Phd Position in Adaptive Molecular Dynamics - FRANCE

Title: Adaptive Molecular Dynamics

Description: 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],
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.

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].

References (available at http://i3d.inrialpes.fr/~redon)
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[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).


Environment
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This position is offered at the “Rhone-Alpes” Research Unit of INRIA,
located near Grenoble and Lyon. The Unit counts more than 500 people,
within 25 research teams and 10 support services.

The starting date will be between september 2007 and december 15,
2007.

Duration: 3-years position.

Salary and benefits : 1529€ NET / month + full health insurance and
social benefits included - salary will be upgraded to 1611 € NET /
month the 3rd year.

For more information / to apply:
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- Visit http://i3d.inrialpes.fr/~redon/AMQ
- Contact us: stephane.redon@xxxxxxxx



Stephane


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Stephane Redon
INRIA Rhone-Alpes Research Unit
Zirst - 655 avenue de l'Europe - Montbonnot
38334 Saint Ismier Cedex - France
http://i3d.inrialpes.fr/~redon

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