Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

Toward the Jamming Threshold of Sphere Packings: Tunneled Crystals

We have discovered a new family of three-dimensional crystal sphere packings that are strictly jammed (i.e., mechanically stable) and yet possess an anomalously low density. This family constitutes an uncountably infinite number of crystal packings that are subpackings of the densest crystal packings and are characterized by a high concentration of self-avoiding "tunnels" (chains of vacancies) that permeate the structures. The fundamental geometric characteristics of these tunneled crystals command interest in their own right and are described here in some detail. These include the lattice vectors (that specify the packing configurations), coordination structure, Voronoi cells, and density fluctuations. The tunneled crystals are not only candidate structures for achieving the jamming threshold (lowest-density rigid packing), but may have substantially broader significance for condensed matter physics and materials science.Comment: 19 pages, 5 figure

Analysis of strain and stacking faults in single nanowires using Bragg coherent diffraction imaging

Coherent diffraction imaging (CDI) on Bragg reflections is a promising technique for the study of three-dimensional (3D) composition and strain fields in nanostructures, which can be recovered directly from the coherent diffraction data recorded on single objects. In this article we report results obtained for single homogeneous and heterogeneous nanowires with a diameter smaller than 100 nm, for which we used CDI to retrieve information about deformation and faults existing in these wires. The article also discusses the influence of stacking faults, which can create artefacts during the reconstruction of the nanowire shape and deformation.Comment: 18 pages, 6 figures Submitted to New Journal of Physic

Can one predict DNA Transcription Start Sites by studying bubbles?

It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.Comment: 4 pages, 3 figures, accepted for publication in physical review letter

Density-functional study of Cu atoms, monolayers, and coadsorbates on polar ZnO surfaces

The structure and electronic properties of single Cu atoms, copper monolayers and thin copper films on the polar oxygen and zinc terminated surfaces of ZnO are studied using periodic density-functional calculations. We find that the binding energy of Cu atoms sensitively depends on how charge neutrality of the polar surfaces is achieved. Bonding is very strong if the surfaces are stabilized by an electronic mechanism which leads to partially filled surface bands. As soon as the surface bands are filled (either by partial Cu coverage, by coadsorbates, or by the formation of defects), the binding energy decreases significantly. In this case, values very similar to those found for nonpolar surfaces and for copper on finite ZnO clusters are obtained. Possible implications of these observations concerning the growth mode of copper on polar ZnO surfaces and their importance in catalysis are discussed.Comment: 6 pages with 2 postscript figures embedded. Uses REVTEX and epsf macro

DNA Renaturation at the Water-Phenol Interface

We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the adsorption is irreversible. The adsorption of the single-stranded DNA is specific to phenol and relies on stacking and hydrogen bonding. We establish the interfacial nature of a DNA renaturation at a high salt concentration. In the absence of shaking, this reaction involves an efficient surface diffusion of the single-stranded DNA chains. In the presence of a vigorous shaking, the bimolecular rate of the reaction exceeds the Smoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA renaturation in these conditions is known as the Phenol Emulsion Reassociation Technique or PERT. Our results establish the interfacial nature of PERT. A comparison of this interfacial reaction with other approaches shows that PERT is the most efficient technique and reveals similarities between PERT and the renaturation performed by single-stranded nucleic acid binding proteins. Our results lead to a better understanding of the partitioning of nucleic acids in two-phase systems, and should help design improved extraction procedures for damaged nucleic acids. We present arguments in favor of a role of phenol and water-phenol interface in prebiotic chemistry. The most efficient renaturation reactions (in the presence of condensing agents or with PERT) occur in heterogeneous systems. This reveals the limitations of homogeneous approaches to the biochemistry of nucleic acids. We propose a heterogeneous approach to overcome the limitations of the homogeneous viewpoint