Research Explorer

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Researcher

An Ghysels

Awards & Distinctions

105 Results

2025

Drug permeation through phospholipid membranes : predicting exact kinetics via path sampling methodology

Sina SafaeiAn Ghysels

Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics

Jose Gavalda-GarciaBhawna DixitAdrián DíazAn GhyselsWim Vranken

A1 Journal Article in JOURNAL OF MOLECULAR BIOLOGY

Investigating protein flexibility using molecular dynamics simulations of α-1 acid glycoprotein and large-scale normal mode analysis of AlphaFold models

Bhawna DixitAn GhyselsWim Vranken

Myelin sheaths can act as compact temporary oxygen storage units as modeled by an electrical RC circuit model

Wouter VervustSina SafaeiKatja WitschasLuc LeybaertAn Ghysels

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein dynamics and conformational heterogeneity in solution are not well captured by AlphaFold and other computational approaches

Wim VrankenBhawna DixitJose Gavalda-GarciaAn Ghysels

Validation of a coarse-grained martini 3 model for molecular oxygen

Samaneh DavoudiPetteri A. VainikkaSiewert J. MarrinkAn Ghysels

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

2024

Advanced molecular dynamics simulation techniques for kinetic analysis of biological systems

Wouter VervustAn Ghysels

An exact algorithm to find a maximum weight clique in a weighted undirected graph

Kati RozmanAn GhyselsDušanka JanežičJanez Konc

A1 Journal Article in SCIENTIFIC REPORTS

Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and unglycosylated AGP

Bhawna DixitWim VrankenAn Ghysels

A1 Journal Article in PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Enhanced molecular docking : novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs

Kati RozmanAn GhyselsBogdan ZavalnijTanja KunejUrban BrenDusanka JanezJanez Konc

A1 Journal Article in JOURNAL OF MOLECULAR STRUCTURE

Exact kinetics of drug permeation through phospholipid membranes via path sampling methodology

Sina SafaeiAn Ghysels

Extending path memory to improve kinetics calculations in rare molecular processes

Elias WilsWouter VervustTitus van ErpAn Ghysels

From 2D toy systems to real drug molecules : exact permeation kinetics through phospholipid membranes

Sina SafaeiAn Ghysels

Investigating the effect of curvature and composition on lipid membrane permeability using molecular dynamics simulations

Samaneh DavoudiAn Ghysels

PyRETIS 3 : conquering rare and slow events without boundaries

Wouter VervustDaniel T. ZhangAn GhyselsSander RoetTitus S. van ErpEnrico Riccardi

A1 Journal Article in JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding oxygen 'buffering' by caveolae using coarse-grained molecular dynamics simulations

Samaneh DavoudiAn Ghysels

2023

Assessing passive permeability of drug releasing liposomes containing saturated fatty acids with molecular dynamics simulations

Samaneh DavoudiAn Ghysels

Capric acid and myristic acid permeability enhancers in curved liposome membranes

Samaneh DavoudiKoen RaemdonckKevin BraeckmansAn Ghysels

A1 Journal Article in JOURNAL OF CHEMICAL INFORMATION AND MODELING

Defining permeability of curved membranes in molecular dynamics simulations

Samaneh DavoudiAn Ghysels

A1 Journal Article in BIOPHYSICAL JOURNAL

Exploring caveolae's role in oxygen 'buffering' through coarse-grained molecular dynamics

Samaneh DavoudiAn Ghysels

Path sampling with memory reduction and replica exchange to reach long permeation timescales

Wouter VervustDaniel T. ZhangTitus S. Van ErpAn Ghysels

A1 Journal Article in BIOPHYSICAL JOURNAL

Pushing path sampling simulations to longer timescales : reducing memory and introducing replica exchange

Wouter VervustAn Ghysels

Understanding the mechanism of oxygen 'buffering' by caveolae using coarse grained molecular dynamics

Samaneh DavoudiAn Ghysels

Understanding the role of caveolae in oxygen buffering : the effect of membrane curvature

Samaneh DavoudiQi WangHemal H. PatelSally C. PiasAn Ghysels

2022

Counting permeant crossings to assess the effect of membrane curvature and composition on the permeability rate

Samaneh DavoudiKoen RaemdonckKevin BraeckmansAn Ghysels

Dissecting conformational dynamics of α-1 acid glycoprotein (AGP) : a study of glycosylated and un-glycosylated mutants

Bhawna DixitWim VrankenAn Ghysels

Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants

Bhawna DixitWim VrankenAn Ghysels

Dissecting the conformational dynamics of α-1 acid glycoprotein (AGP) in cancer : a comparative study of glycosylated and un glycosylated AGP mutants

Bhawna DixitWim VrankenAn Ghysels

Effect of membrane curvature and lipid composition on membrane permeability in liposomal drug delivery

Samaneh DavoudiAn Ghysels

Investigating membrane curvature and composition effect on membrane permeability by counting permeant crossings

Samaneh DavoudiKoen RaemdonckKevin BraeckmansAn Ghysels

Investigating the caveolin protein role in mitochondrial oxygen consumption

Samaneh DavoudiQi WangHemal H. PatelSally C. PiasAn Ghysels

Investigation of the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein using Replica Exchange Transition Interface Sampling

Wouter VervustAn Ghysels

Mechanism of oxygen 'buffering' by caveolae

Samaneh DavoudiQi WangHemal H. PatelSally C. PiasAn Ghysels

Oxygen storage in stacked phospholipid membranes under an oxygen gradient as a model for myelin sheaths

Wouter VervustAn Ghysels

Replica Exchange Transition Interface Sampling to investigate the orthogonal degrees of freedom in protein-drug unbinding pathways of the ABL protein

Wouter VervustAn Ghysels

Replica exchange transition interface sampling to simulate the kinetics of molecular transport through membranes

Understanding membrane permeability of drug releasing liposomes from molecular dynamics simulations : effect of curvature and composition

Samaneh DavoudiKoen RaemdonckKevin BraeckmansAn Ghysels

2021

Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes

Computational tools for protein-ligand binding kinetics in personalized medicine

Wouter VervustAn Ghysels

Exact non-Markovian permeability from rare event simulations

An GhyselsSander RoetSamaneh DavoudiTitus van Erp

A2 Journal Article in PHYSICAL REVIEW RESEARCH

Inhomogeneous solubility-diffusion model gives insight in efficacy of counting crossings method to calculate the membrane permeability

Samaneh DavoudiAn Ghysels

Oxygen permeation pathways through phospholipid membranes in the liquid ordered and liquid disordered phases

Path sampling methodology for membrane permeability simulations

Path sampling methods for protein-ligand binding kinetics

Wouter VervustAn Ghysels

Permeation rates of oxygen through a lipid bilayer using replica exchange transition interface sampling

Enrico RiccardiAndreas KrämerTitus van ErpAn Ghysels

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY B

Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility–diffusion model

Samaneh DavoudiAn Ghysels

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

2020

Assessing counting method efficacy in cell membrane permeability calculations

Samaneh DavoudiAn Ghysels

Membrane permeability of small molecules from unbiased molecular dynamics simulations

Andreas KrämerAn GhyselsEric WangRichard M. VenableJeffery B. KlaudaBernard R. BrooksRichard W. Pastor

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

2019

Permeability of membranes in the liquid ordered and liquid disordered phases

An GhyselsAndreas KrämerRichard M. VenableWalter E. TeagueEdward LymanKlaus GawrischRichard W. Pastor

A1 Journal Article in NATURE COMMUNICATIONS

2018

Effect of chain unsaturation and temperature on oxygen diffusion through lipid membranes from simulations

Oriana De VosTanja Van HeckeAn Ghysels

A1 Journal Article in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY

Membrane permeability: characteristic times and lengths for oxygen, and a simulation-based test of the inhomogeneous solubility-diffusion model

Oriana De VosRichard VenableTanja Van HeckeGerhard HummerRichard PastorAn Ghysels

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

The importance of cell shape sampling to accurately predict flexibility in metal-organic frameworks

Sven RoggeSenne CaroesRuben DemuynckMichel WaroquierVeronique Van SpeybroeckAn Ghysels

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

2017

Correction to “Shape-Selective Diffusion of Olefins in 8-Ring Solid Acid Microporous Zeolites”

An GhyselsSamuel MoorsKaren HemelsoetKristof De WispelaereMichel WaroquierGerman SastreVeronique Van Speybroeck

Position-dependent diffusion tensors in anisotropic media from simulation : oxygen transport in and through membranes

An GhyselsRichard M VenableRichard W PastorGerhard Hummer

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

2016

Discovery of mycobacterium tuberculosis InhA inhibitors by binding sites comparison and ligands prediction

Tanja ŠtularSamo LešnikKaja RožmanJulia SchinkMitja ZdoucAn GhyselsFeng LiuCourtney C AldrichV Joachim HauptSebastian Salentin et al.

A1 Journal Article in JOURNAL OF MEDICINAL CHEMISTRY

Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks

Matthias VandichelJulianna HajekAn GhyselsArthur De VosMichel WaroquierVeronique Van Speybroeck

A1 Journal Article in CRYSTENGCOMM

2015

A comparison of barostats for the mechanical characterization of metal-organic frameworks

Sven RoggeLouis VanduyfhuysAn GhyselsMichel WaroquierToon VerstraelenG MaurinVeronique Van Speybroeck

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics

Kristof De WispelaereB EnsingAn GhyselsEJ MeijerVeronique Van Speybroeck

A1 Journal Article in CHEMISTRY-A EUROPEAN JOURNAL

Exploring new frontiers in modeling complex zeolite-catalyzed reactions using advanced molecular dynamics techniques

Kristof De WispelaereB EnsingAn GhyselsEJ MeijerVeronique Van Speybroeck

Mechanical properties from periodic plane wave quantum mechanical codes: the challenge of the flexible nanoporous MIL-47(V) framework

Danny VanpouckeKurt LejaeghereVeronique Van SpeybroeckMichel WaroquierAn Ghysels

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY C

Normal mode analysis of macromolecular systems with the mobile block Hessian method

An GhyselsVeronique Van SpeybroeckDimitri Van NeckBR BrooksMichel Waroquier

Semi-analytical mean-field model for predicting breathing in metal–organic frameworks

Louis VanduyfhuysAn GhyselsSven RoggeRuben DemuynckVeronique Van Speybroeck

A1 Journal Article in MOLECULAR SIMULATION

Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites

An GhyselsSamuel MoorsKaren HemelsoetKristof De WispelaereMichel WaroquierGerman SastreVeronique Van Speybroeck

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY C

2014

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Yihan ShaoZhengting GanEvgeny EpifanovskyAndrew TB GilbertMichael WormitJoerg KussmannAdrian W LangeAndrew BehnJia DengXintian Feng et al.

A1 Journal Article in MOLECULAR PHYSICS

Critical analysis of the accuracy of models predicting or extracting liquid structure information

Marc Van HouteghemAn GhyselsToon VerstraelenWard PoelmansMichel WaroquierVeronique Van Speybroeck

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics

Andy Van Yperen-De DeyneThierry De MeyerEwald PauwelsAn GhyselsKaren De ClerckMichel WaroquierVeronique Van SpeybroeckKaren Hemelsoet

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

New quasi-1D materials: DFT-study of breathing metal-organic frameworks

Danny VanpouckeJan JaekenStijn De BaerdemackerKurt LejaeghereAn GhyselsMichel WaroquierVeronique Van Speybroeck

Tailoring metal-organic frameworks for adsorption applications

Danny VanpouckeToon VerstraelenMatthias VandichelAn GhyselsKurt LejaeghereVeronique Van Speybroeck

2013

On the thermodynamics of framework breathing: a free energy model for gas adsorption in MIL-53

An GhyselsLouis VanduyfhuysMatthias VandichelMichel WaroquierVeronique Van SpeybroeckBerend Smit

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY C

Oxygen diffusion water, alkanes, and lipid bilayers

An GhyselsRM VenableRW PastorG Hummer

2012

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids : application to methanol

Marc Van HouteghemToon VerstraelenAn GhyselsLouis VanduyfhuysMichel WaroquierVeronique Van Speybroeck

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining

An GhyselsBenjamin T MillerFrank C, IV PickardBernard R Brooks

A1 Journal Article in JOURNAL OF COMPUTATIONAL CHEMISTRY

Empty host breathing profiles of MIL-53 type frameworks with various cations at the nodal points

Louis VanduyfhuysToon VerstraelenMatthias VandichelAn GhyselsMichel WaroquierVeronique Van Speybroeck

Free energy profile of 'breathing' flexible porous frameworks

An GhyselsVeronique Van SpeybroeckMichel WaroquierBerend Smit

Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system

An GhyselsMatthias VandichelToon VerstraelenMonique A van der VeenDirk E De VosMichel WaroquierVeronique Van Speybroeck

A1 Journal Article in THEORETICAL CHEMISTRY ACCOUNTS

Implosion-based mapping procedure between all-atom and coarse-grained normal modes

An GhyselsBT MillerF Pickard IVBR Brooks

Thermodynamics of 'breathing' of metal-organic frameworks: free energy model for adsorption induced transitions

An GhyselsVeronique Van SpeybroeckMichel Waroquier

2011

A theoretical and experimental spectroscopy study on methanol and ethanol conversion over H-SAPO-34

Karen HemelsoetAn GhyselsDavide MoresKristof De WispelaereVeronique Van SpeybroeckBert M WeckhuysenMichel Waroquier

Advanced normal mode analysis for multi-scale modeling

An GhyselsBenjamin T MillerMichel WaroquierBernard R Brooks

Efficient calculation of QM/MM frequencies with the mobile block hessian

An GhyselsH Lee III WoodcockJoseph D LarkinBenjamin T MillerYihan ShaoJing KongDimitri Van NeckVeronique Van SpeybroeckMichel WaroquierBernard R Brooks

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Experimental and theoretical IR study of methanol and ethanol conversion over H-SAPO-34

Karen HemelsoetAn GhyselsDavide MoresKristof De WispelaereVeronique Van SpeybroeckBert M WeckhuysenMichel Waroquier

A1 Journal Article in CATALYSIS TODAY

First principle kinetic studies of zeolite-catalyzed methylation reactions

Veronique Van SpeybroeckJeroen Van der MynsbruggeMatthias VandichelKaren HemelsoetDavid LesthaegheAn GhyselsGuy MarinMichel Waroquier

A1 Journal Article in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Introducing BSSE as an extra energy term in molecular dynamics

Marc Van HouteghemAn GhyselsToon VerstraelenVeronique Van SpeybroeckMichel WaroquierChristine KirschhockJohan Martens

Monte Carlo simulations to understand 'breathing' phenomenon of metal organic frameworks

An GhyselsVeronique Van SpeybroeckMichel WaroquierB Smit

Normal mode analysis in zeolites: toward an efficient calculation of adsorption entropies

Bart De MoorAn GhyselsMarie-Françoise ReyniersVeronique Van SpeybroeckMichel WaroquierGuy Marin

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

Understanding framework flexibility by Monte Carlo simulation

An GhyselsVeronique Van SpeybroeckMichel WaroquierBerend Smit

2010

Comparative study of various normal mode analysis techniques based on partial Hessians

An GhyselsVeronique Van SpeybroeckEwald PauwelsSaron CatakBernard R BrooksDimitri Van NeckMichel Waroquier

A1 Journal Article in JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian

An GhyselsH Lee WoodcockYihan ShaoBernard R BrooksDimitri Van NeckVeronique Van SpeybroeckMichel Waroquier

TAMkin : a versatile package for vibrational analysis and chemical kinetics

An GhyselsToon VerstraelenKaren HemelsoetMichel WaroquierVeronique Van Speybroeck

A1 Journal Article in JOURNAL OF CHEMICAL INFORMATION AND MODELING

2009

Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian Method

An GhyselsMichel Waroquier

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules

An GhyselsVeronique Van SpeybroeckEwald PauwelsDimitri Van NeckBernard R. BrooksMichel Waroquier

A1 Journal Article in Journal of Chemical Theory and Computation

Normal mode analysis of macromolecular systems with the Mobile Block Hessian method

An GhyselsVeronique Van SpeybroeckDimitri Van NeckBernard R. R. BrooksMichel Waroquier

Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method

An GhyselsLee H. WoodcockYihan ShaoBernard R. BrooksVeronique Van SpeybroeckDimitri Van NeckMichel Waroquier

Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

An GhyselsDimitri Van NeckBernard R. BrooksVeronique Van SpeybroeckMichel Waroquier

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

The evaluation of QM/MM full Hessian and some applications

H Lee, III WoodcockAn GhyselsYihan ShaoJing KongBernard R Brooks

The evaluation of the QM/MM full Hessian and some applications

H Lee III WoodcockAn GhyselsYihan ShaoJing KongBernard R Brooks

2008

An efficient approach for the calculation of frequencies in macromolecules

An GhyselsVeronique Van SpeybroeckDimitri Van NeckBernard R. BrooksMichel Waroquier

Calculating reaction rates with partial Hessians: Validation of the mobile block Hessian approach

An GhyselsVeronique Van SpeybroeckToon VerstraelenDimitri Van NeckMichel Waroquier

A1 Journal Article in JOURNAL OF CHEMICAL THEORY AND COMPUTATION

MFI fingerprint: How pentasil-induced IR bands shift during zeolite nanogrowth

David LesthaeghePeter VansteenkisteToon VerstraelenAn GhyselsCEA KIRSCHHOCKJA MARTENSVeronique Van SpeybroeckMichel Waroquier

A1 Journal Article in JOURNAL OF PHYSICAL CHEMISTRY C

Normal modes in partially optimized molecular systems: the Mobile Block Hessian (MBH) approach

An GhyselsVeronique Van SpeybroeckDimitri Van NeckBernard R. BrooksMichel Waroquier

On the development of a partial vibrational analysis within a QM/MM approach

An GhyselsVeronique Van SpeybroeckBernard R. BrooksMichel Waroquier

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

H. Lee WoodcockWenjun ZhengAn GhyselsYihan ShaoJing KongBernard R. Brooks

A1 Journal Article in Journal of Chemical Physics

2007

Cartesian formulation of the mobile block Hessian approach to vibrational analysis in partially optimized systems

An GhyselsDimitri Van NeckMichel Waroquier

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

Vibrational modes in partially optimized molecular systems

An GhyselsDimitri Van NeckVeronique Van SpeybroeckToon VerstraelenMichel Waroquier

A1 Journal Article in JOURNAL OF CHEMICAL PHYSICS

2006

Role of mean free path in spatial phase correlation and nodal screening

BA VAN TIGGELEND ANACHEAn Ghysels

A1 Journal Article in EUROPHYSICS LETTERS