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Coarse-grained molecular dynamics and self-assembly of reacting proteins and chromatin

  • Full or part time
    Prof A Goryachev
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

A project in computational modelling of reactive Brownian dynamics of DNA and proteins inside biological cells is available in the group of Prof. Andrew Goryachev ( The project is suitable for graduates with interest in biomathematics, chemical engineering, applied physics, physical chemistry, biomedical and biological physics.
The aim of this project is to build a coarse-grained particle-based approach for the simulation of Brownian reactive dynamics of large biological molecules and their complexes. The student will use ESPResSo and/or LAMMPS open-source community-developed packages for molecular dynamics, to develop methods for modelling of protein-protein interactions, chemical reactions between proteins, and, ultimately, self-assembly of large spatially complex cellular structures, such as centrosomes. The student will have an opportunity to learn mesoscopic approaches to molecular dynamics and self-assembly, gain expertise in computational methods and acquire practical skills in the design of complex biological models. The student will receive training in nonlinear dynamical systems, bifurcation theory and stability analysis. The project offers an excellent opportunity for the students with background in mathematics, physical sciences and engineering to learn modern cell and developmental biology while contributing to the cutting-edge research, which is published in high-profile journals.

The research focus in the Goryachev group ( is on understanding biophysical mechanisms of symmetry breaking in biological systems. Symmetry breaking manifests itself in a variety of dazzling biological phenomena and our aim is to improve their understanding via construction of predictive mechanistic models. The group works on the interface of soft matter physics, chemical kinetics and cell biology. For our representative publication, please visit the group site. We are looking for motivated, enthusiastic young people with the background in physical, life, computational sciences and engineering who are passionate about research.

Several types of competitive scholarships are available for the prospective PhD students at the University of Edinburgh. Depending on the topic, allied faculty from physics, mathematics and informatics departments are available to co-supervise the project.

Funding Notes

The “Visit Website” button on this page will take you to our Online Application checklist. Please complete each step and download the checklist which will provide a list of funding options and guide you through the application process.

If you would like us to consider you for one of our scholarships you must apply by 5 January 2020 at the latest.


F. Weik et al., ESPResSo 4.0 – an extensible software package for simulating soft matter systems, Eur. Physical J. Special Topics, 227(14), 1789 – 1816, (2019).
C. Svaneborg, LAMMPS framework for dynamic bonding and an application modeling DNA, Computer Phys. Commun., 183, 1793 – 1802, (2012).

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

Research output data provided by the Research Excellence Framework (REF)

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