Fluid of fused spheres as a model for protein solution

In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the fused-sphere particles. The model can be used to study the non-spherical (or dimerized) proteins in solution. Thermodynamic quantities of the system are calculated using a modification of Wertheim's thermodynamic perturbation theory and the results compared with new Monte Carlo simulations under isobaric-isothermal conditions. In particular, we are interested in the liquid-liquid phase separation in such systems. The model fluid serves to evaluate the effect of the shape of the molecules, changing from spherical to more elongated (two fused spheres) ones. The results indicate that the effect of the non-spherical shape is to reduce the critical density and temperature. This finding is consistent with experimental observations for the antibodies of non-spherical shape.Comment: 12 pages, 5 figure

mRNA interactome capture in mammalian cells

Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates. In addition to determining the RBP catalog in a given biological system, mRNA interactome capture allows the examination of changes in protein-mRNA interactions in response to internal and external stimuli, altered cellular programs and disease

Fault slip rates for the active External Dinarides thrust-and-fold belt

We present estimates of slip rates for active faults in the External Dinarides. This thrust-and-fold belt formed in the Adria-Eurasia collision zone by the progressive formation of NE-dipping thrusts in the footwalls of older structures. We calculated the long-term horizontal velocity field, slip rates and related uncertainties for active faults using a thin-shell finite element method. We incorporated active faults with different effective fault frictions, rheological properties, appropriate geodynamic boundary conditions, laterally varying heat flow and topography. The results were obtained by comparing the modeled maximum compressive horizontal stress orientations with the World Stress Map database. The calculated horizontal velocities decrease from the southeastern External Dinarides to the northwestern parts of the thrust-and-fold belt. This spatial pattern is also evident in the long-term slip rates of active faults. The highest slip rate was obtained for the Montenegro active fault, while the lowest rates were obtained for active faults in northwestern Slovenia. Low slip rates, influenced by local active diapirism, are also characteristic for active faults in the offshore central External Dinarides. These findings are contradictory to the concept of Adria as an internally rigid, aseismic lithospheric block because the faults located in its interior release a part of the regional compressive stress. We merged the modeling results and available slip rate estimates to obtain a composite solution for slip rates

Earthquake rates inferred from active faults and geodynamics: the case of the External Dinarides

The goal of earthquake rate models is to define the long-term rate of seismicity above an established magnitude threshold. No earthquake rate models exist for the External Dinarides, although this area is prone to frequent earthquakes that have significant impacts on natural and human environments. In this study, we apply a tectonic/geodynamic approach to build a fault-based and a deformation-based earthquake rate model for the External Dinarides. The main difference between the two models is the inclusion of off-fault seismicity in the deformation-based earthquake rate model. We explore the impact of the moment-balancing uncertainties on the expected number of earthquakes above an established magnitude. The results show comparable earthquake rates for both input models. The slip rate, the elastic modulus and the seismogenic depth play important roles in the variability of earthquake rates, whereas the effects of the corner magnitude and the Gutenberg-Richter β parameter are insignificant. A comparison with the available historical seismic catalogue shows good agreement for MW>5.8 earthquakes

Influence of inherited geometry and fault history on the seismogenic activity and potential of strike-slip fault systems in NW Slovenia: the case study of the Ravne Fault

La zona di faglia Ravne è situata in un area di interazione fra due sistemi regionali di faglie con differente cinematica, entrambi collegati alla convergenza fra Adria e Eurasia: le faglie dinariche orientate NW-SE e le faglie del Sud-alpino orientate E-W. L’analisi di dati di geologia strutturale e di due sequenze sismiche recenti che hanno colpito l’area, ci permette di proporre un modello sismotettonico per la faglia di Ravne, che è stata interessata da diverse fasi tettoniche. La geometria originale e la storia evolutiva della zona di faglia svolgono un ruolo cruciale nella distribuzione recente dell’attività sismica e del potenziale sismogenetico dell’intera struttura. Infatti, la configurazione attuale della faglia Ravne, caratterizzata da fagliazione trascorrente su piani ad alto angolo a profondità crostali, è il risultato dell’iniziale geometria di un thrust orientato NW-SE e avente immersione verso NE, e della sua interazione con i piani di thrust diretti essenzialmente E-W. Partendo dai dati raccolti e tenendo in considerazione sia il quadro geodinamico che le relazioni empiriche, proponiamo tre possibili scenari con relativi potenziali sismogenetici per la possibile futura attività della faglia di Ravne

SHINE: Web Application for Determining the Horizontal Stress Orientation

Interpolating the orientation of the maximum horizontal compressive stress with a well-established procedure is fundamental in understanding the present-day stress field. This paper documents the design principles, strategies and architecture of SHINE (http://shine.rm.ingv.it/), a web-based application for determining the maximum horizontal compressive stress orientation. The interpolation using SHINE can be carried out from a global database or from a custom file uploaded by the user. SHINE satisfies the usability requirements by striving for effectiveness, efficiency and satisfaction as defined by the International Organization for Standardization (ISO) covering ergonomics of human-computer interactions. Our main goal was to build a web-based application with a strong “outside-in” strategy in order to make the interpolation technique available to a wide range of Earth Science disciplines. SHINE is an easy-to-use web application with a straightforward interface guaranteeing quick visualization of the results, which are downloadable in several formats. SHINE is offered as an easy and convenient web service encouraging global data sharing and scientific research collaboration. Within this paper, we present a possible use of SHINE, determining fault kinematics compatibility with respect to the present-day stress field

Towards a seismogenic source model of the Dinarides

Geology-based seismogenic source models are becoming the fundamental input for seismic hazard assessment at the scale of an entire country. In this work, we will illustrate in simple steps the complex process that leads from basic data to a fully-fledged seismogenic source model of the Dinaride thrust belt, running along coastal Croatia, Montenegro and part of Albania. We started from a layer of basic geological and structural data and explored a wide range of indicators of recent tectonic activity, such as drainage anomalies/diversions and displaced or warped geological markers. We then analyzed the interplay of these indicators with known or prospective tectonic structures. To the picture thus obtained, we added a layer with a revised historical seismic catalog and selected a few earthquakes for which we re-estimate epicenter and magnitude. At the end of our analyses we combined all these data in a structured GIS database. With these data at hand, we also compared the longer-term indicators with present-day stress/strain data such as GPS velocities and earthquake focal solutions. Following the approach already developed for the construction of the Database of Individual Seismogenic Sources for Italy, we developed a seismogenic source model for the Dinarides in which the better constrained seismogenic faults have been mapped and parameterized and made ready for use in seismic hazard practice. We believe that our experience in the Dinarides will become useful in unifying and formalizing the process of constructing seismic source models in other countries

Seismogenic sources of the Adriatic domain

We present an overview of the seismogenic source model of the Adriatic domain included in the latest version of the DISS database (http://diss.rm.ingv.it/diss/) and in the European SHARE database (http://diss.rm.ingv.it/SHARE/). The model consists of Composite and Individual Seismogenic Sources located inside and along the margins of the Adria plate. In order to locate and parameterize the sources, we integrated a wide set of geological, geophysical, seismological and geodynamic data, either available from published literature or resulting from our own field work, seismic profile interpretations and numerical modelling studies. We grouped the sources into five regions based on geometrical and kinematic homogeneity criteria. Seismogenic sources of the Central Western Adriatic, North-Eastern Adriatic, Eastern Adriatic and Central Adriatic regions belong to the Northern Apennines, External Dinarides and offshore domains, respectively. They are characterized by NWeSE strike, reverse to oblique kinematics and shallow crustal seismogenic depth. Seismogenic sources of the Southern Western Adriatic region instead are EeW striking, dextral strike-slip faults, cutting both the upper and lower crust. The fastest moving seismogenic sources are the most southern thrusts of the Eastern Adriatic and the strike-slip sources of the Southern Western Adriatic, while the seismogenic sources of the Central Adriatic exhibit the lowest slip rates. Estimates of maximum magnitude are generally in good agreement with the historical and instrumental earthquake records, except for the North-Eastern Adriatic region, where seismogenic sources exhibit a potential for large earthquakes even though no strong events have been reported or registered. All sources included in the database are fully geometrically and kinematically parameterized and can be incorportaed in seismic hazard calculations and earthquake or tsunami scenario simulations

Tsunamis scenarios in the Adriatic Sea

We calculated the expected impact on the Italian coast of the Adriatic Sea of a large set of tsunamis resulting from potential earthquakes generated by major fault zones. Our approach merges updated knowledge on the regional tectonics and scenario-like calculations of expected tsunami impact. We selected six elongated potential source zones. For each of them we determined a Maximum Credible Earthquake and the associated Typical Fault, described by its size, geometry and kinematics. We then let the Typical Fault float along strike of its parent source zone and simulated all tsunamis it could generate. Simulations are based on the solution of the nonlinear shallow water equations through a finite-difference technique. For each run we calculated the wave fields at specified simulation times and the maximum water height field (above mean sea level), then generated travel-time maps and maximum wave height profiles along the target coastline. Maxima were also classified in a three-level code of expected tsunami threat. We found that the southern portion of Apulia facing Albania and the Gargano promontory are especially prone to the tsunami threat. We also found that some bathymetric features are crucial in determining the focalization-defocalization of tsunami energy. We suggest that our results be taken into account in the design of early-warning strategies

Integrating geologic fault data into tsunami hazard studies

We present the realization of a fault-source data set designed to become the starting point in regional-scale tsunami hazard studies. Our approach focuses on the parametric fault characterization in terms of geometry, kinematics, and assessment of activity rates, and includes a systematic classification in six justification levels of epistemic uncertainty related with the existence and behaviour of fault sources. We set up a case study in the central Mediterranean Sea, an area at the intersection of the European, African, and Aegean plates, characterized by a complex and debated tectonic structure and where several tsunamis occurred in the past. Using tsunami scenarios of maximum wave height due to crustal earthquakes (Mw=7) and subduction earthquakes (Mw=7 and Mw=8), we illustrate first-order consequences of critical choices in addressing the seismogenic and tsunamigenic potentials of fault sources. Although tsunamis generated by Mw=8 earthquakes predictably affect the entire basin, the impact of tsunamis generated by Mw=7 earthquakes on either crustal or subduction fault sources can still be strong at many locales. Such scenarios show how the relative location/orientation of faults with respect to target coastlines coupled with bathymetric features suggest avoiding the preselection of fault sources without addressing their possible impact onto hazard analysis results