title: An efficient algorithm to perform local concerted movements of a chain molecule.
abstract: The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling. Here, we propose and validate, on a few pedagogical examples, a novel numerical strategy that generalizes the notion of concerted rotation. The usage of the Denavit-Hartenberg parameters for chain description allows all possible choices for the subset of degrees of freedom to be modified in the move. They can be arbitrarily distributed along the chain and can be distanced between consecutive monomers as well. The efficiency of the methodology capitalizes on the inherent geometrical structure of the manifold defined by all chain configurations compatible with the fixed degrees of freedom. The chain portion to be moved is first opened along a direction chosen in the tangent space to the manifold, and then closed in the orthogonal space. As a consequence, in Monte Carlo simulations detailed balance is easily enforced without the need of using Jacobian reweighting. Moreover, the relative fluctuations of the degrees of freedom involved in the move can be easily tuned. We show different applications: the manifold of possible configurations is explored in a very efficient way for a protein fragment and for a cyclic molecule; the "local backbone volume", related to the volume spanned by the manifold, reproduces the mobility profile of all-α helical proteins; the refinement of small protein fragments with different secondary structures is addressed. The presented results suggest our methodology as a valuable exploration and sampling tool in the context of bio-molecular simulations.
authors.affiliation: Dipartimento di Fisica e Astronomia G. Galilei, Universitá degli Studi di Padova, Via Marzolo 8, I-35131 Padova, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Zamuner
authors.affiliation: SISSA (Scuola Internazionale Superiore di Studi Avanzati), via Bonomea 265, I-34136 Trieste, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: Dipartimento di Fisica e Astronomia G. Galilei, Universitá degli Studi di Padova, Via Marzolo 8, I-35131 Padova, Italy; INFN (Istituto Nazionale di Fisica Nucleare), Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy.
authors.forename: Flavio
authors.initials: F
authors.lastname: Seno
authors.affiliation: Dipartimento di Fisica e Astronomia G. Galilei, Universitá degli Studi di Padova, Via Marzolo 8, I-35131 Padova, Italy; CNISM (Consorzio Nazionale Interuniversitario per le Scienze fisiche della Matera), Unità di Padova, Via Marzolo 8, I-35131 Padova, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Trovato
mesh_terms: D000465:Algorithms; D008962:Models, Theoretical
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