3,945 research outputs found
Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
Understanding the melting of short DNA sequences probes DNA at the scale of
the genetic code and raises questions which are very different from those posed
by very long sequences, which have been extensively studied. We investigate
this problem by combining experiments and theory. A new experimental method
allows us to make a mapping of the opening of the guanines along the sequence
as a function of temperature. The results indicate that non-local effects may
be important in DNA because an AT-rich region is able to influence the opening
of a base pair which is about 10 base pairs away. An earlier mesoscopic model
of DNA is modified to correctly describe the time scales associated to the
opening of individual base pairs well below melting, and to properly take into
account the sequence. Using this model to analyze some characteristic sequences
for which detailed experimental data on the melting is available [Montrichok et
al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce
non-local effects of AT-rich regions to get acceptable results. This brings a
second indication that the influence of these highly fluctuating regions of DNA
on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte
Imperfect Imitation Can Enhance Cooperation
The promotion of cooperation on spatial lattices is an important issue in
evolutionary game theory. This effect clearly depends on the update rule: it
diminishes with stochastic imitative rules whereas it increases with
unconditional imitation. To study the transition between both regimes, we
propose a new evolutionary rule, which stochastically combines unconditional
imitation with another imitative rule. We find that, surprinsingly, in many
social dilemmas this rule yields higher cooperative levels than any of the two
original ones. This nontrivial effect occurs because the basic rules induce a
separation of timescales in the microscopic processes at cluster interfaces.
The result is robust in the space of 2x2 symmetric games, on regular lattices
and on scale-free networks.Comment: 4 pages, 4 figure
Continuous phase transition in polydisperse hard-sphere mixture
In a previous paper (J. Zhang {\it et al.}, J. Chem. Phys. {\bf 110}, 5318
(1999)) we introduced a model for polydisperse hard sphere mixtures that is
able to adjust its particle-size distribution. Here we give the explanation of
the questions that arose in the previous description and present a consistent
theory of the phase transition in this system, based on the Percus-Yevick
equation of state. The transition is continuous, and like Bose-Einstein
condensation a macroscopic aggregate is formed due to the microscopic
interactions. A BMCSL-like treatment leads to the same conclusion with slightly
more accurate predictions.Comment: 7 pages including 5 figures in revte
Fundamental-measure density functional for the fluid of aligned hard hexagons: New insights in fundamental measure theory
In this article we obtain a fundamental measure functional for the model of
aligned hard hexagons in the plane. Our aim is not just to provide a functional
for a new, admittedly academic, model, but to investigate the structure of
fundamental measure theory. A model of aligned hard hexagons has similarities
with the hard disk model. Both share "lost cases", i.e. admit configurations of
three particles in which there is pairwise overlap but not triple overlap.
These configurations are known to be problematic for fundamental measure
functionals, which are not able to capture their contribution correctly. This
failure lies in the inability of these functionals to yield a correct low
density limit of the third order direct correlation function. Here we derive
the functional by projecting aligned hard cubes on the plane x+y+z=0. The
correct dimensional crossover behavior of these functionals permits us to
follow this strategy. The functional of aligned hard cubes, however, does not
have lost cases, so neither had the resulting functional for aligned hard
hexagons. The latter exhibits, in fact, a peculiar structure as compared to the
one for hard disks. It depends on a uniparametric family of weighted densities
through a new term not appearing in the functional for hard disks. Apart from
studying the freezing of this system, we discuss the implications of the
functional structure for new developments of fundamental measure theory.Comment: 10 pages, 9 figures, uses RevTeX
A white dwarf-neutron star relativistic binary model for soft gamma-ray repeaters
A scenario for SGRs is introduced in which gravitational radiation reaction
effects drive the dynamics of an ultrashort orbital period X-ray binary
embracing a high-mass donor white dwarf (WD) to a rapidly rotating low
magnetised massive neutron star (NS) surrounded by a thick, dense and massive
accretion torus. Driven by GR reaction, sparsely, the binary separation
reduces, the WD overflows its Roche lobe and the mass transfer drives unstable
the accretion disk around the NS. As the binary circular orbital period is a
multiple integer number () of the period of the WD fundamental mode (Pons et
al. 2002), the WD is since long pulsating at its fundamental mode; and most of
its harmonics, due to the tidal interaction with its NS orbital companion.
Hence, when the powerful irradiation glows onto the WD; from the fireball
ejected as part of the disk matter slumps onto the NS, it is partially
absorbed. This huge energy excites other WD radial (-mode) pulsations
(Podsiadlowski 1991,1995). After each mass-transfer episode the binary
separation (and orbital period) is augmented significantly (Deloye & Bildsten
2003; Al\'ecyan & Morsink 2004) due to the binary's angular momentum
redistribution. Thus a new adiabatic inspiral phase driven by GR reaction
starts which brings the binary close again, and the process repeats. This model
allows to explain most of SGRs observational features: their recurrent
activity, energetics of giant superoutbursts and quiescent stages, and
particularly the intriguing subpulses discovered by BeppoSAX (Feroci et al.
1999), which are suggested here to be {\it overtones} of the WD radial
fundamental mode (see the accompanying paper: Mosquera Cuesta 2004b).Comment: This paper was submitted as a "Letter to the Editor" of MNRAS in July
17/2004. Since that time no answer or referee report was provided to the
Author [MNRAS publication policy limits reviewal process no longer than one
month (+/- half more) for the reviewal of this kind of submission). I hope
this contribution is not receiving a similar "peer-reviewing" as given to the
A. Dar and A. De Rujula's "Cannonball model for gamma-ray bursts", or to the
R.K. Williams' "Penrose process for energy extraction from rotating black
holes". The author welcomes criticisms and suggestions on this pape
A Cellular Automaton Model for Bi-Directionnal Traffic
We investigate a cellular automaton (CA) model of traffic on a bi-directional
two-lane road. Our model is an extension of the one-lane CA model of {Nagel and
Schreckenberg 1992}, modified to account for interactions mediated by passing,
and for a distribution of vehicle speeds. We chose values for the various
parameters to approximate the behavior of real traffic. The density-flow
diagram for the bi-directional model is compared to that of a one-lane model,
showing the interaction of the two lanes. Results were also compared to
experimental data, showing close agreement. This model helps bridge the gap
between simplified cellular automata models and the complexity of real-world
traffic.Comment: 4 pages 6 figures. Accepted Phys Rev
What do emulsification failure and Bose-Einstein condensation have in common?
Ideal bosons and classical ring polymers formed via self-assembly, are known
to have the same partition function, and so analogous phase transitions. In
ring polymers, the analogue of Bose-Einstein condensation occurs when a ring
polymer of macroscopic size appears. We show that a transition of the same
general form occurs within a whole class of systems with self-assembly, and
illustrate it with the emulsification failure of a microemulsion phase of
water, oil and surfactant. As with Bose-Einstein condensation, the transition
occurs even in the absence of interactions.Comment: 7 pages, 1 figure, typeset with EUROTeX, uses epsfi
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