3,848 research outputs found
Geometrical model for the native-state folds of proteins
No full textWe recently introduced a physical model [T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar, A. Maritan, Geometry and symmetry pre-sculpt the free energy landscape of proteins. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 7960-7964, J.R. Banavar, T.X. Hoang, A. Maritan, F. Seno, A. Trovato, A unified perspective on proteins-a physics approach. Phys. Rev., E 70 (2004) 041905] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and the role played by hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as broad competing minima in the free energy landscape even for a homopolymer. Here we show how the introduction of sequence heterogeneity using a simple scheme of just two types of amino acids, hydrophobic (H) and polar (P), and sequence design allows a selected putative native fold to become the free energy minimum at low temperature. The folding transition exhibits thermodynamic cooperativity, if one neglects the degeneracy between two different low energy conformations sharing the same fold topology
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
No full textThe prion-forming C-terminal domain of the fungal prion HET-s forms infectious amyloid fibrils at physiological pH. The conformational switch from the nonprion soluble form to the prion fibrillar form is believed to have a functional role, as HETs in its prion form participates in a recognition process of different fungal strains. On the basis of the knowledge of the high-resolution structure of the prion forming domain HET-s( 218-289) in its fibrillar form, we here present a numerical simulation of the fibril growth process, which emphasizes the role of the topological properties of the fibrillar structure. An accurate thermodynamic analysis of the way an intervening HET-s chain is recruited to the tip of the growing fibril suggests that elongation proceeds through a dock and lock mechanism. First, the chain docks onto the fibril by forming the longest beta-strands. Then, the re-arrangement in the fibrillar form of all the rest of the molecule takes place. Interestingly, we also predict that one side of the HET-s fibril is more suitable for sustaining its growth with respect to the other. The resulting strong polarity of fibril growth is a consequence of the complex topology of HET-s fibrillar structure, as the central loop of the intervening chain plays a crucially different role in favoring or not the attachment of the C-terminus tail to the fibril, depending on the growth side
Deformazioni oblique nel sistema orogenico Alpi-Appennino: vincoli cinematici
No full textLa continuità laterale delle catene orogeniche è caratteristicamente interrotta da lineamenti trasversali od obliqui la cui attività è coeva con la messa in posto delle principali unità tettoniche: tuttavia molte strutture trasversali sono riconducibili a discontinuità paleogeografiche ereditate da eventi pre-orogenici, oppure a deformazioni successive alle principali fasi di costruzione delle catene. I lineamenti trasversali gocano un ruolo importante nell’evoluzione dei sistemi orogenici in quanto spesso determinano variazioni significative nello stile della deformazione. Le peculiarità dei lineamenti trasversali possono essere messe in evidenza attraverso il contributo di studi multidisciplinari che combinano analisi strutturale, macrotettonica, geodinamica, indagini geofisiche e modellazioni sia numeriche che analogiche. In questo lavoro vengono illustrati i caratteri cinematici principali di alcuni lineamenti trasversali che interrompono la continuità laterale delle principali strutture compressive del sistema Alpi-Appennino. Sono analizzati nel dettaglio lineamenti trasversali presenti nelle Alpi Liguri, nell’Appennino settentrionale, nella zona di giunzione fra l’arco umbro-marchigiano e l’arco laziale-abruzzese ed infine strutture con cinematica complessa rinvenute lungo il limite fra l’Appennino centrale e l’Appennino meridionale. Le associazioni strutturali documentate per questi settori, la cui cinematica risulta estremamente complessa, forniscono la base analitica per un modello di deformazione che trova adeguata collocazione nei canoni della deformazione transpressiva.
Il confronto fra le strutture trasversali documentate in questo studio con analoghe associazioni rinvenute in sistemi transpressivi sia fossili che attivi indica che la presenza di lineamenti paleogeografici obliqui e/o trasversali rispetto alla direzione del trasporto tettonico ha determinato un significativo controllo nei processi di ripartizione della deformazione, caratteristici dei regimi tettonici transpressivi
Real-time Ethernet networks for motion control
No full textCommunication networks have been traditionally employed in motion control applications, especially within factory automation systems. While in the past they were merely used to exchange non time critical data (e.g. parameters and configuration data) nowadays they allow for much more powerful performance. In particular, the recently introduced Real Time Ethernet (RTE) networks, have been explicitly designed in order to cope with very tight time constraints in terms of both determinism and real--time. In this paper we focus on two popular RTE networks, namely Ethernet POWERLINK and EtherCAT, and provide an example of their employment for a coordinated motion control application. In particular, we consider the tracking of a circular trajectory by the coordinated motion of two independent axes where the velocity set--points are transmitted to the electrical drives implementing the axis control by means of the RTE networks. After providing some essential features of the two networks, we describe the configurations adopted for the coordinated motion control application. Then we check the effectiveness of the solution proposed by means of numerical simulations which take into consideration possible error scenarios deriving from the adoption of the communication networks such as transmission errors, communication delays and cable breaks
Complete phase diagram of DNA unzipping: Eye, Y fork and triple point
No full textWe study the unzipping of double stranded DNA by applying a pulling force at a fraction s (0 leq s leq 1) from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase diagram shows a strong ensemble dependence for various values of s. In addition, we show the existence of an eye phase and a triple point
Role of inherited compositional and structural heterogeneity in shear zone development at mid-low levels of the continental crust (the Anzola shear zone; Ivrea-Verbano Zone, Southern Alps)
No full textThe formation of shear zones is crucial to understand the deformation of the crust and the evolution of rifted margins. However, despite their intrinsic importance, a detailed characterization of the compositional and structural patterns of shear zones is often lacking, resulting in poorly constrained models of shear initiation. In this contribution, we reconstruct the pre-shearing lithological, structural and metamorphic proprieties of rocks forming a major, rift-related shear zone with the aim to assess the conditions promoting the strain localization. We focus on the Anzola shear zone, a major extensional structure from one of the best-preserved cross-sections through the middle to lower continental crust of a fossil passive margin, the Ivrea-Verbano Zone (Southern Alps, Italy). Until now, the Anzola shear zone is believed to have developed within a rheologically hard and isotropic gabbro rather than in the surrounding weaker and anisotropic volcano-sedimentary metamorphic sequence. New geological mapping shows that significant pre-existing heterogeneities related to the composition and deformation structures, characterize the Anzola shear zone. Field relationships and geochemistry reveal that the (ultra-)mylonitic rocks overprinted a multi-lithological sequence that have already experienced Variscan deformation and late Variscan High-Temperature metamorphism, at the boundary between amphibolite and granulite facies. Our in-depth trace elements study is shown to be a powerful tool in reconstructing the pre-shearing relationships between wall rocks and mylonites and determining the protoliths of tectonites. Estimated P-T conditions indicate that mylonitic deformation started at high temperature (~820 °C) with presence of melt and continued as solid-state deformation down to amphibolite facies (~650 °C), following a retrograde path. We argue that strain localization was promoted by the combination of rheological boundaries derived from pre-existing conditions, including: i) compositional and structural anisotropies of the volcano-sedimentary metamorphic sequence contrasted by ii) the close intrusion of a nearly isotropic gabbro and iii) the presence of melt within the metamorphic boundary depicted by the transition between granulites (dominated by anhydrous minerals) and amphibolite facies (dominated by hydrous minerals). Our findings finally suggest that pre-existing significant heterogeneities relate to rock composition, deformation and metamorphism represent the preferential loci for strain localization controlling the initiation and development of rift-related structures in the mid to lower crust of passive margins
Depositi post-orogeni dell'Oligocene inferiore interposti tra il Brianzonese e la "Pietra di Finale" (Alpi Liguri): conseguenze paleotettoniche e paleogeografiche. 33, 11-21.
No full textFrom field geology to paleogeographic and geodynamic reconstructions: the synergy of Luciano Cortesogno and Mario Vanossi.
No full textThe role of pre-alpine and Mesozoic tectonics in the present structures of the external sector of the Maritime Alps [Controllo della tettonica pre-alpina e mesozoica sull'assetto attuale dei settori esterni delle Alpi Marittime]
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