Pulse interaction via gain and loss dynamics in passive mode-locking

We study theoretically the effects of pulse interactions mediated by the gain and absorber dynamics in a passively mode-locked laser containing a slow saturable absorber, and operating in a regime with several pulses coexisting in the cavity

Hopf bifurcations in time-delay systems with band-limited feedback

We investigate the steady-state solution and its bifurcations in time-delay systems with band-limited feedback. This is a first step in a rigorous study concerning the effects of AC-coupled components in nonlinear devices with time-delayed feedback. We show that the steady state is globally stable for small feedback gain and that local stability is lost, generically, through a Hopf bifurcation for larger feedback gain. We provide simple criteria that determine whether the Hopf bifurcation is supercritical or subcritical based on the knowledge of the first three terms in the Taylor-expansion of the nonlinearity. Furthermore, the presence of double-Hopf bifurcations of the steady state is shown, which indicates possible quasiperiodic and chaotic dynamics in these systems. As a result of this investigation, we find that AC-coupling introduces fundamental differences to systems of Ikeda-type [Ikeda et al., Physica D 29 (1987) 223-235] already at the level of steady-state bifurcations, e.g. bifurcations exist in which limit cycles are created with periods other than the fundamental ``period-2'' mode found in Ikeda-type systems.Comment: 32 pages, 5 figures, accepted for publication in Physica D: Nonlinear Phenomen

Differential Geometry applied to Acoustics : Non Linear Propagation in Reissner Beams

Although acoustics is one of the disciplines of mechanics, its "geometrization" is still limited to a few areas. As shown in the work on nonlinear propagation in Reissner beams, it seems that an interpretation of the theories of acoustics through the concepts of differential geometry can help to address the non-linear phenomena in their intrinsic qualities. This results in a field of research aimed at establishing and solving dynamic models purged of any artificial nonlinearity by taking advantage of symmetry properties underlying the use of Lie groups. The geometric constructions needed for reduction are presented in the context of the "covariant" approach.Comment: Submitted to GSI2013 - Geometric Science of Informatio

Nucleosome repositioning via loop formation

Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by Schiessel et al. (H. Schiessel, J. Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. {\it Phys. Rev. Lett.} 86:4414-4417). The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model -- being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed and compared to existing experimental findings

Resonant helical deformations in nonhomogeneous Kirchhoff filaments

We study the three-dimensional static configurations of nonhomogeneous Kirchhoff filaments with periodically varying Young's modulus. This type of variation may occur in long tandemly repeated sequences of DNA. We analyse the effects of the Young's modulus frequence and amplitude of oscillation in the stroboscopic maps, and in the regular (non chaotic) spatial configurations of the filaments. Our analysis shows that the tridimensional conformations of long filaments may depend critically on the Young's modulus frequence in case of resonance with other natural frequencies of the filament. As expected, far from resonance the shape of the solutions remain very close to that of the homogeneous case. In the case of biomolecules, it is well known that various other elements, besides sequence-dependent effects, combine to determine their conformation, like self-contact, salt concentration, thermal fluctuations, anisotropy and interaction with proteins. Our results show that sequence-dependent effects alone may have a significant influence on the shape of these molecules, including DNA. This could, therefore, be a possible mechanical function of the ``junk'' sequences.Comment: 18 pages (twocolumn), 5 figures Revised manuscrip

Frequency locking of modulated waves

We consider the behavior of a modulated wave solution to an $\mathbb{S}^1$-equivariant autonomous system of differential equations under an external forcing of modulated wave type. The modulation frequency of the forcing is assumed to be close to the modulation frequency of the modulated wave solution, while the wave frequency of the forcing is supposed to be far from that of the modulated wave solution. We describe the domain in the three-dimensional control parameter space (of frequencies and amplitude of the forcing) where stable locking of the modulation frequencies of the forcing and the modulated wave solution occurs. Our system is a simplest case scenario for the behavior of self-pulsating lasers under the influence of external periodically modulated optical signals