Skip to content. | Skip to navigation


Sections
Document Actions

Dreyer Seminar

What Seminar
When 2012-05-21
from 16:00 to 17:00
Where Seminar room 115, 1st floor, Rogowski building, Schinkelstr. 2
Contact Name Janssen
Contact Email
Add event to calendar vCal
iCal

Large-Scale ab initio Applications in Biophysics

Dr. Jens Dreyer
Computational Biophysics, German Research School for Simulation Sciences

Abstract:

Biological ion channels are pore-forming transmembrane proteins which selectively regulate transport of ions in and out of every living cell. Dysfunction of ion channels are at the basis of several diseases called channelopathies, including, for instance, cystic fibrosis, epileptic seizure, diabetes and migraine [1].
The mechanism of proton transport in ion channels is investigated entirely by first principles molecular dynamics simulations applying Car-Parrinello methods [2]. We focus on the monovalent ion selective channel Gramicidin A [3]. The transport of excess protons along the 1-dimensional wire of water molecules inside the Gramicidin channel is faster (a single conduction event takes about 500 ps) than in any other narrow-pore biological channel conducting H+ or other monovalent ions [4]. We calculate free energy profiles using metadynamics [5] and analyze the subsequent steps of proton transfer, which involves a detailed understanding of the sequence of alternating hydrogen and chemical bond breaking and making processes, the interplay of the electrostatic interactions imposed by the protein, the membrane and the surrounding water molecules. This project of simulating a fundamental biological system in laboratory-feasible conditions fully from first-principles is made possible by access to supercomputing facilities and support through the PRACE (Partnership for Advanced Computing in Europe) 1st regular call.

[1] F. M Ashcroft, Ion channels and diseases, Academic press, 1999. [2] R. Car, M. Parrinello, Phys. Rev. Lett. 1985, 55, 2471. [3] D. A. Kelkar, A. Chattopadhyay, Biochimica et Biophysica Acta 2007, 1768, 2011. [4] T. E. DeCoursey, J. Physiol. 2008, 22, 5305. [5] A. Laio, M. Parrinello, Proc. Nat. Acad. Sci. USA 2002, 99, 12562.

« April 2014 »
Su Mo Tu We Th Fr Sa
12345
6789 1011 12
13141516171819
20212223 2425 26
2728 2930
Upcoming Events
General Assembly 2014/1 AICES,
2014-04-25
Horsch Seminar Room 115, AICES, Rogowski,
2014-04-28
Landis Seminar Room 115, AICES, Rogowski,
2014-05-05
Benner Seminar Room 115, AICES, Rogowski,
2014-05-06
Bordas Seminar Room 115, AICES, Rogowski,
2014-05-12
Upcoming events…
News
Dr. Nicole Faber Presented the Concept of the Charlemagne Distinguished Lecture Series at the DFG Workshop on International Research Marketing 2014-02-18
Prof. Manuel Torrilhon Named Associated Editor to the SIAM Journal of Numerical Analysis 2014-02-18
AICES Participated in RWTH Consulting Days for Students 2014-02-07
AICES Professor Manuel Torrilhon Receives Fellowship from the University of Texas at Austin 2014-02-07
AICES Principal Investigator to Become New Chairman of the Board of Forschungszentrum Jülich 2014-01-24
More news…