Marc Baaden
Laboratoire de Biochimie Théorique, CNRS - UPR 9080
13, rue Pierre et Marie Curie
F-75005 Paris
France
Tel.: +33 1 58 41 51 76
Mail: baaden@ibpc.fr
URL: http://www.baaden.ibpc.fr
Professional Goal
Study of biological and chemical phenomena via theoretical methods based on physical chemistry and
leading to an understanding of processes at the atomic scale. At the same time I try to keep a close
contact to experiment and take advantage of novel approaches such as virtual reality.
Education
-
European PhD Thesis in theoretical chemistry (molecular dynamics), November 2000, Université Louis Pasteur (ULP), Strasbourg,
France and Ecole Polytechnique (ETH), Zürich,
Switzerland,
conducted by Prof. Georges Wipff and Prof. Michel
Burgard (Strasbourg) including a 3 months stay in
Prof. Wilfred van Gunsteren's group (Zürich):
'synergistic effects in liquid-liquid ion extraction.'
-
Diploma thesis ("DEA")
in physical chemistry,
September
1997,
Université Louis Pasteur (ULP), Strasbourg, France,
specialty: spectroscopic methods, directed by Prof. Pierre
Granger and Prof. Alain Strich: 'Ab
initio calculation of NMR chemical shielding tensors.'
-
Degree in chemical engineering ,
June
1997,
Ecole européenne des Hautes études de l'Industrie Chimique
de Strasbourg (EHICS), Strasbourg, France,
Tri-lingual curriculum (French, English, German) in
chemistry, specialty: material science.
-
Degree ('Diplom-Vorprüfung')
in chemistry,
April
1994,
University of Karlsruhe, Germany
-
German school leaving examination ('Abitur') ,
June
1991,
Einstein grammar school of Kehl, Germany,
Bilingual curriculum (German/French).
Research
Chargé de Recherche de 1ère classe
with Prof. Ph. Derreumaux at CNRS Paris
(Since 2007)
Chargé de Recherche de 2ème classe
with Dr R. Lavery at CNRS Paris
(2003 - 2006, 4 years)
Membrane proteins, enzymes and biological function, methodological developments and
applications in interactive molecular graphics and virtual reality.
Results published in Nature, Biophysical Journal, J. Comp. Chem., etc.
EC Research Fellow
with Prof. M.S.P. Sansom at Oxford University (GB)
(2001 - 2002, 2 years)
Computational studies of outer membrane proteins
published in JMB, Biochemistry, Biophysical Journal, etc.
PhD student
with Prof. G. Wipff and Prof. M. Burgard, France
(1997 - 2000, 3 years)
Molecular dynamics simulations of model systems (calixarenes,
TBP, HNO3) providing insight into
molecular recognition, complexation and liquid-liquid
extraction. -
Results published in JPCA, JPCB, Perkin. Trans.,
Inorg. Chem., J. Mol. Liquids, PCCP, etc.
Research internship
with Prof. W. F. van Gunsteren, Switzerland
(2000, 3 months)
Potential of mean force calculations for solute transfer across a
water/chloroform interface.
Diploma work
with Prof. P. Granger and Prof. A. Strich, Strasbourg,
France
(1997, 6 months)
Effect of intramolecular rotation on ab initio
calculated NMR shielding constants in vinylic derivatives. -
Results published in Mol. Phys.
Publications
Supervision
Organisation
Peer review
JACS, Angewandte, Chemistry, Proteins, Biophys J, PCCP and others (~25 per year)
Fellowships
-
ERASMUS grant by the European Union, Bruxelles in 1994
-
PhD fellowship by the French Ministry for Research (26 kEuro, 1998-2000)
-
Marie Curie fellowship by the EU (114 kEuro, 2001-2003)
Grants
- FonFlon, 2006 to 2009, 153 kEuro, Structural fluctuations in enzymes
- FlowVRNano, 2008 to 2010, 223 kEuro, Virtual reality molecular simulations
- BioPac, 2010 to 2014, 132 kEuro, Fuel cell modeling
- Nico_chimera, 2011 to 2014, tba, Nicotinic receptor homologues
Important scientific contributions
-
Recognized for my expertise on outer membrane proteins. Contributed to the elucidation of
an open pore structure of an ion channel close to the human nicotinic receptor.
Teaching
Lecturer
mainly at Université Denis Diderot, Paris 7 (~40 h p.a.)
(2003-2008)
'Vacataire', then teaching assistant
Université Louis Pasteur, Strasbourg (196 h)
(1998-99)
'Vacataire'
Ecole de Chimie, Polymères et Matériaux, Strasbourg (104 h)
(1997/98)
Academic Community Related Activity
-
Co-organiser of the "Bio-Image summer school", Paris, July 2005. - http://www.ecole2005.ibpc.fr/
-
Co-organiser of the "Biomolecular Simulations" conference, Bordeaux, September 2005
-
Scientific secretary of the French "Comité National" of the CNRS
-
Member of the user committee of the national IDRIS supercomputer center
-
Co-author of the book "Itinéraires Bis" to appear at Connaissances et Savoirs in 2009
Distinctions and Affiliations
-
EHICS Excellence award, Strasbourg, France
-
Qualification aux fonctions de Maître de conférences (section
31)
-
Thesis award by the Conseil Scientifique de l'ULP, Strasbourg,
France
-
Young researcher award by the Groupe de Graphisme et Modélisation
Moléculaire in 2003
-
Member of the 'Gesellschaft deutscher Chemiker' and of the
'Société Française de Chimie'
-
Member of the Biophysical Society
Language skills
-
French, German - bilingual.
-
English - written, read and spoken fluently (TOEIC score 945, 23 years
of practice).
-
Japanese - basic skills (4 months introductory class
in Japan).
Computer and IT skills
Operating systems
- Linux, Mac OSX, Unix, Windows.
Networks
- TCP/IP (ftp, http, mail), Microsoft,
Appletalk.
Programming
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Objective-C/C, Fortran, Perl, Python and other
Molecular Modeling
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Gromacs, Yasara, NAMD, Amber, Gromos, Gaussian, Spartan, Macromodel.
Other
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What If, Modeller, VMD, VTK, R, XML, Docbook, LaTeX.
Databases
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PDB, CCDB, Beilstein, bibliographic
(PubMed, ISI, CC, SCI, ...).
Internet
-
Website design for the university, a sports club
and for personal and professional purposes.
Other information
Activities
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Aïkido and Martial Arts (25 years of practice, black belt).
-
Music (6 years of piano).
Traveling
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Europe (A, B, CH, D, E, F, GB, GR, H, I, NL, PL, TR),
Africa (MA), Asia (Japan) and USA.