English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Tools annual

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Presents the access of premium content as premium feature

Premium Content

Global: Zendy Plus annual

Global: Zendy Free Plan

A variety of enhanced statistical and numerical methods are now routinelyused to extract comprehensible and relevant thermodynamic information from thevast amount of complex, high-dimensional data obtained from intensive molecularsimulations. The characterization of kinetic properties, such as diffusioncoefficients, of molecular systems with significantly high energy barriers, onthe other hand, has received less attention. Among others, Markov state models,in which the long-time statistical dynamics of a system is approximated by aMarkov chain on a discrete partition of configuration space, have seenwidespread use in recent years, with the aim of tackling these fundamentalissues. Here we propose a general, automatic method to assess multidimensionalposition-dependent diffusion coefficients within the framework of Markovianstochastic processes and Kramers-Moyal expansion. We apply the formalism toone- and two-dimensional analytic potentials and data from explicit solventmolecular dynamics simulations, including the water-mediated conformations ofalanine dipeptide. Importantly, the developed algortihm presents significantimprovement compared to standard methods when the transport of solute acrossthree-dimensional heterogeneous porous media is studied, for example, theprediction of membrane permeation of drug molecules.

Assessing Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis