V n (t )
0
C
Z in << Z s 2
Vn ⎛ t
I (τ ) ⎞
Vout (t ) = ⎜ ∫
2
⎜ d τ ⎟⎟ + Vn2 (t )
⎝0 C ⎠
I Zs 2
⎛ I (τ )
t
⎞ ∞ 2
V (t ) = ⎜⎜ ∫
2
out d τ ⎟⎟ + ∫ Vn ( jω )d ω
Noisy ⎝0 C ⎠ 0
Op-amp
Noise-less signal
source

ISCAS 2007 12
0
Parametric measurement

ISCAS 2007 12
1
Excitation and Detection

ISCAS 2007 12
2
Example

ISCAS 2007 12
3
Overview of Tutorial

Performance metrics of sensors

Bio-molecular detection and biosensors

• Biosensor systems
• Affinity-based biosensors
• Microarrays and bio-chips
• Biosensor SNR and limits of detection

Integrated sensors

Integrated biosensors (biochips)

• General specifications
• Transducer Structure
• Integrated biosensor microarrays
• Examples

Conclusion

ISCAS 2007 12
4
Integrated Microarrays (Revisited)

Detection
Area

Sensor
What kind of transducer?
Optical
Eltoukhy et al., ISSCC (2004)
Fully electronic?
Hassibi et al., ISSCC (2005)

ISCAS 2007 12
5
Biosensor Chips Gallery

Counter
Sensor
CTIA

ADC

ADC

LO
Electrode Array
Photodiode Array
Spiral Inductor
Array

Bioluminescence Electrochemical biosensor Magnetic particle detection and

detection chip in 0.18µm CMOS microarray in 0.18µm CMOS manipulation in 0.18µm CMOS
Eltoukhy et al., ISSCC 2004 Hassibi et al., ISSCC 2005 Unpublished

ISCAS 2007 12
6
 Example: DNA Sequencing

Real time DNA sequencing through synthesis [Ronaghi ’96]

Polymerase

PPi
DNA sequence

Light intensity
ATP-Sulfurylase
G - T CC
Nucleotides PPi ATP
Luciferase
C T A G
562nm Nucleotide added
ISCAS 2007 12
7
Optical detection (concept)
Excitation Light
650nm Fluorescent tag
z Fluorescence:
– Widely used
– Difficult to integrate
670nm
– Need excitation source
– Need interference filters

z Luminescence
– Lower background
– High sensitivity Luminescence Probe
– Long emission time
– Suited for lab-on-chip
562nm

ISCAS 2007 12
8
System Simulation Model [Salama ’03,’04]

ƒ kt turnover rate of ATP

ƒ ka turnover rate Luciferase Luminescence
ƒ α Luciferase Efficiency Reaction
ƒ V DNA Volume

ƒ System Geometry
ƒ Material properties Optical Path

ƒ Q Quantum efficiency
ƒ idc Dark Current Photon
ƒ tint Integration Time Detection
ƒ σr Read Noise

ISCAS 2007 12
9
Target Application Characteristics

z Small array size (1-1000 spots)

z Large spots (≈150μmx150μm)
z Long integration times (1s to 3min)

z Challenge: Detect below 10-6 lux over 30sec @ room

temperature

z Off-the-shelf CCD&CMOS sensors are not suited

– Small pixels: High Leakage, low sensitivity
– Off-chip ADC and processing

ISCAS 2007 13
0
ADC Requirements

z Problem: Detect small signals embedded in large

background at room temperature
– Assume:
– Photodiode Area = 150μmx150μm
– Photon Flux= 0.04 ph/sec/μm2
– Quantum Efficiency (QE) = 40%
– Dark Current Density (jdc)= 1 nA/cm2
– Integration Time= 30 sec
– Signal = 10Ke-
– Background = 1.3Me-
– Total noise (shot+read) = 2Ke-
z Solution: Use an ADC with averaging

ISCAS 2007 13
1
SNR vs. ADC with Averaging

18
16
14
12
SNR(dB)

10
8
6
4
2
0
8 9 10 11 12 13 14 15 16
ADC resolution (#Bits)
ISCAS 2007 13
2
System Detection Limit

50
13-bit w/o averaging
13-bit 128 averaged digitizations
40 Shot Noise Limit

30
SNR(dB)

20

10 2.2X10-7lux

10-6 10-5 10-4

Photon flux (lux)
ISCAS 2007 13
3
Chip Characteristics

ƒ 0.18µm CMOS (CIS) process

ƒ4M, 1 poly
8x16 Pixel Array ƒ 5mm x 5mm (492K transistors)
ƒ 8 x 16 pixel array (230μm sq.)
ƒ P+/N/Psub photodiode
Ramp ƒ Pseudo-differential pixel
128 channel ADC
ƒ Per-pixel 2-step 13-bit ADC
ƒ Integrated ramp generator
DSP SIMD Array ƒ Per-column DSP
ƒ 320 Mbits/s readout rate
Averaging done in digital ALU (1 per column)]
ƒ Static power: 26mW
ISCAS 2007 13
4
 Chip Block Diagram

2
Pixel Pixel
Reset
Pixel Array
Pixel Pixel

Ramp 2
ADC ADC
Generator 128 channel
ADC ADC
13-bit ADC
Shift/Load
12
Output 8
8x20 SR 8x20 SR
DSP SIMD
Control 3
ALU ALU Array
20
64x20 64x20
SRAM SRAM
ISCAS 2007 13
5
Pixel Level ADC [Fowler ’98, Yang ’99]
z Scalable and extendable
z Simple and robust circuit implementations
z Suited to deep submicron implementation
z Low power consumption
z Also, we wanted eliminate multiplexing to reduce noise
injection

ISCAS 2007 13
6
13bit ADC with Averaging

Step 1

Vin 1x 9 Bit Single

Slope ADC 1010 01001

4 Bit DAC
Step 2
-
9 Bit Single
+ + 16x
Slope ADC
010001011

1010010001011

13 bits
ISCAS 2007 13
7
Pseudo-Differential Pixel

Measured Dark signal (mV/sec)

1.8V
8
BIAS
M2
VREF
VSET
6
Reset Out

M1
4

0.4 0.6 0.8 1 1.2 1.4

VSET (V)

ISCAS 2007 13
8
 Per Pixel Analog chain

1.8V
BIAS
Positive Ramp
VREF M2 +
_
VSET + +
Reset _
+ _
_

M1 Negative Ramp

4-bit DAC Column DSP

4 Register Counter

Pixel 13-bit 2-step ADC

ISCAS 2007 13
9
Pixel Noise Model [El Gamal ’99]

ƒ is the noise charge due to integration

ƒ is the reset noise (KTC noise)
ƒ is the readout circuit noise
ƒ is the flicker noise (1/f noise)
ƒ is the offset FPN
ƒ All noise components are independent

ISCAS 2007 14
0
 System Operation

0 1 N
Ramp Reset

Ramp

16X Gain
Accumulate/
Store

B1 S1 S4
… Correlated
Pixel B2 B4
S2

Output B3 S3 Multiple
Sampling
Background Signal+Background

ISCAS 2007 14
1
 Experimental Results
S1 S4
Experiment: S2
Frames = 50
Tint = 80sec S3
N = 16
ΔTi = 25μs Tint

Technique Offset Reset 1/f Read Loss

9 2X -15.44dB

9 9 2X -6.94dB

9 9 4X -9.42dB

9 9 2X/N -2.05dB

9 9 9 4X/N -1.12dB

ISCAS 2007 14
2
Measured Pyrosequencing Reaction

930 1.3 fmol ATP

920 Tint= 25 sec
910
900
890
DN

880
870
860
850
840
830

0 100 200 300 400 500 600 700

Time(sec)
ISCAS 2007 14
3
 Electrochemical Detection (Concept)
1. Molecular binding changes the characteristics of the electrode-
electrolyte interface
2. An electronic sensor can detects the changes

Electrolyte
ions Rb Rb

Rd Cd R d′ C d′

RI CI R I′ C I′
Electrode e-

ISCAS 2007 14
4
Electrochemical Detection (Examples)

Interdigitated Electrodes

1 2

2 1 2

1. Park et al., Science (2002)

2. Schienle et al., JSSCC (2004)

ISCAS 2007 14
5
Electrochemical Detection (Examples)
Ion-Sensitive FET (ISFET) Devices

Reference
Reference (R) (R)

R
R
+

D
G
Cgsgs
C ggmm rrds
ds
S + + + D S
Channel
Channel

1. Fritz et al., PNAS (2002)

2. Wong et al., IEEE Trans. Electron Devices (1989)

ISCAS 2007 14
6
 Electrochemical Detection (Pros and Cons)
Advantages:

Potentially label-free (Bergveld, IEEE TBE, 1970)

Dense sensor arrays (Dill et al. , ACA, 2000)
Electrical manipulation (Cheng et al., Nature, 1998)
Continuously monitor reactions
Low cost

Disadvantages:

High level of ionic background

Sensitive to parasitics
Unstable electrode-electrolyte interfaces

ISCAS 2007 14
7
 Transducer Design

50µm
Solution
Impedance
100µm

(ZS)

20µm

Solution
PBS
Working Electrode Counter Electrode
Al Interface Impedance Interface Impedance

The solution impedance (ZS) has no information about the binding

ISCAS 2007 14
8
Transducer Design

Passivation
Opening
Passivation

Si3N4

SiO2
M5
SiO2
M4 Al/1%Si
Metal Layers

M3

M2
Si3N4

M1
Silicon

0.18µm CMOS
ISCAS 2007 14
9
Differential Transducer Design

(C)

Input signal

(ZS) (ZS)

Reference Electrode
Working Electrode

Affinity-Based
Biosensor

(W) + Vout
- (R)

In differential transducers, output signal becomes

independent of (ZS)
ISCAS 2007 15
0
Differential Transducer Implementation

Hassibi et al. , ISCCC (2005)

Capacitance = 0.1-1nF, Resistance = 103-105Ω
ISCAS 2007 15
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Differential Detection
A Binding Sites B Analyte

C C

W R W R

C C

C C

ZCW ZCR ZCW ZCR

W R W R
ZWR ZWR
ISCAS 2007 15
2
Fully Differential Sensor

ZLOAD
Solution
W
ZCW
VB1
VC
C ZWR A VOUT
VB2
ZCR
R

ZLOAD

ISCAS 2007 15
3
Pixel Architecture

Vb_1
L11
L12
Solution s11 s12 s13

W
Vcm

7-Bit Control Bus

Out
Z CW sA

C Z WR sO
A sOUT

Z CR
R Control Register
s22 s23
s21
L21
L22
Vb_2

ISCAS 2007 15
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Op-amp Architecture

Gain-boosted folded cascode with

switched-biasing*
0.35µm dual-gate I/O devices (2.2mW,
83dB gain, 95MHz BW)

vOUT

vOUT vOUT

IN(+)
IN(+)

vBIAS vBIAS
IN( )

vBIAS

*Klumperink et al., JSSC (2000)

ISCAS 2007 15
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Pixel Output Noise PSD

Φ Φ
No switched-biasing
Φ Φ
Output Noise Power (V2/Hz)

6dB Φ = 0,Φ Φ =Φ clk

Φ = clk, Φ = clk
10-6

10-7
10Hz-1MHZ noise power
26µV rms (input referred)

10 100
Frequency (Hz)
ISCAS 2007 15
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Pixel Layout

160µm

120µm
ISCAS 2007 15
7
 Pixel Layout

160µm

Working Reference

120µm
Metal 5

Common

ISCAS 2007 15
8
 Pixel Layout

160µm

Working Reference
Opening

Metal 5 M5

M4

M3

M2

Common M1

0.18µ
0.18µm CMOS

ISCAS 2007 15
9
Pixel Layout

160µm

Working Reference

ZWR

120µm
ZCR
ZCW

Sensor

Common

ISCAS 2007 16
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Pixel Layout

160µm

Working Reference

120µm
Sensor

Common

ISCAS 2007 16
1
CMOS Electrochemical Biosensor Array

Wax I/O pins

I/O pads and the bondwires must be

isolated from the solution

ISCAS 2007 16
2
MODE(1): Impedance Spectroscopy

Load-line parasitics
ZL 54Ω || 85fF
W
250µA
CW
Z

VC VOUT
ZWR

C 450fF A
80µA
Z CR

⎧ 1 1 ⎫
R VOUT = AZ L ⎨ − ⎬VCM
ZL ⎩ Z CW Z CR ⎭

ISCAS 2007 16
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MODE(1): Impedance Spectroscopy

5
100mM Tris Acetate (PH=8.3)
Impedance Magnitude (kΩ)

100mM Tris Acetate (PH=8.3) +BSA

4.5

4.0 Al BSA
Si3N4
3.5 SiO2

3.0

2.5
102 103 104
Frequency (Hz)
Impedance magnitude of electrode-electrolyte interface with
and without bovine serum albumin (BSA) on surface
ISCAS 2007 16
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MODE(2): Current Measurement
60-220Ω

Conversion
100pF gain: 500V/nA/sec
ICW W
500mV output swing

VC VOUT
C A

ICR
R
100pF

ISCAS 2007 16
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MODE(2): Current Measurement
60-220Ω

ICW Conversion
100pF gain: 500V/nA/sec
C W
500mV output swing

VOUT
A

Low
VOUT
High

T
A
Reset VOUT (T ) = ∫ I CW ( τ )dτ
S1 C0
Integrate

ISCAS 2007 16
6
MODE(3): Differential ISFET

W
CW 450fF
C
W

RWR CWR
RC
VC VOUT
C A
R
CR
C 450fF
CR
R
Gain: 50V/V

ISCAS 2007 16
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MODE(2): Current Measurement
60-220Ω

Conversion
100pF gain: 500V/nA/sec
ICW W
500mV output swing

VC VOUT
C A

ICR
R
100pF

ISCAS 2007 16
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MODE(3): Differential ISFET

W
CW 450fF
C
W

RWR CWR
RC
VC VOUT
C A
R
CR
C 450fF
CR
R
Gain: 50V/V

ISCAS 2007 16
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CMOS Electrochemical Biosensor Array

ISCAS 2007 17
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Conclusion - Tutorial
Bio-molecular detection and bio-chip design is an extremely important yet
challenging area in biotechnology

Detection in biosensors is mostly limited by the stochastic nature of

biological system

Bio-chip design is a system-level design problem

Integration of Bio-chips using standard CMOS processes is practical and

has the potential to lead into Bio-chip SoCs

Enables inexpensive, hand-held, high throughput biosensors for variety of

industrial, environmental and biomedical applications

ISCAS 2007 17
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 BIO-CHIPS

FACT NOT FICTION

NECESSARY NOT COOL

ISCAS 2007 17
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