Quantum ESPRESSO: One Further Step toward the Exascale.

We review the status of the Quantum ESPRESSO software suite for electronic-structure calculations based on plane waves, pseudopotentials, and density-functional theory. We highlight the recent developments in the porting to GPUs of the main codes, using an approach based on OpenACC and CUDA Fortran offloading. We describe, in particular, the results achieved on linear-response codes, which are one of the distinctive features of the Quantum ESPRESSO suite. We also present extensive performance benchmarks on different GPU-accelerated architectures for the main codes of the suite.

Multidimensional view of amyloid fibril nucleation in atomistic detail.

Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We exploited 8 different collective variables to compute the free energy of hundreds of putative aggregate structures, with variable content of parallel and antiparallel ß-sheets and different packing among the sheets. This allowed characterizing in detail a possible nucleation pathway for the formation of amyloid fibrils: first the system forms a relatively large ordered nucleus of antiparallel ß-sheets, and then a few parallel sheets start appearing. The relevant nucleation process culminates at this point: when a sufficient number of parallel sheets is formed, the free energy starts to decrease toward a new minimum in which this structure is predominant. The complex nucleation pathway we found cannot be described within classical nucleation theory, namely employing a unique simple reaction coordinate like the total content of ß-sheets.

Biased Molecular Simulations for Free-Energy Mapping: A Comparison on the KcsA Channel as a Test Case.

The calculation of free-energy landscapes in proteins is a challenge for modern numerical simulations. As to the case of potassium ion channels is concerned, it is particularly interesting because of the nanometric dimensions of the selectivity filter, where the complex electrostatics is highly relevant. The present study aims at comparing three different techniques used to bias molecular dynamics simulations, namely Umbrella Sampling, Steered Molecular Dynamics, and Metadynamics, never applied all together in the past to the same channel protein. Our test case is represented by potassium ions permeating the selectivity filter of the KcsA channel.

Computational Analysis of Current and Noise Properties of a Single Open Ion Channel.

This paper presents a computational analysis of the noise associated with the ion current in single open ion channels. The study is performed by means of a coupled molecular dynamics/Monte Carlo approach able to simulate the conduction process on the basis of all microscopic information today available from protein structural data and atomistic simulations. The case of potassium ions permeating the KcsA channel is considered in the numerical calculations. The results show a noise spectrum different from what is theoretically predicted for Poisson noise, confirmed by the existence of a correlation in ion-exit events.