Tightness of slip-linked polymer chains

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops which can exchange length between each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip-links it incorporates and its competition with other segments. When self-avoiding interactions are included, scaling arguments can be used to predict the statistics of segment sizes for certain paraknot configurations.Comment: 10 pages, 6 figures, REVTeX

Dark matter production from cosmic necklaces

Cosmic strings have gained a great interest, since they are formed in a large class of brane inflationary models. The most interesting story is that cosmic strings in brane models are distinguished in future cosmological observations. If the strings in brane models are branes or superstrings that can move along compactified space, and also if there are degenerated vacua along the compactified space, kinks interpolate between degenerated vacua become ``beads'' on the strings. In this case, strings turn into necklaces. In the case that the compact manifold in not simply connected, a string loop that winds around a nontrivial circle is stable due to the topological reason. Since the existence of the (quasi-)degenerated vacua and the nontrivial circle is a common feature of the brane models, it is important to study cosmological constraints on the cosmic necklaces and the stable winding states. In this paper, we consider dark matter production from loops of the cosmic necklaces. Our result suggests that necklaces can put stringent bound on certain kinds of brane models.Comment: 27 pages, 5 figures, added many comments and 3 figures, accepted for publication in JCA

Cosmic Necklaces from String Theory

We present the properties of a cosmic superstring network in the scenario of flux compactification. An infinite family of strings, the (p,q)-strings, are allowed to exist. The flux compactification leads to a string tension that is periodic in 'p'. Monopoles, appearing here as beads on a string, are formed in certain interactions in such networks. This allows bare strings to become cosmic necklaces. We study network evolution in this scenario, outlining what conditions are necessary to reach a cosmologically viable scaling solution. We also analyze the physics of the beads on a cosmic necklace, and present general conditions for which they will be cosmologically safe, leaving the network's scaling undisturbed. In particular, we find that a large average loop size is sufficient for the beads to be cosmologically safe. Finally, we argue that loop formation will promote a scaling solution for the interbead distance in some situations.Comment: 14 pages, 5 figures; v3, typos corrected, comments added, published versio

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

Primordial black holes from cosmic necklaces

Cosmic necklaces are hybrid topological defects consisting of monopoles and strings. We argue that primordial black holes(PBHs) may have formed from loops of the necklaces, if there exist stable winding states, such as coils and cycloops. Unlike the standard scenario of PBH formation from string loops, in which the kinetic energy plays important role when strings collapse into black holes, the PBH formation may occur in our scenario after necklaces have dissipated their kinetic energy. Then, the significant difference appears in the production ratio. In the standard scenario, the production ratio $f$ becomes a tiny fraction $f\sim 10^{-20}$, however it becomes $f \sim 1$ in our case. On the other hand, the typical mass of the PBHs is much smaller than the standard scenario, if they are produced in the same epoch. As the two mechanisms may work at the same time, the necklaces may have more than one channel of the gravitational collapse. Although the result obtained in this paper depends on the evolution of the dimensionless parameter $r$, the existence of the winding state could be a serious problem in some cases. Since the existence of the winding state in brane models is due to the existence of a non-tivial circle in the compactified space, the PBH formation can be used to probe the structure of the compactified space. Black holes produced by this mechanism may have peculiar properties.Comment: 22pages, 3 figures, added many comments, +1 figure, accepted for publication in JHE