Горячая PhD-позиция на альпийском курорте во Франции!!!
Тема - компьютерное моделирование макромолекул, разработка алгоритмов и их применение на различных биологических объектах.
Шлите резюме на stephane.redon_at_inria.fr, s.grudinin_at_fz-juelich.de
Вся информация:
A) Advisors
- Stephane Redon - INRIA, i3D team - http://i3d.inrialpes.fr/~redon
- Serge Crouzy (bio-physicist, HDR) - CEA, LBMC
B) Topic
Title: Generalized Adaptive Molecular Dynamics
An average human cell contains several billion molecules. Understanding the complexity underlying the mechanisms and interactions of these molecules would have wide-ranging applications. For example, gaining a precise understanding of how proteins fold and interact would have a tremendous impact on drug design.
One way to understand molecular mechanisms is through modeling and simulation. Unfortunately, the cost of molecular simulations increases with the size of the simulated systems. This makes it extremely difficult to study large systems (e.g. viruses) over long time periods. To address this problem, researchers typically have to increase the processing power (which might be expensive), or make arbitrary simplifications to the system (which might bias the study).
We have recently developed an adaptive simulation method [1,2,4,6], which rigorously and automatically predicts the most mobile groups in a simulated molecular system, and simulates these groups only. This method allows the user to adapt the simulation to available resources, while guaranteeing that a good approximation is found under the imposed constraints [3,4]. We now want to generalize the adaptive simulation theory.
In the current approach, the simulated degrees of freedom are the torsion angles of a molecule, which describe rotations around covalent bonds [4]. The first generalization sought is to handle other types of degrees of freedom (e.g., bond lengths and angles). Especially, we want to generalize the adaptive simulation theory to rigid body joints, in order to adaptively refine simulations of groups of molecules.
A second generalization is to handle kinematic cycles in molecules. In the current theory, the kinematic graph of a molecule has to be acyclic. This allows us to simulate proteins and the flexibility of the amino-acids side chains, but may be insufficient to model other types of biological molecules (for examples, sugars, DNA, etc.). To generalize the adaptive theory to cycles, new algorithms have to be designed.
A third generalization is to adaptively handle restraints in molecular systems (e.g. inter-atomic distances restraints, symmetry restraints, etc.). These restraints are necessary to help biologists design and manipulate models of complex, macro-molecular systems.
If time allows, other extensions will be explored. For example, a challenging task in macro-molecular simulation is the efficient sampling of the conformational space available to the system. Other possible generalizations may thus include (adaptive) multiple time step methods, hybrid Monte-Carlo simulations, etc.
The PhD candidate will develop the mathematics of the generalized adaptive simulation theory, will design and implement the corresponding algorithms, and will validate the work on various biological applications, in collaboration with bio-physicists and biologists at CEA [5].
C) References (available at http://i3d.inrialpes.fr/~redon)
[1] S. Redon and M. C. Lin. "An Efficient, Error-Bounded Approximation Algorithm for Simulating Quasi-Statics of Complex Linkages". Proceedings of ACM Symposium on Solid and Physical Modeling, 2005.
[2] S. Redon, N. Galoppo and M. C. Lin. "Adaptive Dynamics of Articulated Bodies". ACM Transactions on Graphics, 25(3), 2005.
[3] S. Morin and S. Redon. "A Force-Feedback Algorithm for Adaptive Articulated-Body Dynamics Simulation". Proceedings of IEEE International Conference on Robotics and Automation, 2007.
[4] http://i3d.inrialpes.fr/~redon/AMQ
[5] CEA is a French government-funded technological research organisation (http://www.cea.fr/english_portal).
[6] R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam, S. Crouzy, M. Vivaudou, and S. Redon. "Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design". Bioinformatics 2007 23(13):i408-i417 (ISMB/ECCB 2007).
D) For more information / to apply:
- Visit http://i3d.inrialpes.fr/~redon/AMQ
- Contact us: stephane.redon @ inria.fr
