Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.

Synchronization reveals topological scales in complex networks

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular structures corresponding to well-defined communities of nodes emerge in different time scales, ordered in a hierarchical way. The analysis also provides a useful connection between synchronization dynamics, complex networks topology, and spectral graph analysis.

Auditory cues support place navigation in rats when associated with a visual cue.

Rats, like other crepuscular animals, have excellent auditory capacities and they discriminate well between different sounds [Heffner HE, Heffner RS, Hearing in two cricetid rodents: wood rats (Neotoma floridana) and grasshopper mouse (Onychomys leucogaster). J Comp Psychol 1985;99(3):275-88]. However, most experimental literature concerning spatial orientation almost exclusively emphasizes the use of visual landmarks [Cressant A, Muller RU, Poucet B. Failure of centrally placed objects to control the firing fields of hippocampal place cells. J Neurosci 1997;17(7):2531-42; and Goodridge JP, Taube JS. Preferential use of the landmark navigational system by head direction cells in rats. Behav Neurosci 1995;109(1):49-61]. To address the important issue of whether rats are able to achieve a place navigation task relative to auditory beacons, we designed a place learning task in the water maze. We controlled cue availability by conducting the experiment in total darkness. Three auditory cues did not allow place navigation whereas three visual cues in the same positions did support place navigation. One auditory beacon directly associated with the goal location did not support taxon navigation (a beacon strategy allowing the animal to find the goal just by swimming toward the cue). Replacing the auditory beacons by one single visual beacon did support taxon navigation. A multimodal configuration of two auditory cues and one visual cue allowed correct place navigation. The deletion of the two auditory or of the one visual cue did disrupt the spatial performance. Thus rats can combine information from different sensory modalities to achieve a place navigation task. In particular, auditory cues support place navigation when associated with a visual one.

Functional and topological characterization of transcriptional cooperativity in yeast

This work was supported by grants from Spanish Ministry of Science andInnovation (MICINN) BIO2011-22568 & BIO2008-205.

A topological view of the replicon.

The replication of circular DNA faces topological obstacles that need to be overcome to allow the complete duplication and separation of newly replicated molecules. Small bacterial plasmids provide a perfect model system to study the interplay between DNA helicases, polymerases, topoisomerases and the overall architecture of partially replicated molecules. Recent studies have shown that partially replicated circular molecules have an amazing ability to form various types of structures (supercoils, precatenanes, knots and catenanes) that help to accommodate the dynamic interplay between duplex unwinding at the replication fork and DNA unlinking by topoisomerases.

Tarracomap: Development of an archaeological application on Google Maps navigation System

This paper describes the result of a research about diverse areas of the information technology world applied to cartography. Its final result is a complete and custom geographic information web system, designed and implemented to manage archaeological information of the city of Tarragona. The goal of the platform is to show on a web-focused application geographical and alphanumerical data and to provide concrete queries to explorate this. Various tools, between others, have been used: the PostgreSQL database management system in conjunction with its geographical extension PostGIS, the geographic server GeoServer, the GeoWebCache tile caching, the maps viewer and maps and satellite imagery from Google Maps, locations imagery from Google Street View, and other open source libraries. The technology has been chosen from an investigation of the requirements of the project, and has taken great part of its development. Except from the Google Maps tools which are not open source but are free, all design has been implemented with open source and free tools.

Augmented state Kalman filtering for AUV navigation

Addresses the problem of estimating the motion of an autonomous underwater vehicle (AUV), while it constructs a visual map ("mosaic" image) of the ocean floor. The vehicle is equipped with a down-looking camera which is used to compute its motion with respect to the seafloor. As the mosaic increases in size, a systematic bias is introduced in the alignment of the images which form the mosaic. Therefore, this accumulative error produces a drift in the estimation of the position of the vehicle. When the arbitrary trajectory of the AUV crosses over itself, it is possible to reduce this propagation of image alignment errors within the mosaic. A Kalman filter with augmented state is proposed to optimally estimate both the visual map and the vehicle position

Topological origins of chromosomal territories.

Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.

Topological phases in small quantum Hall samples

Topological order has proven a useful concept to describe quantum phase transitions which are not captured by the Ginzburg-Landau type of symmetry-breaking order. However, lacking a local order parameter, topological order is hard to detect. One way to detect it is via direct observation of anyonic properties of excitations which are usually discussed in the thermodynamic limit, but so far has not been realized in macroscopic quantum Hall samples. Here we consider a system of few interacting bosons subjected to the lowest Landau level by a gauge potential, and theoretically investigate vortex excitations in order to identify topological properties of different ground states. Our investigation demonstrates that even in surprisingly small systems anyonic properties are able to characterize the topological order. In addition, focusing on a system in the Laughlin state, we study the robustness of its anyonic behavior in the presence of tunable finite-range interactions acting as a perturbation. A clear signal of a transition to a different state is reflected by the system's anyonic properties.