Wiki Entry 1-Introduction
In the past, nanopores have been fabricated to use in the single molecule detection of DNA by studying the length and conformation of the DNA strand as it travels through the pore. By electronically studying these parameters, insight into DNA sequencing methods can be obtained. The paper by Mitsui et al attempts to understand the mechanism of formation of nanopores after their fabrication using a method called ion-beam sculpting. When an ion beam is transmitted through the pores, atoms within the material diffuse to the nanopore creating ridges along the periphery, and eventually closing the pore. This diffusive process creates structures that resemble volcanoes. It is proposed that the surface electric field and geometry of the pores lead to this unique observation.
Si3.5N4 is grown on a silicon substrate at a thickness of 0.25 μm and a 30 μm square window is patterned using lithography. The silicon substrate is etched below the Si3.5N4 layer creating a square membrane ready to be drilled to create pores. A 10 nm gallium ion beam at 50 keV is subsequently used to create a 100 nm diameter pore size. The closing of this pore is then studied by exposing the samples to an Ar+ beam 300 μm in diameter. A channeltron single-ion counting detector counts the number of ions passing through the pore as a function of exposure time in order to determine at what time the diffusion of ions leads to the 100 nm pore closing completely.
Ion-Beam Induced Pore Closing
The first experiment involves the study of a single nanopore. The sample is treated with a 3 keV Ar+ ion beam and imaged using AFM at 0, 4, 8, and 15 seconds of exposure time. The images shown in Figure 1 reveal the pore closing over time until complete closure is achieved after 15 seconds. At this point, the diffusion of matter to the pore seems to stop. Ridges similar to a volcano grow around the pore until it closes. These ridges have a height of 15-25 nm above the membrane surface.
The second set of experiments involves creating an array of 100 nm pores spaced 1 μm apart. The AFM images reveal the formation of volcanic ridges along the pore periphery. Figure 2 is obtained using a single line scan diagonally connecting the corner pores of the array and demonstrates the evolution of the pores after four exposures to Ar+. Analysis of the image reveals the corner pores to be completely filled while the pores toward the center of the array sample are essentially unaffected by the ion treatment. Furthermore, a larger volcanic ridge indicates a more complete pore closure which is observed in the corner pores. This behavior of pore closure is justified by the hypothesis that the corner pores are exposed to more mobile atoms than the pores in the center of the array. From Figure 2b you can see that after the second exposure, only the outer pores close. Then after the third and fourth exposure (Figure 2c and 2d), the size of the ridges on the outer pores decrease in size and matter diffuses to cover the interior pores on the array. As a result, the size of the ridges at the corner pores decrease in size while the inner pores develop ridges. However, the innermost pore is still not covered after the last exposure.
In order to overcome this “screening effect” of inner pores by outer pores, a gold substrate is added to the bottom of the sample array. When the array is treated with Ar+, the height of the volcanoes is not only uniform along the array but also appear to have increased in size. The gold backing almost entirely diminishes the “screening effect”.
Explaining the Volcano Formation
These observations beg the question of what drives the formation of these nano-sized volcanoes. According to Mitsui et al, the surface electric field of the sample, estimated to be around 4x106 V/cm, results in “transporting and trapping charged matter”. This field induced by the ion-beam enables matter to diffuse longer distances than previously observed. At some point, this diffusing matter is trapped by the electric field of the pore. When the pore has entirely closed, the electric field causing diffusion dissipates and the pore is no longer capable of trapping matter. As a result, the matter creating the volcanic ridge is able to travel to the innermost pores of the array and facilitate pore closing. In this way, the excess diffusive matter is “recycled”. So why is it that adding a gold backing layer enables all the pores to close uniformly regardless of their position on the array (i.e., inner vs. outer pores)? The reason for this is that the gold layer provides the counter charge necessary to cancel out the effects of something called “the enhanced sputtering effect”. When the high energy ion beam excites the charged matter on the surface of the material, something called sputtering occurs where atoms are expelled from the material. As a result, there are fewer particles left to diffuse and close the pores. Gold provides a countercharge that holds these charged particles on the surface so that there are more of them to diffuse and close pores.