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DSPC simulation under transition temperature
- mferraro
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10 years 7 months ago #2058
by mferraro
DSPC simulation under transition temperature was created by mferraro
Hi guys,
I have a question regarding simulation of 3 DSPC bilayers obtained through self-assembly procedure.
They just differ in the number of molecules and obviously in box dimensions. In order to observe DSPC behavior at 300 K (under 328 K, its Tm), I run self-assembly at this temperature for the 3 systems. All systems share the same hydration state (6 water for each DSPC molecule).
From a visual inspection, two of the simulated systems seem to be fluid (looking at conformation of the acyl chains!), whereas in the third system (the smaller one) the formation of a lattice of acyl chains can be observed, solid ordered state I think. This happens just in one leaflet while the other one shows disordered state.
What could this strange and not reproducible behavior be due to?
Any idea will be really appreciated!
Thanks!
Maria.
I have a question regarding simulation of 3 DSPC bilayers obtained through self-assembly procedure.
They just differ in the number of molecules and obviously in box dimensions. In order to observe DSPC behavior at 300 K (under 328 K, its Tm), I run self-assembly at this temperature for the 3 systems. All systems share the same hydration state (6 water for each DSPC molecule).
From a visual inspection, two of the simulated systems seem to be fluid (looking at conformation of the acyl chains!), whereas in the third system (the smaller one) the formation of a lattice of acyl chains can be observed, solid ordered state I think. This happens just in one leaflet while the other one shows disordered state.
What could this strange and not reproducible behavior be due to?
Any idea will be really appreciated!
Thanks!
Maria.
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- jaakko
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10 years 7 months ago #2104
by jaakko
Replied by jaakko on topic DSPC simulation under transition temperature
Hi Maria,
it could be related to, e.g., the size of the patches or it could be related to the simulation length. How large are the bilayer patches and how long are the simulations?
it could be related to, e.g., the size of the patches or it could be related to the simulation length. How large are the bilayer patches and how long are the simulations?
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- mferraro
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10 years 6 months ago #2137
by mferraro
Replied by mferraro on topic DSPC simulation under transition temperature
Hi Jaakko,
1 system = 218 DSPC box after 200 ns of self-assembly= 9.12132 9.12132 5.80448
2 system= 204 DSPC box after 200 ns of self-assembly= 8.63644 8.63644 6.04551
3 system= 192 DSPC box after 200 ns of self-assembly= 8.12610 8.12610 6.46400
Only system 3 shows the transition in one leaflet at 300 K, whereas 1 and 2 do not (at the same temperature)
I solved this problem rising up the temperature until 330 K, but I'm very curious to know something more about that. I've already noticed that self-assembly procedure is very sensible to the initial conditions, so I would not be surprised if not suitable box dimensions influenced DSPC behavior in this way.
Thank you again for caring about this issue!
Maria.
1 system = 218 DSPC box after 200 ns of self-assembly= 9.12132 9.12132 5.80448
2 system= 204 DSPC box after 200 ns of self-assembly= 8.63644 8.63644 6.04551
3 system= 192 DSPC box after 200 ns of self-assembly= 8.12610 8.12610 6.46400
Only system 3 shows the transition in one leaflet at 300 K, whereas 1 and 2 do not (at the same temperature)
I solved this problem rising up the temperature until 330 K, but I'm very curious to know something more about that. I've already noticed that self-assembly procedure is very sensible to the initial conditions, so I would not be surprised if not suitable box dimensions influenced DSPC behavior in this way.
Thank you again for caring about this issue!
Maria.
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10 years 6 months ago #2138
by jaakko
Replied by jaakko on topic DSPC simulation under transition temperature
Hi Maria,
I don't remember from the top of my head how Martini DSPC should behave at 300 K but just based on your observations the Tm is probably closer to 300 K than the experimental one. I would simulate the boxes for much longer, phase transitions can take a lot of time to occur. In general, the periodic effects in smaller boxes enhance ordering but the differences in lipid numbers in your boxes are so small that I doubt one could notice the difference between them.
I don't remember from the top of my head how Martini DSPC should behave at 300 K but just based on your observations the Tm is probably closer to 300 K than the experimental one. I would simulate the boxes for much longer, phase transitions can take a lot of time to occur. In general, the periodic effects in smaller boxes enhance ordering but the differences in lipid numbers in your boxes are so small that I doubt one could notice the difference between them.
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10 years 6 months ago #2158
by siewert
Replied by siewert on topic DSPC simulation under transition temperature
There are two other factors to consider:
(i) after self-assembly you may have ended up with an asymmetric distribution of the lipids. So one monolayer might be more packed than the other, and perhaps this has triggered the formation of a gel phase in the one layer
(ii) freezing or gel formation is a stochastic process, and might occur at any given point in time (assuming you are below Tm).
By the way, it is not clear to me why you start with a self-assembly process if you are interested in the formation of gel phases.
(i) after self-assembly you may have ended up with an asymmetric distribution of the lipids. So one monolayer might be more packed than the other, and perhaps this has triggered the formation of a gel phase in the one layer
(ii) freezing or gel formation is a stochastic process, and might occur at any given point in time (assuming you are below Tm).
By the way, it is not clear to me why you start with a self-assembly process if you are interested in the formation of gel phases.
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- mferraro
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10 years 6 months ago #2243
by mferraro
Replied by mferraro on topic DSPC simulation under transition temperature
Thanks a lot guys!
Siewert,
it's just a curiosity. I'm surely interested in self-assembly, not directly in gel-formation, but I saw this event in my systems and so I was curious to know how it was possible to observe that just in a system and not in the others.
For my information, I could say!
Anyway, your explanation have extensively satisfied my thirst of knowledge! :)
Thanks again!
Maria.
Siewert,
it's just a curiosity. I'm surely interested in self-assembly, not directly in gel-formation, but I saw this event in my systems and so I was curious to know how it was possible to observe that just in a system and not in the others.
For my information, I could say!
Anyway, your explanation have extensively satisfied my thirst of knowledge! :)
Thanks again!
Maria.
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