Diffusion in correlated random potentials, with applications to DNA.
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) approximately 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 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) >> 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.
Slutsky
Michael
M
Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. mich@mit.edu
Kardar
Mehran
M
Mirny
Leonid A
LA
D001665:Binding Sites; D001692:Biological Transport; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D004548:Elasticity; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009038:Motion; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
D004268:DNA-Binding Proteins; D009707:Nucleosomes; D014157:Transcription Factors; D004247:DNA