U.S. patent application number 14/607629 was filed with the patent office on 2015-05-28 for manufacturable sub-3 nanometer palladium gap devices for fixed electrode tunneling recognition.
The applicant listed for this patent is International Business Machines Corporation. Invention is credited to Yann Astier, Jingwei Bai, Michael A. Guillorn, Satyavolu S. Papa Rao, Joshua T. Smith.
Application Number | 20150144888 14/607629 |
Document ID | / |
Family ID | 52105085 |
Filed Date | 2015-05-28 |
United States Patent
Application |
20150144888 |
Kind Code |
A1 |
Astier; Yann ; et
al. |
May 28, 2015 |
MANUFACTURABLE SUB-3 NANOMETER PALLADIUM GAP DEVICES FOR FIXED
ELECTRODE TUNNELING RECOGNITION
Abstract
A technique is provided for manufacturing a nanogap in a
nanodevice. An oxide is disposed on a wafer. A nanowire is disposed
on the oxide. A helium ion beam is applied to cut the nanowire into
a first nanowire part and a second nanowire part which forms the
nanogap in the nanodevice. Applying the helium ion beam to cut the
nanogap forms a signature of nanowire material in proximity to at
least one opening of the nanogap.
Inventors: |
Astier; Yann; (White Plains,
NY) ; Bai; Jingwei; (Los Angeles, CA) ;
Guillorn; Michael A.; (Yorktown Heights, NY) ; Papa
Rao; Satyavolu S.; (Poughkeepsie, NY) ; Smith; Joshua
T.; (Croton on Hudson, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
International Business Machines Corporation |
Armonk |
NY |
US |
|
|
Family ID: |
52105085 |
Appl. No.: |
14/607629 |
Filed: |
January 28, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
13921383 |
Jun 19, 2013 |
|
|
|
14607629 |
|
|
|
|
Current U.S.
Class: |
257/30 |
Current CPC
Class: |
H01L 29/413 20130101;
H01L 21/263 20130101; G01N 27/4145 20130101; G01N 33/48721
20130101 |
Class at
Publication: |
257/30 |
International
Class: |
G01N 33/487 20060101
G01N033/487 |
Claims
1. A structure utilized in sequencing, the structure comprising: an
oxide on a wafer; a nanowire on the oxide; a tapered lateral area
of the nanowire from applying a helium ion beam, the tapered
lateral area forming a first nanowire part and a second nanowire
part, wherein the first nanowire part and the second nanowire part
form a first nanogap; the tapered lateral area forms a bridge
connecting the first nanowire part and the second nanowire part;
and a second nanogap in the bridge forming a first extension from
the first nanowire part and a second extension from the second
nanowire part.
2. The structure of claim 1, wherein the second nanogap is thinner
than the first nanogap.
3. The structure of claim 1, wherein the nanowire is tapered in
order for the first extension and the second extension to have
rounded shapes after the second nanogap is cut.
Description
DOMESTIC PRIORITY
[0001] This is a divisional application of U.S. non-provisional
application Ser. No. 13/921,383 filed Jun. 19, 2013, the entire
contents of which are incorporated by reference herein.
BACKGROUND
[0002] The present invention relates generally to nanodevices, and
more specifically, to manufacturing a sub-3 nanometer palladium
nanogap.
[0003] Nanopore sequencing is a method for determining the order in
which nucleotides occur on a strand of deoxyribonucleic acid (DNA).
A nanopore (also referred to as pore, nanochannel, hole, etc.) can
be a small hole in the order of several nanometers in internal
diameter. The theory behind nanopore sequencing is about what
occurs when the nanopore is submerged in a conducting fluid and an
electric potential (voltage) is applied across the nanopore. Under
these conditions, a slight electric current due to conduction of
ions through the nanopore can be measured, and the amount of
current is very sensitive to the size and shape of the nanopore. If
single bases or strands of DNA pass (or part of the DNA molecule
passes) through the nanopore, this can create a change in the
magnitude of the current through the nanopore. Other electrical or
optical sensors can also be positioned around the nanopore so that
DNA bases can be differentiated while the DNA passes through the
nanopore.
[0004] The DNA can be driven through the nanopore by using various
methods, so that the DNA might eventually pass through the
nanopore. The scale of the nanopore can have the effect that the
DNA may be forced through the hole as a long string, one base at a
time, like thread through the eye of a needle. Recently, there has
been growing interest in applying nanopores as sensors for rapid
analysis of biomolecules such as deoxyribonucleic acid (DNA),
ribonucleic acid (RNA), protein, etc. Special emphasis has been
given to applications of nanopores for DNA sequencing, as this
technology holds the promise to reduce the cost of sequencing below
$1000/human genome.
SUMMARY
[0005] According to one embodiment, a method for manufacturing a
nanogap in a nanodevice is provided. The method includes disposing
an oxide on a wafer, disposing a nanowire on the oxide, and
applying a helium ion beam to cut the nanowire into a first
nanowire part and a second nanowire part to form the nanogap in the
nanodevice. Applying the helium ion beam to cut the nanogap forms a
signature of nanowire material in proximity to at least one opening
of the nanogap.
[0006] According to one embodiment, a method for manufacturing a
nanogap in a nanodevice is provided. The method includes disposing
an oxide on a wafer, disposing a nanowire on the oxide, and
applying a helium ion beam to taper the nanowire laterally into a
first nanowire part and a second nanowire part. The first nanowire
part and the second nanowire part form a first nanogap in the
nanodevice. Applying the helium ion beam to taper the nanowire
laterally forms a bridge connecting the first nanowire part and the
second nanowire part. A second nanogap is cut in the bridge to form
a first extension from the first nanowire part and form a second
extension from the second nanowire part.
[0007] According to one embodiment, a structure utilized in
sequencing. The structure includes an oxide on a wafer, a nanowire
on the oxide, and a tapered lateral area of the nanowire from
applying a helium ion beam. The tapered lateral area forms a first
nanowire part and a second nanowire part, and the first nanowire
part and the second nanowire part form a first nanogap. The tapered
lateral area forms a bridge connecting the first nanowire part and
the second nanowire part. A second nanogap in the bridge forms a
first extension from the first nanowire part and forms a second
extension from the second nanowire part.
[0008] Additional features and advantages are realized through the
techniques of the present invention. Other embodiments and aspects
of the invention are described in detail herein and are considered
a part of the claimed invention. For a better understanding of the
invention with the advantages and the features, refer to the
description and to the drawings.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
[0009] The subject matter which is regarded as the invention is
particularly pointed out and distinctly claimed in the claims at
the conclusion of the specification. The forgoing and other
features, and advantages of the invention are apparent from the
following detailed description taken in conjunction with the
accompanying drawings in which:
[0010] FIG. 1A illustrates a cross-sectional view of a method of
forming a nanodevice according to an embodiment.
[0011] FIG. 1B illustrates a top view of the nanodevice according
to an embodiment.
[0012] FIG. 1C illustrates a cross-sectional view of a nanogap cut
in a nanowire according to an embodiment.
[0013] FIG. 1D illustrates a top view of the nanogap in the
nanodevice according to an embodiment.
[0014] FIG. 2A is a picture via a transmission electron microscope
(TEM) of a nanowire according to an embodiment.
[0015] FIG. 2B is a TEM picture of a first nanogap cut by a helium
ion beam under certain conditions according to an embodiment.
[0016] FIG. 2C is a TEM picture of a second nanogap cut by a helium
ion beam under certain conditions according to an embodiment.
[0017] FIG. 2D is a TEM picture of a third nanogap cut by a helium
ion beam under certain conditions according to an embodiment.
[0018] FIG. 2E is a TEM picture of a unique signature surrounding
the nanogap according to embodiment.
[0019] FIG. 2F is a TEM picture of the nanogap with residual
palladium according to an embodiment.
[0020] FIG. 2G is a TEM picture of the nanogap with the residual
palladium removed according to an embodiment.
[0021] FIG. 3A schematically illustrates an array of nanodevices
each having a nanogap formed by the helium ion beam according to
embodiments.
[0022] FIG. 3B schematically illustrates testing each individual
nanodevice in the array to determine whether residual palladium is
in the nanogap according to embodiments.
[0023] FIG. 4A illustrates a top view of the nanodevice in which
the nanowire is intentionally tapered by the helium ion beam
according to an embodiment.
[0024] FIG. 4B illustrates a top view of the nanodevice with left
and right extensions respectively extending from left and right
electrodes to form a second nanogap according to an embodiment.
[0025] FIG. 4C illustrates an enlarged, partial top view of the
nanodevice showing a bridge according to an embodiment.
[0026] FIG. 4D illustrates the enlarged, partial top view of the
nanodevice in which the bridge is cut forming the two extensions
according to an embodiment.
[0027] FIG. 4E illustrates another enlarged, partial top view of
the nanodevice with the two extensions according to an
embodiment.
[0028] FIG. 5A illustrates a sequencing system utilizing the
nanodevice according to an embodiment.
[0029] FIG. 5B illustrates an enlarged, partial view of the system
showings the two extensions according to an embodiment.
[0030] FIG. 6 is a flow diagram illustrating a method for
manufacturing a nanogap of the nanodevice in the nanowire according
to an embodiment.
[0031] FIG. 7 is a flow diagram illustrating a method for
manufacturing nanogaps in the nanowire of the nanodevice according
to an embodiment.
[0032] FIG. 8 is a block diagram that illustrates an example of a
computer (computer test setup) having capabilities, which may be
included in and/or combined with embodiments.
DETAILED DESCRIPTION
[0033] The fabrication of a sub-3 nm gap between two palladium
electrodes has been pursued to create a device capable of
recognizing individual DNA bases by tunneling current measurements.
This base recognition device is the key component of generation 4
single molecule sequencing technology. Towards this end, several
approaches have been proposed or pursued to achieve a sub-3 nm gap
between electrodes, such as a focused transmission electron
microscope (TEM) beam cutting, or scanning tunneling microscope
electrodes. The primary problem with all of these solutions is that
none of them provides a clear cut path to scaling up
(manufacturing) production of the tunneling devices.
Reproducibility or consistency of the nanogaps at these dimensions
has also been a challenge. Importantly, manufacturing approaches
commonly used to achieve high-fidelity nanoscale features like
electron beam (e-beam) lithography can be inadequate to realize the
needed gap sizes.
[0034] Embodiments are configured to use a focused helium beam to
mill through palladium (Pd) nanowires to fabricate sub-3 nm gap
devices for DNA base recognition. Dividing a continuous palladium
nanowire in this way to create two separate palladium electrodes
provides a high throughput and reproducible path for sub-3 nm gap
creation with a unique and identifiable process signature. The
focused helium beam method also permits tapering of the nanowire to
enhance tunneling recognition capabilities. For example, the
electrodes can be sharpened to a finer tip closer to the gap to
reduce the probability of tunneling signatures originating from
multiple bases simultaneously. In addition, the helium beam cutting
method can be applied to any substrate in contrast to the TEM
approach, which is confined to globally or locally thin
substrates.
[0035] FIG. 1A illustrates a cross-sectional view of a method of
forming a nanogap in a nanodevice 100 according to an embodiment.
The nanodevice 100 has an electrically insulating substrate 102
which may be a silicon wafer. An oxide layer 104 may be deposited
(e.g., grown) on the substrate 102. The oxide layer 104 is a
dielectric material, and may be any dielectric material including
silicon dioxide.
[0036] A nanowire 106 is deposited on the oxide layer 104. FIG. 1B
illustrates a top view of the nanodevice 100. The material of the
nanowire may be palladium. The palladium nanowires 106 can be
fabricated on the dielectric oxide layer 104 using, for example,
e-beam lithography and lift-off. The nanowires 106 can also be
defined by optical lithography and reactive ion etching. The width
W of the nanowires 106 may range from a few nanometers to
micrometers (e.g., 3 nm to 8 .mu.m) and the thickness T may vary
from 2 nm to 50 nm.
[0037] With the palladium nanowire 106 in place, a helium ion
microscope 120 with a focused He ion beam is used to controllably
create sub-3 nm gaps by varying the exposure conditions. FIG. 1C
illustrates a cross-sectional view of a sub-3 nm nanogap 110 cut in
the nanowire 106, while FIG. 1D illustrates a top view of the
nanogap 110. The cutting by the helium microscope 120 results in
palladium electrode 106A (e.g., left nanowire electrode) and
palladium electrode 106B (e.g., right nanowire electrode) which
together form the nanowire 106. The width of the nanogap 110 is
shown by D1. The width D1 of the nanogap 110 is formed to be less
than 3 nanometers (e.g., 1 or 2 nm) via He ions irradiated from the
helium ion microscope 120. Similar to an electron microscope, one
skilled in the art understands the operation of the helium ion
microscope 120 at discussed herein.
[0038] An example of commercially available helium ion microscopes
are the ORION.TM. Helium ion Microscope from Carl Zeiss SMT and the
Multiple Ion Beam Microscopes from Carl Zeiss SMT.
[0039] The following example shows the gap cutting conditions of
the helium ion microscope 120 for palladium nanowires 106 with
specific dimensions in which the width is approximately (.about.)
20 nm and the thickness is approximately 10 nm (where the thickness
is 1 nm Ti and 9 nm Pd). In the example exposure conditions (to
control the helium ion microscope 120), the beam current is 0.4 pA
(picoamperes), the beam spot size is 3.4 to 5 .ANG. (angstroms),
the step size is 5 .ANG., the working distance may be 7.354 mm
(millimeters), and the aperture (opening) is 5 .mu.m.
[0040] By varying parameters (in the helium ion microscope 120)
such as the exposure time per pixel, a nanogap can be reproducibly
fabricated with a distance (D1) less than 3 nm. At 30 kV
(kilovolts), 2 .mu.s/pixel (exposure time) on a 15 nm wide and 10
nm thick palladium nanowire (line) in FIG. 2A yields a 4 nm gap
(e.g., nanogap.sub.--1) in FIG. 2B. By reducing the exposure time
per pixel, the width of the gap can be made smaller. In this case,
a 1 .mu.s/pixel exposure time generates a 3 nm gap
(nanogap.sub.--2) shown in FIG. 2C, and 0.5 .mu.s/pixel exposure
time generates a gap (nanogap.sub.--3) (e.g., between 1 and 3 nm)
that is below the resolution of the helium microscope shown in FIG.
2D.
[0041] Note that in FIGS. 2A, 2B, 2C, and 2D (along with FIGS. 2E
through 2G) the evaporated palladium lines (i.e., nanowires 106)
are cut by a focused helium beam, and the resulting gaps are
respectively shown by the arrows pointing to nanogap.sub.--1,
nanogap.sub.--2, and nanogap.sub.--3. FIG. 2E reveals electrode
nanogaps of less than 3 nm (e.g., 2.77 nm). Also, as seen in FIG.
2E, use of the helium ion beam provides a unique signature
according to an embodiment. Note the (unique) signature splash of
palladium particles/dots 205 surrounding the nanogap is a result of
He ion beam exposure according to embodiments. The palladium dots
205 may have sizes ranging from 2 to 8 nm in diameter. The
palladium dots 205 surrounding the nanogap 110 are not observed
with TEM cutting on thin membranes (i.e., thin electrodes).
[0042] FIG. 2F shows one palladium gap with residual palladium 210
still connecting (i.e., bridging) the electrodes 106A and 106B
after cutting with the helium ion beam. In this case, the focusing
of the electron beam in the TEM (or He ion beam) is used to remove
the residual palladium 210 yielding the nanogap 110 shown in FIG.
2G. The nanogap 110 is 2.97 nm. The structures in FIGS. 2A through
2G were imaged with high resolution transmission electron
microscopy (TEM).
[0043] FIG. 3A illustrates an array of nanodevices 100 each having
a nanogap 110 formed by the helium ion beam of the helium ion
microscope 120 according to embodiments. FIG. 3B illustrates how
each individual nanodevice 100 may be tested to determine if there
is residual palladium dot/particle 205 in the gap 110 between
electrodes 106A and 106B. Voltage of voltage source 310 is applied
to the electrodes 106A and 106B to generate a current measured by
an ammeter 315, and the amount of current determines if there is a
residual palladium particle 205 in the gap 110. Assume that there
is a residual particle 205A bridging (i.e., physically and/or
electrically connecting) the electrode 106A to electrode 106B, and
in such a case, the measured current by ammeter 315 may be
nanoamperes to microamperes because of the residual particle 205A.
If no residual particle 205A is present (in gap 110) between
electrode 106A and electrode 106B, the measured current may be in
the range of 200pA at 400 mV bias.
[0044] When it is determined during manufacturing that residual
particles 205A are connecting the two electrodes 106A and 106B,
there are two options. The occasional nanodevices 100 having the
residual particles 205A in the gap 110 may be discarded, while the
remaining nanodevices 100 in the array on the wafer 102 are
utilized for sequencing as discussed herein. Alternatively and/or
additionally, the nanodevices 100 having the residual particle 205A
may be further treated with an electron beam of a transmission
electron microscope (and/or He ion beam) in the gap 110 to clear
the residual particle 205A. Removing the residual particle 205A
with the electron beam results in the clear nanogap 110 shown in
FIGS. 1C and 1D. Out of the array of nanodevices 100 on the wafer
102, there may be only a few nanodevices 100 that have the residual
particle 205A remaining in the gap 110, and the residual particle
205A is cut (removed) by the electron beam of the transmission
electron microscope even though the gap 110 has already been
(originally) cut using the helium ion beam of the helium ion
microscope 120.
[0045] Cutting a sub-3 nm gap with an electron beam (from start to
finish) requires an enormous amount of time and skill as compared
with a helium ion beam. Therefore, even if a few (e.g., 15%) out of
an array of nanodevices 100 on wafer 102 have a residual particle
205A in the gap 110 (originally cut by the helium ion beam), the
time to then remove the residual particle 205A using the electron
beam (for the few nanodevices 100) is much less than the time
required to cut gaps for an array of nanodevices using the electron
beam. TEM requires sample mounting (i.e., nanodevice 100 mounting)
and high vacuum which takes up to 30 minutes (min) for any given
sample inserted in the TEM. Then, each gap takes about 20 min to
cut exclusively by TEM. The TEM touch up of previously He beam cut
gaps only requires a few milliseconds of beam exposure to remove
residual Pd (e.g., from the nanogap 110).
[0046] FIG. 4A illustrates a top view of the nanodevice 100 in
which the nanowire 106 has been intentionally tapered by the He ion
beam in the vicinity of the nanogap 112 according to an embodiment.
The helium ion microscope 120 is controlled to cut the nanowire
laterally on side A and side B without cutting completely through
the nanowire 106. This intentionally leaves a palladium bridge 405
connecting the left electrode 106A to the right electrode 106B. The
nanogap 112 is cut with a width D2 that is larger than the width
D1.
[0047] The helium ion microscope 120 (and/or an electron
microscope) is controlled to cut a smaller nanogap 114 in the
palladium bridge 405 resulting in extension 405A and extension 405B
in FIG. 4B. FIG. 4B illustrates a top view of the nanodevice 100
with left extension 405A extending from and as part of electrode
106A, and with right extension 405B extending from and as part of
electrode 106B. The newly formed nanogap 114 has a width that may
equal and/or be less than the width D1 of nanogap 110. The width D2
of the nanogap 112 may be 4 to 10 nm and the width of the smaller
nanogap D3 (formed between extensions 405A and 405B) may be, e.g.,
0.3, 0.4, 0.5, 0.7, . . . 1 through 2 nm (to fit/accommodate the
diameter (size) base/nucleotide to be sequenced). By having a
larger nanogap 112 (D2) during DNA sequencing, the larger nanogap
112 ensures that multiple DNA bases are not interacting with the
electrodes 106A and 106B because the distance (D2) between the
electrodes 106A and 106B (e.g., 7 nm or more) is too large for
tunneling current to travel. As understood by one skilled in the
art, the DNA is moved into nanogap 114 between the extensions 405A
and 405B (of the respective electrodes 106A and 106B). The
dimension X of the extensions 405A and 405B may be made to
accommodate a single base in the nanogap 114. For example, the
dimension X has a distance smaller than the separation/spacing
between bases of the molecule being tested. The distance X of the
extensions 405A and 405B may be 3, 4, 5, 6, 7 angstroms depending
on (base separation distance of) the target molecule being
sequenced. Therefore, if the distance X is 3.5 .ANG., the nanogap
114 between extensions 405A and 405B can (only) have a single base
at a time and the measured tunneling current can identify the
particular base presently in the nanogap 114 without simultaneously
measuring tunneling current from neighboring bases that may be in
the larger nanogap 112. The dimension X1 of the nanowire 106 may be
20.
[0048] In FIGS. 4A and 4B, view 410 is a dashed circle of an
enlarged portion shown in FIGS. 4C, 4D, and 4E. The views 410 in
FIGS. 4C, 4D, and 4E are partial views; the substrate 102 and oxide
104 are not shown so as not to obscure the figures.
[0049] FIG. 4C illustrates a partial top view of the nanodevice 100
in which the palladium bridge 405 is shown as rounded portions
(physically and electrically) connecting the left and right
electrodes 106A and 106B in the nanogap 112. FIG. 4D illustrates
the partial top view of the nanodevice 100 in which the palladium
bridge 405 has been further cut (via the helium ion beam and/or
electron beam of the helium ion microscope 120) into the two
separate extensions 405A and 405B (shown as rounded portions
extending from electrodes 106A and 106B). This results in the
smaller nanogap 114 only between extensions 405A and 405B.
[0050] FIG. 4E illustrates the partial top view of the nanodevice
100 in which the two extensions 405A and 405B are shown as
triangular shaped portions extending from electrodes 106A and 106B
according to an embodiment. The nanogap 114 is between the
triangular shaped portions.
[0051] FIG. 5A illustrates a system 500 for sequencing using the
nanodevice 100 according to an embodiment. As discussed above, the
nanodevice 100 includes the electrically insulating substrate 102
(wafer), oxide 104, electrodes 106A and 106B (with respective
extensions 405A and 405B not shown for the sake of clarity), and
nanogap 110 (or nanogaps 112 and 114).
[0052] The system includes electrically insulating films 503 and
506. A backside cavity 504 forms a suspended membrane making up the
nanogap 110 (nanogap 112 and 114). The electrodes 507 and 508 are
metal contact pads, which may be any metal.
[0053] In the system 500, a top reservoir 514 is attached and
sealed to the top of the insulating film 506, and a bottom
reservoir 515 is attached and sealed to the bottom of the
insulating film 503. Electrode 512 is in the top reservoir 514, and
electrode 513 is in the bottom reservoir 515. Electrodes 512 and
513 may be silver/silver chloride, or platinum for example. The
reservoirs 514 and 515 are the inlet and outlet respectively for
buffer solution 550, and reservoirs 514 and 515 hold the DNA and/or
RNA samples for sequencing. The buffer solution 550 is an
electrically conductive solution (such as an electrolyte) and may
be a salt solution such as NaCl.
[0054] The system 500 shows a target molecule 511, which is the
molecule being analyzed and/or sequenced. As an example DNA sample,
the system 500 may include a single stranded DNA molecule 511,
which is passing through the nanogap 110 (nanogaps 112 and 114).
The DNA molecule 511 has bases 530 (A, G, C, and T) represented as
blocks.
[0055] The DNA molecule 511 is pulled through the nanogap 110
(nanogaps 112 and 114) by a vertical electrical field generated by
the voltage source 517. When voltage is applied to electrodes 512
and 513 by the voltage source 517, the voltage generates the
electric field (between reservoirs 514 and 515) that controllably
(e.g., by turning on and off the voltage source 517) drives the DNA
molecule 511 into and through the nanogap 110 (nanogaps 112 and
114). Also, the voltage of the voltage source 517 can produce the
gate bias between electrodes 507 and 508. Note that the electrodes
507, 508, 106A, and 106B, nanogap 110 (114) may operate as a
transistor. The voltage across the nanogap 110 (nanogaps 112 and
114) from the voltage source 517 can be the gate for controlling
the transistor. Metal pads (electrodes) 507 and 508 are the drain
and source respectively for the transistor device. Voltage applied
by voltage source 519 to electrodes 507 and 508 also builds the
electrical field, which can hold the base 530 in the nanogap 110
for sequencing. Note that metal pads 507 and 508 are electrically
connected to electrodes 106A and 106B having the nanogap 110
(nanogaps 112 and 114).
[0056] Note that a nanopore 580 is formed in layers 506 and 104
which is larger than the nanogap 110 (112 and 114). The nanogap 110
(112 and 114) is in the nanopore 580. The nanopore 580 connects top
reservoir 514 to bottom reservoir 515 as understood by one skilled
in the art. Ammeter 518 monitors the ionic current change when DNA
(or RNA) molecule 511 goes through nanogap 110 (112 and 114) (which
is within the nanopore 580). The ionic current (measured by the
ammeter 518) flows through electrode 512, into the buffer solution
550, through the nanopore 580 (to interact with the base 530 when
the target molecule 511 is present in the nanopore 580), out
through the electrode 513. Voltage generated by the voltage source
519 produces the voltage between source 508 and drain 507. Another
ammeter 520 monitors the source-drain transistor current from
nanogap 110 (112 and 114) (of the transistor through the buffer
solution 550) to detect nucleotide (i.e., base) information when
the DNA/RNA molecule 511 passes through the nanogap 110 (112 and
114).
[0057] For example, when a base 530 is in the nanopore 580 (between
the nanogap 110 (or nanogaps 112 and 114) of the nanowire 106) and
when voltage is applied by the voltage source 519, source-drain
transistor current flows to source 508, into the right nanowire
electrode 106B, into the buffer solution 550 (between the nanogap)
to interact with the base 530 positioned therein, into left
nanowire electrode 106A, out through the drain 507, and to the
ammeter 520. The ammeter 520 is configured to measure the change in
source-drain current when each type of base 530 is present in the
nanogap 110 (nanogaps 112 and 114) (between the left and right
electrodes 106A and 106B) and also when no base 530 (of the DNA
molecule 511) is present. The respective bases 530 are determined
by the amplitude of the source-drain transistor current when each
respective base in present in the nanogap 110 (or nanogaps 112 and
114) of the nanopore 580. As discussed for FIGS. 4B, 4D, and 4E,
FIG. 5B illustrates a partial view of the system 500 with
extensions 405A and 405B extending from electrodes 106A and 106B
respectively. The single base is (only) within the nanogap 114
although other bases 530 may be in the larger nanogap 112.
[0058] When the single base 530 is present in the nanogap 114 and
when voltage is applied by the voltage source 519, source-drain
transistor current flows to source 508, into the right nanowire
electrode 106B, into right extension 405B, into the buffer solution
550 (between the nanogap 114) to interact with the base 530
positioned therein, into left extension 405A, into left nanowire
electrode 106A, out through the drain 507, and to the ammeter 520.
The ammeter 520 is measure the tunneling current (source-drain
current) when the base 530 is present in the nanogap 114. This same
process occurs for the rectangular and triangular shaped extensions
405A and 405B shown in FIGS. 4B and 4E.
[0059] FIG. 6 illustrates a method for manufacturing a nanogap in
the nanowire 106 (of the nanodevice 100) which can be utilized for
DNA, RNA sequencing according to an embodiment. Reference can be
made to FIGS. 1-5 discussed herein.
[0060] An oxide 104 is disposed (e.g., grown) on top of a substrate
102 (wafer) at block 605, and the nanowire 106 is disposed on top
of the oxide 104 at block 610. The lift-off process may be utilized
to dispose and pattern the metal of the nanowire 106. As understood
by one skilled in the art a positive resist process or a negative
resist process may be utilized to dispose and pattern the nanowire
106.
[0061] A helium ion beam is applied via the helium ion microscope
120 to cut the nanowire 106 into a first nanowire part (e.g.,
electrode 106A) and a second nanowire part (e.g., electrode 106B)
to form the nanogap 110 in the nanodevice 100 at block 615.
[0062] When the helium ion beam is applied (via the helium ion
microscope 120) to cut the nanogap 110, a signature of nanowire
material (e.g., palladium particles/dots 205) is formed in the
proximity to the openings of the nanogap 110 (e.g., as shown in
FIGS. 2E and 3B) at block 620.
[0063] The signature of the nanowire material comprises nanowire
material particles (e.g., palladium particles/dots 205) in
proximity to the openings of the nanogap 110 as a result of the
helium ion beam. The He beam energy vaporizes the palladium which
may redeposit in round droplets when the He beam is switched
off.
[0064] As a result of applying the helium ion beam, voltage is
applied by the voltage source 310 to determine that a nanowire
material particle (i.e., palladium particle 205A) is lodged in the
nanogap 110 in which the nanowire material particle connects the
first nanowire part and the second nanowire part (i.e., connects
electrode 106A to electrode 106B). When it is determined that the
nanowire material particle is lodged in the nanogap 110, the
nanowire material particle in the nanogap 110 is removed by
applying an electron beam and/or a helium ion beam. Note that the
helium ion microscope 120 may be configured to irradiate both
electron beams and helium ion beams as desired. Alternatively
and/or additionally, when it is determined that the nanowire
material particle is lodged in the nanogap 110, the particular
nanodevice 100 having the nanowire particle lodged in the nanogap
110 out of an array of good nanodevices 100 (shown in FIG. 3A)
having nanogaps 110 (with no lodged palladium particles 205 as
determined in FIG. 3B).
[0065] The nanowire 106 may be (only) palladium and/or other
metals. The substrate/wafer 102 may be silicon, germanium, etc. The
oxide 104 may be silicon dioxide, and/or other dielectric
materials.
[0066] FIG. 7 illustrates a method for manufacturing nanogaps 112
and 114 (which may be the same as nanogap 110) in the nanowire 106
(of the nanodevice 100) which can be utilized for DNA, RNA
sequencing according to an embodiment. Reference can be made to
FIGS. 1-5 discussed herein.
[0067] An oxide 104 is disposed (e.g., grown) on top of a substrate
102 (wafer) at block 705, and the nanowire 106 is disposed on top
of the oxide 104 at block 710. The lift-off process may be utilized
to dispose and pattern the metal of the nanowire 106. As understood
by one skilled in the art a positive resist process or a negative
resist process may be utilized to dispose and pattern the nanowire
106.
[0068] A helium ion beam is applied via the helium ion microscope
120 to taper the nanowire 106 laterally (e.g., on side A and side B
but not in between) into a first nanowire part (e.g., electrode
106A in FIG. 4A) and a second nanowire part (e.g., electrode 106B),
where the first nanowire part and the second nanowire part form a
first nanogap (e.g., nanogap 112) in the nanodevice 100 at block
715.
[0069] Applying the helium ion beam to taper the nanowire laterally
intentionally forms a bridge 405 connecting the first nanowire part
(electrode 106A) and the second nanowire part (electrode 106B) at
block 720.
[0070] Further applying the helium ion beam and/or an electron beam
cut a second nanogap (e.g., nanogap 114) in/through the bridge 405
to form a first extension (e.g., extension 405A) from/on the first
nanowire part (electrode 106A) and form a second extension (e.g.,
extension 405B) from/on the second nanowire part (electrode 106B)
at block 725.
[0071] The second nanogap 114 is thinner than the first nanogap 112
(i.e., D3<D2). The nanowire 106 is tapered in order for the
first extension 405A and the second extension 405B to have
rectangular shapes after the second nanogap 114 is cut as shown in
FIGS. 4A and 4B. The nanowire 106 is tapered in order for the first
extension 405A and the second extension 405B to have rounded shapes
after the second nanogap 114 is cut as shown in FIGS. 4C and 4D.
The nanowire 106 is tapered in order for the first extension 405A
and the second extension 405B to have triangular shapes after the
second nanogap 114 is cut as shown in FIG. 4E.
[0072] The second nanogap 114 is formed by (i.e., is in between)
the first extension 405A and the second extension 405B. The size
(e.g., the distance X of the extensions 405A and 405B) of the
second nanogap 114 accommodates a single base or a single
nucleotide of the target molecule 511 in which the target molecule
511 may include a deoxyribonucleic acid molecule, a ribonucleic
acid molecule, and/or a protein that is to be sequenced in the
system 500. The size of the second nanogap 114 allows (only) the
single base or the single nucleotide to be sequenced via a measured
current (of ammeter 520) while in the second nanogap 114 between
the first and second extensions.
[0073] The first extension 405A and the second extension 405B both
extend into the first nanogap 112.
[0074] FIG. 8 illustrates an example of a computer 800 (e.g., as
part of the computer test setup for testing and analysis) which may
implement, control, and/or regulate the respective voltages of the
voltage sources, respective measurements of the ammeters, and
display screens for displaying various current amplitude (including
ionic current and transistor (source to drain current)) as
discussed herein. The computer 800 also stores the respective
electrical current amplitudes of each base tested and measured to
be compared against the baselines current amplitudes of different
bases, which is utilized to identify the bases of the tested/target
molecule.
[0075] Various methods, procedures, modules, flow diagrams, tools,
applications, circuits, elements, and techniques discussed herein
may also incorporate and/or utilize the capabilities of the
computer 800. Moreover, capabilities of the computer 800 may be
utilized to implement features of exemplary embodiments discussed
herein. One or more of the capabilities of the computer 800 may be
utilized to implement, to connect to, and/or to support any element
discussed herein (as understood by one skilled in the art) in FIGS.
1-7. For example, the computer 800 which may be any type of
computing device and/or test equipment (including ammeters, voltage
sources, current meters, connectors, etc.). Input/output device 870
(having proper software and hardware) of computer 800 may include
and/or be coupled to the nanodevices and structures discussed
herein via cables, plugs, wires, electrodes, patch clamps, etc.
Also, the communication interface of the input/output devices 870
comprises hardware and software for communicating with, operatively
connecting to, reading, and/or controlling voltage sources,
ammeters, and current traces (e.g., magnitude and time duration of
current), etc., as discussed and understood herein. The user
interfaces of the input/output device 870 may include, e.g., a
track ball, mouse, pointing device, keyboard, touch screen, etc.,
for interacting with the computer 800, such as inputting
information, making selections, independently controlling different
voltages sources, and/or displaying, viewing and recording current
traces for each base, molecule, biomolecules, etc.
[0076] Generally, in terms of hardware architecture, the computer
800 may include one or more processors 810, computer readable
storage memory 820, and one or more input and/or output (I/O)
devices 870 that are communicatively coupled via a local interface
(not shown). The local interface can be, for example but not
limited to, one or more buses or other wired or wireless
connections, as is known in the art. The local interface may have
additional elements, such as controllers, buffers (caches),
drivers, repeaters, and receivers, to enable communications.
Further, the local interface may include address, control, and/or
data connections to enable appropriate communications among the
aforementioned components.
[0077] The processor 810 is a hardware device for executing
software that can be stored in the memory 820. The processor 810
can be virtually any custom made or commercially available
processor, a central processing unit (CPU), a data signal processor
(DSP), or an auxiliary processor among several processors
associated with the computer 800, and the processor 810 may be a
semiconductor based microprocessor (in the form of a microchip) or
a macroprocessor.
[0078] The computer readable memory 820 can include any one or
combination of volatile memory elements (e.g., random access memory
(RAM), such as dynamic random access memory (DRAM), static random
access memory (SRAM), etc.) and nonvolatile memory elements (e.g.,
ROM, erasable programmable read only memory (EPROM), electronically
erasable programmable read only memory (EEPROM), programmable read
only memory (PROM), tape, compact disc read only memory (CD-ROM),
disk, diskette, cartridge, cassette or the like, etc.). Moreover,
the memory 820 may incorporate electronic, magnetic, optical,
and/or other types of storage media. Note that the memory 820 can
have a distributed architecture, where various components are
situated remote from one another, but can be accessed by the
processor 810.
[0079] The software in the computer readable memory 820 may include
one or more separate programs, each of which comprises an ordered
listing of executable instructions for implementing logical
functions. The software in the memory 820 includes a suitable
operating system (O/S) 850, compiler 840, source code 830, and one
or more applications 860 of the exemplary embodiments. As
illustrated, the application 860 comprises numerous functional
components for implementing the features, processes, methods,
functions, and operations of the exemplary embodiments.
[0080] The operating system 850 may control the execution of other
computer programs, and provides scheduling, input-output control,
file and data management, memory management, and communication
control and related services.
[0081] The application 860 may be a source program, executable
program (object code), script, or any other entity comprising a set
of instructions to be performed. When a source program, then the
program is usually translated via a compiler (such as the compiler
840), assembler, interpreter, or the like, which may or may not be
included within the memory 820, so as to operate properly in
connection with the O/S 850. Furthermore, the application 860 can
be written as (a) an object oriented programming language, which
has classes of data and methods, or (b) a procedure programming
language, which has routines, subroutines, and/or functions.
[0082] The I/O devices 870 may include input devices (or
peripherals) such as, for example but not limited to, a mouse,
keyboard, scanner, microphone, camera, etc. Furthermore, the I/O
devices 870 may also include output devices (or peripherals), for
example but not limited to, a printer, display, etc. Finally, the
I/O devices 870 may further include devices that communicate both
inputs and outputs, for instance but not limited to, a NIC or
modulator/demodulator (for accessing remote devices, other files,
devices, systems, or a network), a radio frequency (RF) or other
transceiver, a telephonic interface, a bridge, a router, etc. The
I/O devices 870 also include components for communicating over
various networks, such as the Internet or an intranet. The I/O
devices 870 may be connected to and/or communicate with the
processor 810 utilizing Bluetooth connections and cables (via,
e.g., Universal Serial Bus (USB) ports, serial ports, parallel
ports, FireWire, HDMI (High-Definition Multimedia Interface),
etc.).
[0083] In exemplary embodiments, where the application 860 is
implemented in hardware, the application 860 can be implemented
with any one or a combination of the following technologies, which
are each well known in the art: a discrete logic circuit(s) having
logic gates for implementing logic functions upon data signals, an
application specific integrated circuit (ASIC) having appropriate
combinational logic gates, a programmable gate array(s) (PGA), a
field programmable gate array (FPGA), etc.
[0084] As will be appreciated by one skilled in the art, aspects of
the present invention may be embodied as a system, method or
computer program product. Accordingly, aspects of the present
invention may take the form of an entirely hardware embodiment, an
entirely software embodiment (including firmware, resident
software, micro-code, etc.) or an embodiment combining software and
hardware aspects that may all generally be referred to herein as a
"circuit," "module" or "system." Furthermore, aspects of the
present invention may take the form of a computer program product
embodied in one or more computer readable medium(s) having computer
readable program code embodied thereon.
[0085] Any combination of one or more computer readable medium(s)
may be utilized. The computer readable medium may be a computer
readable signal medium or a computer readable storage medium. A
computer readable storage medium may be, for example, but not
limited to, an electronic, magnetic, optical, electromagnetic,
infrared, or semiconductor system, apparatus, or device, or any
suitable combination of the foregoing. More specific examples (a
non-exhaustive list) of the computer readable storage medium would
include the following: an electrical connection having one or more
wires, a portable computer diskette, a hard disk, a random access
memory (RAM), a read-only memory (ROM), an erasable programmable
read-only memory (EPROM or Flash memory), an optical fiber, a
portable compact disc read-only memory (CD-ROM), an optical storage
device, a magnetic storage device, or any suitable combination of
the foregoing. In the context of this document, a computer readable
storage medium may be any tangible medium that can contain, or
store a program for use by or in connection with an instruction
execution system, apparatus, or device.
[0086] A computer readable signal medium may include a propagated
data signal with computer readable program code embodied therein,
for example, in baseband or as part of a carrier wave. Such a
propagated signal may take any of a variety of forms, including,
but not limited to, electro-magnetic, optical, or any suitable
combination thereof. A computer readable signal medium may be any
computer readable medium that is not a computer readable storage
medium and that can communicate, propagate, or transport a program
for use by or in connection with an instruction execution system,
apparatus, or device.
[0087] Program code embodied on a computer readable medium may be
transmitted using any appropriate medium, including but not limited
to wireless, wireline, optical fiber cable, RF, etc., or any
suitable combination of the foregoing.
[0088] Computer program code for carrying out operations for
aspects of the present invention may be written in any combination
of one or more programming languages, including an object oriented
programming language such as Java, Smalltalk, C++ or the like and
conventional procedural programming languages, such as the "C"
programming language or similar programming languages. The program
code may execute entirely on the user's computer, partly on the
user's computer, as a stand-alone software package, partly on the
user's computer and partly on a remote computer or entirely on the
remote computer or server. In the latter scenario, the remote
computer may be connected to the user's computer through any type
of network, including a local area network (LAN) or a wide area
network (WAN), or the connection may be made to an external
computer (for example, through the Internet using an Internet
Service Provider).
[0089] Aspects of the present invention are described below with
reference to flowchart illustrations and/or block diagrams of
methods, apparatus (systems) and computer program products
according to embodiments of the invention. It will be understood
that each block of the flowchart illustrations and/or block
diagrams, and combinations of blocks in the flowchart illustrations
and/or block diagrams, can be implemented by computer program
instructions. These computer program instructions may be provided
to a processor of a general purpose computer, special purpose
computer, or other programmable data processing apparatus to
produce a machine, such that the instructions, which execute via
the processor of the computer or other programmable data processing
apparatus, create means for implementing the functions/acts
specified in the flowchart and/or block diagram block or
blocks.
[0090] These computer program instructions may also be stored in a
computer readable medium that can direct a computer, other
programmable data processing apparatus, or other devices to
function in a particular manner, such that the instructions stored
in the computer readable medium produce an article of manufacture
including instructions which implement the function/act specified
in the flowchart and/or block diagram block or blocks.
[0091] The computer program instructions may also be loaded onto a
computer, other programmable data processing apparatus, or other
devices to cause a series of operational steps to be performed on
the computer, other programmable apparatus or other devices to
produce a computer implemented process such that the instructions
which execute on the computer or other programmable apparatus
provide processes for implementing the functions/acts specified in
the flowchart and/or block diagram block or blocks.
[0092] The flowchart and block diagrams in the Figures illustrate
the architecture, functionality, and operation of possible
implementations of systems, methods and computer program products
according to various embodiments of the present invention. In this
regard, each block in the flowchart or block diagrams may represent
a module, segment, or portion of code, which comprises one or more
executable instructions for implementing the specified logical
function(s). It should also be noted that, in some alternative
implementations, the functions noted in the block may occur out of
the order noted in the figures. For example, two blocks shown in
succession may, in fact, be executed substantially concurrently, or
the blocks may sometimes be executed in the reverse order,
depending upon the functionality involved. It will also be noted
that each block of the block diagrams and/or flowchart
illustration, and combinations of blocks in the block diagrams
and/or flowchart illustration, can be implemented by special
purpose hardware-based systems that perform the specified functions
or acts, or combinations of special purpose hardware and computer
instructions.
[0093] The terminology used herein is for the purpose of describing
particular embodiments only and is not intended to be limiting of
the invention. As used herein, the singular forms "a", "an" and
"the" are intended to include the plural forms as well, unless the
context clearly indicates otherwise. It will be further understood
that the terms "comprises" and/or "comprising," when used in this
specification, specify the presence of stated features, integers,
steps, operations, elements, and/or components, but do not preclude
the presence or addition of one more other features, integers,
steps, operations, element components, and/or groups thereof.
[0094] The corresponding structures, materials, acts, and
equivalents of all means or step plus function elements in the
claims below are intended to include any structure, material, or
act for performing the function in combination with other claimed
elements as specifically claimed. The description of the present
invention has been presented for purposes of illustration and
description, but is not intended to be exhaustive or limited to the
invention in the form disclosed. Many modifications and variations
will be apparent to those of ordinary skill in the art without
departing from the scope and spirit of the invention. The
embodiment was chosen and described in order to best explain the
principles of the invention and the practical application, and to
enable others of ordinary skill in the art to understand the
invention for various embodiments with various modifications as are
suited to the particular use contemplated
[0095] The flow diagrams depicted herein are just one example.
There may be many variations to this diagram or the steps (or
operations) described therein without departing from the spirit of
the invention. For instance, the steps may be performed in a
differing order or steps may be added, deleted or modified. All of
these variations are considered a part of the claimed
invention.
[0096] While the preferred embodiment to the invention had been
described, it will be understood that those skilled in the art,
both now and in the future, may make various improvements and
enhancements which fall within the scope of the claims which
follow. These claims should be construed to maintain the proper
protection for the invention first described.
* * * * *