dorsal/arxiv
View SchemaThe long reach of DNA sequence heterogeneity in diffusive processes
| Authors | Michael Slutsky, Mehran Kardar, Leonid A. Mirny |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0310008 |
| URL | https://arxiv.org/abs/q-bio/0310008 |
| DOI | 10.1103/PhysRevE.69.061903 |
| Journal | Phys. Rev. E 69, 061903 (2004) |
Abstract
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with $\xi_c\approx$ 10 nm. We investigate such transport processes by the mean first passage time (MFPT) formalism, and find diffusion times which exhibit strong sample to sample fluctuations. For a a displacement $N$, the average MFPT is diffusive, while its standard deviation over the ensemble of energy profiles scales as $N^{3/2}$ with a large prefactor. Fluctuations are thus dominant for displacements smaller than a characteristic $N_c \gg \xi_c$: typical values are much less than the mean, and governed by an anomalous diffusion rule. Potential biological consequences of such random walks, composed of rapid scans in the vicinity of favorable energy valleys and occasional jumps to further valleys, is discussed.
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"abstract": "Many biological processes involve one dimensional diffusion over a correlated\ninhomogeneous energy landscape with a correlation length $\\xi_c$. Typical\nexamples are specific protein target location on DNA, nucleosome repositioning,\nor DNA translocation through a nanopore, in all cases with $\\xi_c\\approx$ 10\nnm. We investigate such transport processes by the mean first passage time\n(MFPT) formalism, and find diffusion times which exhibit strong sample to\nsample fluctuations. For a a displacement $N$, the average MFPT is diffusive,\nwhile its standard deviation over the ensemble of energy profiles scales as\n$N^{3/2}$ with a large prefactor. Fluctuations are thus dominant for\ndisplacements smaller than a characteristic $N_c \\gg \\xi_c$: typical values are\nmuch less than the mean, and governed by an anomalous diffusion rule. Potential\nbiological consequences of such random walks, composed of rapid scans in the\nvicinity of favorable energy valleys and occasional jumps to further valleys,\nis discussed.",
"arxiv_id": "q-bio/0310008",
"authors": [
"Michael Slutsky",
"Mehran Kardar",
"Leonid A. Mirny"
],
"categories": [
"q-bio.BM",
"cond-mat.dis-nn",
"cond-mat.soft",
"physics.bio-ph"
],
"doi": "10.1103/PhysRevE.69.061903",
"journal_ref": "Phys. Rev. E 69, 061903 (2004)",
"title": "The long reach of DNA sequence heterogeneity in diffusive processes",
"url": "https://arxiv.org/abs/q-bio/0310008"
},
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