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Since C ( d ) as defined in Eq. (19) would average out the large dimer correlations with the essentially uncorrelated bonds between two dimers, we have defined C odd ( d ) = 1 i max ∑ i = 1 i max 〈 σ z ( 2 i − 1 ) σ z ( 2 i − 1 + d ) 〉, (20).
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Two hydrogen-bond clusters between two dimers are important to stabilize the tetramer.
The reconstruction of semiconductor surfaces to minimize the number of dangling bonds [9] may cause different kinds of binding sites on the surface, e.g. one site may be between the two atoms of a surface dimer, while another is within a trench between two dimers [10].
Also in this model, there is one free-parameter: the association constant between two dimers k+, which was chosen to be in agreement with the previous studies [14], [15].
The interactions between two dimers are repeated seven times to allow formation of the observed 14-mer.
This approach allowed for an unbiased analysis of the similarity between two dimers, which could have been overemphasized by global alignment over the entire dimers.
The hot spot is located in the interface between two dimers and is formed by α3 of one molecule and the oligomerization domain of another molecule.
Filament formation is thought to occur by the interaction of the charged residues (exposed by coiled coil formation) between two dimers.
Thus, the interaction energy between two dimers was calculated by where Emm is the molecular mechanical energy of the selected system consisting of all bonded and nonbonded energy terms in the CHARMM potential energy function.
The formation of ppa dimers is reported and the energetic difference between two dimer structures is presented.
In view of the data presented here and in the recent report by Proud and co-authors, the Kakuta model could be considered in the context of a hexameric eIF2Bα2β2δ2 regulatory subcomplex: as a possible interface between three dimers, instead of three monomers, especially because it was in fact based on crystal packing contacts among three dimers.
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