223 research outputs found
Controlled DNA compaction within chromatin: the tail-bridging effect
We study the mechanism underlying the attraction between nucleosomes, the
fundamental packaging units of DNA inside the chromatin complex. We introduce a
simple model of the nucleosome, the eight-tail colloid, consisting of a charged
sphere with eight oppositely charged, flexible, grafted chains that represent
the terminal histone tails. We demonstrate that our complexes are attracted via
the formation of chain bridges and that this attraction can be tuned by
changing the fraction of charged monomers on the tails. This suggests a
physical mechanism of chromatin compaction where the degree of DNA condensation
can be controlled via biochemical means, namely the acetylation and
deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte
Linear Response in Complex Systems: CTRW and the Fractional Fokker-Planck Equations
We consider the linear response of systems modelled by continuous-time random
walks (CTRW) and by fractional Fokker-Planck equations under the influence of
time-dependent external fields. We calculate the corresponding response
functions explicitely. The CTRW curve exhibits aging, i.e. it is not
translationally invariant in the time-domain. This is different from what
happens under fractional Fokker-Planck conditions
Dynamics of Annealed Systems under External Fields: CTRW and the Fractional Fokker-Planck Equations
We consider the linear response of a system modelled by continuous-time
random walks (CTRW) to an external field pulse of rectangular shape. We
calculate the corresponding response function explicitely and show that it
exhibits aging, i.e. that it is not translationally invariant in the
time-domain. This result differs from that of systems which behave according to
fractional Fokker-Planck equations
Organized condensation of worm-like chains
We present results relevant to the equilibrium organization of DNA strands of
arbitrary length interacting with a spherical organizing center, suggestive of
DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in
which a wrapping state is transformed into a complex multi-leafed, rosette
structure as the adhesion energy is reduced. The statistical mechanics of the
"melting" of a rosette can be mapped into an exactly soluble one-dimensional
many-body problem.Comment: 15 pages, 2 figures in a pdf fil
Polymer reptation and nucleosome repositioning
We consider how beads can diffuse along a chain that wraps them, without
becoming displaced from the chain; our proposed mechanism is analogous to the
reptation of "stored length" in more familiar situations of polymer dynamics.
The problem arises in the case of globular aggregates of proteins (histones)
that are wound by DNA in the chromosomes of plants and animals; these beads
(nucleosomes) are multiply wrapped and yet are able to reposition themselves
over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let
Circuit Topology Analysis of Polymer Folding Reactions
Analytical BioScience
Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity, and scaling
Analytical BioScience
Semi-classical buckling of stiff polymers
A quantitative theory of the buckling of a worm like chain based on a
semi-classical approximation of the partition function is presented. The
contribution of thermal fluctuations to the force-extension relation that
allows to go beyond the classical Euler buckling is derived in the linear and
non-linear regime as well. It is shown that the thermal fluctuations in the
nonlinear buckling regime increase the end-to-end distance of the semiflexible
rod if it is confined to 2 dimensions as opposed to the 3 dimensional case. Our
approach allows a complete physical understanding of buckling in D=2 and in D=3
below and above the Euler transition.Comment: Revtex, 17 pages, 4 figure
Kinetic proofreading of gene activation by chromatin remodeling
Gene activation in eukaryotes involves the concerted action of histone tail
modifiers, chromatin remodellers and transcription factors, whose precise
coordination is currently unknown. We demonstrate that the experimentally
observed interactions of the molecules are in accord with a kinetic
proofreading scheme. Our finding could provide a basis for the development of
quantitative models for gene regulation in eukaryotes based on the
combinatorical interactions of chromatin modifiers.Comment: 8 pages, 2 Figures; application adde
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