PhD Studentship in Synthetic Biology - Modelling Genetic Circuits in Space-Time

Newcastle University

Value of award: 100% of UK/EU tuition fees paid and annual living expenses of £14,296.
Number of awards: 1
Start date and duration: September 2017 for 3 years.

Overview

This PhD project will upgrade existing methods for the design, modelling, simulation and construct of genetic circuits by taking into account both time and space. Current single-cell analysis reveals the internal spatial complexity of bacteria. However, synthetic circuits are engineered to satisfy almost exclusively time-based requirements, underrating the influence of spatial constraints.

Far from being a homogeneous compartment, the inside of bacteria is heterogeneously structured. Features as the availability of resources in specific regions or distances between connected modules need to be formally addressed in order to capture reality to a greater extent. For instance, two parts of a circuit (e.g. regulator and promoter) that were close to each other within a cell’s volume would not interact in the same way than if they were situated very far apart. The overall aim of this PhD project is to revisit and update mathematical modelling techniques (e.g. the time-based Gillespie’s algorithm) to include spatial constraints (e.g. 2D/3D Brownian motion of species). This will change the way reaction kinetics (and rates!) are defined while producing more accurate simulations and predictable models. In addition, the characterization of such mechanistic details between parts will be used to improve circuit design and provide insights into structural features of bacteria.

This studentship provides the opportunity to perform interdisciplinary research at the Interdisciplinary Computing and Complex BioSystems (ICOS) research group, which consists of 50 individuals conducting cutting-edge research at the interface of computing science and complex biological systems.

Sponsor

School of Computing Science, Newcastle University.

Name of supervisor(s)

Dr Angel Goni-Moreno

Eligibility Criteria

Candidates should have a strong computer science, mathematics or physics background and a keen interest in developing and applying computational techniques to Synthetic Biology.

An excellent degree in related subjects is expected.

Wet-lab experience is not required, but basic knowledge of molecular biology is a bonus.

The award is available to UK/EU applicants only, due to funding restrictions.

How to apply

You must apply through the University’s online postgraduate application system.  To do this please ‘Create a new account’.  Only mandatory fields need to be completed.  However, you will need to include the following information:

  • Insert programme code 8050F and select 'PhD Computer Science (Computing Science)' as programme of study
  • insert the studentship code CS058 in the studentship/partnership reference field
  • attach covering letter and CV. The covering letter must state title of studentship, quote reference CS058 and describe how your research interests fit with the topic of research project outlined in the advertisement (maximum two pages)
  • You should also send your covering letter and CV by e-mail to cs.pg@ncl.ac.uk.

Contact

For further details, please contact:

Dr Angel Goni-Moreno
E-mail: angel.goni-moreno@ncl.ac.uk
Telephone: +44 (0) 191 208 3859

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Type / Role:

PhD

Location(s):

Northern England