1,000 research outputs found
Modelling critical Casimir force induced self-assembly experiments on patchy colloidal dumbbells
The order of the metal to superconductor transition
We present results from large-scale Monte Carlo simulations on the full
Ginzburg-Landau (GL) model, including fluctuations in the amplitude and the
phase of the matter-field, as well as fluctuations of the non-compact
gauge-field of the theory. {}From this we obtain a precise critical value of
the GL parameter \kct separating a first order metal to superconductor
transition from a second order one, \kct = (0.76\pm 0.04)/\sqrt{2}. This
agrees surprisingly well with earlier analytical results based on a disorder
theory of the superconductor to metal transition, where the value
\kct=0.798/\sqrt{2} was obtained. To achieve this, we have done careful
infinite volume and continuum limit extrapolations. In addition we offer a
novel interpretation of \kct, namely that it is also the value separating
\typeI and \typeII behaviour.<Comment: Minor corrections, present version accepted for publication in PR
The Alexander-Orbach conjecture holds in high dimensions
We examine the incipient infinite cluster (IIC) of critical percolation in
regimes where mean-field behavior has been established, namely when the
dimension d is large enough or when d>6 and the lattice is sufficiently spread
out. We find that random walk on the IIC exhibits anomalous diffusion with the
spectral dimension d_s=4/3, that is, p_t(x,x)= t^{-2/3+o(1)}. This establishes
a conjecture of Alexander and Orbach. En route we calculate the one-arm
exponent with respect to the intrinsic distance.Comment: 25 pages, 2 figures. To appear in Inventiones Mathematica
The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt
The persistence length of a single, intrinsically rigid polyelectrolyte
chain, above the Manning condensation threshold is investigated theoretically
in presence of added salt. Using a loop expansion method, the partition
function is consistently calculated, taking into account corrections to
mean-field theory. Within a mean-field approximation, the well-known results of
Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that
density correlations between counterions and thermal fluctuations reduce the
stiffness of the chain, indicating an effective attraction between monomers for
highly charged chains and multivalent counterions. This attraction results in a
possible mechanical instability (collapse), alluding to the phenomenon of DNA
condensation. In addition, we find that more counterions condense on slightly
bent conformations of the chain than predicted by the Manning model for the
case of an infinite cylinder. Finally, our results are compared with previous
models and experiments.Comment: 13 pages, 2 ps figure
Photoactivatable prodrugs of butyric acid based on new coumarin fused oxazole heterocycles
New coumarin fused oxazoles were investigated as photosensitive units for carboxylic acid groups using butyric acid as a model compound. 6-Oxo-6H-benzopyrano[6,7-d]oxazol-8-yl)methyl derivatives possessing various (hetero)aromatic substituents at position 2 of the heterocyclic system were used in the synthesis of ester conjugates of butyric acid. Photolysis at selected wavelengths in methanol/HEPES buffer (80:20) solutions, monitored by HPLC/UV and 1H NMR, produced the complete release of butyric acid. The shorter irradiation times for cleavage at longer wavelengths occurred for the conjugate with a 4-oxo-4H-benzopyran-2-yl substituent and thus (6-oxo-2-(4-oxo-4H-benzopyran-2-yl)-6H-benzopyrano[6,7-d]oxazol-8-yl)methyl has potential as a candidate photosensitive moiety for butyric acid prodrugs.Thanks are due to the Fundação para a Ciência e Tecnologia (FCT, Portugal) for financial support
to the NMR portuguese network (PTNMR, Bruker Avance III 400-Univ. Minho), FCT and FEDER
(European Fund for Regional Development)-COMPETE-QREN-EU for financial support to the
research centre CQ/UM [PEst-C/QUI/UI0686/2013 (FCOMP-01-0124-FEDER-022716)] and a
PhD grant to A.M.S.S. (SFRH/BD/80813/2011) is also acknowledged
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies.
Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose polycomb repressor complex (PRC) 2 activity, while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and are associated with vulnerability to USP7 loss, a core member of ncPRC1.1. Using the power of primary tumor organoids, our work helps define the mechanisms of epigenetic dysregulation on which SyS cells are dependent
Effective interaction between helical bio-molecules
The effective interaction between two parallel strands of helical
bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using
computer simulations of the "primitive" model of electrolytes. In particular we
study a simple model for B-DNA incorporating explicitly its charge pattern as a
double-helix structure. The effective force and the effective torque exerted
onto the molecules depend on the central distance and on the relative
orientation. The contributions of nonlinear screening by monovalent counterions
to these forces and torques are analyzed and calculated for different salt
concentrations. As a result, we find that the sign of the force depends
sensitively on the relative orientation. For intermolecular distances smaller
than it can be both attractive and repulsive. Furthermore we report a
nonmonotonic behaviour of the effective force for increasing salt
concentration. Both features cannot be described within linear screening
theories. For large distances, on the other hand, the results agree with linear
screening theories provided the charge of the bio-molecules is suitably
renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog
Photoproduction of mesons associated with a leading neutron
The photoproduction of mesons associated with a leading
neutron has been observed with the ZEUS detector in collisions at HERA
using an integrated luminosity of 80 pb. The neutron carries a large
fraction, {}, of the incoming proton beam energy and is detected at
very small production angles, { mrad}, an indication of
peripheral scattering. The meson is centrally produced with
pseudorapidity {
GeV}, which is large compared to the average transverse momentum of the neutron
of 0.22 GeV. The ratio of neutron-tagged to inclusive production is
in the photon-proton
center-of-mass energy range { GeV}. The data suggest that the
presence of a hard scale enhances the fraction of events with a leading neutron
in the final state.Comment: 28 pages, 4 figures, 2 table
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