We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the control parameter discretization allow a treatment independent of the system in question. Analyzing mean first passage times across control parameter space, ...

The smart-darting algorithm is a Monte Carlo based simulation method used to overcome quasiergodicity problems associated with disconnected regions of configurations space separated by high energy barriers. As originally implemented, the smart-darting method works well for clusters at low temperatures with the angular momentum restricted to zero and where there are no transitions to permutation...

Multimodal structures in the sampling density (e.g. two competing phases) can be a serious problem for traditional Markov Chain Monte Carlo (MCMC), because correct sampling of the different structures can only be guaranteed for infinite sampling time. Samples may not decouple from the initial configuration for a long time and autocorrelation times may be hard to determine. We analyze a suitable...

Parallel Tempering (PT) is an effective algorithm to overcome the slow convergence in low-temperature protein simulation by initiating multiple systems to run at multiple temperature levels and randomly switch with neighbor temperature levels. We implemented the PT scheme in the Rosetta to explore the rough energy landscape in protein folding and to improve the success rate of Rosetta in topolo...

Let M be a finite or countable set of models (here we only deal with finite M but Bayes factors make sense for countable M). For each model m ∈ M we have the prior probability of the model pri(m). It does not matter if this prior on models is unnormalized. Each model m has a parameter space Θm and a prior g(θ | m), θ ∈ Θm The spaces Θm can and usually do have different dimensions. That’s the po...

Two nondestructive electromagnetic/magnetic techniques including hysteresis loop and eddy current methodologies have been used to characterize microstructural changes of AISI D2 cold work tool steel as a result of quench and tempering treatments. To measure the fraction retained austenite in quenched microstructure, six specimens were austenitized in the range  of 1000-1130 °C. Samples austenit...