3,849 research outputs found
Stretching of a single-stranded DNA: Evidence for structural transition
Recent experiments have shown that the force-extension (F-x) curve for
single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is
significantly different from thymine [poly(dT)]. Here, we show that the base
stacking interaction is not sufficient to describe the F-x curves as seen in
the experiments. A reduction in the reaction co-ordinate arising from the
formation of helix at low forces and an increase in the distance between
consecutive phosphates of unstacked bases in the stretched state at high force
in the proposed model, qualitatively reproduces the experimentally observed
features. The multi-step plateau in the F-x curve is a signature of structural
change in ssDNA.Comment: 10 pages, 4 figure
Stretching an heteropolymer
We study the influence of some quenched disorder in the sequence of monomers
on the entropic elasticity of long polymeric chains. Starting from the
Kratky-Porod model, we show numerically that some randomness in the favoured
angles between successive segments induces a change in the elongation versus
force characteristics, and this change can be well described by a simple
renormalisation of the elastic constant. The effective coupling constant is
computed by an analytic study of the low force regime.Comment: Latex, 7 pages, 3 postscript figur
Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
We explore in detail the structural, mechanical and thermodynamic properties
of a coarse-grained model of DNA similar to that introduced in Thomas E.
Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101
(2010). Effective interactions are used to represent chain connectivity,
excluded volume, base stacking and hydrogen bonding, naturally reproducing a
range of DNA behaviour. We quantify the relation to experiment of the
thermodynamics of single-stranded stacking, duplex hybridization and hairpin
formation, as well as structural properties such as the persistence length of
single strands and duplexes, and the torsional and stretching stiffness of
double helices. We also explore the model's representation of more complex
motifs involving dangling ends, bulged bases and internal loops, and the effect
of stacking and fraying on the thermodynamics of the duplex formation
transition.Comment: 25 pages, 16 figure
The Yamabe invariant for axially symmetric two Kerr black holes initial data
An explicit 3-dimensional Riemannian metric is constructed which can be
interpreted as the (conformal) sum of two Kerr black holes with aligned angular
momentum. When the separation distance between them is large we prove that this
metric has positive Ricci scalar and hence positive Yamabe invariant. This
metric can be used to construct axially symmetric initial data for two Kerr
black holes with large angular momentum.Comment: 14 pages, 2 figure
Uniqueness and Non-uniqueness in the Einstein Constraints
The conformal thin sandwich (CTS) equations are a set of four of the Einstein
equations, which generalize the Laplace-Poisson equation of Newton's theory. We
examine numerically solutions of the CTS equations describing perturbed
Minkowski space, and find only one solution. However, we find {\em two}
distinct solutions, one even containing a black hole, when the lapse is
determined by a fifth elliptic equation through specification of the mean
curvature. While the relationship of the two systems and their solutions is a
fundamental property of general relativity, this fairly simple example of an
elliptic system with non-unique solutions is also of broader interest.Comment: 4 pages, 4 figures; abstract and introduction rewritte
Perturbative Solutions of the Extended Constraint Equations in General Relativity
The extended constraint equations arise as a special case of the conformal
constraint equations that are satisfied by an initial data hypersurface in
an asymptotically simple spacetime satisfying the vacuum conformal Einstein
equations developed by H. Friedrich. The extended constraint equations consist
of a quasi-linear system of partial differential equations for the induced
metric, the second fundamental form and two other tensorial quantities defined
on , and are equivalent to the usual constraint equations that satisfies
as a spacelike hypersurface in a spacetime satisfying Einstein's vacuum
equation. This article develops a method for finding perturbative,
asymptotically flat solutions of the extended constraint equations in a
neighbourhood of the flat solution on Euclidean space. This method is
fundamentally different from the `classical' method of Lichnerowicz and York
that is used to solve the usual constraint equations.Comment: This third and final version has been accepted for publication in
Communications in Mathematical Physic
A new geometric invariant on initial data for Einstein equations
For a given asymptotically flat initial data set for Einstein equations a new
geometric invariant is constructed. This invariant measure the departure of the
data set from the stationary regime, it vanishes if and only if the data is
stationary. In vacuum, it can be interpreted as a measure of the total amount
of radiation contained in the data.Comment: 5 pages. Important corrections regarding the generalization to the
non-time symmetric cas
The binary black-hole problem at the third post-Newtonian approximation in the orbital motion: Static part
Post-Newtonian expansions of the Brill-Lindquist and Misner-Lindquist
solutions of the time-symmetric two-black-hole initial value problem are
derived. The static Hamiltonians related to the expanded solutions, after
identifying the bare masses in both solutions, are found to differ from each
other at the third post-Newtonian approximation. By shifting the position
variables of the black holes the post-Newtonian expansions of the three metrics
can be made to coincide up to the fifth post-Newtonian order resulting in
identical static Hamiltonians up the third post-Newtonian approximation. The
calculations shed light on previously performed binary point-mass calculations
at the third post-Newtonian approximation.Comment: LaTeX, 9 pages, to be submitted to Physical Review
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