Alberto Pérez de Alba Ortíz

TL;DR: In this article, a framework was proposed to find an optimal set of CVs from a pool of candidates using a combination of artificial neural networks and genetic algorithms, and the successful retrieval of optimal CVs by this framework is illustrated at the hand of two case studies: the well-known conformational change in the alanine dipeptide molecule and the more intricate transition of a base pair in B-DNA.

TL;DR: The challenges in the theoretical description of photoreceptor proteins using multiscale modeling were highlighted at the CECAM workshop in Tel Aviv, Israel as mentioned in this paper, where participants identified grand challenges and discussed the development of new tools to address them.

TL;DR: Transition interface sampling was used to compute rate constants and relative free energies for the transitions between WC and HG, and the results agree with experiments, and provide highly detailed insights into the mechanisms of this important process.

TL;DR: This chapter applies the adaptive path-CV formalism with several enhanced sampling methods-steered MD, metadynamics, and umbrella sampling-to a biologically relevant process: the Watson-Crick to Hoogsteen base-pairing transition in double-stranded DNA.

TL;DR: In this paper, the authors studied the molecular mechanism of the condensation of calcium, a divalent cation, on hyaluronan, a ubiquitous polymer in human tissues.