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Computational design of nanopores for industrial applications

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  • Full or part time
    Prof S Khalid
  • Application Deadline
    Applications accepted all year round
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

TMCS is an EPSRC Centre for Doctoral Training operated by the Universities of Oxford, Bristol and Southampton.
In year one you will be based in Oxford with a cohort of around 12–15 other TMCS students, and will receive in-depth training in fundamental theory, software development, and chemical applications, delivered by academics from all three Universities. Successful completion of the year-one program leads to the award of an Oxford MSc, and progression to the 3-year PhD project detailed below.
The Khalid group is seeking a highly motivated graduate student to work on a collaborative academia/industry project.
Stochastic sensors provide detection of analytes at the single-molecule level. They are highly desirable for industrial applications due to their sensitivity, resolution, relatively low cost and small size. In the simplest case, the sensor element has two states — occupied (by analyte) and unoccupied — and a different output (usually current) is associated with each. As well as revealing the concentration of analyte molecules, stochastic sensors can also distinguish between different types of molecules and proof-of-principle of distinguishing between enantiomers has also been demonstrated. Oxford Nanopore Technologies Ltd (ONT) has used the same principles of stochastic sensing to develop a DNA sequencing device that has revolutionised this field (please https://nanoporetech.com see for details).
In this project we aim to work closely with ONT to develop novel nanopores for the stochastic sensing of a range of analyte molecules, for example biological warfare agents and other toxins. We will use classical molecular dynamics simulations to study a range of pore designs, seeking inspiration from biological pores. The student will learn state-of-the-art simulation methodologies and apply these to understanding the principle of molecular recognition within the confined geometries of nanopores, ultimately he or she will eventually design his or her own pores and we will seek to get these tested experimentally. The project will involve site visits to Oxford Nanopore Technologies; the world leader in exploiting nanopores for next generation sequencing and close collaboration with existing members of the Khalid research group.

If you wish to discuss any details of the project informally, please contact Professor Syma Khalid, Email: [email protected] Tel: +44 (0) 2380 59 4176

Funding Notes

Funding will be subject to normal EPSRC rules. UK and EU students will be eligible for full-fee studentships. In addition, UK students will be eligible for an annual stipend at or above £14,296 each year.

Applicants would typically be expected to have a first class degree (or overseas equivalent) in chemistry or a closely related discipline. TMCS is committed to promoting equal opportunities in science, and we particularly welcome applications from women. Applications should be made as soon as possible, but will be considered throughout the year until the programme is full. Deadlines for upcoming recruitment rounds and further information on the application process can be found at our website: www.tmcs.ac.uk

Please ensure that you specify clearly that you are making a project-specific application and give the name of the project in your application


Manara R.A, Wallace E.J and Khalid S (2015) ” DNA sequencing with MspA: Molecular Dynamics simulations reveal free energy differences between sequencing and non-sequencing mutants” Scientific Reports, 5:12783.

Manara R.A, Guy A.T, Wallace E.J and Khalid S (2015) ” Free-Energy Calculations Reveal the Subtle Differences in the Interactions of DNA Bases with alpha-Hemolysin” J

Guy, A.T, Piggot T.J. and Khalid S, (2012) “Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study”, Biophysical Journal, 103(5):1028-36
ournal of Chem. Theory and Comput. 11(2):810-6

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