First passage time of N excluded-volume particles on a line.
Motivated by recent single-molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target sequence). At lower particle densities, one observes an expected reduction of the mean first passage time proportional to N(-2), with corrections at higher concentrations. We explicitly take adsorption and desorption effects, to and from the DNA, into account. For this general case, we also consider finite-size effects when the continuum approximation based on the number density of particles breaks down. Moreover, we address the first-passage-time problem of a tagged particle diffusing among other particles.
Sokolov
Igor M
IM
Institut für Physik, Humboldt Universität zu Berlin, Newtonstrasse 15, 12489 Berlin, Germany. igor.sokolov@physik.hu-berlin.de
Metzler
Ralf
R
Pant
Kiran
K
Williams
Mark C
MC
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry*
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA