Open Positions

Master and Semester Projects

We offer the opportunity to make master and semester projects in the following areas:

1. Nanoscale biosensors

2. Study of protein translocation through nanopore sensors

3. Study of protein secretion from single cells using nanopore sensors 

4. Multiplexed Single-Cell systems for protein profiling, inclduing development of novel methodologies to enable highly multiplexed single-cell analysis

Current Project Proposals:

Simulating the Interfacial Nanopore: Enhancing Fundamental Understanding of the Governing Nanoscale Dynamics

Overview

Solid-state nanopores have become powerful sensors for the label-free detection of biomolecules (DNA, mRNA, proteins), with pulled glass nanopores among the most common owing to their simple fabrication. However, with glass nanopipettes we lack subnanometre size precision, dynamic size control and the ability to reliably form the smallest apertures (<10 nm) without losing sensitivity.

Thus far their applicability to single-molecule characterisation has been limited; indeed, with characterising proteins posing one of the foremost problems in the field of single-molecule sensing, a new approach is required. One such approach is a pipette-based interfacial nanopore, which leverages the ease and reproducibility of glass nano- and micro-pipettes in combination with an elastic surface to form an in-situ adaptive solid-state nanopore at their interface.

These dynamic pipette-surface interfacial nanopores can select aperture size with high resolution and modify their size during measurements. With these pores we observe increased DNA dwell times compared to glass nanopipettes, enhancing their sensing capabilities. Moreover, pore formation post pipette pulling increases size reproducibility, negating issues arising from variabilities in fabrication and allowing us to form pores of less than 10 nm.

However, the pore geometry, the translocation and pore formation dynamics, and the electrical properties of the interfacial nanopore are poorly understood. Indeed, the nanoscale nature of the pore makes direct optical observation impossible, while the complex geometry also limits electron methods. Therefore, an understanding derived from computational simulation of the physics underlying these processes is of paramount importance.

Project Goals

The project should elucidate several characteristics of the interfacial nanopore through simulation. The project will therefore be primarily computational, but some time in the lab will be necessary to become familiar with the system. (A more practically oriented project is possible if the student should wish, as comparative measurements are required). The student can choose to tackle several issues as they see fit:

(i)             Predict pore geometry arising from elastomer deformation.

(ii)            Consider electrical properties of the nanopore, including surface effects, electric field, and predict the pore response to DNA and other translocating analytes.

(iii)           Consider effect of electroosmotic flow and electrophoretic flow arising from applied voltages and salt gradients.

(iv)           Model nanopore instability arising from mechanical vibrations.

Given that this work is novel, a strong student project can expect publication. Should you have any questions, please do not hesitate to reach out ().

Project Type

Master Thesis preferred, but Semester Project or Bachelor Thesis can be considered.

Requirements

Strong background in Physics or related subject (engineering, materials science, chemistry etc.). Experience using COMSOL or other simulation packages is helpful but not necessary.