Dr. ir. An Ghysels

FWO postdoc (WE05)
an.ghysels@ugent.be
+32 (0)9 264 65 37
Technologiepark 903, 9052 Zwijnaarde
Office n°022

http://lib.ugent.be/bibliografie/801002053326

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

Submitted / In revision / In press

Time quantification for Metropolis Monte Carlo simulations of adspecies at surfaces, M. Eckert, A. Krishtal, A. Ghysels, D. Geldof, V. Van Speybroeck, C. Van Alsenoy, A. Bogaerts, Journal of Physical Chemistry C, In revision, 2012, IF:4.805, 23/231 [Q1]

Published online

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, Published online, 2013, IF: 4.805, 22/225 [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: 3.333, 7/32 [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: 4.583, 25/152 [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: 2.162, 63/134 [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]
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]
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]

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

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
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

2008

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
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]

2007

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
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

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

2013

Oxygen diffusion water, alkanes, and lipid bilayers, A. Ghysels, ACS Spring Meeting, New Orleans, USA, COMP 420 / http://abstracts.acs.org/chem/245nm/program/view.php, 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, 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, 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

Dissertations

(D1), Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian method, A. Ghysels, Supervisor(s): Prof. Dr. Michel Waroquier, 19/05/2009
(D2), Propagation of seismic waves: analysis of the random phase / Propagation des ondes sismiques : analyse de la phase aléatoire, A. Ghysels, Supervisor(s): Prof. Dr. Frank Verheest, 2005