G-quartet biomolecular nanowires

We present a first-principle investigation of quadruple helix nanowires, consisting of stacked planar hydrogen-bonded guanine tetramers. Our results show that long wires form and are stable in potassium-rich conditions. We present their electronic bandstructure and discuss the interpretation in terms of effective wide-bandgap semiconductors. The microscopic structural and electronic properties of the guanine quadruple helices make them suitable candidates for molecular nanoelectronics.Comment: 7 pages, 3 figures, to be published in Applied Physics Letters (2002

First principle theory of correlated transport through nano-junctions

We report the inclusion of electron-electron correlation in the calculation of transport properties within an ab initio scheme. A key step is the reformulation of Landauer's approach in terms of an effective transmittance for the interacting electron system. We apply this framework to analyze the effect of short range interactions on Pt atomic wires and discuss the coherent and incoherent correction to the mean-field approach.Comment: 5 pages, 3 figure

Surface nano-patterning through styrene adsorption on Si(100)

We present an ab initio study of the structural and electronic properties of styrene molecules adsorbed on the dimerized Si(100) surface at different coverages, ranging from the single-molecule to the full monolayer. The adsorption mechanism primarily involves the vinyl group via a [2+2] cycloaddition process that leads to the formation of covalent Si-C bonds and a local surface derelaxation, while it leaves the phenyl group almost unperturbed. The investigation of the functionalized surface as a function of the coverage (e.g. 0.5 -- 1 ML) and of the substrate reconstruction reveals two major effects. The first results from Si dimer-vinyl interaction and concerns the controlled variation of the energy bandgap of the interface. The second is associated to phenyl-phenyl interactions, which gives rise to a regular pattern of electronic wires at surface, stemming from the pi-pi coupling. These findings suggest a rationale for tailoring the surface nano-patterning of the surface, in a controlled way.Comment: 19 pages (preprint), 4 figures, supplementary materia

Cochlear Implant Outcomes and Genetic Mutations in Children with Ear and Brain Anomalies

Background. Specific clinical conditions could compromise cochlear implantation outcomes and drastically reduce the chance of an acceptable development of perceptual and linguistic capabilities. These conditions should certainly include the presence of inner ear malformations or brain abnormalities. The aims of this work were to study the diagnostic value of high resolution computed tomography (HRCT) and magnetic resonance imaging (MRI) in children with sensorineural hearing loss who were candidates for cochlear implants and to analyse the anatomic abnormalities of the ear and brain in patients who underwent cochlear implantation. We also analysed the effects of ear malformations and brain anomalies on the CI outcomes, speculating on their potential role in the management of language developmental disorders. Methods. The present study is a retrospective observational review of cochlear implant outcomes among hearing-impaired children who presented ear and/or brain anomalies at neuroimaging investigations with MRI and HRCT. Furthermore, genetic results from molecular genetic investigations (GJB2/GJB6 and, additionally, in selected cases, SLC26A4 or mitochondrial-DNA mutations) on this study group were herein described. Longitudinal and cross-sectional analysis was conducted using statistical tests. Results. Between January 1, 1996 and April 1, 2012, at the ENT-Audiology Department of the University Hospital of Ferrara, 620 cochlear implantations were performed. There were 426 implanted children at the time of the present study (who were <18 years). Among these, 143 patients (64 females and 79 males) presented ear and/or brain anomalies/lesions/malformations at neuroimaging investigations with MRI and HRCT. The age of the main study group (143 implanted children) ranged from 9 months and 16 years (average = 4.4; median = 3.0). Conclusions. Good outcomes with cochlear implants are possible in patients who present with inner ear or brain abnormalities, even if central nervous system anomalies represent a negative prognostic factor that is made worse by the concomitant presence of cochlear malformations. Common cavity and stenosis of the internal auditory canal (less than 2 mm) are negative prognostic factors even if brain lesions are absent

Interplay of coarsening, aging, and stress hardening impacting the creep behavior of a colloidal gel

We explore the dynamical and mechanical characteristics of an evolving gel in diffusing wave spectroscopy (DWS) and rheometry, aiming to assess how the gel evolution impacts the creep response of the system. Our gel is formed by inducing the aggregation of thermosensitive colloids by a variation in temperature. We find experimental evidence that the long time evolution of this gel is due to two distinct processes: A coarsening process that involves the incorporation of mobile particles into the network structure and an aging process that triggers intermittent rearrangement events. While coarsening is the main process governing the evolution of the elastic properties of the gel, aging is the process determining structural relaxation. The combination of both processes in addition to stress hardening governs the creep behavior of the gel, a creep behavior that is determined by three distinct contributions: an instantaneous elastic, a delayed elastic, and a loss contribution. The systematic investigation of these contributions in recovery experiments provides evidence that losses and delayed elastic storage have a common origin, both being due to intermittent local structural relaxation events

Anisotropies of tactile distance perception on the face

The distances between pairs of tactile stimuli oriented across the width of the hand dorsum are perceived as about 40% larger than equivalent distances oriented along the hand length. Clear anisotropies of varying magnitudes have been found on different sites on the limbs and less consistently on other parts of the body, with anisotropies on the center of the forehead, but not on the belly. Reported anisotropies on the center of the forehead, however, might reflect an artefact of categorical perception from the face midline, which might be comparable to the expansion of tactile distance perception observed for stimuli presented across joint boundaries. To test whether tactile anisotropy is indeed a general characteristic of the tactile representation of the face, we assessed the perceived distance between pairs of touches on the cheeks and three locations on the forehead: left, right, and center. Consistent with previous results, a clear anisotropy was apparent on the center of the forehead. Importantly, similar anisotropies were also evident on the left and right sides of the forehead and both cheeks. These results provide evidence that anisotropy of perceived tactile distance is not a specific feature of tactile organization at the limbs but it also exists for the face, and further suggest that the spatial distortions found for tactile distances that extend across multiple body parts are not present for stimuli that extend across the body midline

Systems approaches and algorithms for discovery of combinatorial therapies

Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification of control parameters presents an extreme challenge due to the combinatorial explosion of control possibilities in combination therapy and to the incomplete knowledge of the systems biology of cells. In this review paper we describe the main current and proposed approaches to the design of combinatorial therapies, including the empirical methods used now by clinicians and alternative approaches suggested recently by several authors. New approaches for designing combinations arising from systems biology are described. We discuss in special detail the design of algorithms that identify optimal control parameters in cellular networks based on a quantitative characterization of control landscapes, maximizing utilization of incomplete knowledge of the state and structure of intracellular networks. The use of new technology for high-throughput measurements is key to these new approaches to combination therapy and essential for the characterization of control landscapes and implementation of the algorithms. Combinatorial optimization in medical therapy is also compared with the combinatorial optimization of engineering and materials science and similarities and differences are delineated.Comment: 25 page

Self-assembled guanine ribbons as wide-bandgap semiconductors

We present a first principle study about the stability and the electronic properties of a new biomolecular solid-state material, obtained by the self-assembling of guanine (G) molecules. We consider hydrogen-bonded planar ribbons in isolated and stacked configurations. These aggregates present electronic properties similar to inorganic wide-bandgap semiconductors. The formation of Bloch-type orbitals is observed along the stacking direction, while it is negligible in the ribbon plane. Global band-like conduction may be affected by a dipole-field which spontaneously arises along the ribbon axis. Our results indicate that G-ribbon assemblies are promising materials for biomolecular nanodevices, consistently with recent experimental results.Comment: 7 pages, 3 figures, to be published in Physica

Functional characterization of the sea urchin sns chromatin insulator in erythroid cells

Chromatin insulators are regulatory elements that determine domains of genetic functions. We have previously described the characterization of a 265 bp insulator element, termed sns, localized at the 3' end of the early historic H2A gene of the sea urchin Paracentrotus lividus. This sequence contains three cis-acting elements (Box A, Box B, and Box C+T) all needed for the enhancer-blocking activity in both sea urchin and human cells. The goal of this Study was to further characterize the sea urchin sns insulator in the erythroid environment. We employed colony assays in human (K562) and mouse (MEL) erythroid cell lines. We tested the capability of sns to interfere with the communication between the 5HS2 enhancer of the human beta-globin LCR and the gamma-globin promoter. We found that the sns sequence displays directional enhancer-blocking activity. By the use of antibodies against known DNA binding proteins, in electrophoretic mobility shift assays, we demonstrated the binding of the erythroid-specific GATA-1 and the ubiquitous Oct-1 and Sp1 transcription factors. These factors bind to Box A, Box B, and Box C+T, respectively, in both K562 and MEL nuclear extracts. These results may have significant implications for the conservation of insulator function ill evolutionary distant organisms and may prove to be of practical benefit in gene transfer applications for erythroid disorders such as hemoglobinopathies and thalassemias