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 a double pendulums chain model, and DNA roto-torsional dynamics

It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an extension of this approach based on considering a chain of double pendulums with certain characteristics. Here we study a simplified model of this kind, focusing on its general features and nonlinear travelling wave excitations; in particular, we show that some of the degrees of freedom are actually slaved to others, allowing for an effective reduction of the relevant equations

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

Assessing the volcanic hazard for Rome. 40Ar/39Ar and In-SAR constraints on the most recent eruptive activity and present-day uplift at Colli Albani Volcanic District

We present new 40Ar/39Ar data which allow us to refine the recurrence time for the most recent eruptive activity occurred at Colli Albani Volcanic District (CAVD) and constrain its geographic area. Time elapsed since the last eruption (36 kyr) overruns the recurrence time (31 kyr) in the last 100 kyr. New interferometric synthetic aperture radar data, covering the years 1993–2010, reveal ongoing inflation with maximum uplift rates (>2 mm/yr) in the area hosting the most recent (<200 ka) vents, suggesting that the observed uplift might be caused by magma injection within the youngest plumbing system. Finally, we frame the present deformation within the structural pattern of the area of Rome, characterized by 50 m of regional uplift since 200 ka and by geologic evidence for a recent (<2000 years) switch of the local stress-field, highlighting that the precursors of a new phase of volcanic activity are likely occurring at the CAVD

Quit Playing With Your Watch: Perceptions Of Smartwatch Use

This study identified perceptions and social norms that may affect smartwatch adoption. Interviews were conducted to identify perceptions of smartwatch use and norms that might affect those perceptions. Smartwatch use was found to activate norms associated with wristwatch use – specifically, smartwatch users’ peers took offense to the users looking at their wristwatches. This study also found that norms prevent the use of smartwatches’ voice controls in public and various perceptions of smartwatch use and ownership

Pancreatic cystosis in cystic fibrosis. Sometimes a bike ride can help you decide

Pancreatic cystosis (PC) is an uncommon manifestation of pancreas involvement in cystic fibrosis (CF), characterized by the presence of multiple macrocysts partially or completely replacing pancreas. Only few reports are available from literature and management (surgery vs follow up) is commonly based on the presence of symptoms or complications due to local mass effect, although evidence-based recommendations are still not available. We here report the case of a young adult CF patient with PC, in which cardiopulmonary exercise testing (CPET) provided important information to be integrated to the radiological finding of inferior vena cava compression by the multicystic pancreas complex. Through the analysis of oxygen kinetic cardiodynamic phase pattern, CPET may be helpful to safely exclude significant mass effects on blood venous return and to improve the decision-making process on whether to consider surgery or not in patients with PC

Weierstrass's criterion and compact solitary waves

Weierstrass's theory is a standard qualitative tool for single degree of freedom equations, used in classical mechanics and in many textbooks. In this Brief Report we show how a simple generalization of this tool makes it possible to identify some differential equations for which compact and even semicompact traveling solitary waves exist. In the framework of continuum mechanics, these differential equations correspond to bulk shear waves for a special class of constitutive laws.Comment: 4 page