System Design to Resolve Four System Design to Resolve Four Micron Beads above a Solid State Micron Beads above a Solid State
Nanopore using Gradient Index Nanopore using Gradient Index OpticsOptics
Presented by: Edward GraefPresented by: Edward Graef
Southeast Missouri State UniversitySoutheast Missouri State University
MicroEP REU 2007MicroEP REU 2007
OutlineOutline
IntroductionIntroduction The NanoporeThe Nanopore The BeadThe Bead Fiberscopes and BorescopesFiberscopes and Borescopes Optics ChoicesOptics Choices
The Proposed SetupThe Proposed SetupAnalytical Ray TracingAnalytical Ray Tracing
Gradient LensGradient LensTheoretical Angular MagnificationTheoretical Angular MagnificationResultsResults
Experimental resultsExperimental resultsConclusionsConclusionsFuture ResearchFuture ResearchReferencesReferencesAcknowledgementsAcknowledgements
The NanoporeThe NanoporeTwo chambers filled with an Two chambers filled with an electrolytic solution are separated by a electrolytic solution are separated by a solid-state nanoporesolid-state nanoporeA voltage is applied over the nanopore A voltage is applied over the nanopore and an open pore current is and an open pore current is establishedestablishedNegatively charged DNA is pulled Negatively charged DNA is pulled through the nanopore by an electric through the nanopore by an electric forceforceWhile the molecule is inside the pore While the molecule is inside the pore the ion flow is reduced due to reduced the ion flow is reduced due to reduced cross-sectional area available for cross-sectional area available for conduction, resulting in a blockage conduction, resulting in a blockage currentcurrent
Iopen
Iblockage
I have a Bead on youI have a Bead on youThe bead consists of a 1 to 4 micron diameter chromium The bead consists of a 1 to 4 micron diameter chromium oxide sphere.oxide sphere.It is then coated in a layer of a protein called streptavidin.It is then coated in a layer of a protein called streptavidin.This streptavidin is then used to latch on to a vitamin This streptavidin is then used to latch on to a vitamin called biotin, or Bcalled biotin, or B77..The biotin then attaches to a single site edge on a piece The biotin then attaches to a single site edge on a piece of dsDNA.of dsDNA.Now the bead acts as a handle that can be used to pull Now the bead acts as a handle that can be used to pull the DNA through the nanopore at a slower rate.the DNA through the nanopore at a slower rate.
Streptavidin
BiotinChromium
Oxide
dsDNA
OPTIPSOPTIPS
XYZ micrometer
1-axis Nanopositioner
Needle/Pipette
•No line of sight•Fiber optic cable guides light•Makes z-axis motion visible
CCD Camera
The scope of my research The scope of my research
1mm
100 μm
100 μm
1mm
Fiber Optics
PDMS
Chip with pore
30 μm
Fiber-, Bore-, and Endo- scopes. Oh my!Fiber-, Bore-, and Endo- scopes. Oh my!Fiberscope—A fiberscope is a flexible fiber optic bundle with an Fiberscope—A fiberscope is a flexible fiber optic bundle with an eyepiece at one end, and a lens at the other. All fiberscopes eyepiece at one end, and a lens at the other. All fiberscopes introduce a certain amount of image distortion.introduce a certain amount of image distortion.Borescope—A borescope is an optical device consisting of a rigid or Borescope—A borescope is an optical device consisting of a rigid or flexible tube with an eyepiece on one end, an objective lens on the flexible tube with an eyepiece on one end, an objective lens on the other linked together by a relay optical system in between. other linked together by a relay optical system in between. Boroscopes have much less image distortion than a fiberscope.Boroscopes have much less image distortion than a fiberscope.
Fiberscope Image of clock Borescope image of Colon
So many choices…So many choices…
Conventional optics Conventional optics are much larger are much larger than the area that than the area that is available.is available.
GRIN lenses can be GRIN lenses can be made much smaller made much smaller than conventional than conventional optics, on the order optics, on the order of ~250 of ~250 μμm.m.
Conventional Optics
Gradient Index Optics
Which one is better? Conventional or Gradient Index Optics?
Bigger isn’t betterBigger isn’t better
These lens are small.These lens are small.The ones chosen for our The ones chosen for our application are smaller application are smaller than pencil lead.than pencil lead.Handling is Handling is extremelyextremely difficult.difficult.These lenses allow the These lenses allow the light to travel through a light to travel through a gradient index.gradient index.Simulations allow us to Simulations allow us to consider the separation consider the separation between the fiber, the between the fiber, the lens, and the sample.lens, and the sample.
Through the GRIN glassThrough the GRIN glass
These lenses are complicated to accurately These lenses are complicated to accurately simulate.simulate.The Gradient Index EquationThe Gradient Index Equation
Where nWhere n00, r, r00, , δδ and and α α22 are constants that define the individual are constants that define the individual lenses and are provided by the manufacturer.lenses and are provided by the manufacturer.
To receive the 1To receive the 1stst order approximation, assume order approximation, assume αα2 2 is zero.is zero.
Use this equation along with a modified EUse this equation along with a modified Eüler’s üler’s program to plot the ray trace of our GRIN lenses.program to plot the ray trace of our GRIN lenses.
1/22 4
22
0 00N= 1 r r
r rn
Vpython attackVpython attackGRIN Lens Approximation using vpythonGRIN Lens Approximation using vpython
GRIN Lens Fiber Optic
First Base LineFirst Base Line
The base line image The base line image is of a 30 micron by is of a 30 micron by 30 micron window in 30 micron window in a SiN sample. a SiN sample.
This was taken so as This was taken so as to compare any other to compare any other images to a baseline images to a baseline to try and determine to try and determine magnification.magnification.
Through the GRIN glassThrough the GRIN glass
ImageJ was used as ImageJ was used as for all image analysis.for all image analysis.
The picture shows the The picture shows the results of viewing the results of viewing the window through a window through a GRIN lens with a 1 GRIN lens with a 1 micron space micron space between the fiber between the fiber optic and the lens.optic and the lens.
ConclusionsConclusions
Magnification by measuring image sizes, Magnification by measuring image sizes, MMGRINGRIN/M/MBASEBASE, was calculated to be 88% of actual , was calculated to be 88% of actual
image size.image size.
Even though image resolution is lost somewhat Even though image resolution is lost somewhat due to the optical fiber, the box is still resolvable. due to the optical fiber, the box is still resolvable.
Therefore, it should be possible to view a needle Therefore, it should be possible to view a needle tip as it approaches the surface of a nanopore tip as it approaches the surface of a nanopore when viewing the needle from the side using a when viewing the needle from the side using a lab built fiberscope or a preassembled lab built fiberscope or a preassembled boroscope.boroscope.
ReferencesReferences1.1. Decker, Cees. “Solid-state nanopores.” Nature nanotechnology. Vol.2 No.4, Decker, Cees. “Solid-state nanopores.” Nature nanotechnology. Vol.2 No.4,
2007.2007.2.2. Hecht, Eugene, Hecht, Eugene, Optics:4Optics:4thth Edition Edition, Addison Wesely, San Francisco, 2002., Addison Wesely, San Francisco, 2002.3.3. Marchand,Erich W., Marchand,Erich W., Gradient Index OpticsGradient Index Optics, Academic Press, New York, 1978., Academic Press, New York, 1978.4.4. Schaub, Richard D., et. al. “Assessing acute platelet adhesion on opaque Schaub, Richard D., et. al. “Assessing acute platelet adhesion on opaque
metallic and polymeric biomaterials with fiber optic microscopy.” Journal of metallic and polymeric biomaterials with fiber optic microscopy.” Journal of Biomedical Materials Research Vol. 49 Is. 4, 1999.Biomedical Materials Research Vol. 49 Is. 4, 1999.
5.5. Siegman, Anthony E., Siegman, Anthony E., LasersLasers, University Science Books, Sausalito, 1986., University Science Books, Sausalito, 1986.
This work was supported by National Science Foundation award EEC-0097714. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and
do not necessarily reflect the views of the National Science Foundation.
AcknowledgementsAcknowledgements
Mentor Dr. Jiali LiMentor Dr. Jiali Li
Grad. Student Ryan RollingGrad. Student Ryan Rolling
Grad. Student Brad LeddenGrad. Student Brad Ledden
Prof. Ken VickersProf. Ken Vickers
The NanoporeThe Nanopore
The nanopores used for this experiment were constructed by taking The nanopores used for this experiment were constructed by taking a 4in. Si wafer and depositing a 275nm layer of SiN on both sides of a 4in. Si wafer and depositing a 275nm layer of SiN on both sides of the wafer through low pressure chemical vapor deposition (LPCVD). the wafer through low pressure chemical vapor deposition (LPCVD). A positive photoresist is then applied to both sides of the wafer, one A positive photoresist is then applied to both sides of the wafer, one side of which is then patterned by photolithography to expose side of which is then patterned by photolithography to expose windows of SiN. windows of SiN. The wafer is then subjected to a reactive ion etch (RIE) to remove The wafer is then subjected to a reactive ion etch (RIE) to remove the exposed SiN. After the RIE procedure, the wafer is then placed the exposed SiN. After the RIE procedure, the wafer is then placed in a KOH bath to etch through the Si wafer and create a freestanding in a KOH bath to etch through the Si wafer and create a freestanding SiN membrane on the back side. SiN membrane on the back side. A focused ion beam (FIB) milling process is then used to make a A focused ion beam (FIB) milling process is then used to make a hole in the free-standing membrane between 80 and 100 nm in hole in the free-standing membrane between 80 and 100 nm in diameter. Once the FIB hole is made, a Transmission Electron diameter. Once the FIB hole is made, a Transmission Electron Microscope (TEM) is used to image the hole. This allows the size of Microscope (TEM) is used to image the hole. This allows the size of the hole to be determined accurately. the hole to be determined accurately. The ion beam sculpting chamber is then used to close the FIB hole The ion beam sculpting chamber is then used to close the FIB hole to the appropriate dimension for use in single molecule detection. to the appropriate dimension for use in single molecule detection. Typically, Ar+ is used, although He+, Ne+, Kr+ and Xe+ have been Typically, Ar+ is used, although He+, Ne+, Kr+ and Xe+ have been used as well for nanopore fabrication.used as well for nanopore fabrication.
Nanopore PictureNanopore Picture
50nm SiNKOH etch [111]
SiN WindowPore Location
Magnifying the ResultsMagnifying the Results
Magnification with respect to working distance.Magnification with respect to working distance. Negative magnification means real image.Negative magnification means real image.
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0
An
gu
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Ma
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543210Working distance (mm)
Magnification = -.076×Working dist.
