Order-by-Disorder in the XY Pyrochlore Antiferromagnet Revisited

We investigate the properties of the XY pyrochlore antiferromagnet with local planar anisotropy. We find the ground states and show that the configurational ground state entropy is subextensive. By computing the free energy due to harmonic fluctuations and by carrying out Monte Carlo simulations, we confirm earlier work indicating that the model exhibits thermal order-by-disorder leading to low temperature long-range order consisting of discrete magnetic domains. We compute the spin wave spectrum and show that thermal and quantum fluctuations select the same magnetic structure. Using Monte Carlo simulations, we find that the state selected by thermal fluctuations in this XY pyrochlore antiferromagnet can survive the addition of sufficiently weak nearest-neighbor pseudo-dipolar interactions to the spin Hamiltonian. We discuss our results in relation to the Er2Ti2O7 pyrochlore antiferromagnet.Comment: 13 pages, 6 figure

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes.

Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid

Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness

DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional directed walk'. Motivated by a recent experiment on single lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the torsional directed walk problem and solve it analytically in the appropriate force regime. Our technique affords a direct physical determination of the microscopic twist stiffness C and twist-stretch coupling D relevant for DNA functionality. The theory quantitatively fits existing experimental data for relative extension as a function of overtwist over a wide range of applied force; fitting to the experimental data yields the numerical values C=120nm and D=50nm. Future experiments will refine these values. We also predict that the phenomenon of reduction of effective twist stiffness by bend fluctuations should be testable in future single-molecule experiments, and we give its analytic form.Comment: Plain TeX, harvmac, epsf; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.Comment: 13 pages, 5 figure

Effects of supercoiling on enhancer-promoter contacts.

Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer-promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains

Validation of differential pulse polarographic method of ascorbic acid assay in food – Comparison with the chromatographic reference method

The objective of the study was to demonstrate the applicability of differential pulse polarography (DPP) technique of the ascorbic acid (AA) assay for the analysis of food samples with various matrices. The following validation parameters were determined: selectivity, linearity, precision, accuracy, limit of detection, and limit of quantification. The limits of detection and quantification were 0.17 and 0.5 mg ascorbic acid per 100 g food, respectively. The average recovery of added ascorbic acid from all matrices was 96.3–103.6%. The values of the coefficient of variation calculated on the basis of AA contents for food matrices were in the range 2–9.26% and Horrat values were 0.37–1.10. Ascorbic acid values of the samples obtained from the polarographic method were compared with those obtained from high-performance liquid chromatography with diode-array detection (HPLC-DAD) used as the reference method. The analytical parameters determined showed that the polarographic method was equivalent to the chromatographic method. Validation of the polarographic method of ascorbic acid assay indicates that it can be applied for the analysis of ascorbic acid concentration in food products that do not contain isoascorbic acid. This means that the method can be recommended for routine determinations

Studies of global and local entanglements of individual protein chains using the concept of knotoids.

We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn't require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.

Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres. The pushing direction is such that within each topologically associating domain (TAD) cohesin rings forming handcuffs move from the source of supercoiling, constituted by RNA polymerase with associated DNA topoisomerase TOP1, towards borders of TADs, where supercoiling is released by topoisomerase TOPIIB. Cohesin handcuffs are pushed by continuous flux of supercoiling that is generated by transcription and is then progressively released by action of TOPIIB located at TADs borders. Our model explains what can be the driving force of chromatin loop extrusion and how it can be ensured that loops grow quickly and in a good direction. In addition, the supercoiling-driven loop extrusion mechanism is consistent with earlier explanations proposing why TADs flanked by convergent CTCF binding sites form more stable chromatin loops than TADs flanked by divergent CTCF binding sites. We discuss the role of supercoiling in stimulating enhancer promoter contacts and propose that transcription of eRNA sends the first wave of supercoiling that can activate mRNA transcription in a given TAD

Promotion of cultural heritage — regional and traditional Polish meat products

The diverse culinary heritage of various countries in the European Union (EU) has been attracting attention for a very long time. This type of high-quality traditional food should be fully exploited and promoted as a common good that is part of the history of given countries. In order to distinguish individual products and their value (not only cultural, but also qualitative), the EU created special awarding signs (quality schemes) that conform to the quality of traditional products: Protected Designation of Origin (PDO), Protected Geographical Indication (PGI), or Traditional Speciality Guaranteed (TSG). One of the first associations with Polish cuisine would undoubtedly be meat dishes, which play an important role in preserving the tradition. The most popular types of meat in Poland are pork, beef, and then poultry. In addition, game animals are very popular, including wild birds (black grouse and larks). This type of dishes is prepared according to traditional recipes handed down from generation to generation. Products typical of the region obtained from local crops and animal breeding are used in their preparation. Thanks to this, traditional dishes acquire specific taste values, which cannot be recreated in other parts of the country