Scientific Publications Summary

Publications in international peer-reviewed journals

1.) M. Baaden, P. Granger and A. Strich: "Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X", Mol.Phys.98, 2000, 329-342. (Abstract ; Download edited article)

2.)B. Lambert, V. Jacques, A. Shivanyuk, S.E. Matthews, A. Tunayar, M. Baaden, G. Wipff, V. Boehmer and J.F. Desreux: "Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes", Inorg.Chem.39, 2000, 2033-2041. (Abstract ; Download edited article)

3.) M. Baaden, G. Wipff, M.R. Yaftian, M. Burgard and D. Matt: "Cation coordination by calix[4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study", J.Chem.Soc. Perkin Trans.2.2000, 1315-1321. (Abstract ; Download edited article)

4.) M. Baaden, F. Berny, C. Madic and G. Wipff: "M3+ lanthanide cation solvation by acetonitrile: The role of cation size, counterions, and polarization effects investigated by molecular dynamics and quantum mechanical simulations", J.Phys.Chem.A.104, 2000, 7659-7671. (Abstract ; Download edited article)

5.) M. Baaden, M. Burgard, C. Boehme and G. Wipff: "Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations", Phys.Chem.Chem.Phys.3, 2001, 1317-1325. (Abstract ; Download edited article)

6.) M. Baaden, M. Burgard and G. Wipff: "TBP at the water-oil interface: the effect of TBP concentration and water acidity investigated by molecular dynamics simulations", J.Phys.Chem.B.105, 2001, 11131-11141. (Abstract ; Download edited article)

7.) M. Baaden, R. Schurhammer and G. Wipff: "Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/"oil"/TBP solutions with a comparison of supercritical CO2 and chloroform", J.Phys.Chem.B.106, 2002, 434-441. (Abstract ; Download edited article)

8.) M. Baaden, F. Berny, R. Schurhammer, C. Madic and G. Wipff: "Theoretical studies on lanthanide cation extraction by picolinamides: ligand-cation interactions and interfacial behavior", Solv.Extr.Ion.Exch.21, 2003, 199-219. (Abstract ; Download edited article)

9.)J.D. Campbell, P.C. Biggin, M. Baadenand M.S.P. Sansom: "Extending the structure of an ABC transporter to atomic resolution: modelling and simulation studies of Msba", Biochemistry42, 2003, 3666-3673. (Abstract ; Download edited article)

10.) M. Baaden, C. Meier and M.S.P. Sansom: "A molecular dynamics investigation of mono- and dimeric states of the outer membrane enzyme Ompla", J.Mol.Biol.331, 2003, 177-189. (Abstract ; Download edited article)

11.)J.D. Faraldo-Gomez, L.R. Forrest, M. Baaden, P.J. Bond, C. Domene, G. Patargias, J. Cuthbertson and M.S.P. Sansom: "Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations", Proteins57, 2004, 783-791. (Abstract ; Download edited article)

12.) M. Baadenand M.S.P. Sansom: "OmpT: molecular dynamics simulations of an outer membrane enzyme", Biophys.J.87, 2004, 2942-2953. (Abstract ; Download edited article)

13.)R.J. Law, C. Capener, M. Baaden, P.J. Bond, J. Campbell, G. Patargias, Y. Arinaminpathy and M.S.P. Sansom: "Membrane protein structure quality in molecular dynamics simulation", J.Mol.Graph.Model.24, 2005, 157-165. (Abstract ; Download edited article)

14.)K. Tai, M. Baaden, S. Murdock, B. Wu, M.H. Ng, S. Johnston, R. Boardman, H. Fangohr, K. Cox, J.W. Essex and M.S.P. Sansom: "Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database", J.Mol.Graph.Model.25, 2007, 896-902. (Abstract ; Download edited article)

15.)K. Cox, P.J. Bond, A. Grottesi, M. Baadenand M.S.P. Sansom: "Outer Membrane Proteins: Comparing X-Ray and NMR Structures by MD Simulations in Lipid Bilayers", Eur. Biophys. J.37, 2008, 131-141. (Download edited article)

16.)M. Neri, M. Baaden, V. Carnevale, C. Anselmi, A. Maritan and P. Carloni: "Microseconds Dynamics Simulations of the Outer-Membrane Protease T", Biophys.J.94, 2008, 71-78. (Download edited article)

17.)M.P. Durrieu, R. Lavery and M. Baaden: "Interactions between neuronal fusion proteins explored by molecular dynamics", Biophys.J.94, 2008, 3436-3446. (Download edited article)

18.)N. Bocquet, H. Nury, M. Baaden, C. Le Poupon, J.P. Changeux, M. Delarue and P.J. Corringer: "X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation", Nature, 457, 2009, 111-114. (Download edited article)

19.)O. Delalande, N. Frey, G. Grasseau and M. Baaden: "Complex Molecular Assemblies at hand via Interactive Simulations", 2009, J. Comput. Chem.30, 2009, 2375-2387. (Download edited article)

20.)M.P. Durrieu, P.J. Bond, M.S.P. Sansom, R. Lavery and M. Baaden: "Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states", ChemPhysChem, 10, 2009, 1548-1552. (Download edited article)

21.)D. K. Sinha, P.Neveu, N. Gagey, I. Aujard, C. Ben-brahim-Bouzidi, T. Le Saux, C. Rampon, C. Gauron, B. Goetz, S. Dubruille, M. Baaden, M. Volovitch, D. Bensimon, S. Vriz and L. Jullien : "Photocontrol of protein activity in a single cell of a live organism", ChemBioChem, 11, 2010, 653-663. (Download edited article)

22.)H. Nury, F. Poitevin, C. Van Renterghem, J.P. Changeux, P.J. Corringer, M. Delarue and M. Baaden: "One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue", PNAS, early edition, 2010. (Abstract ; Download edited article open access)

Invited contributions to international peer-reviewed journals

23.) M. Baaden, F. Berny, C. Boehme, N. Muzet, R. Schurhammer and G. Wipff: "Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study", J.Alloys&Compounds.303, 2000, 104-111. (Abstract ; Download edited article)

24.)L. Troxler, M. Baaden, V. Bohmer and G. Wipff: "Complexation of M3+ lanthanide cations by calix[4]arene-CMPO ligands: a molecular dynamics study in methanol solution and at a water/chloroform interface", Supramol.Chem.12, 2000, 27-51. (Abstract ; Download edited article)

25.) M. Baaden, F. Berny and G. Wipff: "The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation", J.Mol.Liq.90, 2001, 1-9. (Abstract ; Download edited article)

26.)P.J. Corringer, M. Baaden, N. Bocquet, M. Delarue, V. Dufresne, H. Nury, M. Prevost, C. Van Renterghem: "Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues", J.Physiol., 588, 2010, 565-72. (Download edited article)

Peer-reviewed conferences proceedings

27.) M. Baaden, F. Berny, N. Muzet, R. Schurhammer and G. Wipff : "Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores", 2000, in Proceedings of the Euradwaste 1999 conference, edited by C. Davies, pp. 390-393, EC, Luxembourg.

28.)E. Krieger, L. Leger, M.P. Durrieu, N. Taib, P. Bond, M. Laguerre, R. Lavery, M.S.P. Sansom and M. Baaden: "Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure", 2007, in ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications, edited by C.B.G.R. Joubert, F. Peters, T. Lippert, M. Buecker, B. Gibbon, and B. Mohr, Vol. 38, pp. 729-736, John von Neumann Institute for Computing, Juelich, Germany. (Download edited article)

29.)N. Frey, O. Delalande, G. Grasseau and M. Baaden: "A VR framework for interacting with molecular simulations", 2008, in Proceedings of the 2008 ACM symposium on Virtual reality software and technology, edited by E. Kruiff, pp. 91-94, ACM, Bordeaux, France. (Download edited article)

30.)N. Frey, O. Delalande, G. Grasseau and M. Baaden: "From Interactive to Immersive Molecular Dynamics", 2008, in Proceedings of the International Workshop on Virtual Reality and Physical Simulation (VRIPHYS'08),edited by F. Faure and M. Teschner, pp. 89-96, Eurographics, Grenoble, France.

31.)O. Delalande, N. Frey, B. Laurent, M. Guroult, B. Hartmann and M. Baaden: "Multi-resolution and multi-physics approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device", Pac. Symp. Biocomput., 2010, 205-15. (Download edited article)

NB:28 to 31 are also invited presentations to peer-reviewed, internationally established conferences.

Peer-reviewed chapters in collective volumes

32.) M. Baaden, F. Berny, N. Muzet, L. Troxler and G. Wipff : "Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: a molecular dynamics investigation", 2000, in Calixarenes for separations, ACS Symposium Series 757, edited by G. Lumetta, R.D. Rogers, and A.S. Gopalan, pp. 71-85, Oxford University Press, New York. (Abstract)

33.) M. Baadenand R. Lavery : "There's plenty of room in the middle: multi-scale modelling of biological systems", 2007, in Recent Advances in Protein engineering, Research signpost, India, edited by A.G. de Brevern, pp. 173-195, Research Signpost, Trivandrum, Kerala, India.

34.)S. Khalid and M. Baaden: "Molecular dynamics studies of outer membrane proteins : a story of barrels", 2009, in Molecular Simulations and Biomembranes: From Biophysics to Function, edited by P.C. Biggin and M.S.P. Sansom, Royal Society of Chemistry, United Kingdom (in press).

Further dissemination of my work

35.)CSC News3, 2007, 10-11; 12. Tietoyhteys3, 2007, 10-11; 12-13. DEISA Newsletter5, 2007. DEISA Newsletter5, 2008. iSGTW 1/2008; iSGTW 10/2008. CORDIS News 11/2007. Supercomputing online 11/2007 and more.

36.)"Toucher, dformer et assembler des molcules du bout des doigts ", Les cahiers de l'ANR(in press).

Organisation of International conferences and schools

37.)"Bioimage summer school" (http://www.ecole2005.ibpc.fr), multidisciplinary international summer school, ENS, Paris, 11-22 july 2005 (co-organiser with F. Amblard, V. Croquette, M. Dahan, J.P. Henry, R. Lavery and A. Triller).

38.)"Biomolecular Simulations", satellite meeting of the 5th EBSA congress and of the 15th international IUPAB congress of biophysics, Bordeaux, 1-2 september 2005 (co-organiser with J. Elezgaray, M. Laguerre and M.S.P. Sansom).

Other scientific publications

1.)M. Baaden: "Molecular Modeling with the ChemOffice Ultra 4.5 program suite.", published on web, 1999, CambridgeSoft Corporation. (Download a PDF version of my ChemOffice Ultra 4.5 Review)

2.)M. Baaden: "Etudes de molcules extractantes en solution et aux interfaces liquide-liquide: aspects structuraux et mcanistiques des effets de synergie", Ph.D. Thesis, 2000, Universit Louis Pasteur, Strasbourg (N: 3630), 2 vol., 218/42 pages. (Abstract ; Download PhD thesis, vol. 1 (6.9MB) ; Download PhD thesis, vol. 2 (73.6MB))

3.) M. Baaden, F. Berny, G. Wipff; Contribution to the AMBER Parameter Database. Accessible online at http://www.pharmacy.manchester.ac.uk/bryce/amber.

4.)General Discussion, Faraday Discuss.144, 2010, 203222. (Download edited article)

5.)General Discussion, Faraday Discuss.144, 2010, 445466. (Download edited article)

Other publications

6.)"Itineraires Bis.", a book about early career research at CNRS (in French). (Amazon Page ; Itineraires Bis on FaceBook)