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Modeling diffusional transport in the interphase cell nucleus
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10.1063/1.2753158
/content/aip/journal/jcp/127/4/10.1063/1.2753158
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/4/10.1063/1.2753158
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Comparison of the continuous and discrete random walk chain models and the test system (disconnected obstacles). Upper panel: Diffusion coefficient dependent on the geometric volume fraction. Lower panel: Diffusion coefficient dependent on the effective volume fraction. Circles: smallest particle, squares: medium sized particle, triangles: largest particle, and diamonds: medium sized particle in the test system. Blank: Discrete random walk chain model. Solid: Continuous random walk chain model.

Image of FIG. 2.
FIG. 2.

Mean square displacement of the largest particle vs time. The continuous lines are linear fits through the first five points of the curve (blank squares and blank triangles) to illustrate the deviation from linearity for the long-time diffusion in the denser systems. The dashed lines are power law fits yielding the anomalous diffusion exponent . Blank circles: Random walk chain model (effective volume with 68% and geometric volume with 20%). Solid circles: Continuous random walk chain model (effective volume with 68% and geometric volume with 20%). Blank squares: Random walk chain model (effective volume with 73%, geometric volume with 23%, and ). Solid squares: Continuous random walk chain model (effective volume with 78%, geometric volume with 26%, and ). Triangles: Self-avoiding random walk chain model (effective volume with 81%, geometric volume with 12.5%, chain length , , and ).

Image of FIG. 3.
FIG. 3.

Upper panel: Start conformation of the Monte Carlo algorithm. Forty six cubes, chains with , are homogeneously distributed on the lattice. Lower panel: Relaxed conformation after time steps of the Monte Carlo algorithm combined with the bond fluctuation method. The chains constitute a dense network, comparable with chromosome territories inside the cell nucleus. To highlight the topological structure of the chain network, the 46 chromosomes are alternately colored here with red and blue.

Image of FIG. 4.
FIG. 4.

Energy distribution as a function of time . Geometric occupation volume: 6.4%. Circles, ; squares, . Blank, ; solid, .

Image of FIG. 5.
FIG. 5.

Relaxation time vs chain length on a logarithmic scale. Geometric occupation volume: 6.4%. The solid line is a power law fit with an exponent of 2.5. Squares, ; circles, .

Image of FIG. 6.
FIG. 6.

Upper panel: Anomalous translational diffusion exponent as a function of chain length . Geometric occupation volume: 6.4%. Circles, ; squares, ; triangles, . Lower panel: Center of mass vs time . Squares, and ; circles, and . Solid, cubic lattice; blank, cubic lattice. Straight line, linear fit; dashed line, power law fit.

Image of FIG. 7.
FIG. 7.

Comparison of the random walk chain model and the self-avoiding random walk chain model. Upper panel: Diffusion coefficient dependent on the geometric volume fraction. Lower panel: Diffusion coefficient dependent on the effective volume fraction. Blank: Random walk chain model. Solid: Self-avoiding random walk chain model. Diamonds: middle sized particle in the test system. Circles: smallest particle, squares: middle sized particle, and triangles: largest particle. Stars: largest particle in the SAW system with different persistence lengths of 0.5, 1, 2, and 3 with a constant geometric occupation volume of 6.12%, respectively. Crosses: largest particle in the SAW system with different persistence lengths of 0.5, 1, 2, and 3 with a constant geometric occupation volume of 7.95%, respectively.

Image of FIG. 8.
FIG. 8.

Upper panel: Diffusion coefficient as a function of chain length for different occupation volumes. Solid symbols: smallest particle. Blank symbols: largest particle. Circles denote 6.4% occupation volume, squares with 8% occupation volume, and triangles with 10% occupation volume. Lower panel: Diffusion coefficient as a function of persistence length for different occupation volumes. Circles, 46 chains with (4.6% occupation volume); squares, 46 chains with (6.12% occupation volume); triangles, 46 chains with (7.95% occupation volume).

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/content/aip/journal/jcp/127/4/10.1063/1.2753158
2007-07-30
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Modeling diffusional transport in the interphase cell nucleus
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/4/10.1063/1.2753158
10.1063/1.2753158
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