576 research outputs found
Effects of Sequence Disorder on DNA Looping and Cyclization
Effects of sequence disorder on looping and cyclization of the
double-stranded DNA are studied theoretically. Both random intrinsic curvature
and inhomogeneous bending rigidity are found to result in a remarkably wide
distribution of cyclization probabilities. For short DNA segments, the range of
the distribution reaches several orders of magnitude for even completely random
sequences. The ensemble averaged values of the cyclization probability are also
calculated, and the connection to the recent experiments is discussed.Comment: 8 pages, 4 figures, LaTeX; accepted to Physical Review E; v2: a
substantially revised version; v3: references added, conclusions expanded,
minor editorial corrections to the text; v4: a substantially revised and
expanded version (total number of pages doubled); v5: new Figure 4, captions
expanded, minor editorial improvements to the tex
Stretching semiflexible filaments with quenched disorder
We study the effect of quenched randomness in the arc-length dependent
spontaneous curvature of a wormlike chain under tension. In the weakly bending
approximation in two dimensions, we obtain analytic results for the
force-elongation curve and the width of transverse fluctuations. We compare
quenched and annealed disorder and conclude that the former cannot always be
reduced to a simple change in the stiffness of the pure system. We also discuss
the effect of a random transverse force on the stretching response of a
wormlike chain without spontaneous curvature.Comment: 5 pages, minor changes, added references, final version as published
in PR
Nucleation at the DNA supercoiling transition
Twisting DNA under a constant applied force reveals a thermally activated
transition into a state with a supercoiled structure known as a plectoneme.
Using transition state theory, we predict the rate of this plectoneme
nucleation to be of order 10^4 Hz. We reconcile this with experiments that have
measured hopping rates of order 10 Hz by noting that the viscosity of the bead
used to manipulate the DNA limits the measured rate. We find that the intrinsic
bending caused by disorder in the base-pair sequence is important for
understanding the free energy barrier that governs the transition. Both
analytic and numerical methods are used in the calculations. We provide
extensive details on the numerical methods for simulating the elastic rod model
with and without disorder.Comment: 18 pages, 15 figure
Barut-Girardello coherent states for u(p,q) and sp(N,R) and their macroscopic superpositions
The Barut-Girardello coherent states (BG CS) representation is extended to
the noncompact algebras u(p,q) and sp(N,R) in (reducible) quadratic boson
realizations. The sp(N,R) BG CS take the form of multimode ordinary
Schr\"odinger cat states. Macroscopic superpositions of 2^{n-1} sp(N,R) CS (2^n
canonical CS, n=1,2,...) are pointed out which are overcomplete in the N-mode
Hilbert space and the relation between the canonical CS and the u(p,q) BG-type
CS representations is established. The sets of u(p,q) and sp(N,R) BG CS and
their discrete superpositions contain many states studied in quantum optics
(even and odd N-mode CS, pair CS) and provide an approach to quadrature
squeezing, alternative to that of intelligent states. New subsets of weakly and
strongly nonclassical states are pointed out and their statistical properties
(first- and second-order squeezing, photon number distributions) are discussed.
For specific values of the angle parameters and small amplitude of the
canonical CS components these states approaches multimode Fock states with one,
two or three bosons/photons. It is shown that eigenstates of a squared
non-Hermitian operator A^2 (generalized cat states) can exhibit squeezing of
the quadratures of A.Comment: 29 pages, LaTex, 5 figures. Improvements in text, corrections in some
formulas. To appear in J. Phys. A, v. 3
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
Disordered, stretched, and semiflexible biopolymers in two dimensions
We study the effects of intrinsic sequence-dependent curvature for a two
dimensional semiflexible biopolymer with short-range correlation in intrinsic
curvatures. We show exactly that when not subjected to any external force, such
a system is equivalent to a system with a well-defined intrinsic curvature and
a proper renormalized persistence length. We find the exact expression for the
distribution function of the equivalent system. However, we show that such an
equivalent system does not always exist for the polymer subjected to an
external force. We find that under an external force, the effect of
sequence-disorder depends upon the averaging order, the degree of disorder, and
the experimental conditions, such as the boundary conditions. Furthermore, a
short to moderate length biopolymer may be much softer or has a smaller
apparent persistent length than what would be expected from the "equivalent
system". Moreover, under a strong stretching force and for a long biopolymer,
the sequence-disorder is immaterial for elasticity. Finally, the effect of
sequence-disorder may depend upon the quantity considered
Uncertainty Relations in Deformation Quantization
Robertson and Hadamard-Robertson theorems on non-negative definite hermitian
forms are generalized to an arbitrary ordered field. These results are then
applied to the case of formal power series fields, and the
Heisenberg-Robertson, Robertson-Schr\"odinger and trace uncertainty relations
in deformation quantization are found. Some conditions under which the
uncertainty relations are minimized are also given.Comment: 28+1 pages, harvmac file, no figures, typos correcte
The Semiclassical and Quantum Regimes of Superradiant Light Scattering from a Bose-Einstein Condensate
We show that many features of the recent experiments of Schneble et al. [D.
Schneble, Y. Torii, M. Boyd, E.W. Streed, D.E. Pritchard and W. Ketterle,
Science vol. 300, p. 475 (2003)], which demonstrate two different regimes of
light scattering by a Bose-Einstein condensate, can be described using a
one-dimensional mean-field quantum CARL model, where optical amplification
occurs simultaneously with the production of a periodic density modulation in
the atomic medium. The two regimes of light scattering observed in these
experiments, originally described as ``Kapiza-Dirac scattering'' and
``Superradiant Rayleigh scattering'', can be interpreted as the semiclassical
and quantum limits respectively of CARL lasing.Comment: 10 pages, 5 figures - to appear in Journal of Optics
Repertoires of the Nucleosome-Positioning Dinucleotides
It is generally accepted that the organization of eukaryotic DNA into chromatin is strongly governed by a code inherent in the genomic DNA sequence. This code, as well as other codes, is superposed on the triplets coding for amino acids. The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides, with AA/TT and RR/YY giving the strongest signals, all with a period of 10.4 bases. Every base-pair stack in the DNA duplex has specific deformation properties, thus favoring DNA bending in a specific direction. The appearance of the corresponding dinucleotide at the distance 10.4 xn bases will facilitate DNA bending in that direction, which corresponds to the minimum energy of DNA folding in the nucleosome. We have analyzed the periodic appearances of all 16 dinucleotides in the genomes of thirteen different eukaryotic organisms. Our data show that a large variety of dinucleotides (if not all) are, apparently, contributing to the nucleosome positioning code. The choice of the periodical dinucleotides differs considerably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observed for CG dinucleotides in the genome of the honey bee A. mellifera. Also, the dinucleotide CG appears as the only periodical component in the human genome. This observation seems especially relevant since CpG methylation is well known to modulate chromatin packing and regularity. Thus, the selection of the dinucleotides contributing to the chromatin code is species specific, and may differ from region to region, depending on the sequence context
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