The looping probability of random heteropolymers helps to understand the scaling properties of biopolymers

Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study the scaling properties of loop formation in polymers of the size of typical biological systems. Combining it with self--adjusting simulated--tempering simulations, we can calculate numerically the looping properties of several realizations of the random interactions within the chain. Differently from homopolymers, random heteropolymers display at different temperatures a continuous set of scaling exponents. The necessity of using self--averaging quantities makes finite--size effects dominant at low temperatures even for long polymers, shadowing the length--independent character of looping probability expected in analogy with homopolymeric globules. This could provide a simple explanation for the small scaling exponents found in experiments, for example in chromosome folding

Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin

Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square displacement of chromatin loci varies from a Rouse-like scaling to a more constrained subdiffusion, depending on cell type, genomic region and time scale. With a simple polymeric model, we show that such a Rouse-like dynamics occurs when the parameters of the model are chosen so that contacts are local along the chain, while in presence of non-local contacts, we observe subdiffusion at short time scales with exponents smaller than 0.5. Such exponents are independent of the detailed choice of the parameters and build a master curve that depends only on the mean locality of the resulting contacts. We compare the loop-extrusion model with a polymeric model with static links, showing that also in this case only the presence of nonlocal contacts can produce low-exponent subdiffusion. We interpret these results in terms of a simple analytical model

Geometries for Possible Kinematics

The algebras for all possible Lorentzian and Euclidean kinematics with $\frak{so}(3)$ isotropy except static ones are re-classified. The geometries for algebras are presented by contraction approach. The relations among the geometries are revealed. Almost all geometries fall into pairs. There exists $t \leftrightarrow 1/(\nu^2t)$ correspondence in each pair. In the viewpoint of differential geometry, there are only 9 geometries, which have right signature and geometrical spatial isotropy. They are 3 relativistic geometries, 3 absolute-time geometries, and 3 absolute-space geometries.Comment: 40 pages, 7 figure

Obvious enhancement of the total reaction cross sections for 27,28^{27,28}P with 28^{28}Si target and the possible relavent mechanisms

The reaction cross sections of $^{27,28}$P and the corresponding isotones on Si target were measured at intermediate energies. The measured reaction cross sections of the N=12 and 13 isotones show an abrupt increase at $$. The experimental results for the isotones with $Z\leq 14$ as well as $$P can be well described by the modified Glauber theory of the optical limit approach. The enhancement of the reaction cross section for $^{28}$P could be explained in the modified Glauber theory with an enlarged core. Theoretical analysis with the modified Glauber theory of the optical limit and few-body approaches underpredicted the experimental data of $^{27}$P. Our theoretical analysis shows that an enlarged core together with proton halo are probably the mechanism responsible for the enhancement of the cross sections for the reaction of $^{27}$P+$^{28}$Si.Comment: 16 pages, 5 figures, to be published in Phys.Rev.

Phenolic Characterisation and Antioxidant Capacity of Young Wines Made From Different Grape Varieties Grown in Helanshan Donglu Wine Zone (China)

The Helanshan Donglu wine zone (China) is one of the most successful wine region of China, and the phenolic characterisation and antioxidant capacity of the primarily young, monovarietal wines from there were evaluated. The result showed that Helanshan Donglu wines contained abundant phenolic compounds, especially flavan-3-ols, and possessed high antioxidant capacity. In different grape varieties, the phenolic profiles varied greatly in both red and white wines. For red wines, Cabernet Sauvignon represented the highest total phenols (2 631 mg/L GAE), total flavonoids (1 840.83 mg/L CTE) and antioxidant capacity. Gamay and Cabernet Gernischt possessed the highest total flavan-3-ols (1 108.08 mg/L CTE) and total anthocyanins (258.78 mg/L CGE). Amongst the white wines, Chardonnay and Chenin blanc showed the highest phenolic contents and antioxidant capacity. (+)-Catechin and (-)-epicatechin were dominant phenolic constituents in both the red and white wines. Gallic acid and salicylic acid were the second most abundant in red wines, while gentisic acid was the second most abundant in white wines

A comprehensive study of the open cluster NGC 6866

We present CCD $UBVRI$ photometry of the field of the open cluster NGC 6866. Structural parameters of the cluster are determined utilizing the stellar density profile of the stars in the field. We calculate the probabilities of the stars being a physical member of the cluster using their astrometric data and perform further analyses using only the most probable members. The reddening and metallicity of the cluster were determined by independent methods. The LAMOST spectra and the ultraviolet excess of the F and G type main-sequence stars in the cluster indicate that the metallicity of the cluster is about the solar value. We estimated the reddening $E(B-V)=0.074 \pm 0.050$ mag using the $U-B$ vs $B-V$ two-colour diagram. The distance modula, the distance and the age of NGC 6866 were derived as $\mu = 10.60 \pm 0.10$ mag, $d=1189 \pm 75$ pc and $t = 813 \pm 50$ Myr, respectively, by fitting colour-magnitude diagrams of the cluster with the PARSEC isochrones. The Galactic orbit of NGC 6866 indicates that the cluster is orbiting in a slightly eccentric orbit with $e=0.12$. The mass function slope $x=1.35 \pm 0.08$ was derived by using the most probable members of the cluster.Comment: 14 pages, including 16 figures and 7 tables, accepted for publication in MNRAS. Table 4 in the manuscript will be published electronicall

Mass Hierarchy Determination Using Neutrinos from Multiple Reactors

We report the results of Monte Carlo simulations of a medium baseline reactor neutrino experiment. The difference in baselines resulting from the 1 km separations of Daya Bay and Ling Ao reactors reduces the amplitudes of 1-3 oscillations at low energies, decreasing the sensitivity to the neutrino mass hierarchy. A perpendicular detector location eliminates this effect. We simulate experiments under several mountains perpendicular to the Daya Bay/Ling Ao reactors, considering in particular the background from the TaiShan and YangJiang reactor complexes. In general the hierarchy can be determined most reliably underneath the 1000 meter mountain BaiYunZhang, which is 44.5 km from Daya Bay. If some planned reactors are not built then nearby 700 meter mountains at 47-51 km baselines gain a small advantage. Neglecting their low overhead burdens, hills near DongKeng would be the optimal locations. We use a weighted Fourier transform to avoid a spurious dependence on the high energy neutrino spectrum and find that a neural network can extract quantities which determine the hierarchy marginally better than the traditional RL + PV.Comment: 22 pages, added details on the neural network (journal version

Modelling genome-wide topological associating domains in mouse embryonic stem cells

Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre. However, coarse-grained polymer models based on 5C data can be used to extract the single-cell conformations of single TADs. Here, we extend this approach to analyse around 2500 TADs in murine embryonic stem cells based on high-resolution Hi-C data. This allowed to predict the cell-to-cell variability in single contacts within genome-wide TADs and correlations between them. Based on these results, we predict that TADs are more similar to ideal chains than to globules in terms of their physical size and three-dimensional shape distribution. Furthermore, we show that their physical size and the degree of structural anisotropy of single TADs are correlated with the level of transcriptional activity of the genes that it harbours. Finally, we show that a large number of multiplets of genomic loci co-localize more often than expected by random, and these loci are particularly enriched in promoters, enhancers and CTCF-bound sites. These results provide the first genome-wide structural reconstruction of TADs using polymeric models obeying the laws of thermodynamics and reveal important universal trends in the correlation between chromosome structure and transcription