664 research outputs found
Phase diagram of force-induced DNA unzipping in exactly solvable models
The mechanical separation of the double helical DNA structure induced by
forces pulling apart the two DNA strands (``unzipping'') has been the subject
of recent experiments. Analytical results are obtained within various models of
interacting pairs of directed walks in the (1,1,...,1) direction on the
hypercubic lattice, and the phase diagram in the force-temperature plane is
studied for a variety of cases. The scaling behaviour is determined at both the
unzipping and the melting transition. We confirm the existence of a cold
denaturation transition recently observed in numerical simulations: for a
finite range of forces the system gets unzipped by {\it decreasing} the
temperature. The existence of this transition is rigorously established for
generic lattice and continuum space models.Comment: 19 pages, 5 eps figures; revised version with minor changes,
presentation simplified in the text with details in appendix. Accepted for
publication in Phys. Rev.
Facilitated diffusion on confined DNA
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the
DNA to reach a target faster. This process is known as facilitated diffusion,
and we investigate its dynamics in the physiologically relevant case of
confined DNA. The confining geometry and DNA elasticity are key parameters: we
find that facilitated diffusion is most efficient inside an isotropic volume,
and on a flexible polymer. By considering the typical copy numbers of proteins
in vivo, we show that the speedup due to sliding becomes insensitive to fine
tuning of parameters, rendering facilitated diffusion a robust mechanism to
speed up intracellular diffusion-limited reactions. The parameter range we
focus on is relevant for in vitro systems and for facilitated diffusion on
yeast chromatin
Polymer packaging and ejection in viral capsids: shape matters
We use a mesoscale simulation approach to explore the impact of different
capsid geometries on the packaging and ejection dynamics of polymers of
different flexibility. We find that both packing and ejection times are faster
for flexible polymers. For such polymers a sphere packs more quickly and ejects
more slowly than an ellipsoid. For semiflexible polymers, however, the case
relevant to DNA, a sphere both packs and ejects more easily. We interpret our
results by considering both the thermodynamics and the relaxational dynamics of
the polymers. The predictions could be tested with bio-mimetic experiments with
synthetic polymers inside artificial vesicles. Our results suggest that phages
may have evolved to be roughly spherical in shape to optimise the speed of
genome ejection, which is the first stage in infection.Comment: 4 pages, 4 figure
Actomyosin contraction induces droplet motility
While cell crawling on a solid surface is relatively well understood, and
relies on substrate adhesion, some cells can also swim in the bulk, through
mechanisms that are still largely unclear. Here, we propose a minimal model for
in-bulk self-motility of a droplet containing an isotropic and compressible
contractile gel, representing a cell extract containing a disordered actomyosin
network. In our model, contraction mediates a feedback loop between
myosin-induced flow and advection-induced myosin accumulation, which leads to
clustering and a locally enhanced flow. Interactions of the emerging clusters
with the droplet membrane break flow symmetry and set the whole droplet into
motion. Depending mainly on the balance between contraction and diffusion, this
motion can be either straight or circular. Our simulations and analytical
results provide a framework allowing to study in-bulk myosin-driven cell
motility in living cells and to design synthetic motile active matter droplets
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