4,047 research outputs found
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
Size, shape, and flexibility of RNA structures
Determination of sizes and flexibilities of RNA molecules is important in
understanding the nature of packing in folded structures and in elucidating
interactions between RNA and DNA or proteins. Using the coordinates of the
structures of RNA in the Protein Data Bank we find that the size of the folded
RNA structures, measured using the radius of gyration, , follows the Flory
scaling law, namely, \AA where N is the number of
nucleotides. The shape of RNA molecules is characterized by the asphericity
and the shape parameters that are computed using the eigenvalues
of the moment of inertia tensor. From the distribution of , we find
that a large fraction of folded RNA structures are aspherical and the
distribution of values shows that RNA molecules are prolate (). The
flexibility of folded structures is characterized by the persistence length
. By fitting the distance distribution function to the worm-like
chain model we extracted the persistence length . We find that \AA. The dependence of on implies the average length of
helices should increases as the size of RNA grows. We also analyze packing in
the structures of ribosomes (30S, 50S, and 70S) in terms of , ,
, and . The 70S and the 50S subunits are more spherical compared to
most RNA molecules. The globularity in 50S is due to the presence of an
unusually large number (compared to 30S subunit) of small helices that are
stitched together by bulges and loops. Comparison of the shapes of the intact
70S ribosome and the constituent particles suggests that folding of the
individual molecules might occur prior to assembly.Comment: 28 pages, 8 figures, J. Chem. Phys. in pres
The Errors of Karen Franklin's Pretextuality
In her recent article, Hebephilia: Quintessence of Diagnostic Pretextuality (published in Behavioral Sciences and the Law, 2010), Karen Franklin expands on her previous argument that psychologists and psychiatrists should not diagnose as abnormal hebephilia, the sexual preference for early pubescent children. She supports her argument with a series of claims about the contents of the empirical literature and the scientists who produced it. The present document provides fact-checking of those claims, revealing that Franklin's conclusions are based largely on demonstrable falsehoods
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
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
Reachability in Parametric Interval Markov Chains using Constraints
Parametric Interval Markov Chains (pIMCs) are a specification formalism that
extend Markov Chains (MCs) and Interval Markov Chains (IMCs) by taking into
account imprecision in the transition probability values: transitions in pIMCs
are labeled with parametric intervals of probabilities. In this work, we study
the difference between pIMCs and other Markov Chain abstractions models and
investigate the two usual semantics for IMCs: once-and-for-all and
at-every-step. In particular, we prove that both semantics agree on the
maximal/minimal reachability probabilities of a given IMC. We then investigate
solutions to several parameter synthesis problems in the context of pIMCs --
consistency, qualitative reachability and quantitative reachability -- that
rely on constraint encodings. Finally, we propose a prototype implementation of
our constraint encodings with promising results
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
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
Microscopic formulation of the Zimm-Bragg model for the helix-coil transition
A microscopic spin model is proposed for the phenomenological Zimm-Bragg
model for the helix-coil transition in biopolymers. This model is shown to
provide the same thermophysical properties of the original Zimm-Bragg model and
it allows a very convenient framework to compute statistical quantities.
Physical origins of this spin model are made transparent by an exact mapping
into a one-dimensional Ising model with an external field. However, the
dependence on temperature of the reduced external field turns out to differ
from the standard one-dimensional Ising model and hence it gives rise to
different thermophysical properties, despite the exact mapping connecting them.
We discuss how this point has been frequently overlooked in the recent
literature.Comment: 11 pages, 2 figure
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