Related papers: A Second Look at Canonical Sampling of Biomolecule…
We investigate limit models resulting from a dimensional analysis of quite general heterogeneous catalysis models with fast sorption (i.e.\ exchange of mass between the bulk phase and the catalytic surface of a reactor) and fast surface…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
We explore the effect of sampling rates when measuring data given by $Mf$ for special operators $M$ arising in Thermoacoustic Tomography. We start with sampling requirements on $Mf$ given $f$ satisfying certain conditions. After this we…
We describe a general radiative equilibrium and temperature correction procedure for use in Monte Carlo radiation transfer codes with sources of temperature-independent opacity, such as astrophysical dust. The technique utilizes the fact…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
We address the problem of evaluating the transfer entropy (TE) produced by biochemical reactions from experimentally measured data. Although these reactions are generally non-linear and non-stationary processes making it challenging to…
Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for parameter estimation that return point estimates of the…
High speed camera imaging is a powerful tool to probe the spatiotemporal features of unsteady processes in plasmas, usually assuming light fluctuations to be a proxy for the plasma density fluctuations. In this article, we systematically…
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…
Over the recent years the importance of numerical experiments has gradually been more recognized. Nonetheless, sufficient documentation of how computational results have been obtained is often not available. Especially in the scientific…
Molecular dynamics simulations of a quasi-harmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such…
Fast and accurate sampling method is in high demand, in order to bridge the large gaps between molecular dynamic simulations and experimental observations. Recently, integrated tempering enhanced sampling method (ITS) has been proposed and…
Time-resolved studies have so far relied on rapidly triggering a photo-induced dynamic in chemical or biological ions or molecules and subsequently probing them with a beam of fast moving photons or electrons that crosses the studied…
Simple data correlation of flashpoint data of binary mixture has been developed on a basic of rational reciprocal function. The new approximation requires has only two coefficients and needs the flashpoint temperature of the pure flammable…
Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data and it has been shown that replica-averaged…
Light absorption and scattering of plasmonic metal nanoparticles can lead to non-equilibrium charge carriers, intense electromagnetic near-fields, and heat generation, with promising applications in a vast range of fields, from chemical and…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
Many biochemical systems appearing in applications have a multiscale structure so that they converge to piecewise deterministic Markov processes in a thermodynamic limit. The statistics of the piecewise deterministic process can be obtained…
Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly…