Electrophoretic mobility does not always reflect the charge on an oil droplet (2008)
Knecht, V., Risselada, H.J., Mark, A.E., Marrink, S.J.
Electrophoresis is widely used to determine the electrostatic potential of colloidal particles. Oil droplets in pure water show negative or positive electrophoretic mobilities depending on the pH....
Phase transformations of lipid aggregates at molecular resolution (2007)
De Vries, A. H., Fuhrmans, M., Risselada, J., Siwko, M. E., Knecht, V., Marrink, S. J.
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study (2007)
Siwko, M. E., Marrink, S. J., De Vries, A. H., Kozubek, A., Mark, A. E.
The question of why plants release isoprene when heat stressed has been continuously debated for more than half a century. In this work we use molecular dynamics simulation techniques to directly...
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study (2007)
Siwko, M. E., Marrink, S. J., De Vries, A. H., Kozubek, A., Mark, A. E.
The question of why plants release isoprene when heat stressed has been continuously debated for more than half a century. In this work we use molecular dynamics simulation techniques to directly...
Antimicrobial peptides in action (2006)
Leontiadou, H., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations of the magainin MG-H2 peptide interacting with a model phospholipid membrane have been used to investigate the mechanism by which antimicrobial peptides act. Multiple...
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail (2006)
Knecht, V., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations have been used to study the phase behavior of a dipalmitoylphosphatidylcholine (DPPC)/palmitic acid (PA)/water 1:2:20 mixture in atomic detail. Starting from a random...
Antimicrobial peptides in action (2006)
Leontiadou, H., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations of the magainin MG-H2 peptide interacting with a model phospholipid membrane have been used to investigate the mechanism by which antimicrobial peptides act. Multiple...
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail (2006)
Knecht, V., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations have been used to study the phase behavior of a dipalmitoylphosphatidylcholine (DPPC)/palmitic acid (PA)/water 1:2:20 mixture in atomic detail. Starting from a random...
Simulation studies of pore and domain formation in a phospholipid monolayer (2005)
Knecht, V., Muller, M., Bonn, M., Marrink, S. J., Mark, A. E.
Despite extensive study the phase behavior of phospholipid monolayers at an air-water interface is still not fully understood. In particular recent vibrational sum-frequency generation (VSFG) spectra...
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model (2005)
Marrink, S. J., Risselada, J., Mark, A. E.
The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to...
Molecular structure of the lecithin ripple phase (2005)
De Vries, A. H., Yefimov, S., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two...
Simulation studies of pore and domain formation in a phospholipid monolayer (2005)
Knecht, V., Muller, M., Bonn, M., Marrink, S. J., Mark, A. E.
Despite extensive study the phase behavior of phospholipid monolayers at an air-water interface is still not fully understood. In particular recent vibrational sum-frequency generation (VSFG) spectra...
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model (2005)
Marrink, S. J., Risselada, J., Mark, A. E.
The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to...
Molecular structure of the lecithin ripple phase (2005)
De Vries, A. H., Yefimov, S., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two...
Coarse grained model for semiquantitative lipid simulations (2004)
Marrink, S. J., De Vries, A. H., Mark, A. E.
This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range...
Molecular view of hexagonal phase formation in phospholipid membranes (2004)
Important biological processes, such as vesicle fusion or budding, require the cell matrix to undergo a transition from a lamellar to a nonlamellar state. Although equilibrium properties of membranes...
The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study (2004)
De Vries, A. H., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations have been used to study the properties of mixed dioleoylphosphatidylcholine/ dioleoylphospatidylethanolamine bilayers as a function of phosphatidylcholine...
Molecular dynamics simulations of hydrophilic pores in lipid bilayers (2004)
Leontiadou, H., Mark, A. E., Marrink, S. J.
Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the...
Coarse grained model for semiquantitative lipid simulations (2004)
Marrink, S. J., De Vries, A. H., Mark, A. E.
This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range...
Molecular view of hexagonal phase formation in phospholipid membranes (2004)
Important biological processes, such as vesicle fusion or budding, require the cell matrix to undergo a transition from a lamellar to a nonlamellar state. Although equilibrium properties of membranes...
The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study (2004)
De Vries, A. H., Mark, A. E., Marrink, S. J.
Molecular dynamics simulations have been used to study the properties of mixed dioleoylphosphatidylcholine/ dioleoylphospatidylethanolamine bilayers as a function of phosphatidylcholine...
Molecular dynamics simulations of hydrophilic pores in lipid bilayers (2004)
Leontiadou, H., Mark, A. E., Marrink, S. J.
Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the...
Simulation of MscL Gating in a bilayer under stress (2003)
Colombo, G., Marrink, S. J., Mark, A. E.
The initial stages of the gating of the mechanoselective channel of large conductance from Mycobacterium tuberculosis have been studied in atomic detail using molecular dynamics simulation...
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields (2003)
Tieleman, D. P., Leontiadou, H., Mark, A. E., Marrink, S. J.
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the...
Simulation of MscL Gating in a bilayer under stress (2003)
Colombo, G., Marrink, S. J., Mark, A. E.
The initial stages of the gating of the mechanoselective channel of large conductance from Mycobacterium tuberculosis have been studied in atomic detail using molecular dynamics simulation...
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields (2003)
Tieleman, D. P., Leontiadou, H., Mark, A. E., Marrink, S. J.
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the...
Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile (2002)
Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development...
Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile (2002)
Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development...
Molecular dynamics simulations of mixed micelles modeling human bile (2002)
Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development...
Molecular dynamics simulations of mixed micelles modeling human bile (2002)
Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development...
Effect of Undulations on Surface Tension in Simulated Bilayers (2001)
To understand the effect of the finite size of simulation cells on the equilibrium properties of bilayers, an extensive series of glycerolmonoolein bilayer molecular dynamics simulations in which the...
Pinczewski, W.V., Sheppard, Adrian P., Marrink, S.J., Knackstedt, Mark A., Sahimi, Muhammad
The invasion percolation model is used to investigate the effect of correlated heterogeneity on capillary dominated displacements in porous media. The breakthrough and residual saturations are shown...
Effect of Undulations on Surface Tension in Simulated Bilayers (2001)
To understand the effect of the finite size of simulation cells on the equilibrium properties of bilayers, an extensive series of glycerolmonoolein bilayer molecular dynamics simulations in which the...
Marrink, S.J., Knackstedt, Mark A., Sheppard, Adrian P., Pinczewski, W.V., Sahimi, Muhammad
The invasion percolation model is used to investigate the effect of correlated heterogeneity on capillary dominated displacements in porous media. The breakthrough and residual saturations are shown...
Effect of undulations on surface tension in simulated bilayers (2001)
To understand the effect of the finite size of simulation cells on the equilibrium properties of bilayers, an extensive series of glycerolmonoolein bilayer molecular dynamics simulations in which the...
Effect of undulations on surface tension in simulated bilayers (2001)
To understand the effect of the finite size of simulation cells on the equilibrium properties of bilayers, an extensive series of glycerolmonoolein bilayer molecular dynamics simulations in which the...
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation (2000)
Tieleman, D.P., Marrink, S.J., Mark, A.E.
Using an atom based force field, molecular dynamics (MD) simulations of 54 dodecylphosphocholine (DPC) surfactant molecules in water at two different concentrations above the critical micelle...
Definition of percolation thresholds on self-affine surfaces (2000)
Knackstedt, Mark A., Paterson, Lincoln, Marrink, S.J.
We study the percolation transition on a two-dimensional substrate with long-range self-affine correlations. We find that the position of the percolation threshold on a correlated lattice is no...
Finite size scaling for percolation on elongated lattices in two and three dimensions (2000)
Knackstedt, Mark A., Marrink, S.J.
We derive scaling laws for the percolation properties of an elongated lattice, i.e., those with dimensions of L^(d-1)×nL in d dimensions, where n denotes the aspect ratio of the lattice. Based on...
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation (2000)
Mark, A.E., Tieleman, D.P., Marrink, S.J.
Using an atom based force field, molecular dynamics (MD) simulations of 54 dodecylphosphocholine (DPC) surfactant molecules in water at two different concentrations above the critical micelle...
Definition of percolation thresholds on self-affine surfaces (2000)
Knackstedt, Mark A., Paterson, Lincoln, Marrink, S.J.
We study the percolation transition on a two-dimensional substrate with long-range self-affine correlations. We find that the position of the percolation threshold on a correlated lattice is no...
Finite size scaling for percolation on elongated lattices in two and three dimensions (2000)
Knackstedt, Mark A., Marrink, S.J.
We derive scaling laws for the percolation properties of an elongated lattice, i.e., those with dimensions of L^(d-1)×nL in d dimensions, where n denotes the aspect ratio of the lattice. Based on...
Percolation thresholds on elongated lattices (1999)
Knackstedt, Mark A., Marrink, S.J.
We investigate the percolation thresholds of both random and invasion percolation in two and three dimensions on elongated lattices; lattices with a geometry of L^(d−1) × nL in d dimensions, where...
Percolation thresholds on elongated lattices (1999)
Knackstedt, Mark A., Marrink, S.J.
We investigate the percolation thresholds of both random and invasion percolation in two and three dimensions on elongated lattices; lattices with a geometry of L^(d−1) × nL in d dimensions, where...
A Computer Perspective of Membranes: Molecular Dynamics Studies of Lipid Bilayer Systems (1997)
This paper was followed by two others from Stouch and coworkers, on the diffusion of small molecules in lipid membranes [70,97]. The membrane model explored in these studies is a fully hydrated DMPC...
Berendsen, H.J.C., Jähnig, F., Marrink, S.J.
To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced,...
Molecular dynamics simulation of a charged biological membrane (1996)
Marrink, S.J., López Cascales, J.J., Berendsen, H.J.C.
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as...
Free volume properties of a simulated lipid membrane (1996)
Berendsen, H.J.C., Sok, R.M., Marrink, S.J.
In this paper, an extensive analysis of free volume related properties of a lipid membrane is given. Using percolation theory, and comparing the free volume properties to those of a soft polymer,...
Berendsen, H.J.C., Jähnig, F., Marrink, S.J.
To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced,...
Molecular dynamics simulation of a charged biological membrane (1996)
Marrink, S.J., López Cascales, J.J., Berendsen, H.J.C.
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as...
Free volume properties of a simulated lipid membrane (1996)
Berendsen, H.J.C., Sok, R.M., Marrink, S.J.
In this paper, an extensive analysis of free volume related properties of a lipid membrane is given. Using percolation theory, and comparing the free volume properties to those of a soft polymer,...
Marrink, S J, Jähnig, F, Berendsen, H J
To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced,...
Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations.
Marrink, S J, Berger, O, Tieleman, P, Jähnig, F
Lipid adhesion forces can be measured using several experimental techniques, but none of these techniques provide insight on the atomic level. Therefore, we performed extensive nonequilibrium...
Marrink, S J, Jähnig, F, Berendsen, H J
To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced,...
Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations.
Marrink, S J, Berger, O, Tieleman, P, Jähnig, F
Lipid adhesion forces can be measured using several experimental techniques, but none of these techniques provide insight on the atomic level. Therefore, we performed extensive nonequilibrium...