Project: Simulation of transmembrane transport | Positions | Beckstein Lab

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Project: Simulation of transmembrane transport

Project: Simulation of transmembrane transport

A central process in maintaining life is the transport of ions or small molecules such as nutrients across the cell membrane by secondary active transporter proteins. Although the three-dimensional structures of some of these transporters are known, their detailed molecular mechanism is not fully understood and key steps in the transport cycle have remained elusive, namely where transported molecules and ions bind and how binding triggers the transport event. Lack of such insights hampers a deeper understanding of the fundamental principles by which transporters act as molecular machines that transduce energy through macromolecular conformational changes. In this project you will use molecular dynamics (MD) computer simulations to determine how a large transported molecule may fit through a transporter protein that according to experimental structural data appears to be too narrow.

Solving this puzzle will be the first important step in understanding the physical mechanism of transport in this class of proteins. The project is carried out in close collaboration with experimental colleagues in the UK and results from the theoretical work will determine the direction of experiments to be done. This project may lead to a full PhD project.

In this project you will

  • carry out molecular dynamics simulations of membrane proteins, including advanced simulation techniques to simulate conformational changes
  • write code to quantitatively analyze your simulations (and learn the Python programming language to do so)
  • learn to run simulations on supercomputers

Discuss: “Project: Simulation of transmembrane transport”

August 19, 2015 at 1:25 pm #

Dear Prof. O. Beckstein
I read about your project and I liked it, I have some experience in this field so I would appreciate if you would let me join your project.
I wanted to know if there is any opportunity to join this project as a long-distance student?
Regards
Mahdi Moosaei

Posted by  mahdi moosaei
August 19, 2015 at 2:24 pm #

Dear Mahdi Moosaei,

This project is a rotation project for students enrolled in the PhD porgram in Physics (or Chemistry and Biochemistry) at Arizona State University. If you are part of these programs then you will be able to select this project in the next few days. Otherwise I encourage you to apply to our Graduate Program in Physics.

Best wishes,
Oliver Beckstein

Posted by  Oliver Beckstein

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