How the all-atom simulation and the ising-based theory reconcilewith each other on the helix-coil transition.
In this report, we addressed a somewhat basic question about how the twoextreme models, the all-atom model and the Ising-based model, can beconsistent with each other regarding the polypeptide helix-coil transition.Comparisons of several physical properties were made between the resultsof the all-atom simulations and those of the Ising-based theories. Fromthe equilibrium point of view, the two models were found to exhibit aqualitatively similar trend, which is significant considering the extremedifference in precision between the two models. On the other hand, fromthe kinetic viewpoint, there appeared a difference in relaxation behaviorbetween the two models; i.e., so-called stretched exponential relaxationwas observed in the all-atom simulation whereas the kinetic Ising modelshowed simple exponential relaxation. A plausible source of the observeddifference is briefly discussed.
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M
Takano
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K
Nagayama
A
A
Suyama
Glauber dynamics; Helix-coil transition; Ising model; kinetics; molecular dynamics simulation; relaxation; statistical mechanics; stretched exponential