Scientific Publications Summary =============================== Marc Baaden 1. Research Articles ==================== 2000 ---- 1. M. Baaden, P. Granger and A. Strich; "Dependence of 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. 2. B. Lambert, V. Jacques, A. Shivanyuk, S. E. Matthews, A. Tunayar, M. Baaden, G. Wipff, V. Böhmer, 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. 3. 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, 303-304, 2000, 104-111. 4. M. Baaden, F. Berny, N. Muzet, L. Troxler, G. Wipff; "Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: a molecular dynamics investigation.", in Calixarenes for Separations, 2000, edited by G. Lumetta, R. D. Rogers, and A. S. Gopalan (Oxford University Press, New York), ACS Symposium Series 757, pp. 71-85. 5. 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. 6. M. Baaden, F. Berny, G. Wipff and C. Madic; "A molecular dynamics and quantum mechanics study of M3+ lanthanide cation solvation by acetonitrile: the role of cation size, counterions and polarization effects investigated.", J. Phys. Chem. A, 104, 2000, 7659-7671. 7. 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.", in Proceedings of the Euradwaste 1999 conference, 2000, edited by C. Davies (EC, Luxemburg), pp. 390-393. 8. L. Troxler, M. Baaden, V. Böhmer 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. 2001 ---- 9. 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. 10. 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 11. 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 2002 ---- 12. M. Baaden, R. Schurhammer and G. Wipff; "Molecular dynamics study of the uranyl extraction by TBP: demixing of water / 'oil' / TBP solutions with a comparison of supercritical CO2 and chloroform.", J. Phys. Chem. B, 106, 2002, 434-441 2003 ---- 13. 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 14. J. D. Campbell, P. C. Biggin, M. Baaden and M. S. P. Sansom; "Extending the structure of an ABC transporter to atomic resolution: modelling and simulation studies of Msba.", Biochemistry, 42, 2003, 3666-3673 15. 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 2004 ---- 16. J. D. Faraldo-Gómez, 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.", Proteins, 57, 2004, 783-791 17. M. Baaden M and M. S. P. Sansom "OMPT: Molecular Dynamics simulations of an outer membrane enzyme.", Biophys. J., 87, 2004, 2942-2953 2005 ---- 18. 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 2007 ---- 19. K. Tai, M. Baaden, S. Murdock, B. Wu, M. Hong 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 2. Scientific Presentations and Posters (up to 2005) ==================================================== 1999 ---- 20. M. Baaden, M. Burgard, D. Matt and G. Wipff, "Selective extraction of lanthanide cations by tetra-phosphineoxide substituted calix{4}arenes: a molecular dynamics study at a water/chloroform interface." o Meeting of the SFC-Grand Est, Strasbourg, France, January 21-22, 1999. o Annual meeting of the GDR PRACTIS, Avignon, France, Febuary 25th, 1999. o Journée de l'école doctorale de Chimie Physique of Strasbourg, France, April, 1999. o PRACTIS Atelier "Modélisation", Seyssins, France, November 25th 1999. 21. M. Baaden, M. Burgard, D. Matt and G. Wipff, "Selective extraction of lanthanide cations by tetra-phosphineoxide substituted calix{4}arenes: a molecular dynamics study at a water/chloroform interface." o Short presentation, Journée de l'école doctorale de Chimie Physique of Strasbourg, France, April, 1999. 22. M. Baaden, "Solvation of M3+ lanthanide cations in acetonitrile solution" o Seminar lecture, Strasbourg, France, May, 1999. 23. M. Baaden, L. Troxler and G. Wipff, "Interfacial aspects in liquid-liquid ion extraction." o Lecture, 26th International conference on solution chemistry (26ICSC), Fukuoka, Japan, 27 July 1999. 24. A. Strich, M. Baaden and P. Granger, "Dependence of 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." o 6ème Ecole d'Eté de Physico-Chimie Théorique, Marly-le Roi, September 6-10, 1999. o 11th European seminar on computational methods in quantum chemistry, Zakopane, Poland, September 23-25, 1999. o 2ème rencontre des Chimistes Théoriciens du Grand Est, Reims, October 15th 1999. 2000 ---- 25. M. Baaden, F. Berny, N. Muzet, R. Schurhammer and G. Wipff, "Computer Modeling of liquid - liquid ion extraction." o Euradwaste '99, Luxembourg, November 15-18, 1999. o PRACTIS Atelier "Modélisation", Seyssins, France, November 25th 1999. o 2nd COST D11 workshop on supramolecular chemistry, Strasbourg, France, December 10-12, 1999. o Journées PRACTIS, Villeneuve-lès-Avignon, February 17-18, 2000. 26. M. Baaden, "Etudes de molécules extractantes en solution: aspects structuraux et mécanistiques des effets de synergie" o Doctoriales d'Alsace 1999, Mittelwihr, France, November 1999. o Journées PRACTIS, Villeneuve-lès-Avignon, February 17-18, 2000. 27. M. Baaden, L. Troxler and G. Wipff, "Interfacial aspects in liquid-liquid ion extraction." o Seminar lecture, Oxford, England, 9 June 2000. 28. M. Baaden, "Energy profiles for interface crossing in liquid-liquid ion extraction." o Seminar lecture, Zurich, Switzerland, 24 May 2000. 29. M. Baaden, "Energy profiles for interface crossing in liquid-liquid ion extraction." o CECAM workshop on challenges in Free energy calculations, Lyon, France, 22 June 2000. 2001 ---- 30. M. Baaden, M. S. P. Sansom, "Barrels & corks in a computer, modelling bacterial iron transport systems." o Poster presentation at the Biochemical Society Meeting, University of York, 17-19 December 2001. (Biochemical Soc. Trans. Part 1, 30, 2002, A44) 31. M. Baaden, "Modelling the ligand-gated protein channel and ferric enterobactin receptor FepA." o Seminar, Mathematical Biology Division, National Institute for Medical Research, London, 4 December 2001. 32. M. Baaden, "Modélisation de la protéine membranaire FepA, transporteur bactérien du fer." o Seminar, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, 18 October 2001. 33. M. Baaden, M. S. P. Sansom, "Modelling the FepA protein, a bacterial iron transporter in the outer membrane." o Lecture, Biophysical Chemistry 2001 Conference, Imperial College, London, 21 September 2001. 34. M. Baaden, various seminar lectures, Oxford, England. 2002 ---- 35. M. Baaden, M. S. P. Sansom, "Barrels & corks in a computer, modelling bacterial iron transport systems." o Poster presentation at the Kollman Memorial Symposium, UCSF, San Francisco, 21-22 February 2002. o Poster presentation at the 46th Annual Meeting of the Biophysical Society, San Francisco, 23-27 February 2002. (Biophys. J. Part 2, 82, 2002, 2610) o Poster presentation at the 6èmes Journées Francophones des Jeunes Physico-Chimistes, Marseille, 3-5 July 2002. 36. M. Baaden, "Modelling the ligand-gated protein channel and ferric enterobactin receptor FepA." o Seminar, Laboratory of Molecular Biophysics, Oxford, 5 February 2002 37. M. Baaden, M. S. P. Sansom, "Understanding bacterial iron transport." o Lecture, SFC Eurochem Conference, Toulouse, France, 8 July 2002. 2003 ---- 38. M. Baaden, C. Meier and M. S. P. Sansom; "Molecular dynamics simulations of outer membrane phospholipase A." o Poster presentation at the EURESCO Conference 2003-192 Bionanotechnology: "Euroconference on Biomolecular Devices", Granada, Spain, 9-14 July, 2003. 39. M. Baaden, "La dynamique moléculaire in silico." o Course and tutorial, Ecole Thématique du CNRS, Outils pour étudier la structure et la dynamique des peptides et des protéines, Arcachon, 18-24 Mai 2003. 40. M. Baaden, M. S. P. Sansom, "Les protéines membranaires Ompla et Fepa." o Lecture, GGMM bi-annual conference, Cabourg, France, 7 Mai 2003. 41. M. Baaden, "Protéines membranaires à repliement 'tonneau béta' - modélisation et dynamique moléculaire de l'enzyme OmplA et du transporteur bactérien du fer FepA." o Seminar, Institut Européen de Chimie et Biologie, Bordeaux, 4 April 2003. 42. M. S. P. Sansom, P.Bond, M. Baaden, J.D. Faraldo-Gómez, S. Deol, C. Meier, K. Cox, "Simulation of Outer Membrane Proteins." o Poster presentation at the Gordon Research Conference "Protons & Membrane Reactions", Ventura, CA, United States, 23-28 February 2003. o 47th Annual Meeting of the Biophysical Society, San Antonio, United States, 1-5 March 2003. 2004 ---- 43. M. Baaden, C. Meier and M. S. P. Sansom; "Molecular dynamics simulations of outer membrane phospholipase A." o Poster presentation at the 48th Annual Meeting of the Biophysical Society, Baltimore, United States, 14-18 February 2004. 44. M. Baaden, "Molecular dynamics simulations of outer membrane phospholipase A." o Seminar, Woolf lab, Johns-Hopkins University School of Medicine, Baltimore, 20 February 2004. o Seminar, Osman lab, Mount Sinai School of Medicine, New York, 23 February 2004. o Seminar, Roux lab, Weill Medical College of Cornell University, New York, 26 February 2004. 45. M. Baaden, "Dynamique moléculaire de OmplA, une phospholipase de la membrane externe bactérienne." o Seminar, Huitièmes Entretiens de l'IBPC, Paris, France, 6 April 2004. 46. M. Baaden, M. S. P. Sansom, "La protéine membranaire Ompla." o Seminar, Ben Msik Sciences Faculty, Casablanca, Morocco, 16 June 2004. 2005 ---- 47. M. Baaden, M. S. P. Sansom; "Molecular Dynamics Simulations of an Outer Membrane Enzyme." o Platform presentation at the 49th Annual Meeting of the Biophysical Society, Long Beach, United States, 12-16 February 2005. 48. J. D. Faraldo-Gómez, L. R. Forrest, M. Baaden, P. J. Bond, C. Domene, G. Patargias, J. Cuthbertson, M. S. P. Sansom; "On the convergence of the conformational sampling in molecular dynamics simulations of membrane proteins." o Poster presentation at the 49th Annual Meeting of the Biophysical Society, Long Beach, United States, 12-16 February 2005. 49. M. S. P. Sansom, K. Tai, B. Wu, S. Khalid, M. Baaden; "BioSimGRID: Application to Analysis of Membrane Protein Simulations." o 49th Annual Meeting of the Biophysical Society, Long Beach, United States, 12-16 February 2005. 50. M. Baaden; "Utilisation de VMD et OpenDX." o Presentation at the Journée Visualisation Scientifique, IDRIS, Orsay, France, 8 March 2005. 51. M. Baaden; "Le système SHAMAN: Système HAptique pour MAnipulation Nanoscopique." o Seminar, CEA/DIF Centre DAM-Île de France Bruyères-le-Chatel, 14 April 2005. 52. R. Chater, D. Perahia, K. A. Chihab, S. Moussamih, A. Adlouni, M. Baaden, K. Zakrzewska, R. Lavery, M. El Messal, A. Kettani; "Modélisation moléculaire des mutations du récepteur des lipoprotéines de faible densité impliquées dans l'hypercholesterolémie familiale au Maroc" o Poster presentation at the Xème Symposium ICSN, Gif-sur-Yvette, France, 1-3 June 2005.