Research Projects

Shrinking Kinetics of Solid State Nanopores

Translocation of lambda DNA through solid state nanopore

As part of this project we investigated the Scanning Electron Microscope induced shrinking of Focused Ion Beam drilled nanopores. We demonstrated the ability to tailor the diameter of these pores down to under 10 nm. Pores thus fabricated were then used to detect individual molecules of λ-DNA with the ionic current blockade technique. The mechanism of shrinkage and the internal profile of the pores were also investigated as was the dependence of the pores’ conductance on their geometry. The above videos show TEM tomograms of an FIB drilled 100 nm pore and the real time shrinking of a 70 nm pore. Further information can be found in our paper titled “SEM-induced shrinking of solid-state nanopores for single molecule detection“.

Nanoparticle Separation using Chemically Modified Solid State Nanopores

The translocation of a particle across a nanopore is affected by several factors such as the size and surface charge density of the pore, the applied voltage and other fluidic conditions. In collaboration with Dr. Prashanta Dutta’s group at Washington State University, we experimentally and mathematically investigated the effect of various parameters on nanoparticle translocation and identified the pore surface charge density as a key parameter that determined the velocity of a translocating particle. Our simulations revealed that by tailoring the surface charge density of the nanopore membrane it was possible to increase or decrease the velocity of a translocating particle and even prevent it from translocating across the pore all together. Consequently we demonstrated the electrokinetic separation of 56 nm and 22 nm polystyrene beads using a 150 nm pore fabricated in a silicon nitride membrane by chemically modifying the pore to tailor its surface charge density. More information about this project can be found in our paper titled “Chemically modified solid-state nanopores for high throughput nanoparticle separation.”

Probing Bacterial Flagella Polymorphism with Solid State Nanopores

Bacterial flagella filaments, a part of most bacteria’s locomotory organelles, are long proteinaceous structures comprised of repeated units of a protein monomer called flagellin. These filaments are 20 nm in diameter and several microns in length. In an aqueous medium these filaments acquire helical structures with different pitches that can change reversibly in responses to changes in the medium’s properties such as pH, salinity and temperature. Since these structural changes and the stimuli that trigger them are well characterized we aim study the translocation of bacterial filaments under different fluidic conditions in order to relate these structural changes to the observed current signatures in each case. The ability to efficiently and accurately detect structural changes in proteins can have significant diagnostic potential and this project is an important step in that direction.

FEM Analysis of the Nanofluidic Environment

Simulation of the Nanofluidic Environment

Using existing continuum models, comprising of Stokes equation coupled with the Poisson-Nernst-Planck equations we have simulated the nanofluidic environment around a nanopore in COMSOL. We are currently studying the effect of various parameters such as the applied voltage, membrane charge and buffer concentration on the translocation of analytes and aim to simulate the current signature expected from analytes with different structures.

Translocation Kinetics of Nanoparticles across Solid State Nanopores

As part of my undergraduate curriculum, on a six month internship in Prof. Vinod Subramaniam’s group at the University of Twente in Enschede, I investigated the translocation kinetics of 58 nm latex nanoparticles across solid state nanopores. Translocations were carried out at different applied voltages and buffer concentrations and the dependence of the current drop and translocation times on these parameters was studied.

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