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

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 $\lambda-$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

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$\rm{\acute{e}}$-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

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

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

Flux of cadmium through a laboratory food chain (media-algae-mussel) and its effects

The increasing pollution of the aquatic environment by cadmium is a potentially severe problem and techniques are needed to document the effect of the metal. To investigate the flux of this metal through a laboratory food chain, algae were grown in various cadmium concentrations for subsequent use as contaminated food for mussels. The results showed that in order to make valid deductions, more information about chemical mechanisms and background ecophysiological data is needed, otherwise accumulation reports may become misleading. It was found that the best growth and accumulation results were achieved by harvesting algae from a zinc deficient media containing 7 μmole dm-3 cadmium and at a particular life cycle phase. Two uptake mechanisms are proposed. These "contaminated" algae were fed to mussels under different accumulation regimes. The metal gain and loss were determined and compared to a "baseline" dry body weight which had been calculated from a shell length-body weight relationship. Cadmium accumulation took place in the mussels and after some initial delay, could be correlated to weight loss. Such a weight loss was due to pathological and biochemical changes in the mussels. It was shown that the toxic effect of cadmium could be determined much earlier by the presence of special proteins. The elutant profiles of the gel chromatography study showed the production of metal binding protein as well as a spill over of cadmium into the enzyme pool, caused by a higher uptake than elimination rate. Cadmium on metal binding protein and in the enzyme pool could be related to the poisoning effect of the metal and a pollution history for the mussels identified. The characteristics of the metal binding protein were found to be very similar to those reported for metallothionein and had an approximate molecular weight of 10 600 daltons