Fluctuations of Complex Networks: Electrical Properties of Single Protein Nanodevices

We present for the first time a complex network approach to the study of the electrical properties of single protein devices. In particular, we consider an electronic nanobiosensor based on a G-protein coupled receptor. By adopting a coarse grain description, the protein is modeled as a complex network of elementary impedances. The positions of the alpha-carbon atoms of each amino acid are taken as the nodes of the network. The amino acids are assumed to interact electrically among them. Consequently, a link is drawn between any pair of nodes neighboring in space within a given distance and an elementary impedance is associated with each link. The value of this impedance can be related to the physical and chemical properties of the amino acid pair and to their relative distance. Accordingly, the conformational changes of the receptor induced by the capture of the ligand, are translated into a variation of its electrical properties. Stochastic fluctuations in the value of the elementary impedances of the network, which mimic different physical effects, have also been considered. Preliminary results concerning the impedance spectrum of the network and its fluctuations are presented and discussed for different values of the model parameters.Comment: 16 Pages and 10 Figures published in SPIE Proceedings of the II International Symposium on Fluctuation and Noise, Maspalomas,Gran Canaria,Spain, 25-28 May 200

Insights into ALS pathomechanisms:from flies to humans

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease causing the death of motor neurons with consequent muscle atrophy and paralysis. Several neurodegenerative diseases have been modeled in Drosophila and genetic studies on this model organism led to the elucidation of crucial aspects of disease mechanisms. ALS, however, has lagged somewhat behind possibly because of the lack of a suitable genetic model. We were the first to develop a fly model for ALS and over the last few years, we have implemented and used this model for a large scale, unbiased modifier screen. We also report an extensive bioinformatic analysis of the genetic modifiers and we show that most of them are associated in a network of interacting genes controlling known as well as novel cellular processes involved in ALS pathogenesis. A similar analysis for the human homologues of the Drosophila modifiers and the validation of a subset of them in human tissues confirm and expand the significance of the data for the human disease. Finally, we analyze a possible application of the model in the process of therapeutic discovery in ALS and we discuss the importance of novel “non-obvious” models for the disease

Modelization of Thermal Fluctuations in G Protein-Coupled Receptors

We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently, we have proposed a model based on a coarse graining description, which describes the protein as a network of elementary impedances. The network is built from the knowledge of the positions of the C-alpha atoms of the amino acids, which represent the nodes of the network. Since the elementary impedances are taken depending of the inter-nodes distance, the conformational change of the receptor induced by the capture of the ligand results in a variation of the network impedance. On the other hand, the fluctuations of the atomic positions due to thermal motion imply an impedance noise, whose level is crucial to the purpose of an electrical detection of the ligand capture by the GPCR. Here, in particular, we address this issue by presenting a computational study of the impedance noise due to thermal fluctuations of the atomic positions within a rhodopsin molecule. In our model, the C-alpha atoms are treated as independent, isotropic, harmonic oscillators, with amplitude depending on the temperature and on the position within the protein (alpha-helix or loop). The relative fluctuation of the impedance is then calculated for different temperatures.Comment: 5 pages, 2 figures, Proceeding of the 18-th International Conference on Fluctuations and Noise, 19-23 September 2005, Salamanca, Spain -minor proofreadings

Dispersal of larval and juvenile seabream: Implications for Mediterranean marine protected areas

In the marine context, information about dispersal is essential for the design of networks of marine protected areas (MPAs). Generally, most of the dispersal of demersal fishes is thought to be driven by the transport of eggs and larvae in currents, with the potential contribution of dispersal in later life stages relatively minimal.Using otolith chemistry analyses, we estimate dispersal patterns across a spatial scale of approximately 180. km at both propagule (i.e. eggs and larvae) and juvenile (i.e. between settlement and recruitment) stages of a Mediterranean coastal fishery species, the two-banded seabream Diplodus vulgaris. We detected three major natal sources of propagules replenishing local populations in the entire study area, suggesting that propagule dispersal distance extends to at least 90. km. For the juvenile stage, we detected dispersal of up to 165. km. Our work highlights the surprising and significant role of dispersal during the juvenile life stages as an important mechanism connecting populations. Such new insights are crucial for creating effective management strategies (e.g. MPAs and MPA networks) and to gain support from policymakers and stakeholders, highlighting that MPA benefits can extend well beyond MPA borders, and not only via dispersal of eggs and larvae, but also through movement by juveniles

Resistance and Resistance Fluctuations in Random Resistor Networks Under Biased Percolation

We consider a two-dimensional random resistor network (RRN) in the presence of two competing biased percolations consisting of the breaking and recovering of elementary resistors. These two processes are driven by the joint effects of an electrical bias and of the heat exchange with a thermal bath. The electrical bias is set up by applying a constant voltage or, alternatively, a constant current. Monte Carlo simulations are performed to analyze the network evolution in the full range of bias values. Depending on the bias strength, electrical failure or steady state are achieved. Here we investigate the steady-state of the RRN focusing on the properties of the non-Ohmic regime. In constant voltage conditions, a scaling relation is found between $/_0$ and $V/V_0$, where $$ is the average network resistance, $_0$ the linear regime resistance and $V_0$ the threshold value for the onset of nonlinearity. A similar relation is found in constant current conditions. The relative variance of resistance fluctuations also exhibits a strong nonlinearity whose properties are investigated. The power spectral density of resistance fluctuations presents a Lorentzian spectrum and the amplitude of fluctuations shows a significant non-Gaussian behavior in the pre-breakdown region. These results compare well with electrical breakdown measurements in thin films of composites and of other conducting materials.Comment: 15 figures, 23 page

Intrinsic vulnerability assessment of the south-eastern Murge (Apulia, southern Italy)

Maps of areas with different vulnerability degrees are an integral part of environmental protection and management policies. It is difficult to assess the intrinsic vulnerability of karst areas since the stage and type of karst structure development and its related underground discharge behaviour are not easy to determine. Therefore, some improvements, which take into account dolines, caves and superficial lineament arrangement, have been integrated into the SINTACS R5 method and applied to a karst area of the south-eastern Murge (Apulia, southern Italy). The proposed approach integrates the SINTACS model giving more weight to morphological and structural data; in particular the following parameters have been modified: depth to groundwater, effective infiltration action, unsaturated zone attenuation capacity and soil/overburden attenuation capacity. Effective hydrogeological and impacting situations are also arranged using superficial lineaments and karst density. In order to verify the reliability of the modified procedure, a comparison is made with the original SINTACS R5 index evaluated in the same area. The results of both SINTACS index maps are compared with karst and structural features identified in the area and with groundwater nitrate concentrations recorded in wells. The best fitting SINTACS map is then overlaid by the layout of potential pollution centres providing a complete map of the pollution risk in the area

Stationary Regime of Random Resistor Networks Under Biased Percolation

The state of a 2-D random resistor network, resulting from the simultaneous evolutions of two competing biased percolations, is studied in a wide range of bias values. Monte Carlo simulations show that when the external current $I$ is below the threshold value for electrical breakdown, the network reaches a steady state with a nonlinear current-voltage characteristic. The properties of this nonlinear regime are investigated as a function of different model parameters. A scaling relation is found between $/_0$ and $I/I_0$, where $$ is the average resistance, $_0$ the linear regime resistance and $I_0$ the threshold value for the onset of nonlinearity. The scaling exponent is found to be independent of the model parameters. A similar scaling behavior is also found for the relative variance of resistance fluctuations. These results compare well with resistance measurements in composite materials performed in the Joule regime up to breakdown.Comment: 9 pages, revtex, proceedings of the Merida Satellite Conference STATPHYS2

Tuning the Correlation Decay in the Resistance Fluctuations of Multi-Species Networks

A new network model is proposed to describe the $1/f^\alpha$ resistance noise in disordered materials for a wide range of $\alpha$ values ($0< \alpha < 2$). More precisely, we have considered the resistance fluctuations of a thin resistor with granular structure in different stationary states: from nearly equilibrium up to far from equilibrium conditions. This system has been modelled as a network made by different species of resistors, distinguished by their resistances, temperature coefficients and by the energies associated with thermally activated processes of breaking and recovery. The correlation behavior of the resistance fluctuations is analyzed as a function of the temperature and applied current, in both the frequency and time domains. For the noise frequency exponent, the model provides $0< \alpha < 1$ at low currents, in the Ohmic regime, with $\alpha$ decreasing inversely with the temperature, and $1< \alpha <2$ at high currents, in the non-Ohmic regime. Since the threshold current associated with the onset of nonlinearity also depends on the temperature, the proposed model qualitatively accounts for the complicate behavior of $\alpha$ versus temperature and current observed in many experiments. Correspondingly, in the time domain, the auto-correlation function of the resistance fluctuations displays a variety of behaviors which are tuned by the external conditions.Comment: 26 pages, 16 figures, Submitted to JSTAT - Special issue SigmaPhi200

Shot Noise in Linear Macroscopic Resistors

We report on a direct experimental evidence of shot noise in a linear macroscopic resistor. The origin of the shot noise comes from the fluctuation of the total number of charge carriers inside the resistor associated with their diffusive motion under the condition that the dielectric relaxation time becomes longer than the dynamic transit time. Present results show that neither potential barriers nor the absence of inelastic scattering are necessary to observe shot noise in electronic devices.Comment: 10 pages, 5 figure

ARCHAEOLOGICAL MATERIALS FROM GABII (CENTRAL ITALY): KNOWLEDGE OF OFFERINGS AND RITUALS AT THE INFANT BURIALS THROUGH AN INTEGRATED APPROACH

The ancient Latin city of Gabii is situated 18 km (11.2 miles) to the east of Rome (Central Italy) along the modern Via Prenestina. Gabii was a renowned city in Roman times, particularly during the Republican period and there are various influences in the site that can be identified in Roman culture itself. Gabii is also one of the most significant and important archaeological sites in the territory of the Municipality of Rome and due to its characteristics, it represents today an extraordinary research context. From the excavations carried out in the past it is possible to see how, under the soil, the main structures and buildings of the ancient city are still largely preserved. Among the various testimonies of the past, the tombs, and the micro and macro remains that these contain, represent an opportunity to investigate such practices in the context of Early Iron Age and Orientalizing Latium. In particular, the finds from the Area D baby burials of Gabii enriched the existing dataset so far significantly, allowing us to explore funerary ritual behavior in a more systematic way. This work reports the results of the detailed examination of four tombs (Tombs 30, 50, 51 and 52) of archaeological site. The field strategy for the excavation of the tombs was geared from the start towards both the systematic retrieval of archaeobotanical and zooarchaeological remains and the sampling for organic residue analysis. Aiming for total recovery, the sediments from the tomb fills were sifted in their entirety as their stratigraphic excavation progressed, and samples were taken for flotation. This careful screening allowed for the detection of concentrations of organic material that represent plant and/or animal depositions. The excavation and removal of the grave goods was carried out following strict protocols for residue sampling, minimizing the risk of organic contamination. Samples were analysed by High Temperature Gas Chromatography/Mass Spectrometry (HTGC/MS) and Gas chromatography/Combustion/Isotope ratio mass spectrometry (GC-C-IRMS). For each burial, a subset of vessels including both closed and open shapes was selected, such as cups, open bowl without foot, amphoretta, amphora with dots, Kantharos, plate on a foot, olla, and olpe in bucchero. The results demonstrate the still largely unexploited potential of this sort of integrated studies, encouraging us to expand the application of chemical methods to contexts from other well–controlled excavations