Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
Executive Summary Approximately 46% of all cancer patients are diagnosed when their cancer
has already reached an advanced stage. [1] There is no way to diagnose a disease without
physically seeing a medical professional, and by that time it may be too late. We are proposing a
prototype miniaturized silicon nanowire system that will allow for the diagnosis of disease
through in vivo applications, such as an implantable microchip. Our system will monitor
biomarker levels in the blood and then be able to alert the user when certain diseases are present.
In our research, we will have four main tasks to accomplish:
1. Biomarker screening to determine the benchmark biomarker which the feasibility of our
research will be based around.
2. Find the optimal nanowire distribution to allow for the highest biomarker detection
sensitivity and surface area to nanowire ratio.
3. Miniaturize our system to dimensions ready for possible in vivo applications while
maintaining biomarker detection sensitivity.
4. In vitro testing to ensure the mechanical and functional integrity of the nanowire system.
At the end of our research our prototype nanowire system will be ready for in vivo testing.
Technical Need In disease diagnostics time is the most valuable commodity, and in many cases
a late diagnosis is a death sentence. Current silicone nanowire systems are able to diagnose
disease by analyzing blood samples outside of the body. However, these systems have a
relatively long turnaround time, and are often used after a patient is already showing symptoms
of disease when it is already too late. Miriam is a device currently being developed by the
company Miroculus which will be able to detect dozens of cancers in a single cheap and quick
blood test outside of the body. Miriam utilizes the bioluminescence of microRNA in blood
samples to diagnose disease. In contrast, our system utilizes the electrical properties of
biomarkers to diagnose disease in the body with a faster turnaround time. [2]
We are proposing a miniaturized version of current silicon nanowire systems that will be
designed to be integrated into an implantable microchip to run real time disease diagnostics
within the body. Our miniaturized nanowire system will be designed to diagnose a number of
diseases as soon as they are present in the body. Our system will do this by measuring the level
of characteristic disease biomarkers in the blood. An early diagnostic system such as ours would
revolutionize the healthcare industry by rapidly speeding up the diagnostics process which would
in turn save thousands of lives and up to $16 billion in healthcare costs within the first five years
of implementation. [3]
In addition to the quantitative benefits, our proposal will address the National Academy of
Engineering (NAE) grand challenge of advancing health informatics by allowing for prompt
diagnosis of disease on a large scale and providing a vast amount of biomarker research that has
never been available before.
Technical Goals Our goal is to design and manufacture a fully functional miniaturized silicon
nanowire field-effect transistor (Si-NW FET) system that will allow for the in vivo
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
characterization of biomarkers by coupling this technology into implantable medical devices.
Biomarker detection will be enabled by changes in electrical conductivity caused by the binding
of these molecules to the surface of the nanowires. In order to achieve this goal, the team has
proposed the following four-stage research operation:
1. Conduct a biomarker screening process to select a benchmark biomarker focusing on cancers.
2. Determine the optimal surface area to nanowire distribution ratio to allow for miniaturization.
3. Manufacture a variety of miniaturized nanowire biosensors according to pre-established criteria
based on the optimal surface area to nanowire distribution ratio and target dimension.
4. Perform in vitro testing of miniaturized system to determine overall performance and
functionality.
Technical Approach
Task 1: Biomarker Screening
In order to conduct a biomarker screening
process, the team will focus on nine U.S
Food and Drug Administration (FDA)
approved cancer biomarkers outlined in
the work of Polanski and Anderson [4].
The list of candidate biomarkers are
shown on Table 1 on the right.
The selection of the benchmark biomarker
for the purposes of this research will be
based on criteria including the sensitivity,
specificity and size of the biomarkeraptamer complex. High sensitivity and
specificity values are favorable since they
will allow for very accurate detection and
labeling of the disease present in the blood plasma. In addition to this, the size of the biomarkeraptamer complex is of outmost importance since it will limit the overall dimensions of the
miniaturized system by establishing upper and lower bounds on the nanowire distribution and the
size and flow rate of the microfluidic channel.
Task 2: Nanowire Distribution
The first step in the creation of the Si-NW FET system is to design appropriate aptamer receptors
tailored to the benchmark biomarker. These aptamer receptors will be bound to the surface of the
nanowires through a cross-linker compound. While the most effective cross-linkers have been
demonstrated to be polyethylene glycol based compounds and disuccinimidyl carbonate
compounds [5], the specific binding is not optimized unless the biomarker-aptamer complex is
known. However, cross-linking technologies will be of great use to the research team in order to
allow for the attachment of the aptamer receptor to the nanowire surface, which will then provide
the system with the capability to detect the presence of a target biomarker (via conductivity
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
changes) as it attaches to the aptamer receptor through a lock-and-key type mechanism. The
aptamer receptors will be designed to ensure that the binding effect of the biomarker to the
aptamer is reversible through the development of a biocompatible washing solution.
Prior to proceeding into the miniaturization stage for the Si-NW biosensor, the team will
manufacture a variety of systems based on the selected benchmark biomarker, varied nanowire
distributions and the manufacturing procedures for Si-NW systems outlined elsewhere [6-9].
These procedures include the use of chemical vapor deposition (CVD) technology to grow
nanowires on the surface of a boron doped (p-type) silicon wafer with a top-surface oxide. In
addition to this, gold electrodes will be deposited using thermal evaporation and the microfluidic
channel will be made of polydimethyl siloxane (PDMS) due to its potential to create both
temporary and permanent seals to silicon wafers.
Using these systems, the team will test for the detection sensitivity and use this data to determine
the optimal surface area to nanowire distribution ratio. This optimal ratio will allow for a final
assessment of the success rate of detection of the target biomarker and a re-evaluation step will
be carried out if results are deemed inappropriate. The subsequent miniaturization of the Si-NW
system will be based on safe implant size range and target dimensions of the system.
Task 3: Miniaturization
The miniaturization of the Si-NW FET system will be based on criteria established by the
research team based on a combination of the pre-determined optimal surface area to nanowire
distribution ratio and a safe implant size range and target dimensions.
While team research will be based primarily on maintaining functionality on a miniaturized
version of the Si-NW system, it is important to understand that the greatest challenge faced in
such a task is to recognize that the biomarker-aptamer-cross-linker complex will limit the
potential target dimensions of the system. Based on current research, it is known that most amino
acids have a size on the 0.8 nm range; in addition to this, most biomarkers tend to be on the
range of 25-100 amino acids with most lying on the lower end of the spectrum. With such size
limitations, it is possible to deduce that the PDMS microfluidic channel dimension should have
entry and exit sizes on the range of 1-5 μm in order to allow for comfortable access of the
biomarker into the channel. According to Knopf and Bassi [10], most present-day nanowire
biosensors have microfluidic channels with dimensions close to 6 mm in length and 500 μm in
width. Based on these estimations, a possible target dimension for the miniaturized system is
likely to be on the 1-5 mm2 range. However, many factors including the manufacturing
conditions, the selected benchmark biomarker and the achievable nanowire distributions will
further limit the potential range of sizes achievable during the miniaturization process.
The next step to follow by the research team is to manufacture various Si-NW FET biosensor
systems [6-9] by varying the dimensions of the system according to the optimal surface area to
nanowire distribution ratio and manipulating manufacturing conditions such as the statistical
distribution of nanowire size and mass, temperature, pressure, pH, and deposition time [11]. If
the miniaturization stage is deemed to be inconceivable, the research team will proceed to re-
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
evaluate the feasibility of the project and decide to whether commence the project at stage one,
or proceed to a risk mitigation stage.
Task 4: In-Vitro Testing
In order to maintain proper functionality of the biosensor the miniaturization must guarantee that
the system will be resistant to clogging, allow filtration by biomarker size, allow for laminar
flow of blood plasma and maintain mechanical integrity and conductive behavior for both in
vitro and in vivo applications.
To test the functionality of the various Si-NW systems manufactured in the miniaturization stage,
the research team will carry out an in vitro sensitivity and specificity analysis of the miniaturized
system for the pre-selected benchmark biomarker. Based on the test results, the team will
evaluate the feasibility of maintaining the overall functionality of the system for miniaturized
systems. If the results are deemed successful, the team will proceed to perform in vitro
mechanical and microfluidic analysis of the biosensor by mimicking the conditions that the
system will undergo while implanted in the human body. If the results are deemed inappropriate,
the team will proceed to re-evaluate the feasibility of the project and proceed to a risk mitigation
stage.
The final stage will consist on selecting the systems that perform the best in terms of clogging
resistance, biomarker filtration, flow conditions, mechanical integrity and conductive behavior.
Information of these systems will provide invaluable knowledge regarding a manufacturing
process that will be capable of creating fully functional miniaturized versions of Si-NW FET
biosensors for the first time in history.
Economic and Social Impact The success of our proposal will benefit both the scientific and
medical communities. The study of biomarkers is still in its youth, and our research will provide
a large amount of biomarker research which will prove the validity of utilizing biomarkers in
other scientific applications.
If an in vivo early detection system such as ours is eventually put into widespread use that would
revolutionize the medical field. At that point, there would be no need for the large scale
screening processes that are used today to detect disease early, and that would save thousands of
wasted dollars and a large amount of wasted time. Then the medical community would be able to
focus more time and research on treatment methods because the early diagnosis will already be
taken care of.
If our proposal succeeds it will open the door to possibly providing thousands of people access to
early diagnosis systems that could save their lives and thousands of dollars in healthcare costs. It
would improve the way that society looks at healthcare as a whole.
Government research has shown that in addition to all the of the qualitative benefits that an early
diagnosis system such as ours would have, there would be a monetary return on investment of
approximately $5.60 per dollar invested. [3]
MATSE
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
Project Timeline
Project Year
Project Quarter Q1
Year 1
Q2
Q3
Year 2
Q4
Q5
Q6
Q7
Year 3
Q8
Q9
Q10
Q11
Year 4
Q12
Q13
Q14
Q15
Q16
Task 1: Biomarker Screening
a. Determine list of possible target biomarkers
b. Select a benchmark biomarker
Task 2: Nanowire Distribution
a. Design aptamer receptors tailored to target benchmark biomarker
b. Manufacture SiNW systems with varied nanowire distributions
c. Test detection sensitivity of systems
d. Determine the optimal surface area to nanowire distribution ratio
e. Evaluate success rate of benchmark biomarker and re-evaluate if necessary
Task 3: Miniaturize
a. Determine safe implant size range and target dimensions
b. Manufacture SiNW systems over the range of sizes and nanowire distributions
Task 4: In Vitro Testing
a. Test detection sensitivity of the different miniaturized systems
b. Re-evaluate the feasibility of maintaining functionality of miniaturized systems
c. Test mechanical and microfluidic behavior of systems
d. Determine the systems that meet the target criteria
In case, miniaturization step fails for selected benchmark biomarker
Project Costs
Unit (Person for personnel)
Year 1 (US $)
Year 2 (US $)
Year 3 (US $)
Year 4 (US $)
Total (US $)
Salaries
Principal Investigator (1)
10000
10250
10506
10769
32525
Co-Investigator (4)
16000
16400
16812
17232
66444
Graduate Assistants (2)
31536
32324
33133
33961
130954
Graduate Researcher (1)
6601
6766
6935
7108
27410
Other
Laboratory Supplies
10000
15000
5000
5000
35000
Purchase Services
10000
10000
7500
10000
37500
Travel
1000
1000
1000
1000
4000
Tuition Remission
83300
85383
87465
89548
345695
Total Fringe
14006
14356
14715
15083
58160
F&A Rate: 50.7%
50265
53791
48469
50777
203302
Total Cost
316008
330653
318998
330023
$1,295,682
Deliverables
At the conclusion of Tasks 2, 3, and 4 we will present our findings and our plan to proceed. At
the conclusion of our research we will provide a prototype miniaturized silicon nanowire system
that will be ready for integration into applications for in vivo testing.
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
APPENDIX I: References
[1] Campbell D., “Almost Half of All Cancer Patients Diagnosed Too Late”, The Guardian;
theguardian.com, September 21, 2014
[2] Iozzio C., “Testing For Cancer With a Single Blood Sample”, Smithsonian Magazine;
smithsonianmagcom, October 20, 2014
[3] Hing E., “Wait Times for Treatments in Hospital Emergency Departments”, NCHS Data
Brief No. 102, (2012)
[4] Polanski M., Anderson Leigh N., “A List of Candidate Cancer Biomarkers for Targeted
Proteomics”, Biomarker Insights, Volume 1, Pages 1-48 (2007)
[5] Dorvel B., Reddy B., Bashir R.,“ Effect of Biointerfacing Linker Chemistries on the
Sensitivity of Silicon Nanowires for Protein Detection”, Analytical Chemistry, Volume 85, Issue
20, Pages 1-16 (2013)
[6] Kim K.S, Lee H.S., Yang J.A., Jo M.H. and Hahn S.K., “The Fabrication, Characterization
and application of aptamer-functionalized Si-nanowire FET biosensors”, Nanotechnology,
Volume 20, Issue 23, Pages 1-6 (2009)
[7] Park W., Zheng G., Jiang X. Tian B. and Lieber C.M., “Controlled Synthesis of Millimeter
Long Silicon Nanowires with Uniform Electronic Properties”, Nano Letters, Volume 8, Issue 9,
Pages 3004-3009 (2009)
[8] Leydent M.T., Schuman C., Sharf T., Kevek J., Remcho V.T. and Minot E.D., “Fabrication
and Characterization of Carbon Nanotube Field-Effect Transistor Biosensors”, Organic
Semiconductors in Sensors and Bioelectronics III, Conference Volume 7779 (2010)
[9] Hsu S., Tsai C., Hsu W., Lu F., He J., Cheng K., Hsieh S., Wang H., Sun Y. and Tu L.,
“Fabrication of Silicon Nanowires Field Effect Transistors for Biosensor Applications”,
Bioengineering Conference (NEBEC) 2012 38th Annual Northeast, Pages 5-6 (2012)
[10] Knopf G.K. and Bassi A.S, “Smart Biosensor Technology”, Page 642, Edited by Knopf
G.K. and Bassi A.S, CRC Press, Taylor & Francis Group, Boca Raton, FL 33487-2742 (2008)
[11] Nair P.R. and Alam M.A, “Design Considerations of Silicon Nanowire Biosensors”,
Electron Devices, IEEE Transactions, Volume 54, Issue 12, Pages 3400-3408 (2007)
MATSE
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
APPENDIX II: Timeline
Project Year
Project Quarter Q1
Year 1
Q2
Q3
Year 2
Q4
Q5
Q6
Q7
Year 3
Q8
Q9
Q10
Q11
Year 4
Q12
Task 1: Biomarker Screening
a. Determine list of possible target biomarkers
b. Select a benchmark biomarker
Task 2: Nanowire Distribution
a. Design aptamer receptors tailored to target benchmark biomarker
b. Manufacture SiNW systems with varied nanowire distributions
c. Test detection sensitivity of systems
d. Determine the optimal surface area to nanowire distribution ratio
e. Evaluate success rate of benchmark biomarker and re-evaluate if necessary
Task 3: Miniaturize
a. Determine safe implant size range and target dimensions
b. Manufacture SiNW systems over the range of sizes and nanowire distributions
Task 4: In Vitro Testing
a. Test detection sensitivity of the different miniaturized systems
b. Re-evaluate the feasibility of maintaining functionality of miniaturized systems
c. Test mechanical and microfluidic behavior of systems
d. Determine the systems that meet the target criteria
In case, miniaturization step fails for selected benchmark biomarker
Q13
Q14
Q15
Q16
Miniaturized Silicon Nanowire System for
In Vivo Diagnosis of Disease
MATSE
492W
R. MYERS, J. VILLALBA, L. RIVERA, Y. HE, Z. LI
APPENDIX III: Budget
Materials Science & Engineering (Earth & Mineral Sciences) / The Pennsylvania State University
Miniaturized Silicon Nanowire System for In Vivo Diagnosis of Disease
National Science Foundation
Project Dates: 08/1/2015 - 7/31/2019
Year 1
Year 2
Year 3
Year 4
Total
07/01/2015 - 06/30/2016 07/01/2016 - 06/30/2017 07/01/2017 - 06/30/2018 07/01/2018 - 06/30/2019
Salaries (Category I)
Principal Investigator - Rob Myers
Percent effort: 10%
10000
10250
10506
10769
Co-Investigator - Luis Rivera
Percent effort: 5%
4000
4100
4203
4308
Co-Investigator - Yalong He
Percent effort: 5%
4000
4100
4203
4308
Co-Investigator - Javier Villalba
Percent effort: 5%
4000
4100
4203
4308
Co-Investigator - Alex Lee
Percent effort: 5%
4000
4100
4203
4308
Total Salaries (Category I)
26000
26650
27316
27999
107965
Graduate Assistants (Category II)
(1) Graduate Assistant - To Be Named
Grade 14. Half-time. Fall & Spring.
15768
16162
16566
16980
65477
(1) Graduate Assistant - To Be Named
Grade 14. Half-time. Fall & Spring.
15768
16162
16566
16980
65477
Total Graduate Assistants (Category II)
31536
32324
33133
33961
130954
Wages (Category III)
(1) Graduate Researcher - To Be Named
Grade 14. Half-time. Summer wages.
6601
6766
6935
7108
27410
Total Wages (Category III)
6601
6766
6935
7108
27410
64137
65740
67384
69068
266329
9360
4131
515
9594
4234
528
9834
4340
541
10080
4449
554
38868
17155
2138
Total Fringe
14006
14356
14715
15083
58160
Total Salaries, Wages and Fringe
78143
80097
82099
84151
324490
Modified Total Direct Costs
Laboratory Supplies
Purchased Services
Travel - Domestic (CONUS)
10000
10000
1000
15000
10000
1000
5000
7500
1000
5000
10000
1000
35000
37500
4000
Total Modified Total Direct Costs
99143
106097
95599
100151
400990
Other Direct Costs
Tuition Remission
83300
85383
87465
89548
345695
83300
182443
85383
191479
87465
183064
89548
189699
345695
746685
50265
53791
48469
50777
203302
Total Requested From Sponsor
316008
330653
318998
330023 $1,295,682
Total Project Costs
316008
330653
318998
330023 $1,295,682
Total Salaries and Wages
Fringe
Category I @ 36.%
Category II @ 13.10%
Category III @ 7.80%
Total Other Direct Costs
Total Direct Costs
F&A Costs
F&A Rate: 50.7%