Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Many-body effects in tracer particle diffusion with applications for
  single-protein dynamics on DNA   30% of the DNA in E. coli bacteria is covered by proteins. Such high degree
of crowding affect the dynamics of generic biological processes (e.g. gene
regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully
understood. In this paper, we theoretically address the diffusion constant of a
tracer particle in a one dimensional system surrounded by impenetrable crowder
particles. While the tracer particle always stays on the lattice, crowder
particles may unbind to a surrounding bulk and rebind at another or the same
location. In this scenario we determine how the long time diffusion constant
${\cal D}$ (after many unbinding events) depends on (i) the unbinding rate of
crowder particles $k_{\rm off}$, and (ii) crowder particle line density $\rho$,
from simulations (Gillespie algorithm) and analytical calculations. For small
$k_{\rm off}$, we find ${\cal D}\sim k_{\rm off}/\rho^2$ when crowder particles
are immobile on the line, and ${\cal D}\sim \sqrt{D k_{\rm off}}/\rho$ when
they are diffusing; $D$ is the free particle diffusion constant. For large
$k_{\rm off}$, we find agreement with mean-field results which do not depend on
$k_{\rm off}$. From literature values of $k_{\rm off}$ and $D$, we show that
the small $k_{\rm off}$-limit is relevant for in vivo protein diffusion on a
crowded DNA. Our results applies to single-molecule tracking experiments.

17
The categories of this paper are: q-fin
30
The categories of this paper are: q-alg
36
The categories of this paper are: cmp-lg
9
The categories of this paper are: nlin
24
The categories of this paper are: dg-ga
3
The categories of this paper are: physics
35
The categories of this paper are: mtrl-th
27
The categories of this paper are: comp-gas
19
The categories of this paper are: eess
16
The categories of this paper are: stat
1
The categories of this paper are: cs
23
The categories of this paper are: solv-int
12
The categories of this paper are: nucl-th
29
The categories of this paper are: funct-an
2
The categories of this paper are: math
14
The categories of this paper are: math-ph