1,217 research outputs found
Extreme bendability of DNA double helix due to bending asymmetry
Experimental data of the DNA cyclization (J-factor) at short length scales,
as a way to study the elastic behavior of tightly bent DNA, exceed the
theoretical expectation based on the wormlike chain (WLC) model by several
orders of magnitude. Here, we propose that asymmetric bending rigidity of the
double helix in the groove direction can be responsible for extreme bendability
of DNA at short length scales and it also facilitates DNA loop formation at
these lengths. To account for the bending asymmetry, we consider the asymmetric
elastic rod (AER) model which has been introduced and parametrized in an
earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919
(2009)). Exploiting a coarse grained representation of DNA molecule at base
pair (bp) level, and using the Monte Carlo simulation method in combination
with the umbrella sampling technique, we calculate the loop formation
probability of DNA in the AER model. We show that, for DNA molecule has a
larger J-factor compared to the WLC model which is in excellent agreement with
recent experimental data.Comment: 8 pages, 9 figure
Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops
The equilibrium three dimensional shape of relatively short loops of DNA is
studied using an elastic model that takes into account anisotropy in bending
rigidities. Using a reasonable estimate for the anisotropy, it is found that
cyclized DNA with lengths that are not integer multiples of the pitch take on
nontrivial shapes that involve bending out of planes and formation of kinks.
The effect of sequence inhomogeneity on the shape of DNA is addressed, and
shown to enhance the geometrical features. These findings could shed some light
on the role of DNA conformation in protein--DNA interactions
Topological modes bound to dislocations in mechanical metamaterials
Mechanical metamaterials are artificial structures with unusual properties,
such as negative Poisson ratio, bistability or tunable vibrational properties,
that originate in the geometry of their unit cell. At the heart of such unusual
behaviour is often a soft mode: a motion that does not significantly stretch or
compress the links between constituent elements. When activated by motors or
external fields, soft modes become the building blocks of robots and smart
materials. Here, we demonstrate the existence of topological soft modes that
can be positioned at desired locations in a metamaterial while being robust
against a wide range of structural deformations or changes in material
parameters. These protected modes, localized at dislocations, are the
mechanical analogue of topological states bound to defects in electronic
systems. We create physical realizations of the topological modes in prototypes
of kagome lattices built out of rigid triangular plates. We show mathematically
that they originate from the interplay between two Berry phases: the Burgers
vector of the dislocation and the topological polarization of the lattice. Our
work paves the way towards engineering topologically protected nano-mechanical
structures for molecular robotics or information storage and read-out.Comment: 13 pages, 6 figures; changes to text and figures and added analysis
on mode localization; see
http://www.lorentz.leidenuniv.nl/~paulose/dislocation-modes/ for accompanying
video
Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21
Human chromosome 21 is the only chromosome in human genome that exhibits
oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near
the right telomere). We aim at establishing the existence of similar
periodicity in structure-related sequence features in order to relate this
(G+C)% oscillation to other biological phenomena. The following quantities are
shown to oscillate with the same 500kb periodicity in human chromosome 21:
binding energy calculated by two sets of dinucleotide-based thermodynamic
parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide
density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These
intrinsic quantities are related to structural features of the double helix of
DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and
a putative tendency for nucleosome formation.Comment: submitted to Physical Review
Calculating singlet excited states: comparison with fast time-resolved infrared spectroscopy of coumarins
In contrast to the ground state, the calculation of the infrared (IR) spectroscopy of molecular singlet excited states represents a substantial challenge. Here we use the structural IR fingerprint of the singlet excited states of a range of coumarin dyes to assess the accuracy of density functional theory based methods for the calculation of excited state IR spectroscopy. It is shown that excited state Kohn-Sham density functional theory provides a high level of accuracy and represents an alternative approach to time-dependent density functional theory for simulating the IR spectroscopy of the singlet excited states
Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
The Yakushevich (Y) model provides a very simple pictures of DNA torsion
dynamics, yet yields remarkably correct predictions on certain physical
characteristics of the dynamics. In the standard Y model, the interaction
between bases of a pair is modelled by a harmonic potential, which becomes
anharmonic when described in terms of the rotation angles; here we substitute
to this different types of improved potentials, providing a more physical
description of the H-bond mediated interactions between the bases. We focus in
particular on soliton solutions; the Y model predicts the correct size of the
nonlinear excitations supposed to model the ``transcription bubbles'', and this
is essentially unchanged with the improved potential. Other features of soliton
dynamics, in particular curvature of soliton field configurations and the
Peierls-Nabarro barrier, are instead significantly changed
Fluctuation-Facilitated Charge Migration along DNA
We propose a model Hamiltonian for charge transfer along the DNA double helix
with temperature driven fluctuations in the base pair positions acting as the
rate limiting factor for charge transfer between neighboring base pairs. We
compare the predictions of the model with the recent work of J.K. Barton and
A.H. Zewail (Proc.Natl.Acad.Sci.USA, {\bf 96}, 6014 (1999)) on the unusual
two-stage charge transfer of DNA.Comment: 4 pages, 2 figure
Two-level system with a thermally fluctuating transfer matrix element: Application to the problem of DNA charge transfer
Charge transfer along the base-pair stack in DNA is modeled in terms of
thermally-assisted tunneling between adjacent base pairs. Central to our
approach is the notion that tunneling between fluctuating pairs is rate-limited
by the requirement of their optimal alignment. We focus on this aspect of the
process by modeling two adjacent base pairs in terms of a classical damped
oscillator subject to thermal fluctuations as described by a Fokker-Planck
equation. We find that the process is characterized by two time scales, a
result that is in accord with experimental findings.Comment: original file is revtex4, 10 pages, three eps figure
Photochemistry of framework-supported M(diimine)(CO)₃X complexes in 3D Lithium-Carboxylate metal−organic frameworks: monitoring the effect of framework cations
The structures and photochemical behaviour of two new metal-organic frameworks are reported. Reaction of Re(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylic acid)(CO)₃Cl or Mn(2,2ʹ-bipyʹ-5,5ʹ- dicarboxylic acid)(CO)₃Br with either LiCl or LiBr, respectively, produces single crystals of {Li₂(DMF)₂[(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylate)Re(CO)₃Cl]}n (ReLi) or {Li₂(DMF)₂[(2,2ʹ-bipyʹ- 5,5ʹ-dicarboxylate)Mn(CO)₃Br]}n (MnLi). The structures formed by the two MOFs comprise one-dimensional chains of carboxylate-bridged Li(I) cations that are cross-linked by units of Re(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylate)(CO)₃Cl (ReLi) or Mn(2,2ʹ-bipyʹ-5,5ʹ- dicarboxylate)(CO)₃Br (MnLi). The photophysical and photochemical behaviour of both ReLi and MnLi are probed. The rhenium-containing MOF, ReLi, exhibits luminescence and the excited state behaviour, as established by time-resolved infra-red measurements, are closer in behaviour to that of unsubstituted [Re(bipy)(CO)₃Cl] rather than a related MOF where the Li(I) cations are replaced by Mn(II) cations. These observations are further supported by DFT calculations. Upon excitation MnLi forms a dicarbonyl species which rapidly recombines with the dissociated CO, in a fashion consistent with the majority of the photoejected CO not escaping the MOF channels
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat
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