We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedbackoptimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is applied to a lattice simulation of a homopolymer chain undergoing a coil-to-globule transition upon cooling. We select the optimal number of replicas for differe...

Two different dynamical-parameter algortihms are discussed, simulated tempering and the multisequence method. Using simulated tempering, the folding properties of 300 random sequences in a simple off-lattice model with only two amino-acid types, hydrophobic and hydrophilic, are investigated. A careful statistical analysis shows that the hydrophobic monomers are anticorrelated along the chains f...

We examine three Monte Carlo sampling methods on idealized examples. Implementing the Metropolis algorithm on created functions, we compare the single temperature to four temperatures running in parallel. Using simulated annealing and parallel tempering on the traveling salesman problem, we examine what each of the methods is capable of exploring. We focus specifically on parallel tempering’s a...

I discuss optimized data analysis and Monte Carlo methods. Reweighting methods are discussed through examples, like Lee-Yang zeroes in the Ising model and the absence of deconfinement in QCD. I discuss reweighted data analysis and multi-hystogramming. I introduce Simulated Tempering, and as an example its application to the Random Field Ising Model. I illustrate Parallel Tempering, and discuss ...

This paper addresses issues related to weights and acceptance ratios in generalized ensemble simulation (GES), while comparing two algorithms of GES: serial (e.g., simulated tempering) and parallel (e.g., parallel tempering or replica exchange). We derive a cumulant approximation formula for optimal weights in the serial GES and discuss its effectiveness in practical applications. We compare th...

We review a selection of methods for performing enhanced sampling in 1 molecular dynamics simulations. We consider methods based on collective variable biasing 2 and on tempering, and offer both historical and contemporary perspectives. In collective3 variable biasing, we first discuss methods stemming from thermodynamic integration that 4 use mean force biasing, including the adaptive biasing ...

Acoustic Doppler velocity meters �ADVMs� provide an alternative to more traditional flow measurement devices and proce­ dures such as flumes, weirs, and stage rating for irrigation and drainage canals. However, the requirements for correct calibration are extensive and complex. A three-dimensional computational fluid dynamics �CFD� model was used to design a subcritical rapidly varied flow cont...

We investigate experimentally the subcritical behavior of the Kelvin-Helmholtz instability for a gas-liquid shearing flow in a Hele-Shaw cell. The subcritical curve separating the solutions of a stable plane interface and a fully saturated nonlinear wave train is determined. Experimental results are fitted by a fifth order complex Ginzburg-Landau equation whose linear coefficients are compared ...

The present paper investigates the effects of tempering power law kernel moving average representation a fractional Brownian motion (fBm) on some local and global properties this Gaussian stochastic process. Tempered (TFBM) tempered second kind (TFBMII) are processes that considered in order to investigate role tempering. Tempering does not change fBm including sample paths p-variation, but it ...

Rice bran oil was extracted using hexane, as well as subcritical butane and propane. The quality of rice bran oils obtained using these three solvents was comparatively studied. The results showed that subcritical fluid extraction oil showed higher concentrations of health-conducive components (such as vitamin E, oryzanol, and phytosterol) compared with hexane-extracted oil. Extraction solvent ...