| Dr Fan Wang, Ph.D. |
| LG2A, CNRS FRE 3517 |
| UFR de Pharmacie |
| Université de Picardie Jules Verne |
| 1, rue des Louvels |
| 80036 Amiens Cedex, France |
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| E-mail: fan.wang_at_u-picardie.fr; fan.wang_at_q4md-forcefieldtools.org |
| Web site: http://q4md-forcefieldtools.org/FW |
| Phone number: +33-6-2853-7733 |
| Citizenship: Chinese |
| Date of birth: August 1986 |
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Present situation
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Research scientist associated to the q4md-forcefieldtools project
Searching for a position in the academic field (in computational Chemistry, bioinformatics or scientific calculation). |
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Education
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| Oct 2014 |
Ph.D. in Computational Chemistry
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Title: Sofware developments and structural studies of bioinorganic complexes by molecular dynamics |
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Manuscript: http://q4md-forcefieldtools.org/FW/Thesis |
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Université de Picardie Jules Verne, Amiens, France
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| 2010 |
MS in Computer Science and Technology
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Université de Picardie Jules Verne, Amiens, France
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| 2008 |
BS in Computer Science and Technology
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Université de Picardie Jules Verne, Amiens, France
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| 2007 |
BS in Mathematics
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Université de Picardie Jules Verne, Amiens, France
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| 2005 |
First year undergraduate in Mathematics
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Huazhong University of Science and Technology, Wuhan, China
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Skills and Achievements
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Scientific computing and molecular modeling software: |
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Development of the PyRED (or R.E.D. Python) and R.E.D. Server Development tools (http://q4md-forcefieldtools.org/REDServer-Development) for force field generation (Amber and Glycam force fields).
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Optimization of the R.E.D. IV program (Perl programming language)
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Molecular dynamics simulation using the pmemd and sander programs (AMBER) |
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Visualization (VMD, GaussView, Avogadro, PyMol) |
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Quantum chemistry (Gaussian, GAMESS, Firefly) |
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Babel (file format conversion), BKchem |
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Programming and Operating Systems: |
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Development with other languages : Python, Perl, C/C++, Fortran, Java
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Web development : XHTML, PHP, JavaScript, MySQL, CSS |
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Shell scripting (tcsh, bash, sed, awk)
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Experience with software for mathematics (Matlab, Scilab)
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MPI and OpenMP parallel programming
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Installation and management of Linux on workstations and
cluster of computers (administration, program installation and
compilation, PBS queuing system) |
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Languages
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| Chinese |
native
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| French |
written, read, spoken
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| English |
written, read, spoken
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Research Experience
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Oct 2011 - Nov 2014:
LG2A, CNRS FRE 3517, UFR de pharmacie, Université de Picardie Jules Verne, Amiens, France
Ph.D. student, Supervisor: Professor F.-Y. Dupradeau
- Project: Empirical force field development with an object
oriented programming approach and molecular dynamics simulation of
bioinorganic complexes
- International French-USA project between the Université de
Picardie Jules Verne and the Sanford Burnham Medical
Research Institute (San Diego, USA)
- Scholarship from the "Conseil Régional de Picardie" and the "European Regional Development Fund"
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Jan 2010 - Aug 2010:
Doonya Technologies, Lille, France - Université de Picardie Jules Verne, Amiens, France
Master, Supervisor: Professor A. Lapujade
- Project: Development of the application WebConf for
controlling the conference of Voice Over Internet Protocol (VOIP
Asterisk, QoS, PHP, Javascript, C/C++, Linux shell)
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Publications
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Object oriented programming for Amber force fields: application to the study of bioinorganic complexes by molecular dynamics simulation
F. Wang, J.-P. Becker, P. Cieplak, F.-Y. Dupradeau.(in preparation)
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Beta-hematin crystal formation: first insights from molecular dynamics of small clusters in water
J.-P. Becker, F. Wang, P. Sonnet, F.-Y. Dupradeau, J. Am. Chem. Soc. submitted Jul 28, 2015.
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Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment
J. M. Sanders, M. E. Wampole, C.-P. Chen, D. Sethi, A. Singh,
F.-Y. Dupradeau, F. Wang, B. D. Gray, M. L. Thakur & E. Wickstrom,
J. Phys. Chem. B 2013, 117, 11584-11595.
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Communications
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R.E.D. Python: Application of object oriented programming
to charge derivation and force field library building for the Amber
additive and non-additive force field models
F. Wang, J.-P. Becker, P. Cieplak, F.-Y. Dupradeau, GGMM
2013 meeting (Groupe Graphisme et Modélisation Moléculaire), Ile
d'Oléron, May 21-23, 2013.
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R.E.D. Python: Object oriented programming for Amber force fields
F. Wang, J.-P. Becker, P. Cieplak, F.-Y. Dupradeau, 247th American Chemical Society national meeting, Dallas, TX, March 16-20, 2014.
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Program, web server and tutorials
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R.E.D. Server Development - Performing calculations with the PyRED program : Application to charge derivation, force field library building and force field parameter generation
Fan Wang,[1] Jean-Paul Becker,[1] Piotr Cieplak,[2] François-Yves Dupradeau[1]
[1] FRE CNRS 3517 & UFR de Pharmacie, Université de Picardie - Jules Verne, rue des Louvels, Amiens, France
[2] Sanford | Burnham Medical Resesearch Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
http://q4md-forcefieldtools.org/REDServer-Development
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References
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F.-Y. Dupradeau, Professor of chemistry; LG2A, CNRS FRE 3517, UFR de pharmacie, Université de Picardie Jules Verne, Amiens, France
E-mail: fyd_at_u-picardie.fr, Phone number: +33-3-2282-7498 |
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P. Cieplak, Research Associate Professor; The Sanford Burnham Medical Research Institute, San Diego, USA
E-mail: pcieplak_at_sanfordburnham.org, Phone number: +1-858-646-3100 x 3076 |
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Y. Li, Professor of Computer Science and
Technology; UFR de Mathématiques et d'Informatique, Université de Picardie Jules Verne, Amiens, France
E-mail: yu.li_at_u-picardie.fr, Phone number: +33-3-2282-7872 |
