Literature DB >> 17994964

Algorithms for three-dimensional rigidity analysis and a first-order percolation transition.

M V Chubynsky1, M F Thorpe.   

Abstract

A fast computer algorithm, the pebble game, has been used successfully to analyze the rigidity of two-dimensional (2D) elastic networks, as well as of a special class of 3D networks, the bond-bending networks, and enabled significant progress in studies of rigidity percolation on such networks. Application of the pebble game approach to general 3D networks has been hindered by the fact that the underlying mathematical theory is, strictly speaking, invalid in this case. We construct an approximate pebble game algorithm for general 3D networks, as well as a slower but exact algorithm, the relaxation algorithm, that we use for testing the new pebble game. Based on the results of these tests and additional considerations, we argue that in the particular case of randomly diluted central-force networks on bcc and fcc lattices, the pebble game is essentially exact. Using the pebble game, we observe an extremely sharp jump in the largest rigid cluster size in bond-diluted central-force networks in 3D, with the percolating cluster appearing and taking up most of the network after a single bond addition. This strongly suggests a first-order rigidity percolation transition, which is in contrast to the second-order transitions found previously for the 2D central-force and 3D bond-bending networks. While a first order rigidity transition has been observed previously for Bethe lattices and networks with "chemical order," here it is in a regular randomly diluted network. In the case of site dilution, the transition is also first order for bcc lattices, but results for fcc lattices suggest a second-order transition. Even in bond-diluted lattices, while the transition appears massively first order in the order parameter (the percolating cluster size), it is continuous in the elastic moduli. This, and the apparent nonuniversality, make this phase transition highly unusual.

Entities:  

Year:  2007        PMID: 17994964     DOI: 10.1103/PhysRevE.76.041135

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  11 in total

1.  Two exactly soluble models of rigidity percolation.

Authors:  M F Thorpe; R B Stinchcombe
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2013-12-30       Impact factor: 4.226

2.  Rigidity percolation and geometric information in floppy origami.

Authors:  Siheng Chen; L Mahadevan
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-05       Impact factor: 11.205

3.  Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions.

Authors:  Nicoletta I Petridou; Bernat Corominas-Murtra; Carl-Philipp Heisenberg; Edouard Hannezo
Journal:  Cell       Date:  2021-03-16       Impact factor: 41.582

4.  RIGID GRAPH COMPRESSION: MOTIF-BASED RIGIDITY ANALYSIS FOR DISORDERED FIBER NETWORKS.

Authors:  Samuel Heroy; Dane Taylor; F Bill Shi; M Gregory Forest; Peter J Mucha
Journal:  Multiscale Model Simul       Date:  2018-08-21       Impact factor: 1.930

5.  Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.

Authors:  Dominik Budday; Sigrid Leyendecker; Henry van den Bedem
Journal:  J Chem Inf Model       Date:  2018-10-09       Impact factor: 4.956

6.  Graph rigidity reveals well-constrained regions of chromosome conformation embeddings.

Authors:  Geet Duggal; Carl Kingsford
Journal:  BMC Bioinformatics       Date:  2012-09-21       Impact factor: 3.169

7.  Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains.

Authors:  Josh Czemeres; Kurt Buse; Gennady M Verkhivker
Journal:  PLoS One       Date:  2017-12-21       Impact factor: 3.240

8.  Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone.

Authors:  Gabrielle Stetz; Amanda Tse; Gennady M Verkhivker
Journal:  PLoS One       Date:  2017-11-02       Impact factor: 3.240

9.  Adaptive Regulation of Nitrate Transceptor NRT1.1 in Fluctuating Soil Nitrate Conditions.

Authors:  Mubasher Rashid; Soumen Bera; Alexander B Medvinsky; Gui-Quan Sun; Bai-Lian Li; Amit Chakraborty
Journal:  iScience       Date:  2018-04-06

10.  Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations.

Authors:  Libin Ye; Chris Neale; Adnan Sljoka; Brent Lyda; Dmitry Pichugin; Nobuyuki Tsuchimura; Sacha T Larda; Régis Pomès; Angel E García; Oliver P Ernst; Roger K Sunahara; R Scott Prosser
Journal:  Nat Commun       Date:  2018-04-10       Impact factor: 14.919

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.