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Onderzoeker
An Ghysels
Profiel
Projecten
Publicaties
Activiteiten
Prijzen & Erkenningen
97
Resultaten
2024
An exact algorithm to find a maximum weight clique in a weighted undirected graph
Kati Rozman
An Ghysels
Dušanka Janežič
Janez Konc
A1
Artikel in een tijdschrift
in
SCIENTIFIC REPORTS
2024
Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and unglycosylated AGP
Bhawna Dixit
Wim Vranken
An Ghysels
A1
Artikel in een tijdschrift
in
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
2024
Enhanced molecular docking : novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs
Kati Rozman
An Ghysels
Bogdan Zavalnij
Tanja Kunej
Urban Bren
Dusanka Janez
Janez Konc
A1
Artikel in een tijdschrift
in
JOURNAL OF MOLECULAR STRUCTURE
2024
Exact kinetics of drug permeation through phospholipid membranes via path sampling methodology
Sina Safaei
An Ghysels
C3
Conferentie
2024
From 2D toy systems to real drug molecules : exact permeation kinetics through phospholipid membranes
Sina Safaei
An Ghysels
C3
Conferentie
2024
Investigating the effect of curvature and composition on lipid membrane permeability using molecular dynamics simulations
Samaneh Davoudi
An Ghysels
Proefschrift
2024
PyRETIS 3 : conquering rare and slow events without boundaries
Wouter Vervust
Daniel T. Zhang
An Ghysels
Sander Roet
Titus S. van Erp
Enrico Riccardi
A1
Artikel in een tijdschrift
in
JOURNAL OF COMPUTATIONAL CHEMISTRY
2024
Understanding oxygen 'buffering' by caveolae using coarse-grained molecular dynamics simulations
Samaneh Davoudi
An Ghysels
C1
Conferentie
2024
2023
Assessing passive permeability of drug releasing liposomes containing saturated fatty acids with molecular dynamics simulations
Samaneh Davoudi
An Ghysels
C3
Conferentie
2023
Capric acid and myristic acid permeability enhancers in curved liposome membranes
Samaneh Davoudi
Koen Raemdonck
Kevin Braeckmans
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL INFORMATION AND MODELING
2023
Defining permeability of curved membranes in molecular dynamics simulations
Samaneh Davoudi
An Ghysels
A1
Artikel in een tijdschrift
in
BIOPHYSICAL JOURNAL
2023
Exploring caveolae's role in oxygen 'buffering' through coarse-grained molecular dynamics
Samaneh Davoudi
An Ghysels
C3
Conferentie
2023
Path sampling with memory reduction and replica exchange to reach long permeation timescales
Wouter Vervust
Daniel T. Zhang
Titus S. Van Erp
An Ghysels
A1
Artikel in een tijdschrift
in
BIOPHYSICAL JOURNAL
2023
Pushing path sampling simulations to longer timescales : reducing memory and introducing replica exchange
Wouter Vervust
An Ghysels
C3
Conferentie
2023
Understanding the mechanism of oxygen 'buffering' by caveolae using coarse grained molecular dynamics
Samaneh Davoudi
An Ghysels
C3
Conferentie
2023
Understanding the role of caveolae in oxygen buffering : the effect of membrane curvature
Samaneh Davoudi
Qi Wang
Hemal H. Patel
Sally C. Pias
An Ghysels
C1
Conferentie
2023
2022
Counting permeant crossings to assess the effect of membrane curvature and composition on the permeability rate
Samaneh Davoudi
Koen Raemdonck
Kevin Braeckmans
An Ghysels
C3
Conferentie
2022
Dissecting conformational dynamics of α-1 acid glycoprotein (AGP) : a study of glycosylated and un-glycosylated mutants
Bhawna Dixit
Wim Vranken
An Ghysels
C3
Conferentie
2022
Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants
Bhawna Dixit
Wim Vranken
An Ghysels
C3
Conferentie
2022
Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants
Bhawna Dixit
Wim Vranken
An Ghysels
C3
Conferentie
2022
Effect of membrane curvature and lipid composition on membrane permeability in liposomal drug delivery
Samaneh Davoudi
An Ghysels
C3
Conferentie
2022
Investigating membrane curvature and composition effect on membrane permeability by counting permeant crossings
Samaneh Davoudi
Koen Raemdonck
Kevin Braeckmans
An Ghysels
C3
Conferentie
2022
Investigating the caveolin protein role in mitochondrial oxygen consumption
Samaneh Davoudi
Qi Wang
Hemal H. Patel
Sally C. Pias
An Ghysels
C3
Conferentie
2022
Investigation of the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein using Replica Exchange Transition Interface Sampling
Wouter Vervust
An Ghysels
C3
Conferentie
2022
Mechanism of oxygen 'buffering' by caveolae
Samaneh Davoudi
Qi Wang
Hemal H. Patel
Sally C. Pias
An Ghysels
C3
Conferentie
2022
Oxygen storage in stacked phospholipid membranes under an oxygen gradient as a model for myelin sheaths
Wouter Vervust
An Ghysels
P1
Conferentie
2022
Replica Exchange Transition Interface Sampling to investigate the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein
Wouter Vervust
An Ghysels
C3
Conferentie
2022
Replica exchange transition interface sampling to simulate the kinetics of molecular transport through membranes
An Ghysels
C3
Conferentie
2022
Understanding membrane permeability of drug releasing liposomes from molecular dynamics simulations : effect of curvature and composition
Samaneh Davoudi
Koen Raemdonck
Kevin Braeckmans
An Ghysels
C3
Conferentie
2022
2021
Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes
An Ghysels
Andere
2021
Computational tools for protein-ligand binding kinetics in personalized medicine
Wouter Vervust
An Ghysels
C3
Conferentie
2021
Exact non-Markovian permeability from rare event simulations
An Ghysels
Sander Roet
Samaneh Davoudi
Titus van Erp
A2
Artikel in een tijdschrift
in
PHYSICAL REVIEW RESEARCH
2021
Inhomogeneous solubility-diffusion model gives insight in efficacy of counting crossings method to calculate the membrane permeability
Samaneh Davoudi
An Ghysels
C3
Conferentie
2021
Oxygen permeation pathways through phospholipid membranes in the liquid ordered and liquid disordered phases
An Ghysels
C3
Conferentie
2021
Path sampling methodology for membrane permeability simulations
An Ghysels
C3
Conferentie
2021
Path sampling methods for protein-ligand binding kinetics
Wouter Vervust
An Ghysels
C3
Conferentie
2021
Permeation rates of oxygen through a lipid bilayer using replica exchange transition interface sampling
Enrico Riccardi
Andreas Krämer
Titus van Erp
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY B
2021
Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility–diffusion model
Samaneh Davoudi
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2021
2020
Assessing counting method efficacy in cell membrane permeability calculations
Samaneh Davoudi
An Ghysels
C3
Conferentie
2020
Membrane permeability of small molecules from unbiased molecular dynamics simulations
Andreas Krämer
An Ghysels
Eric Wang
Richard M. Venable
Jeffery B. Klauda
Bernard R. Brooks
Richard W. Pastor
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2020
2019
Permeability of membranes in the liquid ordered and liquid disordered phases
An Ghysels
Andreas Krämer
Richard M. Venable
Walter E. Teague
Edward Lyman
Klaus Gawrisch
Richard W. Pastor
A1
Artikel in een tijdschrift
in
NATURE COMMUNICATIONS
2019
2018
Effect of chain unsaturation and temperature on oxygen diffusion through lipid membranes from simulations
Oriana De Vos
Tanja Van Hecke
An Ghysels
A1
Artikel in een tijdschrift
in
ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY
2018
Membrane permeability: characteristic times and lengths for oxygen, and a simulation-based test of the inhomogeneous solubility-diffusion model
Oriana De Vos
Richard Venable
Tanja Van Hecke
Gerhard Hummer
Richard Pastor
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2018
The importance of cell shape sampling to accurately predict flexibility in metal-organic frameworks
Sven Rogge
Senne Caroes
Ruben Demuynck
Michel Waroquier
Veronique Van Speybroeck
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2018
2017
Correction to “Shape-Selective Diffusion of Olefins in 8-Ring Solid Acid Microporous Zeolites”
An Ghysels
Samuel Moors
Karen Hemelsoet
Kristof De Wispelaere
Michel Waroquier
German Sastre
Veronique Van Speybroeck
Correctie
2017
Position-dependent diffusion tensors in anisotropic media from simulation : oxygen transport in and through membranes
An Ghysels
Richard M Venable
Richard W Pastor
Gerhard Hummer
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2017
2016
Discovery of mycobacterium tuberculosis InhA inhibitors by binding sites comparison and ligands prediction
Tanja Štular
Samo Lešnik
Kaja Rožman
Julia Schink
Mitja Zdouc
An Ghysels
Feng Liu
Courtney C Aldrich
V Joachim Haupt
Sebastian Salentin
et al.
A1
Artikel in een tijdschrift
in
JOURNAL OF MEDICINAL CHEMISTRY
2016
Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks
Matthias Vandichel
Julianna Hajek
An Ghysels
Arthur De Vos
Michel Waroquier
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
CRYSTENGCOMM
2016
2015
A comparison of barostats for the mechanical characterization of metal-organic frameworks
Sven Rogge
Louis Vanduyfhuys
An Ghysels
Michel Waroquier
Toon Verstraelen
G Maurin
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2015
Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics
Kristof De Wispelaere
B Ensing
An Ghysels
EJ Meijer
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
CHEMISTRY-A EUROPEAN JOURNAL
2015
Exploring new frontiers in modeling complex zeolite-catalyzed reactions using advanced molecular dynamics techniques
Kristof De Wispelaere
B Ensing
An Ghysels
EJ Meijer
Veronique Van Speybroeck
C3
Conferentie
2015
Mechanical properties from periodic plane wave quantum mechanical codes: the challenge of the flexible nanoporous MIL-47(V) framework
Danny Vanpoucke
Kurt Lejaeghere
Veronique Van Speybroeck
Michel Waroquier
An Ghysels
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY C
2015
Normal mode analysis of macromolecular systems with the mobile block Hessian method
An Ghysels
Veronique Van Speybroeck
Dimitri Van Neck
BR Brooks
Michel Waroquier
P1
Conferentie
2015
Semi-analytical mean-field model for predicting breathing in metal–organic frameworks
Louis Vanduyfhuys
An Ghysels
Sven Rogge
Ruben Demuynck
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
MOLECULAR SIMULATION
2015
Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites
An Ghysels
Samuel Moors
Karen Hemelsoet
Kristof De Wispelaere
Michel Waroquier
German Sastre
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY C
2015
2014
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Yihan Shao
Zhengting Gan
Evgeny Epifanovsky
Andrew TB Gilbert
Michael Wormit
Joerg Kussmann
Adrian W Lange
Andrew Behn
Jia Deng
Xintian Feng
et al.
A1
Artikel in een tijdschrift
in
MOLECULAR PHYSICS
2014
Critical analysis of the accuracy of models predicting or extracting liquid structure information
Marc Van Houteghem
An Ghysels
Toon Verstraelen
Ward Poelmans
Michel Waroquier
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY B
2014
Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics
Andy Van Yperen-De Deyne
Thierry De Meyer
Ewald Pauwels
An Ghysels
Karen De Clerck
Michel Waroquier
Veronique Van Speybroeck
Karen Hemelsoet
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2014
New quasi-1D materials: DFT-study of breathing metal-organic frameworks
Danny Vanpoucke
Jan Jaeken
Stijn De Baerdemacker
Kurt Lejaeghere
An Ghysels
Michel Waroquier
Veronique Van Speybroeck
C3
Conferentie
2014
Tailoring metal-organic frameworks for adsorption applications
Danny Vanpoucke
Toon Verstraelen
Matthias Vandichel
An Ghysels
Kurt Lejaeghere
Veronique Van Speybroeck
C3
Conferentie
2014
2013
On the thermodynamics of framework breathing: a free energy model for gas adsorption in MIL-53
An Ghysels
Louis Vanduyfhuys
Matthias Vandichel
Michel Waroquier
Veronique Van Speybroeck
Berend Smit
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY C
2013
Oxygen diffusion water, alkanes, and lipid bilayers
An Ghysels
RM Venable
RW Pastor
G Hummer
C3
Conferentie
2013
2012
Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids : application to methanol
Marc Van Houteghem
Toon Verstraelen
An Ghysels
Louis Vanduyfhuys
Michel Waroquier
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2012
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining
An Ghysels
Benjamin T Miller
Frank C, IV Pickard
Bernard R Brooks
A1
Artikel in een tijdschrift
in
JOURNAL OF COMPUTATIONAL CHEMISTRY
2012
Empty host breathing profiles of MIL-53 type frameworks with various cations at the nodal points
Louis Vanduyfhuys
Toon Verstraelen
Matthias Vandichel
An Ghysels
Michel Waroquier
Veronique Van Speybroeck
C3
Conferentie
2012
Free energy profile of 'breathing' flexible porous frameworks
An Ghysels
Veronique Van Speybroeck
Michel Waroquier
Berend Smit
C3
Conferentie
2012
Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system
An Ghysels
Matthias Vandichel
Toon Verstraelen
Monique A van der Veen
Dirk E De Vos
Michel Waroquier
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
THEORETICAL CHEMISTRY ACCOUNTS
2012
Implosion-based mapping procedure between all-atom and coarse-grained normal modes
An Ghysels
BT Miller
F Pickard IV
BR Brooks
C3
Conferentie
2012
Thermodynamics of 'breathing' of metal-organic frameworks: free energy model for adsorption induced transitions
An Ghysels
Veronique Van Speybroeck
Michel Waroquier
C3
Conferentie
2012
2011
A theoretical and experimental spectroscopy study on methanol and ethanol conversion over H-SAPO-34
Karen Hemelsoet
An Ghysels
Davide Mores
Kristof De Wispelaere
Veronique Van Speybroeck
Bert M Weckhuysen
Michel Waroquier
C3
Conferentie
2011
Advanced normal mode analysis for multi-scale modeling
An Ghysels
Benjamin T Miller
Michel Waroquier
Bernard R Brooks
C3
Conferentie
2011
Efficient calculation of QM/MM frequencies with the mobile block hessian
An Ghysels
H Lee III Woodcock
Joseph D Larkin
Benjamin T Miller
Yihan Shao
Jing Kong
Dimitri Van Neck
Veronique Van Speybroeck
Michel Waroquier
Bernard R Brooks
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2011
Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34
Karen Hemelsoet
An Ghysels
Davide Mores
Kristof De Wispelaere
Veronique Van Speybroeck
Bert M Weckhuysen
Michel Waroquier
A1
Artikel in een tijdschrift
in
CATALYSIS TODAY
2011
First principle kinetic studies of zeolite-catalyzed methylation reactions
Veronique Van Speybroeck
Jeroen Van der Mynsbrugge
Matthias Vandichel
Karen Hemelsoet
David Lesthaeghe
An Ghysels
Guy Marin
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2011
Introducing BSSE as an extra energy term in molecular dynamics
Marc Van Houteghem
An Ghysels
Toon Verstraelen
Veronique Van Speybroeck
Michel Waroquier
Christine Kirschhock
Johan Martens
C3
Conferentie
2011
Monte Carlo simulations to understand 'breathing' phenomenon of metal organic frameworks
An Ghysels
Veronique Van Speybroeck
Michel Waroquier
B Smit
C3
Conferentie
2011
Normal mode analysis in zeolites: toward an efficient calculation of adsorption entropies
Bart De Moor
An Ghysels
Marie-Françoise Reyniers
Veronique Van Speybroeck
Michel Waroquier
Guy Marin
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2011
Understanding framework flexibility by Monte Carlo simulation
An Ghysels
Veronique Van Speybroeck
Michel Waroquier
Berend Smit
C3
Conferentie
2011
2010
Comparative study of various normal mode analysis techniques based on partial Hessians
An Ghysels
Veronique Van Speybroeck
Ewald Pauwels
Saron Catak
Bernard R Brooks
Dimitri Van Neck
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF COMPUTATIONAL CHEMISTRY
2010
Efficient calculation of QM/MM frequencies with the Mobile Block Hessian
An Ghysels
H Lee Woodcock
Yihan Shao
Bernard R Brooks
Dimitri Van Neck
Veronique Van Speybroeck
Michel Waroquier
C3
Conferentie
2010
TAMkin : a versatile package for vibrational analysis and chemical kinetics
An Ghysels
Toon Verstraelen
Karen Hemelsoet
Michel Waroquier
Veronique Van Speybroeck
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL INFORMATION AND MODELING
2010
2009
Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian Method
An Ghysels
Michel Waroquier
Proefschrift
2009
Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules
An Ghysels
Veronique Van Speybroeck
Ewald Pauwels
Dimitri Van Neck
Bernard R. Brooks
Michel Waroquier
A1
Artikel in een tijdschrift
in
Journal of Chemical Theory and Computation
2009
Normal mode analysis of macromolecular systems with the Mobile Block Hessian method
An Ghysels
Veronique Van Speybroeck
Dimitri Van Neck
Bernard R. R. Brooks
Michel Waroquier
C1
Conferentie
2009
Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method
An Ghysels
Lee H. Woodcock
Yihan Shao
Bernard R. Brooks
Veronique Van Speybroeck
Dimitri Van Neck
Michel Waroquier
C3
Conferentie
2009
Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach
An Ghysels
Dimitri Van Neck
Bernard R. Brooks
Veronique Van Speybroeck
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2009
The evaluation of QM/MM full Hessian and some applications
H Lee, III Woodcock
An Ghysels
Yihan Shao
Jing Kong
Bernard R Brooks
C3
Conferentie
2009
The evaluation of the QM/MM full Hessian and some applications
H Lee III Woodcock
An Ghysels
Yihan Shao
Jing Kong
Bernard R Brooks
C3
Conferentie
2009
2008
An efficient approach for the calculation of frequencies in macromolecules
An Ghysels
Veronique Van Speybroeck
Dimitri Van Neck
Bernard R. Brooks
Michel Waroquier
C3
Conferentie
2008
Calculating reaction rates with partial Hessians: Validation of the mobile block Hessian approach
An Ghysels
Veronique Van Speybroeck
Toon Verstraelen
Dimitri Van Neck
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2008
MFI fingerprint: How pentasil-induced IR bands shift during zeolite nanogrowth
David Lesthaeghe
Peter Vansteenkiste
Toon Verstraelen
An Ghysels
CEA KIRSCHHOCK
JA MARTENS
Veronique Van Speybroeck
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF PHYSICAL CHEMISTRY C
2008
Normal modes in partially optimized molecular systems: the Mobile Block Hessian (MBH) approach
An Ghysels
Veronique Van Speybroeck
Dimitri Van Neck
Bernard R. Brooks
Michel Waroquier
C3
Conferentie
2008
On the development of a partial vibrational analysis within a QM/MM approach
An Ghysels
Veronique Van Speybroeck
Bernard R. Brooks
Michel Waroquier
C3
Conferentie
2008
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
H. Lee Woodcock
Wenjun Zheng
An Ghysels
Yihan Shao
Jing Kong
Bernard R. Brooks
A1
Artikel in een tijdschrift
in
Journal of Chemical Physics
2008
2007
Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems
An Ghysels
Dimitri Van Neck
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2007
Vibrational modes in partially optimized molecular systems
An Ghysels
Dimitri Van Neck
Veronique Van Speybroeck
Toon Verstraelen
Michel Waroquier
A1
Artikel in een tijdschrift
in
JOURNAL OF CHEMICAL PHYSICS
2007
2006
Role of mean free path in spatial phase correlation and nodal screening
BA VAN TIGGELEN
D ANACHE
An Ghysels
A1
Artikel in een tijdschrift
in
EUROPHYSICS LETTERS
2006