6,436 research outputs found

### Pseudoknots in a Homopolymer

After a discussion of the definition and number of pseudoknots, we reconsider
the self-attracting homopolymer paying particular attention to the scaling of
the number of pseudoknots at different temperature regimes in two and three
dimensions. Although the total number of pseudoknots is extensive at all
temperatures, we find that the number of pseudoknots forming between the two
halves of the chain diverges logarithmically at (in both dimensions) and below
(in 2d only) the theta-temparature. We later introduce a simple model that is
sensitive to pseudoknot formation during collapse. The resulting phase diagram
involves swollen, branched and collapsed homopolymer phases with transitions
between each pair.Comment: submitted to PR

### Boundary Spatiotemporal Correlations in a Self-Organized Critical Model of Punctuated Equilibrium

In a semi-infinite geometry, a 1D, M-component model of biological evolution
realizes microscopically an inhomogeneous branching process for $M \to \infty$.
This implies in particular a size distribution exponent $\tau'=7/4$ for
avalanches starting at a free end of the evolutionary chain. A bulk--like
behavior with $\tau'=3/2$ is restored if `conservative' boundary conditions
strictly fix to its critical, bulk value the average number of species directly
involved in an evolutionary avalanche by the mutating species located at the
chain end. A two-site correlation function exponent ${\tau_R}'=4$ is also
calculated exactly in the `dissipative' case, when one of the points is at the
border. These results, together with accurate numerical determinations of the
time recurrence exponent $\tau_{first}'$, show also that, no matter whether
dissipation is present or not, boundary avalanches have the same space and time
fractal dimensions as in the bulk, and their distribution exponents obey the
basic scaling laws holding there.Comment: 5 pages, 3 eps figure

### Strong gravitational field light deflection in binary systems containing a collapsed star

Large light deflection angles are produced in the strong gravitational field
regions around neutron stars and black holes. In the case of binary systems,
part of the photons emitted from the companion star towards the collapsed
object are expected to be deflected in the direction of the earth. Based on a
semi-classical approach we calculate the characteristic time delays and
frequency shifts of these photons as a function of the binary orbital phase.
The intensity of the strongly deflected light rays is reduced by many orders of
magnitude, therefore making the observations of this phenomenon extremely
difficult. Relativistic binary systems containing a radio pulsar and a
collapsed object are the best available candidates for the detection of the
strongly deflected photons. Based on the accurate knowledge of their orbital
parameters, these systems allow to predict accurately the delays of the pulses
along the highly deflected path, such that the sensitivity to very weak signals
can be substantially improved through coherent summation over long time
intervals. We discuss in detail the cases of PSR 1913+16 and PSR 1534+12 and
find that the system geometry is far more promising for the latter. The
observation of the highly deflected photons can provide a test of general
relativity in an unprecedented strong field regime as well as a tight
constraint on the radius of the collapsed object.Comment: 7 pages, uuencoded, gzip'ed, postscript file with figures included.
Accepted for pubblication in MNRA

### Topological and geometrical entanglement in a model of circular DNA undergoing denaturation

The linking number (topological entanglement) and the writhe (geometrical
entanglement) of a model of circular double stranded DNA undergoing a thermal
denaturation transition are investigated by Monte Carlo simulations. By
allowing the linking number to fluctuate freely in equilibrium we see that the
linking probability undergoes an abrupt variation (first-order) at the
denaturation transition, and stays close to 1 in the whole native phase. The
average linking number is almost zero in the denatured phase and grows as the
square root of the chain length, N, in the native phase. The writhe of the two
strands grows as the square root of N in both phases.Comment: 7 pages, 11 figures, revte

### Ranking knots of random, globular polymer rings

An analysis of extensive simulations of interacting self-avoiding polygons on
cubic lattice shows that the frequencies of different knots realized in a
random, collapsed polymer ring decrease as a negative power of the ranking
order, and suggests that the total number of different knots realized grows
exponentially with the chain length. Relative frequencies of specific knots
converge to definite values because the free energy per monomer, and its
leading finite size corrections, do not depend on the ring topology, while a
subleading correction only depends on the crossing number of the knots.Comment: 4 pages, 5 figure

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