Curiously, many optimization problems can be mapped onto more general versions of the Ising model, in which any two spins can interact, not just neighbors, and the paired spins can be set to favor alignment or opposition.
We favor Alignment A for M1 for several additional reasons.
A higher BP will favor alignment sets with fewer, larger, alignments.
One possible artifact is the NCBI-Blast algorithm favors alignment of sequences in the middle of an alignment over sequences near the two ends.
In qualitative terms, the change of sign in the PCC reflects a competition between two effects: an energetic attraction between DPPE-biotin and saturated lipids, favoring alignment of Lo domains, vs a curvature-induced repulsion of these lipids away from the actin fibers.
Furthermore, an apparent direct physical interaction, which favors alignment between L-VGCCs and RyRs, enables L-VGCCs to function as a preferred source of extracellularly derived Ca2+ in triggering CICR from RyRs and amplifying Ca2+ transients (Lu et al., 1994; Cheng et al., 1996; Wang et al., 2001).
Searching on atom types favors alignments that superimpose atoms of the same type.
On the other hand, it was shown in [8] that the "streaker bee" hypothesis is a plausible mechanism by simulating the case that uninformed individuals can recognize informed bees and favor alignment to these bees.
Given that we know a priori which positions in a profile alignment are allowed to bear a selenocysteine, selenoprofiles favors the alignment to UGA codons only if these are aligned to one such position.
With the aim to explain the nanorod alignment, Zhang et al. hypothesized that a textured ZnO wetting layer formed prior to nanorod growth favors the alignment [22].
This shear rate seemed to provide the optimum flow favoring the alignment of the CW components, probably developing mixed mesophase organizations.
