Today's journal club of the Information Theory Study Group had Hiroshi Yokota (iTHEMS) talk about the replica-permutation method to obtain stable structures. He started off the talk with some introduction of proteins' stable structures. To avoid reaching nonglobally optimal structures, the replica-exchange method used to be applied; however, this method may be computationally expensive and less efficient in some circumstances. Later work has proposed the replica-permutation method by which the candidates of the stable structures are permutated (shuffled) and relaxes the detailed balance condition. He drew an analogy with allocation problems of various volumed cups each filled with water. He finally talked about the application in a paper that examines amyloid ? oligomerization. The audience asked lots of questions about the algorithm per se, physical meaning, and even its potential applications. Thanks, Hiroshi, for the fantastic talk! I as well as arguably all the audience really enjoyed it!
-Ryosuke Iritani (RIKEN iTHEMS)