Person: Li, Jiali
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Li
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Jiali
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Li, Jiali
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Publication DNA molecules and configurations in a solid-state nanopore microscope(Nature Publishing Group, 2003) Li, Jiali; Gershow, Marc; Stein, Derek; Brandin, Eric Richard; Golovchenko, JeneA nanometre scale pore in a solid state membrane provides a new way to electronically probe the structure of single linear polymers, including those of biological interest in their native environments. Previous work with biological protein pores wide enough to pass and sense single stranded DNA molecules demonstrates the power of the nanopore approach, but many future tasks and applications call for a robust solid-state pore whose nanometre scale dimensions and properties may be selected, as one selects the lenses of a microscope. Here we demonstrate a solid-state nanopore microscope capable of observing individual molecules of double stranded DNA and their folding behaviour. We discuss extensions of the nanopore microscope concept to alternative probing mechanisms and applications including the study of molecular structure and sequencing.Publication Ion-Beam Sculpting Time Scales(American Physical Society (APS), 2002) Stein, Derek; Li, Jiali; Golovchenko, JeneA study of ion sculpting dynamics in SiO2 and SiN using periodically pulsed ion beams reveals material transport that depends strongly on the time structure of the pulsed beams. It is found that significant nanoscale matter transport can occur over second long time scales after the ion beam has been extinguished. A simple phenomenological model described the dynamics of ion beam sculpting in terms of two material time scales. The model accounts for the surprising observation of enhanced matter transport affected by pulsed ion beams over continuous ion beam exposure.Publication Detecting Single Stranded DNA with a Solid State Nanopore(American Chemical Society (ACS), 2005) Fologea, Daniel; Gershow, Marc; Ledden, Bradley; McNabb, David S.; Golovchenko, Jene; Li, JialiVoltage biased solid-state nanopores are used to detect and characterize individual single stranded DNA molecules of fixed micrometer length by operating a nanopore detector at pH values greater than ∼11.6. The distribution of observed molecular event durations and blockade currents shows that a significant fraction of the events obey a rule of constant event charge deficit (ecd) indicating that they correspond to molecules translocating through the nanopore in a distribution of folded and unfolded configurations. A surprisingly large component is unfolded. The result is an important milestone in developing solid-state nanopores for single molecule sequencing applications.Publication Feedback-controlled ion beam sculpting apparatus(AIP Publishing, 2004) Stein, Derek M.; McMullan, Ciaran J.; Li, Jiali; Golovchenko, JeneWe report the design of an “ion sculpting” instrument that enables the controlled fabrication of nanometer-sized structures in solid-state materials. The instrument employs a beam of kilo-electron-volt argon ions that impinge on a solid-state membrane containing prefabricated structures such as holes, slits, or cavities whose properties are to be modified. By controlling both the ion beam parameters and sample temperature, the instrument can be adjusted to either deliver or remove material from these articulations, for example opening or closing holes of various shapes. The instrument is unique in its use of feedback control for the crafting of structures that define a hole through which a component of the incident ion beam is permitted to pass and be monitored. Electrostaticion optics refocus ions transmitted unimpeded through the hole, onto a detector capable of registering single ions. The transmission rate is a direct, real-time measure of the transmitting area that is used as a feedback signal to trigger the termination of the ion irradiation process precisely when a desired dimension is obtained. The ions thus serve the dual role of modifying and measuring the size of the nanoscale structures. The sensitivity of the ion beam sculpting apparatus to atomic-scale material rearrangement at the perimeter of a hole also enables the study of ion beam induced material transport at solid-state surfaces. The utility of the instrument as a fabrication tool has been demonstrated by the fabrication of nanopores used for recent single-molecule biophysics studies.Publication Nanopore Fabrication in Amorphous Si: Viscous Flow Model and Comparison to Experiment(American Institute of Physics, 2010) George, H. Bola; Tang, Yuye; Chen, Xi; Li, Jiali; Hutchinson, John; Golovchenko, Jene; Aziz, MichaelNanopores fabricated in free-standing amorphous silicon thin films were observed to close under 3 keV argon ion irradiation. The closing rate, measured in situ, exhibited a memory effect: at the same instantaneous radius, pores that started larger close more slowly. An ion-stimulated viscous flow model is developed and solved in both a simple analytical approximation for the small-deformation limit and in a finite element solution for large deformations. The finite-element solution exhibits surprising changes in cross-section morphology, which may be extremely valuable for single biomolecule detection, and are untested experimentally. The finite-element solution reproduces the shape of the measured nanopore radius versus fluence behavior and the sign and magnitude of the measured memory effect. We discuss aspects of the experimental data not reproduced by the model, and successes and failures of the competing adatom diffusion model.