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 ...

During laser powder bed fusion (L-PBF), materials experience cyclic re-heating as new layers are deposited, inducing an in situ tempering effect. In this study, the effect of phenomenon on martensite during L-PBF was examined for Fe-0.45C steel. Detailed scanning electron microscopy, transmission atom probe tomography, and hardness measurements indicated that initially a quenched-like state aft...

The improvement of simulations of QCD with dynamical Wilson fermions by combining the Hybrid Monte Carlo algorithm with parallel tempering is studied. As an indicator for decorrelation the topological charge is used.

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obt...

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 ...

A method for solving binary optimization problems was proposed by Karandashev and Kryzhanovsky that can be used for finding ground states of spin glass models. By taking a power of the bond matrix the energy landscape of the system is transformed in such a way, that the global minimum should become easier to find. In this paper we test the combination of the new approach with various algorithms...

Motivation: Assembling shotgun sequencing data from repetitive DNA sequences is a non-trivial task. In existing sequence assembly methods repeats are resolved by either using statistical analyses to identify and separate fragments corresponding to repeats, or by using extra information, not contained in the fragments. In this paper we take a different approach. Using the simulated-tempering Mon...