304 research outputs found
Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
We propose a dynamical model for non-specific DNA-protein interaction, which
is based on the 'bead-spring' model previously developed by other groups, and
investigate its properties using Brownian Dynamics simulations. We show that
the model successfully reproduces some of the observed properties of real
systems and predictions of kinetic models. For example, sampling of the DNA
sequence by the protein proceeds via a succession of 3d motion in the solvent,
1d sliding along the sequence, short hops between neighboring sites, and
intersegmental transfers. Moreover, facilitated diffusion takes place in a
certain range of values of the protein effective charge, that is, the
combination of 1d sliding and 3d motion leads to faster DNA sampling than pure
3d motion. At last, the number of base pairs visited during a sliding event is
comparable to the values deduced from single-molecule experiments. We also
point out and discuss some discrepancies between the predictions of this model
and some recent experimental results as well as some hypotheses and predictions
of kinetic models
Theoretical investigation of finite size effects at DNA melting
We investigated how the finiteness of the length of the sequence affects the
phase transition that takes place at DNA melting temperature. For this purpose,
we modified the Transfer Integral method to adapt it to the calculation of both
extensive (partition function, entropy, specific heat, etc) and non-extensive
(order parameter and correlation length) thermodynamic quantities of finite
sequences with open boundary conditions, and applied the modified procedure to
two different dynamical models. We showed that rounding of the transition
clearly takes place when the length of the sequence is decreased. We also
performed a finite-size scaling analysis of the two models and showed that the
singular part of the free energy can indeed be expressed in terms of an
homogeneous function. However, both the correlation length and the average
separation between paired bases diverge at the melting transition, so that it
is no longer clear to which of these two quantities the length of the system
should be compared. Moreover, Josephson's identity is satisfied for none of the
investigated models, so that the derivation of the characteristic exponents
which appear, for example, in the expression of the specific heat, requires
some care
Different mechanics of snap-trapping in the two closely related carnivorous plants Dionaea muscipula and Aldrovanda vesiculosa
The carnivorous aquatic Waterwheel Plant (Aldrovanda vesiculosa L.) and the
closely related terrestrial Venus Flytrap (Dionaea muscipula SOL. EX J. ELLIS)
both feature elaborate snap-traps, which shut after reception of an external
mechanical stimulus by prey animals. Traditionally, Aldrovanda is considered as
a miniature, aquatic Dionaea, an assumption which was already established by
Charles Darwin. However, videos of snapping traps from both species suggest
completely different closure mechanisms. Indeed, the well-described snapping
mechanism in Dionaea comprises abrupt curvature inversion of the two trap
lobes, while the closing movement in Aldrovanda involves deformation of the
trap midrib but not of the lobes, which do not change curvature. In this paper,
we present the first detailed mechanical models for these plants, which are
based on the theory of thin solid membranes and explain this difference by
showing that the fast snapping of Aldrovanda is due to kinematic amplification
of the bending deformation of the midrib, while that of Dionaea unambiguously
relies on the buckling instability that affects the two lobes.Comment: accepted in Physical Review
Extracting Multidimensional Phase Space Topology from Periodic Orbits
We establish a hierarchical ordering of periodic orbits in a strongly coupled
multidimensional Hamiltonian system. Phase space structures can be
reconstructed quantitatively from the knowledge of periodic orbits alone. We
illustrate our findings for the hydrogen atom in crossed electric and magnetic
fields.Comment: 4 pages, 5 figures, accepted for publication in Phys. Rev. Let
High-resolution Fourier-transform XUV photoabsorption spectroscopy of 14N15N
The first comprehensive high-resolution photoabsorption spectrum of 14N15N
has been recorded using the Fourier-transform spectrometer attached to the
Desirs beamline at the Soleil synchrotron. Observations are made in the extreme
ultraviolet (XUV) and span 100,000-109,000 cm-1 (100-91.7 nm). The observed
absorption lines have been assigned to 25 bands and reduced to a set of
transition energies, f values, and linewidths. This analysis has verified the
predictions of a theoretical model of N2 that simulates its photoabsorption and
photodissociation cross section by solution of an isotopomer independent
formulation of the coupled-channel Schroedinger equation. The mass dependence
of predissociation linewidths and oscillator strengths is clearly evident and
many local perturbations of transition energies, strengths, and widths within
individual rotational series have been observed.Comment: 14 pages, 8 figures, one data archiv
Anharmonic stacking in supercoiled DNA
Multistep denaturation in a short circular DNA molecule is analyzed by a
mesoscopic Hamiltonian model which accounts for the helicoidal geometry.
Computation of melting profiles by the path integral method suggests that
stacking anharmonicity stabilizes the double helix against thermal disruption
of the hydrogen bonds. Twisting is essential in the model to capture the
importance of nonlinear effects on the thermodynamical properties. In a ladder
model with zero twist, anharmonic stacking scarcely affects the thermodynamics.
Moderately untwisted helices, with respect to the equilibrium conformation,
show an energetic advantage against the overtwisted ones. Accordingly
moderately untwisted helices better sustain local fluctuational openings and
make more unlikely the thermally driven complete strand separation.Comment: In pres
Hydrogen atom in crossed electric and magnetic fields: Phase space topology and torus quantization via periodic orbits
A hierarchical ordering is demonstrated for the periodic orbits in a strongly
coupled multidimensional Hamiltonian system, namely the hydrogen atom in
crossed electric and magnetic fields. It mirrors the hierarchy of broken
resonant tori and thereby allows one to characterize the periodic orbits by a
set of winding numbers. With this knowledge, we construct the action variables
as functions of the frequency ratios and carry out a semiclassical torus
quantization. The semiclassical energy levels thus obtained agree well with
exact quantum calculations
Classical and quantum mechanical plane switching in CO2
Classical plane switching takes place in systems with a pronounced 1:2
resonance, where the degree of freedom with lowest frequency is
doubly-degenerate. Under appropriate conditions, one observes a periodic and
abrupt precession of the plane in which the doubly-degenerate motion takes
place. In this article, we show that quantum plane switching exists in CO2 :
Based on our analytical solutions of the classical Hamilton's equations of
motion, we describe the dependence on vibrational angular momentum and energy
of the frequency of switches and the plane switching angle. Using these
results, we find optimal initial wave packet conditions for CO2 and show,
through quantum mechanical propagation, that such a wave packet indeed displays
plane switching at energies around 10000 cm-1 above the ground state on time
scales of about 100 fs.Comment: accepted for publication in the Journal of Chemical Physic
Renormalisation group determination of the order of the DNA denaturation transition
We report on the nature of the thermal denaturation transition of homogeneous
DNA as determined from a renormalisation group analysis of the
Peyrard-Bishop-Dauxois model. Our approach is based on an analogy with the
phenomenon of critical wetting that goes further than previous qualitative
comparisons, and shows that the transition is continuous for the average
base-pair separation. However, since the range of universal critical behaviour
appears to be very narrow, numerically observed denaturation transitions may
look first-order, as it has been reported in the literature.Comment: 6 pages; no figures; to appear in Europhysics Letter
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