Shrinking of Solid-state Nanopores by Direct Thermal Heating
© Asghar et al; licensee Springer. 2011
Received: 11 February 2011
Accepted: 4 May 2011
Published: 4 May 2011
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© Asghar et al; licensee Springer. 2011
Received: 11 February 2011
Accepted: 4 May 2011
Published: 4 May 2011
Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.
The use of α-hemolysin protein nanopores inspired the fabrication of solid-state nanopores. Solid-state nanopores have emerged as novel biosensors for single molecule analysis of DNA, proteins, etc. [1–7]. Solid-state nanopores are more stable than protein nanopores under various experimental conditions like pH, salinity, and temperature [8–11]. When a single bio-molecule electrophoretically passes through a nanopore, it gives significant current blockage pulses.
The diameter of the nanopore should be almost at the same scale as the size of the translocating species. The pores fabricated with conventional processes result into initial diameters larger than the size of species of interest [12–16]. The nanopore diameter is then reduced using transmission electron microscope (TEM) or field emission scanning electron microscope (FESEM) to induce the shrinking [15, 17] and FIB for the sculpting processes . During the TEM shrinking process, the viscous flow of SiO2 membrane is induced by an electron beam of optimal intensity. The nanopore shrinks or expands based on the surface-tension-driven mass flow. The nanopore, fulfilling the condition r < t/2, would shrink under the electron beam at optimal conditions where r is the radius of the pore and t is the thickness of the membrane. TEM beam exposure depletes oxygen from the oxide at depletion rate of about 10% per hour . Higher shrinking rates can be achieved through FESEM induced shrinking .
The FESEM induced shrinking mechanism is putatively not surface tension driven, but explained by radiolysis. The crystalline structure of the nanopore is disturbed under a high energy FESEM electron beam. This results in pore shrinkage due to the diffusion of Si and oxygen atoms toward the edge of the pore to overcome the crystalline defects present at the edge. The stoicheometry of the SiO2 is expected to be different than a normal oxide layer due to radiolysis. Different shrinking rates were reported by using different acceleration voltages during FESEM exposure . The nanopore was found to be always shrinking independent of the ratio of the pore's diameter and membrane thickness under FESEM .
During the FIB sculpting process, the nanopore is exposed to an energetic ion beam. The accelerating ions drilled a nanopore in a thin oxide membrane due to sputtering of the surface, or these reduced the pore diameter due to atom diffusion or surface tension driven mass flow [18, 19]. The FIB sculpting process is also dependent on the substrate temperature. Under an Argon ion beam, the pore closed at room temperature while it opened at temperatures close to 0°C .
Chemical composition of the material around the nanopore periphery changes during TEM or FESEM induced shrinking processes. This produces variable modifications of nanopore surface properties. These processes make the nanopore unfavorable for molecule analysis due to increased surface charge and electrical noise in the desired signal. In addition, all these shrinking processes are time consuming because they can only process one nanopore at a time. In this article, we report a simple and novel method to shrink nanopores using direct thermal heating. High temperature treatment (>1000°C), or annealing, promotes the viscous flow of the silicon dioxide (SiO2) membrane and results in morphological changes that depend on the ratio of nanopore diameter to membrane thickness. Residual stress in the SiO2 membrane is also reduced during high temperature annealing. Surface composition of the nanopore is maintained in this approach, as opposed to being inevitably changed in the electron or ion irradiation approaches previously reported. Annealing has been extensively used in semiconductor industry to reduce leakage current in thin films , to repair gate oxide damage from electrical stress , and to minimize residual stress in amorphous films .
EDS analysis of pore at different steps of the process.
Before FIB drilling
After FIB drilling
The physics of nanopore shrinkage and expansion can be explained by taking into account the surface tension of the viscous oxide membrane . At high temperature, the oxide membrane softens and deforms to find a structural morphology with lower surface free energy F. For simplicity, the nanopore is considered cylindrical with radius r and oxide membrane thickness t. The change in free energy with respect to radius can be calculated using the simple mathematical relation ΔF = γΔA = 2πγ (rt - r 2), where γ is the surface tension of the fluid and ΔA is the change in the surface area [15, 25]. From the above relation, it can be concluded that surface free energy of the nanopore having r < t/2 can be lowered by reducing r, whereas for nanopores having r > t/2, their surface free energy can be lowered by increasing size [15, 25]. The ratio of radius to membrane thickness along with the exact geometry of the nanopore, are considered important factors in estimating a decision on whether the pore will shrink or expand. The decisive ratio of nanopore radius and membrane thickness was also verified experimentally. A 250 nm diameter pore in a 300 nm membrane shrank (Figure 2), while a 350 nm diameter pore in 300 nm membrane expanded (Figure 4) at 1150°C. Experiments performed on 150 nm thick membranes also showed similar results (data not shown). Interestingly, nanopore shrinking similar to TEM shrinking can be achieved at high temperature. The major advantage provided is that TEM processes one pore at a time, whereas this approach can process a whole wafer in one run. We believe that viscous flow is induced in the oxide membranes which results in nanopores shrinking or expanding. Similar dynamics of pore closing and opening have been reported in films of mercury and air holes in water sheets . The holes used in these studies were of micrometer scale. The larger holes increased in size while the smaller holes closed down due to surface tension . Similar kinetics have also been observed when 20 nm thick gold sheets with 10 to 30 nm pores were subjected to an annealing process . Mathematical modeling and experiments proved that pores with diameters smaller than the gold film thickness tend to shrink while pores with diameters larger than the film thickness tend to expand during the thermal annealing process . Similar diffusion kinetics of oxide membranes to shrink or expand the nanopores during high temperature annealing process may be applicable.
The fabrication process started by oxidizing a double-side-polished, boron-doped silicon (100) wafer. The initial oxide thickness was 400 nm. Positive photoresist (PR) S1813 (Shipley Microposit J2 PR, Marlborough, MA, USA) was coated on one side of the wafer and square windows were opened after development. PR was coated on the other side followed by buffered hydrofluoric acid wet etching to remove oxide from square windows. The wafer was then washed with de-ionized (DI) water and dried with nitrogen. The wafer was submerged in acetone to remove the remaining PR. In order to make free-standing membranes, anisotropic etching was performed using 20% TMAH in DI water at 90°C (Mallinckrodt Baker, Inc. Phllipsburg, NJ, USA). Self-limiting etch was stopped once 30 × 30 μm2 square windows were achieved in SiO2. The thickness of the SiO2 membranes were then reduced to 300 nm by reactive ion etching (RIE) using tetraflouromethane at 100 W and gas flow rate of 15 sccm. The etch rate of the RIE was characterized using a reflectometer (Ocean Optic, Dunedin, FL, USA). All samples were cleaned with piranha solution before FIB (Carl Zeiss, Peabody, MA, USA) drilling. The free-standing oxide membranes were drilled with the FIB to create the initial pores. The FIB process was optimized first in terms of drilling time and milling current while the acceleration voltage of 30 kV was fixed. HRTEM (Hitachi High Technologies America, Inc., Schaumburg, IL, USA) operating at 300 kV was used to image the nanopores and to characterize their diameters.
The heating furnace was first turned on to raise the temperature to the desired range. All samples were put together in a horizontal carrier inside the furnace. The samples were allowed to heat up for 30 s before starting the actual processing time. The nitrogen flow rate of 20 sccm was maintained throughout the shrinking process. After the desired amount of time, the samples were taken out of furnace to cool down to room temperature. All the samples were cleaned with argon-oxygen plasma for 5 min before and after every thermal processing step to avoid hydrocarbon contamination.
We demonstrated a new technique to shrink nanopores in oxide membranes with nanometer precision. The shrinking process is controlled and repeatable. In contrast to TEM or FESEM shrinking methods, our process can be used to shrink many napopore dyes in parallel. We processed 5 to 10 dyes in one run and achieved similar shrinking rates. Our technique has an additional advantage in that it did not change the chemical composition of the pore walls. The oxide layer is softened under high temperature and is allowed to diffuse due to surface diffusion of viscous oxide.
energy dispersive X-ray spectroscopy
field emission scanning electron microscope
focused ion beam
high-resolution transmission electron microscope
reactive ion etching
transmission electron microscope
We are thankful to the staff at Nanotechnology Research and Teaching Facility for their help in fabrication. Partial chip characterization was carried out at UTA Characterization Center for Materials and Biology (C2MB). The work was supported by grants from The Metroplex Research Consortium for Electronic Devices and Materials (MRCEDM), Arlington, Texas and National Science Foundation CAREER grant number ECCS-0845669.
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.