STM study on the self-assembly of oligothiophene-based organic semiconductors

The self-assembly properties of a series of functionalized regioregular oligo(3-alkylthiophenes) were investigated by using scanning tunneling microscopy (STM) at the liquid-solid interface under ambient conditions. The characteristics of the 2-D crystals formed on the (0001) plane of highly ordered pyrolitic graphite (HOPG) strongly depend on the length of the p-conjugated oligomer backbone, on the functional groups attached to it, and on the alkyl substitution pattern on the individual thiophene units. Theoretical calculations were performed to analyze the geometry and electronic density of the molecular orbitals as well as to analyze the intermolecular interactions, in order to obtain models of the 2-D molecular ordering on the substrate.

Control of gene expression by modulated self-assembly

Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here, we capture the effects of modulated self-assembly in gene expression with a novel quantitative framework. We show that this mechanism provides precision and flexibility, two seemingly antagonistic properties, to the sensing of diverse cellular signals by systems that share common elements present in transcription factors like p53, NF-kappa B, STATs, Oct and RXR. Applied to the nuclear hormone receptor RXR, this framework accurately reproduces a broad range of classical, previously unexplained, sets of gene expression data and corroborates the existence of a precise functional regime with flexible properties that can be controlled both at a genome-wide scale and at the individual promoter level.

Assembly of viral genomes from metagenomes

Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.

About tree-depth

In this work I present recent scientific papers related to the concept of tree-depth: different characterizations, a game theoretic approach to it and recently discovered applications. The focus in this work is presenting all the ideas in a self-contained way, such that they can be easily understood with little previous knowledge. Apart from that all the ideas are presented in a homogeneous way with clear examples and all the lemmas, some of which didn’t have proofs in the papers, are presented with rigorous proofs.

Self-assembly of metallated TPP porphyrin by external dipyridyl ligands

Póster presentado en: XXII International Congress and General Assembly of the International Union of Crystallography (UICr), 22–30 Agosto 2011. Madrid, España

Self-assembly of metalloporphyrins: first TPP-bipy coordination polymer with CoII (TPP=meso-tetraphenylporphyrin and bipy=4,4´-bipyridine)

Póster presentado en: 11th International Symposium on Applied Bioinorganic Chemistry. 2-5 Diciembre 2011. Barcelona, España (ISABC 2011)

Self-assembly of iron TCPP (meso-tetra(4-carboxyphenyl)porphyrin) into a chiral 2D coordination polymer

Artículo Polyhedron 2011