- 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
An Ghysels
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Published
2019
Permeability of membranes in the liquid ordered and liquid disordered phases , , Nature Communications , 10, 5616 , 2019 , IF: 11.80 , 5/69 [Q1]
2018
Effect of Chain Unsaturation and Temperature on Oxygen Diffusion through Lipid Membranes from Simulations , , Advances in Experimental Medicine and Biology , Oxygen Transport to Tissue XL, 399-404 , 2018 , IF: 1.760 , 38/85 [Q2]
Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model , , Journal of Chemical Theory and Computation (JCTC) , 14 (7), 3811-3824 , 2018 , IF: 5.245 , 4/35 [Q1]
The Importance of Cell Shape Sampling To Accurately Predict Flexibility in Metal-Organic Frameworks , , Journal of Chemical Theory and Computation , 14 (3), 1186-1197 , 2018 , IF: 5.313 , 6/36 [Q1]
2017
Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes , , Journal of Chemical Theory and Computation (JCTC) , 13 (6), 2962-2976 , 2017 , IF: 5.245 , 28/146 [Q1]
2016
Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction , , Journal of Medicinal Chemistry , 59 (24), 11069-11078 , 2016 , IF: 5.589 , 3/59 [Q1]
Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks , , CrystEngComm , 18 (37), 7056-7069 , 2016 , IF: 3.849 , 4/26 [Q1]
2015
A comparison of barostats for the mechanical characterization of metal-organic frameworks , , Journal of Chemical Theory and Computation (JCTC) , 11 (12), 5583-5597 , 2015 , IF: 5.301 , 5/35 [Q1]
Mechanical properties from periodic plane wave QM codes: the challenge of the flexible nanoporous MIL-47 (V) framework , , Journal of Physical Chemistry C , 119, 23752-23766 , 2015 , IF: 4.509 , 38/271 [Q1]
Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites , , Journal of Physical Chemistry C , 119, 41, 23721-23734 , 2015 , IF: 4.509 , 38/271 [Q1]
Semi-Analytical mean-field model for predicting breathing in Metal-Organic Frameworks , , Molecular Simulation , 41, 16-17, 1311-1328 , 2015 , IF: 1.678 , 99/144 [Q3]
Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics , , Chemistry - A European Journal , 21 (26), 9385-9396 , 2015 , IF: 5.771 , 24/163 [Q1]
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , , Molecular Physics , 113 (2), 184-215 , 2015 , IF: 1.837 , 20/35 [Q3]
2014
Critical analysis of the accuracy of models predicting or extracting liquid structure information , , Journal of Physical Chemistry B , 118 (9), 2451–2470 , 2014 , IF: 3.302 , 44/139 [Q2]
Exploring the Vibrational Fingerprint of the Electronic Excitation Energy via Molecular Dynamics , , Journal of Chemical Physics , 140 (2014), 134105 , 2014 , IF: 2.952 , 8/34 [Q1]
2013
On the thermodynamics of framework breathing: A free energy model for gas adsorption in MIL-53 , , Journal of Physical Chemistry C , 117, 11540-11554 , 2013 , IF: 4.835 , 29/251 [Q1]
2012
Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol , , Journal of Chemical Physics , 137 (10), 104506 , 2012 , IF: 3.164 , 8/34 [Q1]
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining , , 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 , , 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 , , 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 , , 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 , , 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 , , 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 , , 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 , , 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 , , Journal of Chemical Physics , 130 (8), 084107 , 2009 , IF: 3.093 , 6/33 [Q1]
Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules , , Journal of Chemical Theory and Computation (JCTC) , 5 (5), 1203-1215 , 2009 , IF: 4.804 , 2/33 [Q1]
2008
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit , , Journal of Chemical Physics , 129 (21), 214109 , 2008 , IF: 3.149
Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach , , 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 , , Journal of Physical Chemistry C , 112 (25), 9186-9191 , 2008 , IF: 3.396 , [Q1]
2007
Vibrational Modes in partially optimized molecular systems , , 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 , , Journal of Chemical Physics , 127 (16), 164108 , 2007 , IF: 3.044
2006
Role of mean free path in spatial phase correlation and nodal screening , , EPL (Europhysics letters) , 74 (6), 999-1005 , 2006
P1 publications
2015
Normal mode analysis of macromolecular systems with the mobile block Hessian method , , AIP Conference Proceedings , 1642 (2015), 559 , 2015
Miscellaneous
Correction to “Shape-Selective Diffusion of Olefins in 8-Ring Solid Acid Microporous Zeolites” , , JOURNAL OF PHYSICAL CHEMISTRY C , 2017 , pubs.acs.org
Dissertations
(D1) , Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian method , , 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 , , Supervisor(s): Prof. Dr. Frank Verheest , 2005
2015
Keynote
Understanding The Flexibility In Metal-Organic Frameworks From molecular To Thermodynamic Insights , , CHITEL2015 , Torino, Italy , Sun, 26/07/2015 to Fri, 31/07/2015 2014
Invited talk
Critical analysis of liquid structure models , , WATOC 2014 , Santiago de Chile, Chile , Sun, 05/10/2014 to Fri, 10/10/2014 2007
Invited talk
Normal modes in partially optimized molecular structures: the mobile block Hessian (MBH) approach , , Group meeting at research group of B. Brooks , Lab. of Comp. Biology, NHLBI, NIH, Maryland, US , Tue, 06/11/2007 Invited talk
Normal modes in partially optimized systems: the Mobile Block Hessian (MBH) approach , , Meeting with SCM , Amsterdam, the Netherlands , Sat, 22/09/2007 2017
Modeling diffusion of adsorbates in nanoporous materials , , EUROMAT 2017 , Thessaloniki, Greece , Sun, 17/09/2017 to Fri, 22/12/2017
Oxygen permeability through lipid membranes , , 45th Annual Meeting of the International Society on Oxygen Transport to Tissue , Halle-Saale, Germany , Tue, 22/08/2017
2016
Insights in the Behaviour of MOFs through Molecular Modeling: from Force Field Derivation to Thermodynamic Analysis , , DAMP , Montpellier, France , Thu, 17/11/2016
Oxygen diffusion in and through lipid membranes , , CECAM workshop Membranes – Complex dynamics and composition , Helsinki, Finland , Thu, 18/08/2016
Unraveling the mechanical behaviour of MOFs: A thermodynamic exploration , , DAMP , Montpellier, France , Mon, 18/07/2016
Diffusion in nanoporous materials: Assessing the long time scale from short molecular dynamics trajectories , , ACS - Division of Computers in Chemistry , San Diego, USA , Sun, 13/03/2016 to Thu, 17/03/2016
Metal-organic frameworks under pressure: A thermodynamic exploration , , MolSim 2016: Understanding Molecular Simulations , Amsterdam, The Netherlands , Fri, 08/01/2016
2015
Unraveling the breathing in Metal-Organic Frameworks: from force fields to thermodynamic insights , , EUROMAT2015 , Warsaw, Poland , Sun, 20/09/2015 to Thu, 24/09/2015
Exploring New Frontiers in Modeling Complex Zeolite-Catalyzed Reactions Using Advanced Molecular Dynamics Techniques , , 24th North American Catalysis Society Meeting (NAM24) , Pittsburgh, PA, USA , O-Th-408-13 , Sun, 14/06/2015 to Fri, 19/06/2015
Unraveling the breathing in Metal-Organic Frameworks: from force fields to thermodynamic insights , , IAP PL3 meeting , Mons, Belgium , Thu, 05/02/2015
The vibrational fingerprint of the electronic excitation energy of molecular systems via Molecular Dynamics , , IAP, joint WP1/PL1 meeting , Mons, Belgium , Thu, 05/02/2015
2014
Molecular dynamics study of shape-selective diffusion in 8-ring acidic zeolites , , WATOC 2014 Satellite Meeting on Large Condensed and Biological Systems , Concepción, Chili , Mon, 13/10/2014 to Tue, 14/10/2014
Molecular dynamics study of shape-selective diffusion in 8-ring acidic zeolites , , 6 th FEZA Conference 2014 , Leipzig, Germany , 105 , Mon, 08/09/2014 to Thu, 11/09/2014
Tailoring Metal-organic frameworks for adsorption applications , , 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 , , NCCC XV , Noordwijkerhout , 1 , Mon, 10/03/2014 to Wed, 12/03/2014
2013
Oxygen diffusion water, alkanes, and lipid bilayers , , 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 , , 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 , , ISQBP 2012 President’s Meeting , Långholmen, Stockholm , p. 9 , Sun, 17/06/2012 to Wed, 20/06/2012
2011
Understanding framework flexibility by Monte Carlo simulation , , ACS Spring 2011 National Meeting & Exposition , Anaheim, California, USA , 14-COMP , Sun, 27/03/2011 to Thu, 31/03/2011
Advanced normal mode analysis for multi-scale modeling , , ACS Spring 2011 National Meeting & Exposition , Anaheim, California, USA , Abstract COMP309 , Sun, 27/03/2011 to Thu, 31/03/2011
Investigating framework flexibility with Monte Carlo simulations , , 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 , , 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 , , International Conference of Computational Methods in Sciences and Engineering (ICCMSE 2009) , Rhodos, Greece Tue, 29/09/2009 to Sun, 04/10/2009
4 pages
The evaluation of the QM/MM full Hessian and some applications , , 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 , , University of California - Berkeley, CA, USA , Tue, 11/08/2009
2008
On the development of a partial vibrational analysis within a QM/MM approach , , 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 , , Workshop on Mechanistic Analysis of Biological Systems with Novel Computational models , Telluride, Colorado, Us , Mon, 24/03/2008 to Fri, 28/03/2008
2017
Benchmarking free energy methods for breathing in Metal-Organic Frameworks , , MARVEL School on Variationally Enhanced Sampling 2017 , Lugano, Switzerland , Tue, 14/02/2017 to Fri, 17/02/2017
The importance of unit cell fluctuations for free energy profiles of flexible crystals , , MolSim 2017 , Amsterdam The Netherlands , Mon, 09/01/2017 to Fri, 20/01/2017
2016
Diffusion of O2 in cell membranes , , Chemical Research in Flanders Symposium (CRF-1) , Blankenberge, Belgium , Mon, 24/10/2016 to Wed, 26/10/2016
A thermodynamic approach to accurately determine pressure profiles for MOFs to assess their flexibility and loss of crystallinity , , MOF-2016: 5th International Conference on Metal-Organic Frameworks & Open Framework Compounds , Long Beach, CA, USA , Mon, 12/09/2016
Benchmarking free energy methods for breathing in Metal-Organic Frameworks , , MOF2016 , Long Beach, CA, USA , Sun, 11/09/2016 to Thu, 15/09/2016
A thermodynamic approach to accurately determine pressure profiles for MOFs to assess their flexibility and loss of crystallinity , , Theory and Applications of Computational Chemistry 2016 , Seattle, WA, USA , Wed, 31/08/2016
2015
Benchmarking free energy methods for breathing in Metal-Organic Frameworks , , IAP Annual Meeting , Hasselt, Belgium , Fri, 11/09/2015
The vibrational fingerprint of the electronic excitation energy of molecular systems via molecular dynamics , , Next generation quantum based molecular dy-namics: challenges and perspectives , Bremen, Germany , Mon, 13/07/2015 to Fri, 17/07/2015
Benchmarking free energy methods for breathing in Metal-Organic Frameworks , , Hands-on workshop density-functional theory and beyond: First-principles simulations of molecules and materials , Berlin, Germany , Mon, 13/07/2015 to Thu, 23/07/2015
Modeling breathing of Mil-53: from force fields to thermodynamic insights , , Flexibility and disorder in Metal-Organic Frameworks , Paris, France , Wed, 03/06/2015 to Fri, 05/06/2015
Selective diffusion of small hydrocarbons in acidic zeolites with 8-rings , , 2nd Euro-Asia Zeolite Conference , Nice, France , Sun, 25/01/2015 to Wed, 28/01/2015
2014
Position-dependent diffusion profiles in inhomogeneous media , , 6 th FEZA Conference 2014 , Santiago de Chile, Chile , Sun, 05/10/2014 to Fri, 10/10/2014
Selective diffusion of small hydrocarbons through acidic zeolites with 8- membered rings , , WATOC 2014 , Santiago de Chile, Chile , Sun, 05/10/2014 to Fri, 10/10/2014
New quasi-1D materials: DFT-study of breathing metal-organic frameworks , , IAP P7/05 Annual meeting 2014 , Louvain-La-Neuve, Belgium , Fri, 19/09/2014
2013
Vibrational fingerprint of spectroscopic properties , , Annual IAP Meeting , Ghent, Belgium , Wed, 18/09/2013
Vibrational Fingerprint of Spectroscopic Properties , , 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 , , 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 , , ICTAC-14 , Vlissingen, The Netherlands , Tue, 26/06/2012 to Sat, 30/06/2012
Free energy profile of "breathing" flexible porous frameworks , , 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 , , 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 , , 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 , , 5th Int. FEZA Conference , Valencia, Spain , Sun, 03/07/2011 to Thu, 07/07/2011
Predicting breathing with MOFs with Monte Carlo simulations , , 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 , , 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 , , 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 , , 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 , , 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 , , Doctoral Symposium , Ghent Univeristy, Faculty of Engineering, Ghent, Belgium , Wed, 03/12/2008
Normal modes in partially optimized molecular systems , , SimBioMa 2008 , Konstanz, Germany , Wed, 02/04/2008 to Sat, 05/04/2008
2007
Normal modes in partially optimized molecular systems , , Doctoral Symposium , Ghent Univeristy, Faculty of Engineering, Ghent, Belgium , Wed, 05/12/2007
Normal modes in partially optimized molecular systems , , Molecular Quantum Mechanics Conference , Budapest, Hungary , Tue, 29/05/2007 to Sun, 03/06/2007
2015
Normal mode analysis of macromolecular systems with the mobile block Hessian method , , AIP Conference Proceedings , 1642 (2015), 559 , 2015