SoftSimu Movie Gallery
Welcome to our movie gallery. Feel free to use these. In exchange we would highly appreciate if you could reference the source whenever you use one of these (SoftSimu: www.softsimu.org).Controlling micellar fission using electrostatics
Fission, or a rupture, of a charged micelle. Fission is induced by electrostatics. Fission proceeds through the formation of a narrow and long stalk. This stalk is highly interdigitated and ordered. The life-time of the stalk can be controlled by controlling the electrostatic interactions (compare with the other movie).
Reference:
Micelle fission through surface instability and formation of an interdigitating stalk.
M. Sammalkorpi, M. Karttunen, M. Haataja
J. Am. Chem. Soc. 130, 17977-17980 (2008). [On-line]
Micellar fission
Fission, or a rupture, of a charged micelle. Fission is induced by electrostatics. Fission proceeds through the formation of a narrow and long stalk. This stalk is highly interdigitated and ordered. The life-time of the stalk can be controlled by controlling the electrostatic interactions.
Reference:
Micelle fission through surface instability and formation of an interdigitating stalk.
M. Sammalkorpi, M. Karttunen, M. Haataja
J. Am. Chem. Soc. 130, 17977-17980 (2008). [On-line]
Molecular Dynamics simulations of the enzyme Catechol-O-Methyl Transferase
Catechol-O-methyltransferase (COMT) is an enzyme responsible for the inactivation, for example, catecholamine neurotransmitters, including dopamine, epinephrine and norepinephrine. Inhibitors for COMT activity are needed in the treatment neurodegenerative diseases, e.g., Parkinson's disease.
References:
Extensive
Molecular Dynamics simulations of the enzyme Catechol-O-Methyl Transferase:
Methodological issues,
A. Bunker, P.T. Männistö, J.-F. St.-Pierre, T. Róg, P. Pomorski, and M. Karttunen,
SAR and QSAR in Env. Res. 19, 179-189 (2008). [On-line]
Cold denaturation of proteins
Proteins assume a unique three-dimensional structure under physiological conditions. This structure becomes gradually unstable as temperature is raised or lowered. At about 60C the ordered structure of proteins becomes unstable. This phenomenon is called denaturation. It is also observed at low temperatures, around -20C. While denaturation at high temperature can be easily explained, the mechanism behind denaturation at low temperature, i.e. cold denaturation, remains to be explained. We have simulated cold denaturation with an explicit solvent and found that this phenomenon can be explained by the formation clathrate cages around hydrophobic residues.
Reference:
Microscopic mechanism for cold denaturation
,
C.L. Dias, T. Ala-Nissila, M. Karttunen, I. Vattulainen, and M. Grant
Phys. Rev. Lett. 100, 118101 (2008). [On-line]
Ethanol molecule hydrogen bonding to a POPC lipid
A movie showing how ethanol forms hydrogen bonds with (POPC) lipids. Snapshot from a molecular dynamics simulations of ethanol, water and 128 POPC lipids. Water has been removed for clarity.
References:
Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers
M. Patra et al.,
Biophys. J. 90, 1121-1135 (2006). [Online];
Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations
B.W. Lee, et al.,
Fluid Phase Equilibria 225, 63-68 (2004) [online]
No phosphorylation:Biomineralization: Face-Specific Adsorption of an Osteopontin Phosphopeptide on Calcium Oxalate
Osteopontin is abundant in bone and eggshell and is it intimately related to formation of atherosclerotic plaque, and kidney stones. We are study the interaction between osteopontin and the biomineral calcium oxalate monohydrate to understand how crystal growth can be modulated or/and inhibited. That is important, for example, in the formation of kidney stones as they most commonly contain calcium oxalate monohydrate. The movie shows absorption of ostepontin adsorbing on a calcium oxalate surface.Reference: Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide, B. Grohe, J. O'Young, A. Ionescu, G. Lajoie, K.A. Rogers, M. Karttunen, H.A. Goldberg and, G.K. Hunter, J. Am. Chem. Soc. 129, 14946-14951, 2007. [On-line]
Translocation of polymer through a narrow hole under an electric field.
Molecular dynamics simulation of spontaneous translocation of a polymer of length N=100 through a narrow hole. The process is driven by an applied electric field.
Reference:
Dynamical Scaling Exponents for Polymer Translocation through a Nanopore.
Kaifu Luo, Santtu T.T. Ollila, Ilkka Huopaniemi, Tapio Ala-Nissila, Pawel Pomorski, Mikko Karttunen,
See-Chen Ying, Aniket Bhattacharya.
Phys. Rev. E. (Rapid Comm.) 78, 050901(R) (2008). [On-line]
Sterol flip-flop in a lipid bilayer
A movie of ketosterol molecule undergoing a flip-flop in a lipid bilayer. To our knowledge this is the first time a sterol flip-flop has been seen in a simulation.Reference: Replacing the cholesterol hydroxyl group by the ketone group facilitates sterol flip-flop and promotes membrane fluidity, T. Rog, L.M. Stimson, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, J. Phys. Chem. B. 112 1946-1952 (2008). [On-line]
Lipid diffusion and correlations (DPPC bilayer simulation).
The arrows show the displacement of each lipid in one monlayer averaged over 5ns. Look for the streams that form and disappear.
Reference: Lateral diffusion in lipid membranes through collective flows,
E. Falck, T. Rog, M. Karttunen, I. Vattulainen, J. Am. Chem. Soc.,
129, 14946-14951, 2007
[On-line]
Cholesterol molecule (rotated)
Atomic scale model of cholesterol.Reference: Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvonen, and Ilpo Vattulainen Biophys. J. 87, 1076-1091 (2004).
Translocation of a polyethylene chain (N=100) through a narrow hole.
Molecular dynamics simulation of spontaneous translocation of a polyethylene molecule of length N=100 through a narrow hole.Reference: P. Pomorski and M. Karttunen, in preparation.
Ethanol in a lipid bilayer
Molecular dynamics simulations of ethanol, water and 128 DPPC lipids. Water has been removed for clarity. After a while, two ethanols are tagged such it is easier to follow their trajectories.
References:
Under the influence of alcohol: The effect of ethanol and methanol on lipid bilayers
M. Patra et al.,
Biophys. J. 90, 1121-1135 (2006). [Online];
Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations
B.W. Lee et al.,
Fluid Phase Equilibria 225, 63-68 (2004). [online];
Terama et al., J. Phys. Chem. B 112, 4131-4139 (2008). [On-line]
Xenon molecules interacting with a lipid bilayer
Molecular dynamics simulations of Xenon (150), water and 128 DPPC lipids. Water has been removed for clarity.
Reference:
Exploring the effect of Xenon on biomembranes
L.M. Stimson, I. Vattulainen, T. Rog, and M. Karttunen
Cell. Mol. Biol. Lett. 10 563-565 (2005).
[Online].
Simple system under shear flow conditions
Simple molecular system under shear flow (Lees-Edwards boundary conditions). The plane of zero shear is in the middle (dashed line). Two particles are marked with green color to illusrate the behavior of the individual particles.DPD simulations of liposome formation
References:How would you integrate the equations of motion in dissipative particle dynamics simulations? Petri Nikunen, Mikko Karttunen, and Ilpo Vattulainen Comp. Phys. Comm. 153, 407-421 (2003) [Online];
Towards better integrators for dissipative particle dynamics simulations, G. Besold, I. Vattulainen, M. Karttunen, and J.M. Polson, Phys. Rev. E, vol. 63, pp. R7611-R7614 (2000). [Online].
Quick Time format
DPD simulations of a A3B7 block copolymer
References:
How would you integrate the equations of motion in dissipative particle dynamics simulations?
Petri Nikunen, Mikko Karttunen, and Ilpo Vattulainen
Comp. Phys. Comm. 153, 407-421 (2003) [Online];
All in MPG format:
Spots in 2D Lamellae in 2D
Spheres in 3D
Lamellae in 3D Self-organization in 3D
Network in 2D
Network in 3D
Simulations of Turing systems
References:
Morphological transitions and bistability in Turing systems
T. Leppänen, M. Karttunen, R.A. Barrio, and K. Kaski
Phys. Rev. E 70, 066202 (2004).
[online]
A new dimension to Turing patterns,
T. Leppänen, M. Karttunen, K. Kaski, R. A. Barrio, and L. Zhang,
Physica D 168-169C, 35-44 (2002).
[Online];
Dimensionality effects in Turing pattern formation
Leppänen et al.,
Int. J. Mod. Phys. B 17, 5541-5553 (2003).
[cond-mat/0306121];
The effect of noise on Turing patterns
Leppänen, et al.,
Prog. Theor. Phys. (suppl.) 150, 367-370 (2003).
[Online]
MPG format
Phase slip in a superconducting wire
A movie showing a phase slip. The z-axis is the length of the superconducting wire and the x- and y-axes represent the real and the imaginary parts of the order parameter.References:
Instabilities and resistance fluctuations in thin accelerated superconducting rings, Mikko Karttunen, K.R. Elder, Martin B. Tarlie, Martin Grant, Phys. Rev. E 66, 026115 (2002). [online] [preprint]
More movies of superconducting ringsSelected for the September 1, 2002 issue of the Virtual Journal of Applications of Superconductivity
Sliding charge-density waves
Sliding charge-density waves under a driven force. The formation of dislocations is clearly visible.References:
Defects, Order, and Hysteresis in Driven Charge-Density Waves,
Mikko Karttunen, Mikko Haataja, K. R. Elder, and Martin Grant,
Phys. Rev. Lett., vol. 83, pp. 3518-3521 (1999).
[Online]
[preprint]
More CDW movies
DPD simulation of liposome formation
Liposome (vesicle) formation. The movie shows a cross section of the system visualizing the formation of a double layer. Water has been removed from the visualization for claity. One tracer molecule is colored using green.Reference:
MD simulation of a cholesterol-DPPC bilayer
A movie of DPPC-Chol systems (128 lipids). Cholesterols are marked with green color.Reference:
More lipid membrane movies + publications
MD simulation of alpha-hemolysin pore
MD simulation of Staphylococcus aureus toxin alpha-hemolysin in a lipid bilayer.
Reference:
Patra and Karttunen, in preparation
Simulation of cellular aggergates
Video of a cellular aggregate made of soft elastic particles swelling due to increased inflation pressure. The contact forces on the membranes are color coded (cold -> hot: small force -> large force)
Reference:
Cell aggregation: Packing soft grains,
Jan A. Astrom and Mikko Karttunen,
Phys. Rev. E 73 062301 (2006).[Online]
Forest fire simulation 1: Uniform background
Time development of the temperature field in a simulation of slow combustion in 2-d when the background reactant concentration is uniform. Growth sites emerge due to thermal fluctuations -- there are growing clusters of various sizes present in the system. Growth is radial since the background is uniform. After some time, growing clusters collide. Red denotes 'hot' and blue 'cold'. Due to dissipation the centers of the clusters start to cool.
Reference:
Nucleation, growth, and scaling in slow combustion,
M. Karttunen, N. Provatas, T. Ala-Nissila,
and M. Grant,
J. Stat. Phys. 90 1401-1411 (1998).[Online]
Forest fire simulation 2: Random background
Time development of the temperature field in a simulation of slow combustion in 2-d when the background reactant concentration is random. Growth sites emerge due to thermal fluctuations -- there are growing clusters of various sizes present in the system. After some time, growing clusters collide. Red denotes 'hot' and blue 'cold'. Due to dissipation the centers of the clusters start to cool as time passes.
Reference:
Nucleation, growth, and scaling in slow combustion,
M. Karttunen, N. Provatas, T. Ala-Nissila,
and M. Grant,
J. Stat. Phys. 90 1401-1411 (1998).[Online]