Laboratory of Computational Chemistry and Biochemistry
Institute of Chemical Sciences and Engineering
Swiss Federal Institute of Technology EPF Lausanne
Group Röthlisberger
Tel: +41 1 633 4194
Fax: +41 21 693 0320
michel.cuendet[at]epfl.ch
Official affiliation :
Group of Prof. van Gunsteren
Lab of Physical Chemistry
Hönggerberg HCI G227
ETH Zürich
Theoretical studies on thermostated dynamics and the Jarzynski identity
Advanced nonequillibrium methods for free energy calculations
Integration algorithms for molecular dynamics simulation
Steered molecular dynamics application :
The T cell receptor - peptide - MHC complex
QM/MM study of the copper protein azurin
M. Cascella, M. A. Cuendet, I. Tavernelli and U. Röthlisberger, "Optical spectra characterization in metalloproteins: Cu(II) photoexcitation in azurin by hybrid TDDFT-molecular dynamics simulations", submitted to Phys. Rev. Lett. (2006)
M. A. Cuendet, W. F. van Gunsteren, "On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm", submitted to J. Chem. Phys. (2006)
M. A. Cuendet, "The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles", J. Chem. Phys. 125 : 144109 (2006)
M. A. Cuendet, "Statistical mechanical derivation of the Jarzynski identity for non-Hamiltonian thermostated dynamics", Phys. Rev. Lett. 96(1) : 120602 (2006).
A. Labbi, M. Cuendet, "Predictive Data Mining for Project Portfolio Risk Management" in "Handbook of Integrated Risk Management for E-Business : Measuring, Modeling, and Managing Risk", J. Ross Publishing (2005), p. 151 (ISBN 193215907X).
M. Cuendet, A. Labbi, "Consistent AdaBoost for boosting stumps", Proceedings of the International Conference on Machine Learning and Applications - ICMLA 2002, Las Vegas, Nevada, USA. CSREA Press (2002) p. 117.
M. Cuendet, A. Labbi, "Some theoretical and practical perspectives on boosting weak predictors", IBM Research technical paper RZ3402 (2002).
A.Labbi, M. Cuendet, "Boosted decision trees for project risk assessment and pricing", IBM Research technical paper RZ340 (2002).
"Aspects of nonequilibrium molecular dynamics", First Maxwell Institute Colloquium on Applications of Mathematics, University of Edinburgh (UK), November 23, 2006.
"A steered molecular dynamics study of the TCR-pMHC complex" (poster only), Gordon Research Conference on Computational Chemistry, Les Diablerets (CH), October 8-13, 2006.
"Derivation of the Jarzynski identity for non-Hamiltonian thermostated dynamics", CECAM Workshop: Theory of single molecule force experiments and simulations, Lyon (F), September 26-29, 2006.
"Statistical mechanical derivation of the Jarzynski identity for thermostated dynamics", (talk for the first poster price), 367. WE-Heraeus-Seminar: Biomolecular Simulation: From Physical Principles to Biological Function, Bad Honnef (D), May 22-24, 2006.
"Binding free energy profiles of specific immune recognition complexes", High performance computing for the life sciences (2nd Annual Vital-IT Symposium), Geneva (CH), April 7, 2006.
"Association free energy profile of the TCR-pMHC complex determined by steered molecular dynamics", Computer Simulation and Theory of Macromolecules, Hünfeld (D), May 19-21, 2005.
"A statistical mechanical proof of the Jarzynski identity, ... and little remarks about Gromacs", 15th Annual BIOMOS Meeting, Burg Arras (D), August 31, 2005.
"Predictive Analysis for Project Portfolio Risk Management", Tenth International Congress on Computational and Applied Mathematics ICCAM, Leuven (BE), 2002.
