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The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan
Published on: June 29, 2018
Exchanging Replicas with Unequal Cost, Infinitely and Permanently
Sander Roet1, Daniel T Zhang1, Titus S van Erp1
1Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491Trondheim, Norway.
Abstract:
We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different types of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble-based criterion in which the other ensembles represent an environment that might or might not participate in the Monte Carlo move. In addition, based on a recent algorithm for computing permanents, we effectively increase the exchange rate to infinite without the steep factorial scaling as a function of the number of replicas. We illustrate the effectiveness of this replica exchange methodology by combining it with a quantitative path sampling method, replica exchange transition interface sampling (RETIS), in which the costs for a Monte Carlo move can vary enormously as paths in a RETIS algorithm do not have the same length and the average path lengths tend to vary considerably for the different path ensembles that run in parallel. This combination, coined ∞RETIS, was tested on three model systems.
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