Dr. ir. An Ghysels

FWO postdoc (EA17)
+32 (0)9 264 65 37
Technologiepark 903, 9052 Zwijnaarde
Office n°022

Research interests 

  • Accurate methods for the determination of the normal modes of the chemically active part of an extended molecular system
  • Development of efficient algorithms for the normal mode calculation in large biomolecular systems

A1 publications

2014

Critical analysis of the accuracy of models predicting or extracting liquid structure information , M. Van Houteghem, A. Ghysels, T. Verstraelen, W. Poelmans, M. Waroquier, V. Van Speybroeck , Journal of Physical Chemistry B , 118 (9), 2451–2470 , 2014 , IF: 3.607 , 34/134 [Q2]
Exploring the Vibrational Fingerprint of the Electronic Excitation Energy via Molecular Dynamics , A. Van Yperen-De Deyne, T. De Meyer, E. Pauwels, A. Ghysels, K. De Clerck, M. Waroquier, V. Van Speybroeck, K. Hemelsoet , Journal of Chemical Physics , 140 (2014), 134105 , 2014 , IF: 3.164 , 8/34 [Q1]

2013

On the thermodynamics of framework breathing: A free energy model for gas adsorption in MIL-53 , A. Ghysels, L. Vanduyfhuys, M. Vandichel, M. Waroquier, V. Van Speybroeck, B. Smit , Journal of Physical Chemistry C , 117, 11540-11554 , 2013 , IF: 4.814 , 26/239 [Q1]

2012

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol , M. Van Houteghem, T. Verstraelen, A. Ghysels, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck , Journal of Chemical Physics , 137 (2012), 104506 , 2012 , IF: 3.164 , 8/34 [Q1]
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining , A. Ghysels, B.T. Miller, F.C. Pickard III, B.R. Brooks , Journal of Computational Chemistry , 33(28), 2250–2275 , 2012 , IF: 3.835 , 34/152 [Q1]
Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system , A. Ghysels, M. Vandichel, T. Verstraelen, M. van der Veen, D. De Vos, M. Waroquier, V. Van Speybroeck , Theoretical Chemistry Accounts , 131 (7) 1234-1246 , 2012 , IF: 2.233 , 62/134 [Q2]

2011

Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34 , K. Hemelsoet, A. Ghysels, D. Mores, K. De Wispelaere, V. Van Speybroeck, B.M. Weckhuysen, M. Waroquier , Catalysis Today , 177 (1), 12-24 , 2011 , IF: 3.407 , 12/133 [Q1]
Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies , B. De Moor, A. Ghysels, M-F. Reyniers, V. Van Speybroeck, M. Waroquier, G.B. Marin , Journal of Chemical Theory and Computation (JCTC) , 7(4), 1090-1101 , 2011 , IF: 5.215 , 2/32 [Q1]
Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian , A. Ghysels, H. Lee Woodcock III, J.D. Larkin, B.T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroeck, M. Waroquier, B.R. Brooks , Journal of Chemical Theory and Computation (JCTC) , 7 (2), 496–514 , 2011 , IF: 5.215 , 2/32 [Q1]
First principle kinetic studies of zeolite-catalyzed methylation reactions , V. Van Speybroeck, J. Van der Mynsbrugge, M. Vandichel, K. Hemelsoet, D. Lesthaeghe, A. Ghysels, G.B. Marin, M. Waroquier , JACS (Journal of the American Chemical Society) , 133 (4), 888–899 , 2011 , IF: 9.907 , 11/152 [Q1]

2010

TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics , A. Ghysels, T. Verstraelen, K. Hemelsoet, M. Waroquier, V. Van Speybroeck , Journal of Chemical Information and Modeling (JCIM) , 50 (9), 1736–1750 , 2010 , IF: 3.822 , 2/97 [Q1]
Comparative study of various normal mode analysis techniques based on partial Hessians , A. Ghysels, V. Van Speybroeck, E. Pauwels, S. Catak, B.R. Brooks, D. Van Neck, M. Waroquier , Journal of Computational Chemistry , 31 (5), 994-1007 , 2010 , IF: 4.050 , 28/147 [Q1]

2009

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules , A. Ghysels, V. Van Speybroeck, E. Pauwels, D. Van Neck, B.R. Brooks, M. Waroquier , Journal of Chemical Theory and Computation (JCTC) , 5 (5), 1203-1215 , 2009 , IF: 4.804 , 2/33 [Q1]
Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach , A. Ghysels, D. Van Neck, B.R. Brooks, V. Van Speybroeck, M. Waroquier , Journal of Chemical Physics , 130 (8), 084107 , 2009 , IF: 3.093 , 6/33 [Q1]

2008

Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach , A. Ghysels, V. Van Speybroeck, T. Verstraelen, D. Van Neck, M. Waroquier , Journal of Chemical Theory and Computation (JCTC) , 4 (4) 614-625 , 2008 , IF: 4.274 , [Q1]
MFI Fingerprint: How Pentasil-Induced IR Bands Shift during Zeolite Nanogrowth , D. Lesthaeghe, P. Vansteenkiste, T. Verstraelen, A. Ghysels, C. Kirschhock, J.A. Martens, V. Van Speybroeck, M. Waroquier , Journal of Physical Chemistry C , 112 (25), 9186-9191 , 2008 , IF: 3.396 , [Q1]
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit , H. Lee Woodcock III, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks , Journal of Chemical Physics , 129 (21), 214109 , 2008

2007

Vibrational Modes in partially optimized molecular systems , A. Ghysels, D. Van Neck, V. Van Speybroeck, T. Verstraelen, M. Waroquier , Journal of Chemical Physics , 126 (22), 224102 , 2007 , IF: 3.044
Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems , A. Ghysels, D. Van Neck, M. Waroquier , Journal of Chemical Physics , 127 (16), 164108 , 2007 , IF: 3.044

2006

Role of mean free path in spatial phase correlation and nodal screening , B. A. van Tiggelen, D. Anache, A. Ghysels , EPL (Europhysics letters) , 74 (6), 999-1005 , 2006

A2 publications

P1 publications

Invited talks

2007

Normal modes in partially optimized molecular structures: the mobile block Hessian (MBH) approach , A. Ghysels , Group meeting at research group of B. Brooks , Lab. of Comp. Biology, NHLBI, NIH, Maryland, US , Tue, 06/11/2007
Normal modes in partially optimized systems: the Mobile Block Hessian (MBH) approach , A. Ghysels , Meeting with SCM , Amsterdam, the Netherlands , Sat, 22/09/2007

Talks

2014

Tailoring Metal-organic frameworks for adsorption applications , D.E.P. Vanpoucke, T. Verstraelen, M. Vandichel, A. Ghysels, K. Lejaeghere, V. Van Speybroeck , E-MRS 2014 Spring Meeting , Lille, France , Mon, 26/05/2014 to Fri, 30/05/2014
Molecular dynamics study of diffusion in 8-ring zeolites , S. Moors, A. Ghysels, K. De Wispelaere, K. Hemelsoet, V. Van Speybroeck, M. Waroquier , NCCC XV , Noordwijkerhout , 1 , Mon, 10/03/2014 to Wed, 12/03/2014

2013

Oxygen diffusion water, alkanes, and lipid bilayers , A. Ghysels, R.M. Venable, R.W. Pastor, G. Hummer , ACS Spring Meeting , New Orleans, USA , COMP 420 , Sun, 07/04/2013 to Thu, 11/04/2013
Derivation of generic force field terms & Applications to describe thermodynamics of nanoporous materials , L. Vanduyfhuys, A. Ghysels, T. Verstraelen, M. Vandichel, M. Waroquier, V. Van Speybroeck , IAP P7/05 Platform 3 meeting , Namur, Belgium , Thu, 10/01/2013

2012

Implosion-based mapping procedure between all-atom and coarse-grained normal modes , A. Ghysels, B.T. Miller, F. Pickard IV, B.R. Brooks , ISQBP 2012 President’s Meeting , Långholmen, Stockholm , p. 9 , Sun, 17/06/2012 to Wed, 20/06/2012

2011

Advanced normal mode analysis for multi-scale modeling , A. Ghysels, B.T. Miller, M. Waroquier, B.R. Brooks , ACS Spring 2011 National Meeting & Exposition , Anaheim, California, USA , Abstract COMP309 , Sun, 27/03/2011 to Thu, 31/03/2011
Understanding framework flexibility by Monte Carlo simulation , A. Ghysels, V. Van Speybroeck, M. Waroquier, B. Smit , ACS Spring 2011 National Meeting & Exposition , Anaheim, California, USA , 14-COMP , Sun, 27/03/2011 to Thu, 31/03/2011
Investigating framework flexibility with Monte Carlo simulations , A. Ghysels , 2nd CP2K Tutorial: enabling the power of imagination in MD simulations , Zurich, Switzerland , Mon, 07/02/2011 to Fri, 11/02/2011

2010

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian method , A. Ghysels, H. Lee Woodcock III, Y. Shao, J. Kong, B.R. Brooks, D. Van Neck, V. Van Speybroeck, M. Waroquier , North American Meeting on Industrial and Applied Mathematics (NAMIAM) , Huatulco, Mexico , Mon, 06/12/2010 to Sat, 11/12/2010

2009

Normal mode analysis of macromolecular systems with the Mobile Block Hessian method , A. Ghysels, V. Van Speybroeck, D. Van Neck, B.R. Brooks, M. Waroquier , International Conference of Computational Methods in Sciences and Engineering (ICCMSE 2009) , Rhodos, Greece
4 pages
Tue, 29/09/2009 to Sun, 04/10/2009
The evaluation of the QM/MM full Hessian and some applications , H. Lee Woodcock III, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks , 238th ACS National Meeting , Washington DC , Sun, 16/08/2009 to Thu, 20/08/2009
Towards normal mode analysis in extended molecular systems: the Mobile Block Hessian approach , A. Ghysels , University of California - Berkeley, CA, USA , Tue, 11/08/2009

2008

On the development of a partial vibrational analysis within a QM/MM approach , A. Ghysels , 3rd CMM 'Users Meet Developers' Workshop on QM/MM Simulations , Philadelphia, Pennsylvania, US , Thu, 21/08/2008 to Sat, 23/08/2008
Normal modes in partially optimized systems: the Mobile Block Hessian (MBH) approach , A. Ghysels , Workshop on Mechanistic Analysis of Biological Systems with Novel Computational models , Telluride, Colorado, Us , Mon, 24/03/2008 to Fri, 28/03/2008

Posters

2013

Vibrational fingerprint of spectroscopic properties , A. Van Yperen-De Deyne, T. De Meyer, A. Ghysels, K. Hemelsoet, E. Pauwels, V. Van Speybroeck, M. Waroquier , Annual IAP Meeting , Ghent, Belgium , Wed, 18/09/2013
Vibrational Fingerprint of Spectroscopic Properties , A. Van Yperen-De Deyne, T. De Meyer, A. Ghysels, K. Hemelsoet, E. Pauwels, V. Van Speybroeck, M. Waroquier , TD-DFT , Nantes , Tue, 23/04/2013 to Fri, 26/04/2013

2012

Empty host breathing profiles of MIL-53 type frameworks with various cations at the nodal points , L. Vanduyfhuys, T. Verstraelen, M. Vandichel, A. Ghysels, M. Waroquier, V. Van Speybroeck , MOF2012 , Edinburgh UK , Sun, 16/09/2012 to Wed, 19/09/2012
Thermodynamics of "breathing" of metal-organic frameworks: free energy model for adsorption induced transitions , A. Ghysels, V. Van Speybroeck, M. Waroquier , ICTAC-14 , Vlissingen, The Netherlands , Tue, 26/06/2012 to Sat, 30/06/2012
Free energy profile of "breathing" flexible porous frameworks , A. Ghysels, V. Van Speybroeck, M. Waroquier, B. Smit , DFTM2012 , Ghent University, Het Pand, Ghent, Belgium , Sun, 01/04/2012 to Fri, 06/04/2012

2011

Introducing BSSE as an extra energy term in molecular dynamics , M. Van Houteghem, A. Ghysels, T. Verstraelen, V. Van Speybroeck, M. Waroquier, C. Kirschhock, J.A. Martens , IAP Annual Meeting , Leuven, Belgium , Mon, 21/11/2011 to Tue, 22/11/2011
Monte carlo simulations to understand "breathing" phenomenon of metal organic Frameworks , A. Ghysels, V. Van Speybroeck, M. Waroquier, B. Smit , Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC) , Santiago de Compostela, Spain , Sun, 17/07/2011 to Fri, 22/07/2011
A theoretical and experimental spectroscopy study on methanol conversion over H-SAPO-34 , K. Hemelsoet, A. Ghysels, D. Mores, K. De Wispelaere, V. Van Speybroeck, B.M. Weckhuysen, M. Waroquier , 5th Int. FEZA Conference , Valencia, Spain , Sun, 03/07/2011 to Thu, 07/07/2011
Predicting breathing with MOFs with Monte Carlo simulations , A. Ghysels, V. Van Speybroeck, M. Waroquier, B. Smit , 2011 Mini Stat Mech Meeting , Berkeley, California, US , Fri, 14/01/2011 to Sun, 16/01/2011

2010

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian , A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, D. Van Neck, V. Van Speybroeck, M. Waroquier , Gordon Research Conference - Computational Chemistry , Les Diablerets, Switzerland , Sun, 29/08/2010 to Fri, 03/09/2010
Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method , A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, V. Van Speybroeck, D. Van Neck, M. Waroquier , Quantum Chemistry in Belgium 9th edition , Louvain-la-Neuve, Belgium , Tue, 26/01/2010

2009

Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method , A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, V. Van Speybroeck, D. Van Neck, M. Waroquier , 7th Canadian Computational Chemistry Conference , Halifax, Canada , Mon, 20/07/2009 to Fri, 24/07/2009
An efficient approach for the calculation of frequencies in macromolecules , A. Ghysels, V. Van Speybroeck, D. Van Neck, B.R. Brooks, M. Waroquier , MolSim 2009 course , Universiteit Amsterdam, The Netherlands , Mon, 05/01/2009 to Fri, 16/01/2009

2008

An efficient approach for the calculation of frequencies in macromolecules , A. Ghysels , Doctoral Symposium , Ghent Univeristy, Faculty of Engineering, Ghent, Belgium , Wed, 03/12/2008
Normal modes in partially optimized molecular systems , A. Ghysels, V. Van Speybroeck, D. Van Neck, B.R. Brooks, M. Waroquier , SimBioMa 2008 , Konstanz, Germany , Wed, 02/04/2008 to Sat, 05/04/2008

2007

Normal modes in partially optimized molecular systems , A. Ghysels, D. Van Neck, V. Van Speybroeck, T. Verstraelen, M. Waroquier , Doctoral Symposium , Ghent Univeristy, Faculty of Engineering, Ghent, Belgium , Wed, 05/12/2007
Normal modes in partially optimized molecular systems , A. Ghysels, D. Van Neck, V. Van Speybroeck, T. Verstraelen, M. Waroquier , Molecular Quantum Mechanics Conference , Budapest, Hungary , Tue, 29/05/2007 to Sun, 03/06/2007