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Author Topic: How can I create simulations of DNA and a graphene monolayer?  (Read 537 times)

Offline dveans

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Hello,

I want to make simulations of DNA and a graphene nanolayer, but I don't know of any software to help me make it easier.

Can anyone offer any advice?

Thank You.
« Last Edit: 24/05/2016 08:16:40 by chris »


 

Offline evan_au

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These are two very different molecules.
  • Graphene is 2 dimensional, composed of a single atom (carbon) and very regular
  • DNA is 1 dimensional, composed of many atomic species, and very irregular content.
  • Both of them tend to fold into complex 3D shapes.
A tool optimized for one will probably perform poorly on the other.

What is the common aspect of these two molecules that you want to simulate?
 

Offline chiralSPO

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There are many different types of computational models that span from the simple and computationally cheap "molecular mechanics" to slightly better semi-empirical methods like "extended Hückel" to the very expensive, but much more accurate "Density Functional Theory", which can give excellent analysis and prediction of molecules and molecular interactions, including electronic structure, orbital coupling and charge or spin density localization.

As far as software goes, Gaussian is the one that I have used most, and is often used in academic settings, but it is really freaking expensive. It is capable of all the methods I mentioned above and more--it's really one for the pros. Another fairly expensive program is VASP, which might be better suited to modeling graphene and other 2D or 3D lattices.

There is a freeware program called Avogadro that will do some simple molecular mechanics modeling (UFF = universal force field), but it is annoying to work in, and I don't know how informative the outputs will be for your DNA/graphene system...

Another freeware program, YAeHMOP (available at sourceforge), does extended Hückel calculations, and is actually quite powerful, though the interface is not great...

Good luck!
 
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Offline dveans

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What is the common aspect of these two molecules that you want to simulate?
graphene helps determine the sequence of nucleobases in DNA
 

Offline dveans

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There are many different types of computational models that span from the simple and computationally cheap "molecular mechanics" to slightly better semi-empirical methods like "extended Hückel" to the very expensive, but much more accurate "Density Functional Theory", which can give excellent analysis and prediction of molecules and molecular interactions, including electronic structure, orbital coupling and charge or spin density localization.

As far as software goes, Gaussian is the one that I have used most, and is often used in academic settings, but it is really freaking expensive. It is capable of all the methods I mentioned above and more--it's really one for the pros. Another fairly expensive program is VASP, which might be better suited to modeling graphene and other 2D or 3D lattices.

There is a freeware program called Avogadro that will do some simple molecular mechanics modeling (UFF = universal force field), but it is annoying to work in, and I don't know how informative the outputs will be for your DNA/graphene system...

Another freeware program, YAeHMOP (available at sourceforge), does extended Hückel calculations, and is actually quite powerful, though the interface is not great...

Good luck!

Thank you very much!
 

Offline evan_au

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Quote from: dveans
graphene helps determine the sequence of nucleobases in DNA

Are you developing a next-generation DNA sequencing technology?

Or are you trying to discover the evolutionary tree of DNA? (This is covered in another thread...)
 

Offline dveans

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Quote from: dveans
graphene helps determine the sequence of nucleobases in DNA

Are you developing a next-generation DNA sequencing technology?

Or are you trying to discover the evolutionary tree of DNA? (This is covered in another thread...)

It is only practice part in my diploma, I want to build it, to see that on my own eyes and also how it is works :)
 

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