Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a pair is modelled by a harmonic potential, which becomes anharmonic when described in terms of the rotation angles; here we substitute to this different types of improved potentials, providing a more physical description of the H-bond mediated interactions between the bases. We focus in particular on soliton solutions; the Y model predicts the correct size of the nonlinear excitations supposed to model the ``transcription bubbles'', and this is essentially unchanged with the improved potential. Other features of soliton dynamics, in particular curvature of soliton field configurations and the Peierls-Nabarro barrier, are instead significantly changed

Sine-Gordon solitons, auxiliary fields, and singular limit of a double pendulums chain

We consider the continuum version of an elastic chain supporting topological and non-topological degrees of freedom; this generalizes a model for the dynamics of DNA recently proposed and investigated by ourselves. In a certain limit, the non-topological degrees of freedom are frozen, and the model reduces to the sine-Gordon equations and thus supports well-known topological soliton solutions. We consider a (singular) perturbative expansion around this limit and study in particular how the non-topological field assume the role of an auxiliary field. This provides a more general framework for the slaving of this degree of freedom on the topological one, already observed elsewhere in the context of the mentioned DNA model; in this framework one expects such phenomenon to arise in a quite large class of field-theoretical models.Comment: 18 pages, 2 figure

Solitons in the Yakushevich model of DNA beyond the contact approximation

The Yakushevich model of DNA torsion dynamics supports soliton solutions, which are supposed to be of special interest for DNA transcription. In the discussion of the model, one usually adopts the approximation $\ell_0 \to 0$, where $\ell_0$ is a parameter related to the equilibrium distance between bases in a Watson-Crick pair. Here we analyze the Yakushevich model without $\ell_0 \to 0$. The model still supports soliton solutions indexed by two winding numbers $(n,m)$; we discuss in detail the fundamental solitons, corresponding to winding numbers (1,0) and (0,1) respectively

On the geometry of lambda-symmetries, and PDEs reduction

We give a geometrical characterization of $\lambda$-prolongations of vector fields, and hence of $\lambda$-symmetries of ODEs. This allows an extension to the case of PDEs and systems of PDEs; in this context the central object is a horizontal one-form $\mu$, and we speak of $\mu$-prolongations of vector fields and $\mu$-symmetries of PDEs. We show that these are as good as standard symmetries in providing symmetry reduction of PDEs and systems, and explicit invariant solutions

Heterogeneous effects of spinoff foundations on the means of technology transfer: the role of past academic-industry collaborations

Focusing on the Italian population of academic entrepreneurs, we analyze the effect of establishing a spinoff firm on researchers' attitudes towards carrying out other activities in collaboration with firms, namely, co-publishing and co-patenting. We investigate the heterogeneity in this effect in terms of existing collaborations with firms in the pre-spinoff period. Using a counterfactual analysis on subgroups, we verify that academic entrepreneurs with previous publications with firms diminish their co-publishing and increase their co-patenting after founding a spinoff. Conversely, academic entrepreneurs who had no previous publications with firms increase their co-publishing and decrease their co-patenting. We maintain that such results are related to academics' learning processes connected with their previous technology transfer activities. The policy implications are related to technology transfer aims and contradict the idea that promoting spinoffs is an appropriate "one-size-fits-all" initiative

Poincare' normal forms and simple compact Lie groups

We classify the possible behaviour of Poincar\'e-Dulac normal forms for dynamical systems in $R^n$ with nonvanishing linear part and which are equivariant under (the fundamental representation of) all the simple compact Lie algebras and thus the corresponding simple compact Lie groups. The ``renormalized forms'' (in the sense of previous work by the author) of these systems is also discussed; in this way we are able to simplify the classification and moreover to analyze systems with zero linear part. We also briefly discuss the convergence of the normalizing transformations.Comment: 17 pages; minor corrections in revised versio

Competition between the Modulation Instability and Stimulated Brillouin Scattering in a Broadband Slow Light Device

We observe competition between the modulation instability (MI) and stimulated Brillouin scattering (SBS) in a 9.2-GHz broadband SBS slow light device, in which a standard 20-km-long single-mode LEAF fibre is used as the SBS medium. We find that MI is dominant and depletes most of the pump power when we use an intense pump beam at ~1.55 {\mu}m, where the LEAF fibre is anomalously dispersive. The dominance of the MI in the LEAF-fibre-based system suppresses the SBS gain, degrading the SBS slow light delay and limiting the SBS gain-bandwidth to 126 dB \cdot GHz. In a dispersion-shifted highly nonlinear fibre, the SBS slow light delay is improved due to the suppression of the MI, resulting in a gain-bandwidth product of 344 dB \cdot GHz, limited by our available pump power of 0.82 W