Literature DB >> 36185393

Modeling and simulation of cell nuclear architecture reorganization process.

Qing Cheng1, Pourya Delafrouz2, Jie Liang2, Chun Liu3, Jie Shen1.   

Abstract

We develop a special phase field/diffusive interface method to model the nuclear architecture reorganization process. In particular, we use a Lagrange multiplier approach in the phase field model to preserve the specific physical and geometrical constraints for the biological events. We develop several efficient and robust linear and weakly nonlinear schemes for this new model. To validate the model and numerical methods, we present ample numerical simulations which in particular reproduce several processes of nuclear architecture reorganization from the experiment literature.

Entities:  

Keywords:  Lagrange multiplier; Nuclear architecture reorganization; Phase field approach; chromosome

Year:  2021        PMID: 36185393      PMCID: PMC9524197          DOI: 10.1016/j.jcp.2021.110808

Source DB:  PubMed          Journal:  J Comput Phys        ISSN: 0021-9991            Impact factor:   4.645


  19 in total

Review 1.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

Authors:  T Cremer; C Cremer
Journal:  Nat Rev Genet       Date:  2001-04       Impact factor: 53.242

Review 2.  Chromosome territories.

Authors:  Thomas Cremer; Marion Cremer
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-03       Impact factor: 10.005

Review 3.  Formation of Chromatin Subcompartments by Phase Separation.

Authors:  Fabian Erdel; Karsten Rippe
Journal:  Biophys J       Date:  2018-04-06       Impact factor: 4.033

4.  Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes.

Authors:  Rabia Laghmach; Michele Di Pierro; Davit A Potoyan
Journal:  Biophys J       Date:  2019-09-17       Impact factor: 4.033

5.  Spatial confinement is a major determinant of the folding landscape of human chromosomes.

Authors:  Gamze Gürsoy; Yun Xu; Amy L Kenter; Jie Liang
Journal:  Nucleic Acids Res       Date:  2014-07-02       Impact factor: 16.971

6.  LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation.

Authors:  Irina Solovei; Audrey S Wang; Katharina Thanisch; Christine S Schmidt; Stefan Krebs; Monika Zwerger; Tatiana V Cohen; Didier Devys; Roland Foisner; Leo Peichl; Harald Herrmann; Helmut Blum; Dieter Engelkamp; Colin L Stewart; Heinrich Leonhardt; Boris Joffe
Journal:  Cell       Date:  2013-01-31       Impact factor: 41.582

7.  A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization.

Authors:  S Seirin Lee; S Tashiro; A Awazu; R Kobayashi
Journal:  J Math Biol       Date:  2016-05-30       Impact factor: 2.259

8.  Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement.

Authors:  Nicholas Allen Kinney; Igor V Sharakhov; Alexey V Onufriev
Journal:  Epigenetics Chromatin       Date:  2018-01-22       Impact factor: 4.954

9.  Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.

Authors:  Gamze Gürsoy; Yun Xu; Jie Liang
Journal:  PLoS Comput Biol       Date:  2017-07-13       Impact factor: 4.475

10.  High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis.

Authors:  Qiu Sun; Alan Perez-Rathke; Daniel M Czajkowsky; Zhifeng Shao; Jie Liang
Journal:  Nat Commun       Date:  2021-01-08       Impact factor: 14.919

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