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Theoretical and computational methods for sensory biology

  • Full or part time
  • Application Deadline
    Friday, November 01, 2019
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

The overall goal of this research project is to advance computational modelling techniques such as the molecular dynamics (MD) or free energy perturbation approaches to permit computational studies of biological macromolecules and molecular assemblies that are central to the molecular basis of many sensory processes (including vision, hearing, magnetoreception). For more information please visit http://www.quantbiolab.com.

At present, various biomolecular mechanisms can be studied using advanced computational modelling techniques, which model the motion of every atom in a biomolecular system and the forces acting between them. This elaborate approach roots upon the fundamental laws of nature, such as Newton’s laws of motion, and allows a glimpse of biomolecular mechanisms at the smallest level of detail – down to the individual atoms – which is not otherwise possible through experimental techniques. Due to the large number of atoms typically involved, simulations of complex biomolecular systems are computationally intensive, but with the emergence of ever-increasing supercomputer resources, molecular systems with millions of atoms are within reach of the computational method nowadays. Even with the powerful supercomputers available today, however, the computational complexity still severely limits the range of processes that can be studied directly using all-atom MD simulations: large conformational changes in proteins often take place on the course of milliseconds and are hence too slow to be observed during a simulation. Events that do occur, but are rare, will often be observed with too poor statistics to draw solid conclusions. Furthermore, it is challenging to characterize observed processes quantitatively in a way suitable for comparison with experimental findings.

This project aims to develop ULTRO (UniversaL Tool for modeling biophysical pROcesses) – a unique methodology based on MD simulations, tailored to study a range of mechanical processes in sensory biomolecular structures, which are too slow to be observed in traditional MD simulations. To achieve the goal, ULTRO will employ a modified MD algorithm that is designed to determine the free energy profile along a specific reaction coordinate, which will essentially define the modelled process. As such, ULTRO will provide a hypothesis-driven rather than exploratory approach: a specific process will be tested rather than letting the system move freely to "see what happens". This approach will permit to address a larger range of biophysical processes and will deliver richer in-formation on the specific processes that are suspected to occur in biomolecular sensory systems.

We are looking for a highly motivated PhD candidate with an academic university degree (Master or equivalent) in Physics, Chemistry or related fields. Applicants should have good computing skills, experience and training in computational modelling and a strong interest in computational biophysics. Experience with classical MD simulations and free energy perturbation methods is an advantage. Good English language skills are expected.

Funding Notes

The German Research Foundation (DFG)-funded Research Training Group 1885 Molecular Basis of Sensory Biology is offering a
Ph.D. position (TV-L E13 65%) m/f/d.

The RTG Molecular basis of Sensory Biology (View Website) and the University of Oldenburg are aware of the power of diversity. In order to increase the percentage of female faculty and staff members, female candidates with equal qualification will be given preference. Applicants with disabilities will be preferentially considered in case of equal qualification.

References

https://quantbiolab.com/ --> the lab is moving to Oldenburg (Germany)

https://uol.de/en/sensorybio --> Website of the Research Training group in Oldenburg

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