4,198 research outputs found
Nonlinear charge transport mechanism in periodic and disordered DNA
We study a model for polaron-like charge transport mechanism along DNA
molecules with emphasis on the impact of parametrical and structural disorder.
Our model Hamiltonian takes into account the coupling of the charge carrier to
two different kind of modes representing fluctuating twist motions of the base
pairs and H-bond distortions within the double helix structure of
DNA. Localized stationary states are constructed with the help of a
nonlinear map approach for a periodic double helix and in the presence of
intrinsic static parametrical and/or structural disorder reflecting the impact
of ambient solvent coordinates. It is demonstrated that charge transport is
mediated by moving polarons respectively breather compounds carrying not only
the charge but causing also local temporal deformations of the helix structure
through the traveling torsion and bond breather components illustrating the
interplay of structure and function in biomolecules.Comment: 23 pages, 13 figure
Charge transport in a nonlinear, three--dimensional DNA model with disorder
We study the transport of charge due to polarons in a model of DNA which
takes in account its 3D structure and the coupling of the electron wave
function with the H--bond distortions and the twist motions of the base pairs.
Perturbations of the ground states lead to moving polarons which travel long
distances. The influence of parametric and structural disorder, due to the
impact of the ambient, is considered, showing that the moving polarons survive
to a certain degree of disorder. Comparison of the linear and tail analysis and
the numerical results makes possible to obtain further information on the
moving polaron properties.Comment: 9 pages, 2 figures. Proceedings of the conference on "Localization
and energy transfer in nonlinear systems", June 17-21, 2002, San Lorenzo de
El Escorial, Madrid, Spain. To be publishe
Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers
We investigate the charge transport in synthetic DNA polymers built up from
single types of base pairs. In the context of a polaron-like model, for which
an electronic tight-binding system and bond vibrations of the double helix are
coupled, we present estimates for the electron-vibration coupling strengths
utilizing a quantum-chemical procedure. Subsequent studies concerning the
mobility of polaron solutions, representing the state of a localized charge in
unison with its associated helix deformation, show that the system for
poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess
quantitatively distinct transport properties. While the former supports
unidirectionally moving electron breathers attributed to highly efficient
long-range conductivity the breather mobility in the latter case is
comparatively restrained inhibiting charge transport. Our results are in
agreement with recent experimental results demonstrating that poly(dG)-poly(dC)
DNA molecules acts as a semiconducting nanowire and exhibits better conductance
than poly(dA)-poly(dT) ones.Comment: 11 pages, 5 figure
Modeling the thermal evolution of enzyme-created bubbles in DNA
The formation of bubbles in nucleic acids (NAs) are fundamental in many
biological processes such as DNA replication, recombination, telomeres
formation, nucleotide excision repair, as well as RNA transcription and
splicing. These precesses are carried out by assembled complexes with enzymes
that separate selected regions of NAs. Within the frame of a nonlinear dynamics
approach we model the structure of the DNA duplex by a nonlinear network of
coupled oscillators. We show that in fact from certain local structural
distortions there originate oscillating localized patterns, that is radial and
torsional breathers, which are associated with localized H-bond deformations,
being reminiscent of the replication bubble. We further study the temperature
dependence of these oscillating bubbles. To this aim the underlying nonlinear
oscillator network of the DNA duplex is brought in contact with a heat bath
using the Nos-Hoover-method. Special attention is paid to the
stability of the oscillating bubbles under the imposed thermal perturbations.
It is demonstrated that the radial and torsional breathers, sustain the impact
of thermal perturbations even at temperatures as high as room temperature.
Generally, for nonzero temperature the H-bond breathers move coherently along
the double chain whereas at T=0 standing radial and torsional breathers result.Comment: 19 pages, 7 figure
Probabilistic Linear Solvers: A Unifying View
Several recent works have developed a new, probabilistic interpretation for
numerical algorithms solving linear systems in which the solution is inferred
in a Bayesian framework, either directly or by inferring the unknown action of
the matrix inverse. These approaches have typically focused on replicating the
behavior of the conjugate gradient method as a prototypical iterative method.
In this work surprisingly general conditions for equivalence of these disparate
methods are presented. We also describe connections between probabilistic
linear solvers and projection methods for linear systems, providing a
probabilistic interpretation of a far more general class of iterative methods.
In particular, this provides such an interpretation of the generalised minimum
residual method. A probabilistic view of preconditioning is also introduced.
These developments unify the literature on probabilistic linear solvers, and
provide foundational connections to the literature on iterative solvers for
linear systems
Localization Properties of Electronic States in Polaron Model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers
We numerically investigate localization properties of electronic states in a
static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with
realistic parameters obtained by quantum-chemical calculation. The randomness
in the on-site energies caused by the electron-phonon coupling are completely
correlated to the off-diagonal parts. In the single electron model, the effect
of the hydrogen-bond stretchings, the twist angles between the base pairs and
the finite system size effects on the energy dependence of the localization
length and on the Lyapunov exponent are given. The localization length is
reduced by the influence of the fluctuations in the hydrogen bond stretchings.
It is also shown that the helical twist angle affects the localization length
in the poly(dG)-poly(dC) DNA polymer more strongly than in the
poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy
dependence of the localization length when the system size is relatively small.Comment: 6 pages, 6 figure
Clustering with the Average Silhouette Width
The Average Silhouette Width (ASW) is a popular cluster validation index to estimate the number of clusters. The question whether it also is suitable as a general objective function to be optimized for finding a clustering is addressed. Two algorithms (the standard version OSil and a fast version FOSil) are proposed, and they are compared with existing clustering methods in an extensive simulation study covering known and unknown numbers of clusters. Real data sets are analysed, partly exploring the use of the new methods with non-Euclidean distances. The ASW is shown to satisfy some axioms that have been proposed for cluster quality functions. The new methods prove useful and sensible in many cases, but some weaknesses are also highlighted. These also concern the use of the ASW for estimating the number of clusters together with other methods, which is of general interest due to the popularity of the ASW for this task
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