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Biomedical subjects

Ralf Blossey

Publications and source records attributed to Ralf Blossey.

6 recordsLinked to original sources
PubMed2005

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.

Biophysics↗
PubMed2003

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.

Algorithms↗
PubMed2003

Complex dewetting scenarios captured by thin-film models.

In the course of miniaturization of electronic and microfluidic devices, reliable predictions of the stability of ultrathin films have a strategic role for design purposes. Consequently, efficient computational techniques that allow for a direct comparison with experiment become increasingly important. Here we demonstrate, for the first time, that the full complex spatial and temporal evolution of the rupture of ultrathin films can be modelled in quantitative agreement with experiment. We accomplish this by combining highly controlled experiments on different film-rupture patterns with computer simulations using novel numerical schemes for thin-film equations. For the quantitative comparison of the pattern evolution in both experiment and simulation we introduce a novel pattern analysis method based on Minkowski measures. Our results are fundamental for the development of efficient tools capable of describing essential aspects of thin-film flow in technical systems.

Biomedical Engineering↗
PubMed2003

Self-cleaning surfaces--virtual realities.

In the 19th century, Oscar Wilde stated "We live, I regret to say, in an age of surfaces". Today, we do so even more, and we do not regret it: key advances in the understanding and fabrication of surfaces with controlled wetting properties are about to make the dream of a contamination-free (or 'no-clean') surface come true. Two routes to self-cleaning are emerging, which work by the removal of dirt by either film or droplet flow. Although a detailed understanding of the mechanisms underlying the behaviour of liquids on such surfaces is still a basic research topic, the first commercial products in the household-commodity sector and for applications in biotechnology are coming within reach of the marketplace. This progress report describes the current status of understanding of the underlying mechanisms, the concepts for making such surfaces, and some of their first applications.

Journal Article↗
PubMed2002

Wetting droplet instability and quantum ring formation.

InAs islands on GaAs substrates undergo a morphological change into ring-shaped configurations upon deposition of a GaAs layer after island growth. By invoking an analogy of the InAs islands to wetting droplets on solid substrates, we suggest that this transition might be brought about by a change of the surface free-energy balance at the three-phase contact-line between GaAs, InAs, and vacuum (or As atmosphere). Our scenario can also be tested in conventional liquid systems (e.g., polymers).

Journal Article↗