Multidimensional Free Energy Landscapes from Bias-Exchange Metadynamics
Event details
| Date | 19.11.2015 |
| Hour | 09:30 |
| Speaker | Prof. Alessandro Laio, International School for Advanced Studies (SISSA), Trieste (I) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
Bias exchange [1] is an approach that combines replica exchange [2] with metadynamics [3] and allows, with a moderate computational effort, the simultaneous reconstruction of the free energy as a function of a large number of variables. This allows simulating very complex reactions, like protein folding, in which the reaction coordinate is totally unknown. We will discuss applications of the methodology to protein folding, to amyloid aggregation, and to the study of drug-protein interaction.
[1] S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007).
[2] Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
[3] A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. USA 99,12562 (2002).
Bio:
Abstract:
Bias exchange [1] is an approach that combines replica exchange [2] with metadynamics [3] and allows, with a moderate computational effort, the simultaneous reconstruction of the free energy as a function of a large number of variables. This allows simulating very complex reactions, like protein folding, in which the reaction coordinate is totally unknown. We will discuss applications of the methodology to protein folding, to amyloid aggregation, and to the study of drug-protein interaction.
[1] S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007).
[2] Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
[3] A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. USA 99,12562 (2002).
Bio:
- February 1995: Degree in Nuclear Engineering at Politectnico di Torino. Thesis: A quantum interpretation of the anomalous redshifts in astrophysics and cosmology. Supervisors: Guido Rizzi and Luigi Accardi (University of Rome II).
- Ph.D. degree obtained in October 1999 . Thesis: Simulation of iron at Earth core conditions. Supervisors: Sandro Scandolo, Guido Chiarotti and Erio Tosatti.
- January 2000- December 2001: postdoctoral research assistant in the group of Prof. Ursula Rothlisberger at ETH Zurich.
- January 2002- December 2005: postdoctoral research assistant in the group of Prof. Michele Parrinello in Lugano.
- Since January 2006: Assistant Professor at nternational School for Advanced Studies (SISSA), Trieste (I)
- Current: Associate Professor in Statistical and Biological Physics at SISSA, Trieste.
Practical information
- Informed public
- Free