Numerical analysis of solitons profiles in a composite model for DNA to rsion dynamics

We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the Yakushevich model many features and results but it represents an improvement from both the conceptual and the phenomenological point of view. It provides a more realistic description of DNA and possibly a justification for the use of models which consider the DNA chain as uniform. It shows that the existence of solitons is a generic feature of the underlying nonlinear dynamics and is to a large extent independent of the detailed modelling of DNA. As opposite to the Yakushevich model, where it is needed to use an unphysical value for the torsion in order to induce the correct velocity of sound, the model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Yakushevich solitons, in a fully realistic range of all the physical parameters characterizing the DNA.Comment: 16 pages, 9 figure

Ricostruzione e visualizzazione 3D di un cervello da acquisizioni manuali di sezioni istologiche

In questo lavoro presentiamo il sistema di visualizzazione da noi sviluppato per la rappresentazione tridimensionale di dati medici, ricavati da acquisizioni manuali di un insieme di sezioni parallele di un cervello di primate. Le due principali tecniche discusse sono la ricostruzione della geometria nello spazio 3D e lo studio dei metodi di visualizzazione per poterla rappresentare insieme alle strutture sottocorticali (nel nostro caso cellule neuronali di diversa tipologia). Il lavoro è organizzato come segue: nella prima sezione delineiamo le problematiche che si riscontrano in una vasta classe di esperimenti di neurofisiologia e le ragioni che ci inducono a cercare una risposta ad alcuni di tali problemi. Nella sezione seguente indichiamo i metodi e le strategie utilizzati per la ricostruzione della geometria e la visualizzazione dell'intero complesso dei dati. Successivamente indichiamo i risultati finora raggiunti, supportati da alcune immagini esemplificatrici, e infine indichiamo quali sono le possibili e più interessanti linee di sviluppo futuro, soprattutto per quanto riguarda il modello di ricostruzione delle superfici

SOLITON PROPAGATION IN HOMOGENEOUS AND INHOMOGENEOUS MODELS FOR DNA TORSION DYNAMICS

The existence of solitonic excitations is a generic feature of a broad class of homogeneous models for nonlinear DNA internal torsional dynamics, but many properties of solitonic propagation depend on the actual model one is considering. In this paper we perform a detailed and comparative numerical investigation of the profiles and time evolution of solitons for two different models, the Yakushevich one and the more recent "composite" model of [1], and for two different choices of the potential describing the pairing interaction between bases (harmonic and Morse potential). We consider not only homogeneous DNA chains but also inhomogeneous ones (with sequence of bases corresponding to a real organism, the Human Adenovirus 2). We show that twist solitons can propagate in inhomogeneous chains over biologically significant distances. It is also shown that stable soliton propagation is possible for inhomogeneous chains when dissipation and an external force are present. On a more general level, our results in..

Twist solitons in complex macromolecules: from DNA to polyethylene

DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one first proposed by Peyrard and Bishop (and developed by Dauxois, Barbi, Cocco and Monasson among others), but support topological solitons. We recently developed a ``composite'' version of the Y model, in which the sugar-phosphate group and the base are described by separate degrees of freedom. This at the same time fits experimental data better than the simple Y model, and shows dynamical phenomena, which are of interest beyond DNA dynamics. Of particular relevance are the mechanism for selecting the speed of solitons by tuning the physical parameters of the non linear medium and the hierarchal separation of the relevant degrees of freedom in ``master'' and ``slave''. These mechanisms apply not only do DNA, but also to more general macromolecules, as we show concretely by considering polyethylene.Comment: New version substantially longer, with new applications to Polyethylene. To appear in "International Journal of Non-Linear Mechanics