Literature DB >> 11970130

Energy landscapes, supergraphs, and "folding funnels" in spin systems.

P Garstecki1, T X Hoang, M Cieplak.   

Abstract

Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The resulting supergraph describes both dynamics and statics of the system in a unified coarse-grained sense. We give examples of the supergraphs for several two-dimensional spin and protein-related systems. We demonstrate that disordered ferromagnets have supergraphs akin to those of model proteins whereas spin glasses behave like random sequences of amino acids that fold badly.

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Year:  1999        PMID: 11970130     DOI: 10.1103/physreve.60.3219

Source DB:  PubMed          Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics        ISSN: 1063-651X


  8 in total

1.  BarMap: RNA folding on dynamic energy landscapes.

Authors:  Ivo L Hofacker; Christoph Flamm; Christian Heine; Michael T Wolfinger; Gerik Scheuermann; Peter F Stadler
Journal:  RNA       Date:  2010-05-26       Impact factor: 4.942

2.  Combinatorial vector fields and the valley structure of fitness landscapes.

Authors:  Bärbel M R Stadler; Peter F Stadler
Journal:  J Math Biol       Date:  2010-01-22       Impact factor: 2.259

3.  Aging, memory, and nonhierarchical energy landscape of spin jam.

Authors:  Anjana Samarakoon; Taku J Sato; Tianran Chen; Gai-Wei Chern; Junjie Yang; Israel Klich; Ryan Sinclair; Haidong Zhou; Seung-Hun Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-03       Impact factor: 11.205

4.  Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

Authors:  Marcel Kucharík; Ivo L Hofacker; Peter F Stadler; Jing Qin
Journal:  Bioinformatics       Date:  2014-03-19       Impact factor: 6.937

5.  Energy landscapes of resting-state brain networks.

Authors:  Takamitsu Watanabe; Satoshi Hirose; Hiroyuki Wada; Yoshio Imai; Toru Machida; Ichiro Shirouzu; Seiki Konishi; Yasushi Miyashita; Naoki Masuda
Journal:  Front Neuroinform       Date:  2014-02-25       Impact factor: 4.081

6.  Pseudoknots in RNA folding landscapes.

Authors:  Marcel Kucharík; Ivo L Hofacker; Peter F Stadler; Jing Qin
Journal:  Bioinformatics       Date:  2015-10-01       Impact factor: 6.937

7.  Visualization of protein folding funnels in lattice models.

Authors:  Antonio B Oliveira; Francisco M Fatore; Fernando V Paulovich; Osvaldo N Oliveira; Vitor B P Leite
Journal:  PLoS One       Date:  2014-07-10       Impact factor: 3.240

Review 8.  Design of Artificial Riboswitches as Biosensors.

Authors:  Sven Findeiß; Maja Etzel; Sebastian Will; Mario Mörl; Peter F Stadler
Journal:  Sensors (Basel)       Date:  2017-08-30       Impact factor: 3.576

  8 in total

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