News & Events

Nouroddin Sotoudeh Chafi

Posted on September 21, 2016


Date - September 21, 2016
1:00 pm


Ph.D. Literature Seminar—751

Title “Finding meta stable states in s1p1 receptor by Markov chain method”


Since conformational changes are important in different biological processes like protein folding, signal transduction, a great number of researchers are interested to investigate it in biological macromolecules. The experimental works like X-ray crystallography or nuclear magnetic resonance spectroscopy (NMR) has given more detailed information about the function of the proteins and their structures, but they only provide information about the static of the molecules. For having a dynamic tool, Molecular dynamic (MD) simulation technique has been introduced. MD can describe the dynamic of molecules by using mechanic classic equations of movement which were produced by Newton. MD simulation has some limitations and it is its timescale. Thus far, the best MD simulators could only provide microscecond (10-6 s) trajectories while biological function are in order of miliseconds(10-3). To overcome this problem another mathematical technique recently caught researchers’ attention which is called Markov State Model (MSM). This technique has potential to bridge the timescale gap between MD and biological functions.