1,466 research outputs found
Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics
The chromosome is a key player of cell physiology, and its dynamics provides
valuable information about its physical organization. In both prokaryotes and
eukaryotes, the short-time motion of chromosomal loci has been described as a
Rouse model in a simple or viscoelastic medium. However, little emphasis has
been put on the role played by the folded organization of chromosomes on the
local dynamics. Clearly, stress-propagation, and thus dynamics, must be
affected by such organization, but a theory allowing to extract such
information from data, e.g.\ of two-point correlations, is lacking. Here, we
describe a theoretical framework able to answer this general polymer dynamics
question, and we provide a general scaling analysis of the stress-propagation
time between two loci at a given arclength distance along the chromosomal
coordinate. The results suggest a precise way to detect folding information
from the dynamical coupling of chromosome segments. Additionally, we realize
this framework in a specific theoretical model of a polymer with variable-range
interactions in a viscoelastic medium characterized by a tunable scaling
exponent, where we derive analytical estimates of the correlation functions.Comment: 14 pages including supplementary material
Lamplighter model of a random copolymer adsorption on a line
We present a model of an AB-diblock random copolymer sequential
self-packaging with local quenched interactions on a one-dimensional infinite
sticky substrate. It is assumed that the A-A and B-B contacts are favorable,
while A-B are not. The position of a newly added monomer is selected in view of
the local contact energy minimization. The model demonstrates a
self-organization behavior with the nontrivial dependence of the total energy,
(the number of unfavorable contacts), on the number of chain monomers, :
for quenched random equally probable distribution of A- and
B-monomers along the chain. The model is treated by mapping it onto the
"lamplighter" random walk and the diffusion-controlled chemical reaction of
type with the subdiffusive motion of reagents.Comment: 8 pages, 5 figure
Statistics of randomly branched polymers in a semi-space
We investigate the statistical properties of a randomly branched
3--functional --link polymer chain without excluded volume, whose one point
is fixed at the distance from the impenetrable surface in a 3--dimensional
space. Exactly solving the Dyson-type equation for the partition function
in 3D, we find the "surface" critical
exponent , as well as the density profiles of 3--functional units
and of dead ends. Our approach enables to compute also the pairwise correlation
function of a randomly branched polymer in a 3D semi-space.Comment: 15 pages 7 figsures; section VII is slightly reorganized, discussion
is revise
Necklace-Cloverleaf Transition in Associating RNA-like Diblock Copolymers
We consider a diblock copolymer, whose links are capable
of forming local reversible bonds with each other. We assume that the resulting
structure of the bonds is RNA--like, i.e. topologically isomorphic to a tree.
We show that, depending on the relative strengths of A--A, A--B and B--B
contacts, such a polymer can be in one of two different states. Namely, if a
self--association is preferable (i.e., A--A and B--B bonds are comparatively
stronger than A--B contacts) then the polymer forms a typical randomly branched
cloverleaf structure. On the contrary, if alternating association is preferable
(i.e. A--B bonds are stronger than A--A and B--B contacts) then the polymer
tends to form a generally linear necklace structure (with, probably, some rear
side branches and loops, which do not influence the overall characteristics of
the chain). The transition between cloverleaf and necklace states is studied in
details and it is shown that it is a 2nd order phase transition.Comment: 17 pages, 9 figure
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