Projects: |
- Dissipative Particle Dynamics
- Biomembranes
- Bacterial membranes
- Non-Hamiltonian MD
- Electrokinetics
- Turing patterns
- Wetting
- DNA-cationic lipids
- Self-gravitating systems
- Superconductivity
- Charge-density waves
Biological membranes
We are currently studying various membrane systems including pure DPPC, mixtures of DPPC and cholesterol, cationic lipids (DMTAP and others) with and without DNA, and the effect of alcohol on membranes, to mention a few. Typically, our simulations are done using classical molecular dynamics but we have also done force-field development using a fully quantum mechanical approach as well as coarse-grained modeling using dissipative particle dynamics.More information of these projects will be added later, but below you will find some of our publications and a few movies of these systems. We also provide downloadable configurations and software.
Movies:
- DPPC-cholesterol system (5 Mb). A movie of DPPC-Chol systems (128 lipids). Cholesterols are marked with green color.
- DPPC-cholesterol system (large! 157 Mb). The same as above but in much more detail.
- A CPK model of a cholesterol molecule (0.5 Mb, rotated).
- A full atom model of a cholesterol molecule (0.6 Mb rotated).
Some of our membrane publications:
-
Crumpling of a stiff tethered membrane,
J.A. Åström, J. Timonen, and Mikko Karttunen
Phys. Rev. Lett. 93, 244301 (2004).
[Online]
[cond-mat/0309506]
-
Long-Range Interactions in Molecular Simulations: Accuracy and Speed
Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen
submitted.
[
cond-mat/0410210]
-
Impact of Cholesterol on Voids in Phospholipid Membranes
Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen
J. Chem. Phys. 121, 12676 (2004)
[
cond-mat/0408380]
[online]
Selected for the December 15, 2004 issue of
the Virtual Journal of Biological Physics Research
-
Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers
Michael Patra, Emppu Salonen, Emma Terama, Ilpo Vattulainen, Roland Faller, Bryan W. Lee, Juha Holopainen, and Mikko Karttunen
submitted
[cond-mat/0408122]
- Structural effects of small molecules on phospholipid bilayers investigated
by molecular simulations
B.W. Lee, R. Faller, A.K. Sum, I. Vattulainen, M. Patra, and M. Karttunen
to appear in Fluid Phase Equilibria
For a preprint, please email us.
-
Coarse-Grained Model for Phospholipid/Cholesterol Bilayer
Teemu Murtola, Emma Falck, Michael Patra, Mikko Karttunen, Ilpo Vattulainen
J. Chem. Phys.121 9156-9165 (2004).
[cond-mat/0406764]
[online]
Selected for the November 1, 2004 issue of
the Virtual Journal of Biological Physics Research
-
Lessons of Slicing Membranes: Interplay of Packing, Free Area, and
Lateral Diffusion in Phospholipid/Cholesterol Bilayers
Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen
Biophys. J. 87, 1076-1091 (2004).
[Online]
[cond-mat/0402290]
Selected in Sep. 2004 issue of
Molecular Modeling & Computational Chemistry (MMCC)
-
Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study,
A.A. Gurtovenko, Michael Patra, Mikko Karttunen, and Ilpo Vattulainen
Biophys. J. 86, 3461-3472 (2004).
[online]
[cond-mat/0312400]
Download
equilibrium configuration and parameters
Selected in July 2004 issue of
Molecular Modeling & Computational Chemistry (MMCC)
- Lipid bilayers driven to a wrong lane in molecular dynamics
simulations by truncation of long-range electrostatic interactions
Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen
J. Phys. Chem. B 108, 4485-4494 (2004).
[Online]
Download equilibrium configuration
-
Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating
electrostatic interactions
Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen
Biophys. J. 84, 3636-3645 (2003)
[Online]
[Preprint]
Selected in July 2003 issue of
Molecular Modeling & Computational Chemistry (MMCC)
Download equilibrium configurations
-
Characterization of Sphingosine-Phosphatidylcholine Monlayers: Effects of DNA,
V. Matti J. Säily, Juha-Matti Alakoskela, Samppa J. Ryhänen, Mikko Karttunen, and Paavo K.J. Kinnunen
Langmuir 19, 8956-8963 (2003)
[Online]
See also:
- Systematic comparison of force fields for microscopic simulations of NaCl
in aqueous solutions: Diffusion, free energy of hydration and structural properties,
Michael Patra and Mikko Karttunen,
J. Comp. Chem 25, 678-689 (2004).
[physics/0211059]
All RDFs from ion simulations
-
Novel Methods in Soft Matter Simulations,
Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen (Eds.)
to be published by Springer-Verlag in the Lecture Notes in Physics series
[Contents of the book]
SoftSimu2002
-
Modeling of biologically motivated soft matter systems
Ilpo Vattulainen and Mikko Karttunen
to appear in the Handbook of Theoretical and Computational Nanotechnology, edited by M. Rieth and W. Schommers (American Scientific Publishers)For a preprint, please email us.
- See our publication list.
- Downloadable configurations and software is here