271 research outputs found
Effect of genome sequence on the force-induced unzipping of a DNA molecule
We considered a dsDNA polymer in which distribution of bases are random at
the base pair level but ordered at a length of 18 base pairs and calculated its
force elongation behaviour in the constant extension ensemble. The unzipping
force vs. extension is found to have a series of maxima and minima.
By changing base pairs at selected places in the molecule we calculated the
change in curve and found that the change in the value of force is of
the order of few pN and the range of the effect depending on the temperature,
can spread over several base pairs. We have also discussed briefly how to
calculate in the constant force ensemble a pause or a jump in the
extension-time curve from the knowledge of
Discrete elastic model for stretching-induced flagellar polymorphs
Force-induced reversible transformations between coiled and normal polymorphs
of bacterial flagella have been observed in recent optical-tweezer experiment.
We introduce a discrete elastic rod model with two competing helical states
governed by a fluctuating spin-like variable that represents the underlying
conformational states of flagellin monomers. Using hybrid Brownian dynamics
Monte-Carlo simulations, we show that a helix undergoes shape transitions
dominated by domain wall nucleation and motion in response to externally
applied uniaxial tension. A scaling argument for the critical force is
presented in good agreement with experimental and simulation results.
Stretching rate-dependent elasticity including a buckling instability are
found, also consistent with the experiment
Brane Bremsstrahlung in DBI Inflation
We consider the effect of trapped branes on the evolution of a test brane
whose motion generates DBI inflation along a warped throat. The coupling
between the inflationary brane and a trapped brane leads to the radiation of
non-thermal particles on the trapped brane. We calculate the Gaussian spectrum
of the radiated particles and their backreaction on the DBI motion of the
inflationary brane. Radiation occurs for momenta lower than the speed of the
test brane when crossing the trapped brane. The slowing down effect is either
due to a parametric resonance when the interaction time is small compared to
the Hubble time or a tachyonic resonance when the interaction time is large. In
both cases the motion of the inflationary brane after the interaction is
governed by a chameleonic potential,which tends to slow it down. We find that a
single trapped brane can hardly slow down a DBI inflaton whose fluctuations
lead to the Cosmic Microwave Background spectrum. A more drastic effect is
obtained when the DBI brane encounters a tightly spaced stack of trapped
branes.Comment: 20 pages, 1 figur
Syntectonic mobility of supergene nickel ores of New Caledonia (Southwest Pacific). Evidence from faulted regolith and garnierite veins.
International audienceSupergene nickel deposits of New Caledonia that have been formed in the Neogene by weathering of obducted ultramafic rocks are tightly controlled by fracture development. The relationship of tropical weathering and tectonic structures, faults and tension gashes, have been investigated in order to determine whether fractures have play a passive role only, as previously thought; or alternatively, if brittle tectonics was acting together with alteration. From the observation of time-relationship, textures, and mineralogy of various fracture fills and fault gouges, it may be unambiguously established that active faulting has play a prominent role not only in facilitating drainage and providing room for synkinematic crystallisation of supergene nickel silicate, but also in mobilising already formed sparse nickel ore, giving birth to the very high grade ore nicknamed "green gold"
Theory of High-Force DNA Stretching and Overstretching
Single molecule experiments on single- and double stranded DNA have sparked a
renewed interest in the force-extension of polymers. The extensible Freely
Jointed Chain (FJC) model is frequently invoked to explain the observed
behavior of single-stranded DNA. We demonstrate that this model does not
satisfactorily describe recent high-force stretching data. We instead propose a
model (the Discrete Persistent Chain, or ``DPC'') that borrows features from
both the FJC and the Wormlike Chain, and show that it resembles the data more
closely. We find that most of the high-force behavior previously attributed to
stretch elasticity is really a feature of the corrected entropic elasticity;
the true stretch compliance of single-stranded DNA is several times smaller
than that found by previous authors. Next we elaborate our model to allow
coexistence of two conformational states of DNA, each with its own stretch and
bend elastic constants. Our model is computationally simple, and gives an
excellent fit through the entire overstretching transition of nicked,
double-stranded DNA. The fit gives the first values for the elastic constants
of the stretched state. In particular we find the effective bend stiffness for
DNA in this state to be about 10 nm*kbt, a value quite different from either
B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques
Pairwise stimulations of pathogen-sensing pathways predict immune responses to multi-adjuvant combinations
The immune system makes decisions in response to combinations of multiple microbial inputs. We do not understand the combinatorial logic governing how higher-order combinations of microbial signals shape immune responses. Here, using coculture experiments and statistical analyses, we discover a general property for the combinatorial sensing of microbial signals, whereby the effects of triplet combinations of microbial signals on immune responses can be predicted by combining the effects of single and pairs. Mechanistically, we find that singles and pairs dictate the information signaled by triplets in mouse and human DCs at the levels of transcription, chromatin, and protein secretion. We exploit this simplifying property to develop cell-based immunotherapies prepared with adjuvant combinations that trigger protective responses in mouse models of cancer. We conclude that the processing of multiple input signals by innate immune cells is governed by pairwise effects, which will inform the rationale combination of adjuvants to manipulate immunity
Statistical mechanics of triangulated ribbons
We use computer simulations and scaling arguments to investigate statistical
and structural properties of a semiflexible ribbon composed of isosceles
triangles. We study two different models, one where the bending energy is
calculated from the angles between the normal vectors of adjacent triangles,
the second where the edges are viewed as semiflexible polymers so that the
bending energy is related to the angles between the tangent vectors of
next-nearest neighbor triangles. The first model can be solved exactly whereas
the second is more involved. It was recently introduced by Liverpool and
Golestanian Phys.Rev.Lett. 80, 405 (1998), Phys.Rev.E 62, 5488 (2000) as a
model for double-stranded biopolymers such as DNA. Comparing observables such
as the autocorrelation functions of the tangent vectors and the bond-director
field, the probability distribution functions of the end-to-end distance, and
the mean squared twist we confirm the existence of local twist correlation, but
find no indications for other predicted features such as twist-stretch
coupling, kinks, or oscillations in the autocorrelation function of the
bond-director field.Comment: 10 pages, 13 figures. submitted to PRE, revised versio
The EDELWEISS Experiment : Status and Outlook
The EDELWEISS Dark Matter search uses low-temperature Ge detectors with heat
and ionisation read- out to identify nuclear recoils induced by elastic
collisions with WIMPs from the galactic halo. Results from the operation of 70
g and 320 g Ge detectors in the low-background environment of the Modane
Underground Laboratory (LSM) are presented.Comment: International Conference on Dark Matter in Astro and Particle Physics
(Dark 2000), Heidelberg, Germany, 10-16 Jul 2000, v3 minor revision
Modeling a bacterial ecosystem through chemotaxis simulation of a single cell
International audienceWe present in this paper an artificial life ecosystem in which bacteria are evolved to perform chemotaxis. In this system, surviving bacteria have to overcome the problems of detecting resources (or sensing the environment), modulating their motion to generate a foraging behavior, and communicating with their kin to produce more sophisticated behaviors. A cellâs chemotactic pathway is modulated by a hybrid approach that uses an algebraic model for the receptor clusters activity, an ordinary differential equation for the adaptation dynamics, and a metabolic model that converts nutrients into biomass. The results show some analysis of the motion obtained from some bacteria and their effects on the evolved population behavior. The evolutionary process improves the bacteriaâs ability to react to their environment, enhancing their growth and allowing them to better survive. As future work, we propose to investigate the effect of emergent bacterial communication as new species arise, and to explore the dynamics of colonies
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