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Why do these ambimodal transition states occur?
I don't know that there is a general reason for that. Potential energy surfaces are complicated. Very often, there is an abundance of local minima, separated by potential energy barriers. It is similar to what happens with mountain chains and valleys, but with many dimensions.
One could argue that the opposite ...
4
To question (1), the short answer is yes, such scenarios do exist, but they are rare for m greater than 10 or so due to the large number of possible sequences and the high frequency of substitutions even in very closely related proteins. Those that do exist are often encoded by the same gene, and the deletion of parts of one polypeptide (producing a "...
3
You can use VMD to do this.
Note that the following is only tested on Linux with VMD version 1.9.2, i don't know how it works out on Windows or Apple OS.
The following is from a script that i used to render a trajectory. The first thing to do is to load your xyz file as trajectory. I.e. in a format so that vmd allows you to "slide" through the ...
2
The protein structural terminology in your question needs some work. For example "protein in primary structure embedded in a plane" - the primary structure is the sequence of the protein, and it is not clear how that would be embedded in the plane. Perhaps you mean embedding the graph corresponding to the atomic structure?
Pulling back, however, ...
1
Its a tricky question but anyway when you go through the HK theorem you'll see that there is a part where you have $v_{\mathrm{ext}} - v_{\mathrm{ext}}' = H - H'$ as the electron-electron and other operators are the same for both systems and will therefore cancel. The only important part is the external (nuclear-electron) potential and you get that mapping.
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