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PhD studentship in Computational Modelling for Biology and Chemistry - Developing a General Rule-Based Stochastic Modelling Framework

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  • Full or part time
    Dr H Fellermann
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Number of awards:

1

Start date and duration:

September 2018 for 3 years.

Overview:

Stochastic simulation is a powerful tool for the modelling and analysis of molecular systems, as they occur in chemistry and biology. Unlike more traditional modelling approaches, stochastic simulation algorithms have the advantage that they are not constrained to static state spaces, such as a fixed set of molecules. Instead, they are able to capture molecular systems where reactions can create (a potentially unlimited amount of) novel molecular species. Rule-based models that enable the study of such expanding state spaces can further capture intricate arrangements of molecules rather than merely their chemical concentrations. Examples of such molecular systems include molecular complexification (e.g. protein complexes that bind, move along and potentially modify DNA), or encapsulation within cellular compartments which themselves can undergo reactions such as budding and division.

The objective of this PhD project is to develop a general rule-based stochastic modelling framework that enables computational chemists and biologists to express molecular organizations as they occur within their systems of interest by means of domain specific formal languages. Based on the user’s system specification, the framework will compile an appropriate stochastic simulation algorithm as well as analysis and visualization methods that are tailored to efficiently simulate and analyse a molecular system of interest. Algorithm and tool development will be accompanied by exemplary modelling studies in the areas of synthetic biology, supra-molecular chemistry, DNA nano-technology and molecular computing.

The candidate will have the opportunity to work within a strong research group on Interdisciplinary Computing and Complex Biosystems (ICOS), consisting of 50 individuals who conduct cutting-edge research at the interface of computing science and complex biological systems, and to work closely with experimental scientists from chemistry and biology.

Sponsor:

School of Computing (https://bit.ly/2INuLaV)

Name of supervisor(s):

Dr Harold Fellermann (https://bit.ly/2s9Gk1u)

Eligibility Criteria:

Candidates should have a strong background in computer science, programming, mathematics, or physics, and a keen interest in applying computational techniques in the areas of chemistry and molecular biology. An excellent degree in related subjects is expected. Wet-lab experience is not required, but a background in molecular biology or chemistry is a bonus.

The award is available to UK/EU students only.

How to apply:

You must apply through the University’s online postgraduate application system. To do this please ‘Create a new account’ (https://bit.ly/2s97ju9).
All relevant fields should be completed, but fields marked with a red asterisk must to be completed. The following information will help us to process your application. You will need to:

insert the programme code 8050F in the programme of study section
select ‘PhD Computer Science (full time)’ as the programme of study
insert the studentship code COMP005 in the studentship/partnership reference field
attach a covering letter and CV. The covering letter must state the title of the studentship, quote reference code COMP005 and state how your interests and experience relate to the project
attach degree transcripts and certificates and, if English is not your first language, a copy of your English language qualifications.

Funding Notes

100% of UK/EU tuition fees paid and annual living expenses of £14,777.



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