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pro vyhledávání: '"Poblete, Simon"'
Autor:
Cofas-Vargas, Luis F., Moreira, Rodrigo A., Poblete, Simón, Chwastyk, Mateusz, Poma, Adolfo B.
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensi
Externí odkaz:
http://arxiv.org/abs/2311.08174
Publikováno v:
In Computational Materials Science September 2023 228
Akademický článek
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Publikováno v:
Nucleic Acids Res. 46, 1674 (2018)
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an
Externí odkaz:
http://arxiv.org/abs/1711.00741
Publikováno v:
Biochem. Biophys. Res. Commun. 498, 352 (2018)
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential degrees of free
Externí odkaz:
http://arxiv.org/abs/1709.08691
Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir
Autor:
Fritsch, Sebastian, Poblete, Simon, Junghans, Christoph, Ciccotti, Giovanni, Site, Luigi Delle, Kremer, Kurt
Publikováno v:
Phys. Rev. Lett. 108, 170602 (2012)
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of dif
Externí odkaz:
http://arxiv.org/abs/1112.3151
A molecular dynamics study of a two dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid transitio
Externí odkaz:
http://arxiv.org/abs/1101.4337
Publikováno v:
J. Chem. Phys. 132, 114101 (2010)
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present a general
Externí odkaz:
http://arxiv.org/abs/0907.5497
Publikováno v:
In Biochemical and Biophysical Research Communications 29 March 2018 498(2):352-358
Autor:
Gabba, Matteo, Poblete, Simón, Rosenkranz, Tobias, Katranidis, Alexandros, Kempe, Daryan, Züchner, Tina, Winkler, Roland G., Gompper, Gerhard, Fitter, Jörg
Publikováno v:
In Biophysical Journal 21 October 2014 107(8):1913-1923