Ralf Blossey

Reparametrizing the loop entropy weights: effect on DNA melting curves.

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10(6) base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

The dynamics of the nucleosome: thermal effects, external forces and ATP

With nucleosomes being tightly associated with the majority of eukaryotic DNA, it is essential that mechanisms are in place that can move nucleosomes ‘out of the way’. A focus of current research comprises chromatin remodeling complexes, which are ATP‐consuming protein complexes that, for example, pull or push nucleosomes along DNA. The precise mechanisms used by those complexes are not yet understood. Hints for possible mechanisms might be found among the various spontaneous fluctuations that nucleosomes show in the absence of remodelers. Thermal fluctuations induce the partial unwrapping of DNA from the nucleosomes and introduce twist or loop defects in the wrapped DNA, leading to nucleosome sliding along DNA. In this minireview, we discuss nucleosome dynamics from two angles. First, we describe the dynamical modes of nucleosomes in the absence of remodelers that are experimentally fairly well characterized and theoretically understood. Then, we discuss remodelers and describe recent insights about the possible schemes that they might use.

Morphological transformation of InyGa1-yAs islands, fabricated by Stranski-Krastanov growth

Abstract A remarkable change in topology occurs when In y Ga 1− y As quantum dots, grown by Stranski–Krastanov self-organization, are covered by a thin layer of GaAs. The nano-islands rearrange themselves to form volcano-like islands with distinct, ring-like features. The island topology can be preserved during overgrowth and thus used for the fabrication of ring-shaped quantum structures. The experimental data suggests that two mechanisms, diffusion and dewetting, are driving the transformation from dots to rings.

Reversible electrowetting on superhydrophobic double-nanotextured surfaces.

The paper reports on wetting, electrowetting (EW), and systematic contact angle hysteresis measurements after electrowetting of superhydrophobic silicon nanowire surfaces (NWs). The surfaces consist of C4F8-coated silicon nanowires grown on Si/SiO2 substrate. Different surfaces modulating (i) the dielectric layer thickness and (ii) the nanotexturation were investigated in this study. It was found that the superhydrophobic NWs display different EW behaviors according to their double nanotexturation with varying droplet impalement levels. Some surfaces exhibited a total reversibility to EW with no impalement (contact angle variation of 35+/-2 degrees at 190 VTRMS with deionized water), whereas other surfaces showed nonreversible behavior to EW with partial droplet impalement. A scenario is proposed to explain the unique properties of these surfaces.

Electrowetting and droplet impalement experiments on superhydrophobic multiscale structures

The reversible actuation of droplets on superhydrophobic surfaces under ambient conditions is currently an important field of research due to its potential applicability in microfluidic lab-on-a-chip devices. We have recently shown that Si-nanowire (NW) surfaces allow for reversible actuation provided that the surface structures show certain characteristics. In particular it appears that, for such surfaces, the presence of structures with multiple specific length scales is indeed needed to have a robust reversibility of contact angle changes. Here we report on electrowetting (EW) and impalement experiments on double-scale structured surfaces prepared by a combination of silicon micropillars prepared by an association of optical lithography and silicon etching, and nanowire growth on top of these surfaces. We show that while micropillar surfaces have a low impalement threshold and irreversible EW behaviour, a surface with double-scale texture can show both a very high resistance to impalement and a limited reversibility under EW, provided that the roughness of the micro-scale is large enough--i.e. that the pillars are tall enough. The optimal performance is obtained for a space between pillars that is comparable to the height of the nanostructure.

Exons, Introns, and DNA Thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e., stretches of DNA which do not carry useful information for protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights into the physical mechanisms underlying the evolution of genes.

Slip vs. viscoelasticity in dewetting thin films.

Abstract.Ultrathin polymer films on non-wettable substrates display dynamic features which have been attributed to either viscoelastic or slip effects. Here we show that in the weak- and strong-slip regime, effects of viscoelastic relaxation are either absent or essentially indistinguishable from slip effects. Strong slip modifies the fastest unstable mode in a rupturing thin film, which questions the standard approach to reconstruct the effective interface potential from dewetting experiments.

Spinodal dewetting of thin films with large interfacial slip: implications from the dispersion relation

We compare the dispersion relations for spinodally dewetting thin liquid films for increasing magnitude of interfacial slip length in the lubrication limit. While the shape of the dispersion relation, in particular the position of the maximum, are equal for no-slip up to moderate-slip lengths, the position of the maximum shifts to much larger wavelengths for large slip lengths. Here, we discuss the implications of this fact for recently developed methods to assess the disjoining pressure in spinodally unstable thin films by measuring the shape of the roughness power spectrum. For polystyrene (PS) films on octadecyltrichlorosilane (OTS) covered Si wafers (with slip length b approximately 1 microm), we predict a 20% shift of the position of the maximum of the power spectrum which should be detectable in experiments.

Self-Organized InGaAs Quantum Rings -- Fabrication and Spectroscopy

13 paginas.-- The written version of the plenary and invited lectures of the Spring Meeting of the Condensed Matter Physics section of the Deutsche Physikalische Gesellschaft held from March 24 to 28, 2003 in Dresden, Germany.-- Kramer, Bernhard (Ed.).

Dipolar correlations in structured solvents under nanoconfinement

We study electrostatic correlations in structured solvents confined to nanoscale systems. We derive variational equations of Netz-Orland type for a model liquid composed of finite size dipoles. These equations are solved for both dilute solvents and solvents at physiological concentrations in a slit nanopore geometry. Correlation effects are of major importance for the dielectric reduction and anisotropy of the solvent resulting from dipole image interactions and also lead to a reduction of van der Waals attractions between low dielectric bodies. Finally, by comparison with other recently developed self-consistent theories and experiments, we scrutinize the effect of solvent-membrane interactions on the differential capacitance of the charged liquid in contact with low dielectric substrates. The interfacial solvent depletion driven by solvent-image interactions plays the major role in the observed low values of the experimental capacitance data, while non-locality associated with the extended charge structure of solvent molecules only brings a minor contribution.