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Stochastic Multiscale Model of Evolutionary Competition of Molecules


School of Mathematics

Applications accepted all year round Competition Funded PhD Project (European/UK Students Only)

About the Project

Oligonucleotides are not only the careers of genetic information. They can also form complex 3D structures with diverse chemical properties. Consequently, one can find oligonucleotides that can bind to diverse targets, or that act as drugs. This makes such oligonucleotides suitable for many important biomedical applications, including for cancer immunotherapy or anti-microbial treatments.
Interestingly, the primary experimental protocol used to identify oligonucleotides with specific chemical properties, the SELEX protocol, uses ideas from evolution. Here, a huge number of oligonucleotides is competing for binding sites at the target (e.g. a cancer cell, cell receptor, or bacteria), and the best binding candidate molecules are selected and amplified).
In this project, new mathematical models will be constructed to gain insights into the dynamics of the evolutionary processes of oligonucleotide selection. There are three focus areas associated to this project, and the candidate should contribute to at least one of them:
1) Build realistic models and validate them with data from industrial collaborators that aim to identify oligonucleotides for cancer immunotherapy
2) Develop analytic approximations to Markov processes describing the evolutionary processes to gain new insights into the dynamics of the evolutionary process
3) Develop new simulation methods to improve efficiency of the complex simulations
Methods: Markov Process, Monte Carlo Simulations, Multiscale Modelling, Asymptotic Analysis
Not all methods are required. The only essential requirement is strong academic performance (e.g. evidenced through an excellent 1st class degree in Mathematics, Theoretical Physics or related subjects), and motivation to work in an interdisciplinary environment.

Funding Notes

For UK and EU candidates:
funding may be available through a college or EPSRC scholarship in competition with all other PhD applications;
the scholarship will cover tuition fees, training support, and a stipend at standard rates for 3-3.5 years;
early applications are strongly recommended;

strong candidates are encouraged to make an informal inquiry.

For non-UK/non-EU candidates:
strong applicants with external scholarships will be considered;
exceptionally strong candidates in this category may be awarded a tuition fee waiver (for up to 3 years) in competition with all other PhD applications.

References

https://www.pnas.org/content/113/43/12076/

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