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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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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 ;
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article)
12.) M. Baadenand M.S.P.
Sansom: "OmpT: molecular dynamics
simulations of an outer membrane enzyme",
Biophys.J.87, 2004,
2942-2953. (Abstract ;
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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 ;
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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.
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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.
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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)
Invited contributions to international peer-reviewed
journals
21.) 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)
22.)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)
23.) 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 ;
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edited article)
Peer-reviewed conferences proceedings
24.) 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.
25.)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)
26.)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)
27.)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.
28.)O. Delalande, N. Frey,
B. Laurent, M. Guroult, B. Hartmann and M.
Baaden: "Multi-resolution and
multi-physics approach for interactively locating funtionally
linked ion binding sites by steering small molecules into
electrostatic potential maps using a haptic device",
accepted at Pacific Symposium for Biocomputing
2010.
NB:25 to 28 are also invited
presentations to peer-reviewed, internationally established
conferences.
Peer-reviewed chapters in collective volumes
29.) 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)
30.) 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.
31.)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
32.)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.
33.)"Toucher, dformer et assembler des
molcules du bout des doigts ", Les cahiers de
l'ANR(in press).
Organisation of International conferences and
schools
34.)"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).
35.)"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.
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article)
5.)General Discussion, Faraday
Discuss.144, 2010, 445466.
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article)
