260 research outputs found
Twist-bend instability for toroidal DNA condensates
We propose that semiflexible polymers in poor solvent collapse in two stages.
The first stage is the well known formation of a dense toroidal aggregate.
However, if the solvent is sufficiently poor, the condensate will undergo a
second structural transition to a twisted entangled state, in which individual
filaments lower their bending energy by additionally orbiting around the mean
path along which they wind. This ``topological ripening'' is consistent with
known simulations and experimental results. It connects and rationalizes
various experimental observations ranging from strong DNA entanglement in viral
capsids to the unusually short pitch of the cholesteric phase of DNA in
sperm-heads. We propose that topological ripening of DNA toroids could improve
the efficiency and stability of gene delivery.Comment: 4 pages, 3 figures, RevTeX4 styl
Brownian dynamics of a microswimmer
We report on dynamic properties of a simple model microswimmer composed of
three spheres and propelling itself in a viscous fluid by spinning motion of
the spheres under zero net torque constraint. At a fixed temperature and
increasing the spinning frequency, the swimmer demonstrates a transition from
dissipation-dominated to a pumping-dominated motion regime characterized by
negative effective friction coefficient. In the limit of high frequencies, the
diffusion of the swimmer can be described by a model of an active particle with
constant velocity.Comment: Submitte
Conventional Superconductivity in Fe-Based Pnictides: the Relevance of Intra-Band Electron-Boson Scattering
Various recent experimental data and especially the large Fe-isotope effect
point against unconventional pairings, since the large intra-band impurity
scattering is strongly pair-breaking for them. The strength of the inter-band
impurity scattering in some single crystals may be strong and probably beyond
the Born scattering limit. In that case the proposed s(+-) pairing (hole(h)-
and electron(el)-gaps are of opposite signs) is suppressed but possibly not
completely destroyed. The data imply that the intra-band pairing in the h- and
in the el-band, which are inevitably due to some nonmagnetic el-boson
interaction (EBI), must be taken into account. EBI is either due to phonons
(EPI) or possibly due to excitons (EEI), or both are simultaneously operative.
We discuss their interplay briefly. The large Fe-isotope effect favors the EPI
and the s(+) pairing (the h- and el-gaps are in-phase).Comment: 7 pages, no figures, explanations and argumentations improved,
references adde
Theory of Nucleosome Corkscrew Sliding in the Presence of Synthetic DNA Ligands
Histone octamers show a heat-induced mobility along DNA. Recent theoretical
studies have established two mechanisms that are qualitatively and
quantitatively compatible with in vitro experiments on nucleosome sliding:
Octamer repositiong through one-basepair twist defects and through ten-basepair
bulge defects. A recent experiment demonstrated that the repositioning is
strongly suppressed in the presence of minor-groove binding DNA ligands. In the
present study we give a quantitative theory for nucleosome repositioning in the
presence of such ligands. We show that the experimentally observed octamer
mobilities are consistent with the picture of bound ligands blocking the
passage of twist defects through the nucleosome. This strongly supports the
model of twist defects inducing a corkscrew motion of the nucleosome as the
underlying mechanism of nucleosome sliding. We provide a theoretical estimate
of the nucleosomal mobility without adjustable parameters, as a function of
ligand concentration, binding affinity, binding site orientiation, temperature
and DNA anisotropy. Having this mobility at hand we speculate about the
interaction between a nucleosome and a transcribing RNA polymerase and suggest
a novel mechanism that might account for polymerase induced nucleosome
repositioning.Comment: 23 pages, 4 figures, submitted to J. Mol. Bio
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