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Research GBB Molecular Dynamics Group Publications





Maria Tsanai 2022

Modeling of liquid-liquid phase separation in biological systems

Carlos Ramirez Palacios 2022

Numerical simulations of proteins

Bart Bruininks 2021

On the road to simulating life with molecular detail

Yang Liu 2020 Multiscale membrane models
Peter Kroon 2020 Aggregate, assemble, automate
Ilias Patmanidis 2020 Molecular Dynamics of Bioinspired Nanotubes
Riccardo Alessandri 2019 Multiscale modeling of organic materials. From the Morphology Up
Juanjuan Su 2017 The simulation studies of the interplay of peptides with lipids
Jaakko Uusitalo 2016 Covering all the bases
Floris van Eerden 2016 Photosynthesis in silico
Clement Arnarez 2014 Computational Microscopy of the supramolecular organisation of the respitory chain complexes
Nur Alia Oktaviani 2014 NMR studies of folded and unfolded proteins : method developments and biological insight
Djurre de Jong 2013 A molecular view on the organizational complexity of proteins in membranes
César López Bautista 2012 Carbohydrates: More than meets the eye
Andrzej Rzepiela 2011 Development of multiscale simulation methods
Renee Otten 2011

Protein structure and dynamics by NMR: synergy between biochemistry and pulse sequence design

Marcelo Masman 2010 Development of novel small-size peptides as putative therapeutic drugs
Marc Fuhrmans 2010 Simulation studies of membrane fusion and the role of fusion peptides
Daniela Mueller 2010

The effects of urea and of pH on protein structure studies by molecular dynamics simulation

Ying Xue 2010 The effect of environment on peptide and protein folding: a molecular dynamics study
Jelger Risselada 2009 Fascinating vesicles?
Magdalena Siwko 2008

Disturb or Stabilize? Effects of different molecules on biological membranes

Tsjerk Wassenaar 2006 Molecular Dynamics of Sense and Sensibility in Processing and Analysis of Data
Hao Fan 2006 Refining protein structures: a dynamic approach
Hari Leontiadou 2005 Modelling membranes under stress

Gilles Pieffet


The application of molecular dynamics simulation techniques and free energy calculations to predict protein-protein and protein-ligand interactions

Gerrit Groenhof


Understanding light-induced conformational changes in molecular systems from first principles

Patricia Soto-Becerra


Peptide folding in non-aqueous environments investigated with molecular dynamics simulations: possibilities and limitations

Franciska van Lune


Residual dipolar couplings: a new technique for structure determination of proteins in solution

Berk Hess


Stochastic concepts in molecular simulation

Eiso AB


Structural studies on IIB

Alexander Morozov


Orientational transitions in block-copolymer melts under shear flow

Marc Lensink


Non-adiabatic proton transfer in biomolecular systems

Anton Feenstra


Long term dynamics of proteins and peptides

Marcel Swart


Density Functional Theory Applied to Copper Proteins

Lucia Creveld


Molecular dynamics simulations in rational protein design: stabilisation of Fusarium solani pisi cudinase against anionic surfactants

Pieter Meulenhoff


Interfacial action of phospholipase A 2: A molecular dynamics study.

Bert de Groot


Native State Protein Dynamics, a theoretical approach

Peter Tieleman


Theoretical studies of membrane models: Molecular dynamics of water, lipids and membrane proteins

Bernard van Vlimmeren


Mesoscopic dynamics, simulation of microphase separation dynamics in polymer liquids

Andrea Amadei


Theoretical models for fluid thermodynamics based on the quasi-Gaussian entropy theory

Ton Linssen


Molecular dynamics simulations of haloalkane dehalogenase

Natalia Maurits


Mathematical modeling of complex systems, microphase separation dynamics in polymer liquids

Emile Apol


The quasi-gaussian entropy theory, temperature dependence of thermodynamic properties using distribution functions

David van der Spoel


Structure and dynamics of peptides: Theoretical aspects of protein folding

Henk Bekker


Molecular dynamics simulation methods revised

Alex de Vries


Modelling condensed-phase systems : from quantum chemistry to molecular models (PDF)

Siewert Jan Marrink


Permeation of small molecules across lipid membranes. A molecular dynamics study.

Last modified:07 March 2023 11.34 a.m.