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W Krauth

Publications and source records attributed to W Krauth.

15 recordsLinked to original sources

Absence of thermodynamic phase transition in a model glass former

The glass transition can be viewed simply as the point at which the viscosity of a structurally disordered liquid reaches a universal threshold value. But this is an operational definition that circumvents fundamental issues, such as whether the glass transition is a purely dynamical phenomenon. If so, ergodicity gets broken (the system becomes confined to some part of its phase space), but the thermodynamic properties of the liquid remain unchanged across the transition, provided they are determined as thermodynamic equilibrium averages over the whole phase space. The opposite view claims that an underlying thermodynamic phase transition is responsible for the pronounced slow-down in the dynamics at the liquid-glass boundary. Such a phase transition would trigger the dynamic standstill, and then be masked by it. Here we perform Monte Carlo simulations of a two-dimensional system of polydisperse hard disks far within its glassy phase. The approach allows for non-local moves in a way that preserves micro-reversibility. We find no evidence for a thermodynamic phase transition up to very high densities; the glass is thus indistinguishable from the liquid on purely thermodynamic grounds.

Journal Article↗

Internucleotide protein linkers in Ehrlich ascites cell DNA.

DNA from Ehrlich ascites tumor cells is nicked or gapped by a reaction which is induced by proteases such as autodigested pronase, proteinase K, trypsin, chymotrypsin and subtilisin. The cleavage of the protease-sensitive sites is inhibited by protease inhibitors. The nicks or gaps induced by proteases can be demonstrated by nuclease S1 sensitivity of native DNA and by a change of the sedimentation rate of alkali-denatured DNA. The limit size of denatured DNA released after optimal protease treatment is 8.5 x 10(6) daltons (27 kilo bases). The molecular weight of the native DNA pieces released after nuclease S1 degradation of DNA containing the protease-induced nicks or gaps is in the same order indicating that the protease-sensitive sites are alternatively arranged on the opposite DNA strands at an average distance of 13.5 kilo base pairs. Since the protease-induced nicks or gaps in phosphatase-treated DNA are not attacked by Escherichia coli polymerase I, one or both ends liberated by the protease treatment must be blocked by a material other than phosphate groups. The results are most compatible with peptide/protein linkers joining adjacent single-strand DNA subunits. Alternative explanations such as alkali-stable RNA linkers, protein-protected RNA linkers, site-specific nuclease contaminations in the protease preparations or cellular nucleases activated by the protease treatment are eliminated by the results presented in this paper.

Animals↗

Analysis of the most tightly bound proteins in eukaryotic DNA.

DNA isolated by procedures generally considered to be most efficient for purifying DNA still contains detectable peptide components. The characteristics of this material and the stability of its linkage to DNA were investigated: DNA released from [35S]methionine-labelled cells by SDS in the presence of proteases contains a significant amount of 35S label which is not removed by additional treatment with proteases and phenol and which cosediments and cobands together with DNA on alkaline gradients. Furthermore, some peptide material which is copurified with native DNA and which remains complexed with DNA after alkali treatment can be labelled with 125I and analyzed on SDS-polyacrylamide-gels. The amino acid analysis of hydrolysates of purified DNA gives a rough estimate of the amount of the peptide material which is copurified with DNA. The results indicate that distinct proteins between 54 000 and 68 000 daltons in size are not removed from DNA by phenol, proteases, alkali or by any combination of these treatments. They can only be isolated by degradation of DNA. This extreme stability of the DNA-protein linkage indicates that these proteins are not merely contaminants which are difficult to eliminate but are rather covalently or otherwise bound (alkali-stable) to DNA. The size of these proteins and the stability of their linkage to DNA suggests that they are related to the class of non-histone proteins which are thought to be involved in chromatin structure e.g. by keeping DNA in a supercoiled state. Other possible functions are discussed.

Amino Acids↗