Modeling and simulation of cell nuclear architecture reorganization process

Article history: Available online 4 November 2021

[1]  Zhen Guan,et al.  Convergence analysis for second‐order accurate schemes for the periodic nonlocal Allen‐Cahn and Cahn‐Hilliard equations , 2016, 1610.06973.

[2]  Q. Du,et al.  Energetic variational approaches in modeling vesicle and fluid interactions , 2009 .

[3]  Xiaofeng Yang.  Numerical approximations of the Navier–Stokes equation coupled with volume-conserved multi-phase-field vesicles system: Fully-decoupled, linear, unconditionally energy stable and second-order time-accurate numerical scheme , 2021 .

[4]  Chert,et al.  Applications of semi-implicit Fourier-spectral method to phase field equations , 2004 .

[5]  L. Peichl,et al.  LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation , 2013, Cell.

[6]  Vaibhav Joshi,et al.  A variational interface-preserving and conservative phase-field method for the surface tension effect in two-phase flows , 2020, J. Comput. Phys..

[7]  Qiang Du,et al.  Efficient and stable exponential time differencing Runge-Kutta methods for phase field elastic bending energy models , 2016, J. Comput. Phys..

[9]  Jia Zhao,et al.  A 3D Multi-Phase Hydrodynamic Model for Cytokinesis of Eukaryotic Cells , 2016 .

[10]  Nikolas Provatas,et al.  Phase-Field Methods in Materials Science and Engineering , 2010 .

[11]  Jie Shen,et al.  A phase field model for the mixture of two incompressible fluids and its approximation by a Fourier-spectral method , 2003 .

[12]  Qiang Du,et al.  Simulating the deformation of vesicle membranes under elastic bending energy in three dimensions , 2006, J. Comput. Phys..

[13]  Thomas Cremer,et al.  Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution , 2009, Cell.

[14]  Jia Zhao,et al.  Structure-Preserving Numerical Approximations to a Non-isothermal Hydrodynamic Model of Binary Fluid Flows , 2020, J. Sci. Comput..

[15]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[16]  Andreas Prohl,et al.  Numerical analysis of the Allen-Cahn equation and approximation for mean curvature flows , 2003, Numerische Mathematik.

[17]  Vaibhav Joshi,et al.  A positivity preserving and conservative variational scheme for phase-field modeling of two-phase flows , 2017, J. Comput. Phys..

[18]  Thomas Cremer,et al.  Chromosome territories--a functional nuclear landscape. , 2006, Current opinion in cell biology.

[19]  Jie Shen,et al.  Global constraints preserving SAV schemes for gradient flows , 2019, ArXiv.

[20]  Qing Cheng,et al.  Multiple Scalar Auxiliary Variable (MSAV) Approach and its Application to the Phase-Field Vesicle Membrane Model , 2018, SIAM J. Sci. Comput..

[21]  K. Rippe,et al.  Formation of Chromatin Subcompartments by Phase Separation. , 2018, Biophysical journal.

[22]  Cheng Wang,et al.  Second order convex splitting schemes for periodic nonlocal Cahn-Hilliard and Allen-Cahn equations , 2014, J. Comput. Phys..

[23]  Jonas Paulsen,et al.  Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts , 2017, Genome Biology.

[24]  A. Onufriev,et al.  Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement , 2018, Epigenetics & Chromatin.

[25]  F. Lin,et al.  Numerical approximations of a norm-preserving gradient flow and applications to an optimal partition problem , 2008 .

[26]  Jie Liang,et al.  Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data , 2017, Nucleic acids research.

[27]  Mustafa Mir,et al.  Phase separation drives heterochromatin domain formation , 2017, Nature.

[28]  Jie Liang,et al.  High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis , 2021, Nature communications.

[29]  T. Cremer,et al.  Chromosome territories. , 2010, Cold Spring Harbor perspectives in biology.

[30]  Davit A. Potoyan,et al.  Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes. , 2020, Biophysical journal.

[31]  Yun Xu,et al.  Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model , 2017, PLoS Comput. Biol..

[32]  Bas van Steensel,et al.  Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.

[33]  Lili Ju,et al.  Efficient linear schemes with unconditional energy stability for the phase field elastic bending energy model , 2017 .

[34]  Qi Wang,et al.  Linear second order energy stable schemes for phase field crystal growth models with nonlocal constraints , 2020, Comput. Math. Appl..

[35]  Q. Cheng,et al.  A new interface capturing method for Allen-Cahn type equations based on a flow dynamic approach in Lagrangian coordinates, I. One-dimensional case , 2020, J. Comput. Phys..

[36]  Jie Liang,et al.  CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells , 2020, Genome biology.

[37]  Jia Zhao,et al.  Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions , 2016, PLoS Comput. Biol..

[38]  S. Seirin-Lee.  Role of domain in pattern formation , 2017, Development, growth & differentiation.

[39]  Jie Liang,et al.  Spatial confinement is a major determinant of the folding landscape of human chromosomes , 2014, Nucleic acids research.