Any suggestions for software capable of computing the electrical conductivity of a protein?
I guess this requires, electron effective masses calculations, which means an ab initio approach? My protein is 5-40 amino acids big. I don’t know if there is any semi QM approach that can compute the conductivity, but obviously the throughput of calculations is a concern.
Thank you for your attention to the matter.
/Morten
Dear Morten,
Attached please find three papers: two of them describe the required sofware and the third one covers the experimental and theoretical part of your topic.
Hoping this will be helpful,
Rafik
Hi Morten,
Perhaps this paper describes what you want to do?
DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases: http://journal.frontiersin.org/article/10.3389/fgene.2015.00213/full
They set up a tight-binding hamiltonian for large chunks of DNA and use a Green's function (NEGF) approach for calculating the transmittivity.
You could contact Dmitry Skachkov for the scripts/codes they use, I don't know how easy it is to use them with other bio-systems such as proteins.
Best wishes,
Fedor
Hi Fedor,
thanks for the great suggestion. I will read the paper and try to make contact with Dmitry Skachkov, to see if the script is applicable for proteins aswell and if I can be allowed to use it :)
kind regards
Morten
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