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We consider the theory of \emph{twisted symmetries} of differential equations, in particular $\lambda$ and $\mu$-symmetries, and discuss their geometrical content. We focus on their interpretation in terms of gauge transformations on the one hand, and of coverings on the other one.

In a previous paper we have discussed how the Landau potential (entering in Landau theory of phase transitions) can be simplified using the Poincar\'e normalization procedure. Here we apply this approach to the Landau-deGennes functional for the isotropic-nematic transitions, and transitions between different nematic phases, in liquid crystals. {We give special attention to applying our method in the region near the main transition point, showing in full detail how this can be done via a suitable simple modification of our Poincar\'e-like method. We also consider the question if biaxial phases can branch directly off the fully symmetric state; some partial results in this direction are presented.

We discuss a procedure to simplify the Landau potential, based on Michel's reduction to orbit space and Poincar\'e normalization procedure; and illustrate it by concrete examples. The method makes use, as in Poincar\'e theory, of a chain of near-identity coordinate transformations with homogeneous generating functions; using Michel's insight, one can work in orbit space. It is shown that it is possible to control the choice of generating functions so to obtain a (in many cases, substantial) simplification of the Landau polynomial, including a reduction of the parameters it depends on. Several examples are considered in detail.

We specialize Olver's and Rosenau's side condition heuristics for the determination of particular invariant sets of ordinary differential equations. It turns out that side conditions of so-called LaSalle type are of special interest. Moreover we put side condition properties of symmetric and partially symmetric equations in a wider context. In the final section we present an application to parameter-dependent systems, in particular to quasi-steady state for chemical reactions., Comment: To appear in J. of Lie Theory

When we consider a differential equation $\Delta=0$ whose set of solutions is ${{\cal S}}_\Delta$, a Lie-point exact symmetry of this is a Lie-point invertible transformation $T$ such that $T({{\cal S}}_\Delta)={{\cal S}}_\Delta$, i.e. such that any solution to $\Delta=0$ is tranformed into a (generally, different) solution to the same equation; here we define {\it partial} symmetries of $\Delta=0$ as Lie-point invertible transformations $T$ such that there is a nonempty subset ${{\cal P}} \subset {{\cal S}}_\Delta$ such that $T({{\cal P}}) = {{\cal P}}$, i.e. such that there is a subset of solutions to $\Delta=0$ which are transformed one into the other. We discuss how to determine both partial symmetries and the invariant set ${{\cal P}} \subset {{\cal S}}_\Delta$, and show that our procedure is effective by means of concrete examples. We also discuss relations with conditional symmetries, and how our discussion applies to the special case of dynamical systems. Our discussion will focus on continuous Lie-point partial symmetries, but our approach would also be suitable for more general classes of transformations; the discussion is indeed extended to partial generalized (or Lie-B\"acklund) symmetries along the same lines, and in the appendix we will discuss the case of discrete partial symmetries., Comment: 29 pages, no figures

We discuss how the presence of a suitable symmetry can guarantee the perturbative linearizability of a dynamical system - or a parameter dependent family - via the Poincar\'e Normal Form approach. We discuss this at first formally, and later pay attention to the convergence of the linearizing procedure. We also discuss some generalizations of our main result, Comment: 19 pages, no figures

Symmetry properties are at the basis of integrability. In recent years, it appeared that so called "twisted symmetries" are as effective as standard symmetries in many respects (integrating ODEs, finding special solutions to PDEs). Here we discuss how twisted symmetries can be used to detect integrability of Lagrangian systems which are not integrable via standard symmetries.

We report on numerical investigations concerning the propagation of solitons in a real DNA chain (the Human Adenovirus 2) using a realistic model of DNA torsional dynamics; this takes fully into account the inhomogeneities in the real chain. We find that twist solitons propagate for considerable distances (2-10 times their diameters) before stopping due to phonon emission. Our results show that twist solitons may exist in real DNA chains; and on a more general level that solitonic propagation can take place in highly inhomogeneous media., Comment: 6 pages, 3 figures

We consider generalized (possibly depending on fields as well as on space-time variables) gauge transformations and gauge symmetries in the context of general -- that is, possibly non variational nor covariant -- differential equations. In this case the relevant principal bundle admits the first jet bundle (of the phase manifold) as an associated bundle, at difference with standard Yang-Mills theories. We also show how in this context the recently introduced operation of $\mu$-prolongation of vector fields (which generalizes the $\la$-prolongation of Muriel and Romero), and hence $\mu$-symmetries of differential equations, arise naturally. This is turn suggests several directions for further development. S0ome detailed examples are also given., Comment: 34 pages; PDF file 326 K. To appear in JGP

Nicodemi and Prisco recently proposed a model for X-chromosome inactivation in mammals, explaining this phenomenon in terms of a spontaneous symmetry-breaking mechanism [{\it Phys. Rev. Lett.} 99 (2007), 108104]. Here we provide a mean-field version of their model.

We give a version of Noether theorem adapted to the framework of mu-symmetries; this extends to such case recent work by Muriel, Romero and Olver in the framework of lambda-symmetries, and connects mu-symmetries of a Lagrangian to a suitably modified conservation law. In some cases this "mu-conservation law'' actually reduces to a standard one; we also note a relation between mu-symmetries and conditional invariants. We also consider the case where the variational principle is itself formulated as requiring vanishing variation under mu-prolonged variation fields, leading to modified Euler-Lagrange equations. In this setting mu-symmetries of the Lagrangian correspond to standard conservation laws as in the standard Noether theorem. We finally propose some applications and examples., Comment: 28 pages, to appear in J. Phys. A

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 figures

We propose a mechanism for fixing the velocity of relativistic soliton based on the breaking of the Lorentz symmetry of the sine-Gordon (SG) model. The proposal is first elaborated for a molecular chain model, as the simple pendulum limit of a double pendulums chain. It is then generalized to a full class of two-dimensional field theories of the sine-Gordon type. From a phenomenological point of view, the mechanism allows one to select the speed of a SG soliton just by tuning elastic couplings constants and kinematical parameters. From a fundamental, field-theoretical point of view we show that the characterizing features of relativistic SG solitons (existence of conserved topological charges and stability) may be still preserved even if the Lorentz symmetry is broken and a soliton of a given speed is selected., Comment: 23 pages, no figures

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.

DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits made of a nucleoside and the attached nitrogen bases are described by a single degree of freedom. In this paper we propose and investigate, both analytically and numerically, a ``composite'' version of the Y model, in which the nucleoside and the base are described by separate degrees of freedom. The model proposed here contains as a particular case the Y model and shares with it many features and results, but 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. The model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Y solitons, in a fully realistic range of all the physical parameters characterizing the DNA., Comment: 29 pages

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.

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.

We extend the Poincare'-Lyapounov-Nekhoroshev theorem from torus actions and invariant tori to general (non-abelian) involutory systems of vector fields and general invariant manifolds.

In some cases, solutions to nonlinear PDEs happen to be asymptotically (for large $x$ and/or $t$) invariant under a group $G$ which is not a symmetry of the equation. After recalling the geometrical meaning of symmetries of differential equations -- and solution-preserving maps -- we provide a precise definition of asymptotic symmetries of PDEs; we deal in particular, for ease of discussion and physical relevance, with scaling and translation symmetries of scalar equations. We apply the general discussion to a class of ``Richardson-like'' anomalous diffusion and reaction-diffusion equations, whose solution are known by numerical experiments to be asymptotically scale invariant; we obtain an analytical explanation of the numerically observed asymptotic scaling properties. We also apply our method to a different class of anomalous diffusion equations, relevant in optical lattices. The methods developed here can be applied to more general equations, as clear by their geometrical construction.

Finite group symmetry is commonplace in Physics, in particular through crystallographic groups occurring in condensed matter physics -- but also through the inversions (C,P,T and their combinations) occurring in high energy physics and field theory. The breaking of finite groups symmetry has thus been thoroughly studied, and general approaches exist to investigate it. In Landau theory, the state of a system is described by a finite dimensional variable (the {\it order parameter}), and physical states correspond to minima of a potential, invariant under a group. In this article we describe the basics of symmetry breaking analysis for systems described by a symmetric polynomial; in particular we discuss generic symmetry breakings, i.e. those determined by the symmetry properties themselves and independent on the details of the polynomial describing a concrete system. We also discuss how the plethora of invariant polynomials can be to some extent reduced by means of changes of coordinates, i.e. how one can reduce to consider certain types of polynomials with no loss of generality. Finally, we will give some indications on extension of this theory, i.e. on how one deals with symmetry breakings for more general groups and/or more general physical systems.

It was recently remarked by Lutz [{\it Phys. Rev. A} {\bf 67} (2003), 051402(R)] that the equation for the marginal Wigner distribution in an optical lattice admits a scale-free distribution corresponding to Tsallis statistics. Here we show that this distribution is invariant under an asymptotic symmetry of the equation, hence that this scale-free behavior can be understood in terms of symmetry analysis.

We analyze asymptotic scaling properties of a model class of anomalous reaction-diffusion (ARD) equations. Numerical experiments show that solutions to these have, for large $t$, well defined scaling properties. We suggest a general framework to analyze asymptotic symmetry properties; this provides an analytical explanation of the observed asymptotic scaling properties for the considered ARD equations., Comment: To appear in J. Nonlin. Math. Phys

It is known that many equations of interest in Mathematical Physics display solutions which are only asymptotically invariant under transformations (e.g. scaling and/or translations) which are not symmetries of the considered equation. In this note we extend the approach to asymptotic symmetries for the analysis of PDEs, to the case of difference equations.

Lambda-symmetries of ODEs were introduced by Muriel and Romero, and discussed by C. Muriel in her talk at SPT2001. Here we provide a geometrical characterization of lambda-prolongations, and a generalization of these -- and of lambda-symmetries -- to PDEs and systems thereof.

Integration of nonlinear dynamical systems is usually seen as associated to a symmetry reduction, e.g. via momentum map. In Lax integrable systems, as pointed out by Kazhdan, Kostant and Sternberg in discussing the Calogero system, one proceeds in the opposite way, enlarging the nonlinear system to a system of greater dimension. We discuss how this approach is also fruitful in studying non integrable systems, focusing on systems in normal form., Comment: 16 pages

We give a geometrical interpretation of the notion of $\mu$-prolongations of vector fields and of the related concept of $\mu$-symmetry for partial differential equations (extending to PDEs the notion of $\lambda$-symmetry for ODEs). We give in particular a result concerning the relationship between $\mu$-symmetries and standard exact symmetries. The notion is also extended to the case of conditional and partial symmetries, and we analyze the relation between local $\mu$-symmetries and nonlocal standard symmetries., Comment: 25 pages, no figures, latex. to be published in J. Phys. A

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.

In the Landau theory of phase transitions one considers an effective potential $\Phi$ whose symmetry group $G$ and degree $d$ depend on the system under consideration; generally speaking, $\Phi$ is the most general $G$-invariant polynomial of degree $d$. When such a $\Phi$ turns out to be too complicate for a direct analysis, it is essential to be able to drop unessential terms, i.e. to apply a simplifying criterion. Criteria based on singularity theory exist and have a rigorous foundation, but are often very difficult to apply in practice. Here we consider a simplifying criterion (as stated by Gufan) and rigorously justify it on the basis of classical Lie-Poincar\'e theory as far as one deals with fixed values of the control parameter(s) in the Landau potential; when one considers a range of values, in particular near a phase transition, the criterion has to be accordingly partially modified, as we discuss. We consider some specific cases of group $G$ as examples, and study in detail the application to the Sergienko-Gufan-Urazhdin model for highly piezoelectric perovskites., Comment: 32 pages, no figures. To appear in Annals of Physics

In many relevant cases -- e.g., in hamiltonian dynamics -- a given vector field can be characterized by means of a variational principle based on a one-form. We discuss how a vector field on a manifold can also be characterized in a similar way by means of an higher order variational principle, and how this extends to involutive systems of vector fields., Comment: 31 pages. To appear in International Journal of Geometric Methods in Modern Physics (IJGMMP)

It has been suggested by several authors that nonlinear excitations, in particular solitary waves, could play a fundamental functional role in the process of DNA transcription, effecting the opening of the double chain needed for RNA Polymerase to be able to copy the genetic code. Some models have been proposed to model the relevant DNA dynamics in terms of a reduced number of effective degrees of freedom. Here I discuss advantages and disadvantages of such an approach, and discuss in more detail one of the models, i.e. the one proposed by Yakushevich., Comment: An older review paper (NOT UPDATED), posted here for archival purposes

Let $M$ be smooth $n$-dimensional manifold, fibered over a $k$-dimensional submanifold $B$ as $\pi:M \to B$, and $\vartheta \in \Lambda^k (M)$; one can consider the functional on sections $\phi$ of the bundle $\pi$ defined by $\int_D \phi^* (\vartheta)$, with $D$ a domain in $B$. We show that for $k = n-2$ the variational principle based on this functional identifies a unique (up to multiplication by a smooth function) nontrivial vector field in $M$, i.e. a system of ODEs. Conversely, any vector field $X$ on $M$ satisfying $i_X ({\rm d} \vartheta) = 0$ for some $\vartheta \in \Lambda^{n-2} (M)$ admits such a variational characterization. We consider the general case, and also the particular case $M = P \times R$ where one of the variables (the time) has a distinguished role; in this case our results imply that any Liouville (volume-preserving) vector field on the phase space $P$ admits a variational principle of the kind considered here., Comment: Some misprints corrected

We provide a variational description of any Liouville (i.e. volume preserving) autonomous vector fields on a smooth manifold. This is obtained via a ``maximal degree'' variational principle; critical sections for this are integral manifolds for the Liouville vector field. We work in coordinates and provide explicit formulae.

Standard (Arnold-Liouville) integrable systems are intimately related to complex rotations. One can define a generalization of these, sharing many of their properties, where complex rotations are replaced by quaternionic ones. Actually this extension is not limited to the integrable case: one can define a generalization of Hamilton dynamics based on hyperKahler structures., Comment: 10 pages. To appear in the proceedings of the SPT2002 conference, edited by S. Abenda, G. Gaeta and S. Walcher, World Scientific

We extend Michel's theorem on the geometry of symmetry breaking [L. Michel, {\it Comptes Rendus Acad. Sci. Paris} {\bf 272-A} (1971), 433-436] to the case of pure gauge theories, i.e. of gauge-invariant functionals defined on the space ${\cal C}$ of connections of a principal fiber bundle. Our proof follows closely the original one by Michel, using several known results on the geometry of ${\cal C}$. The result (and proof) is also extended to the case of gauge theories with matter fields., Comment: 24 pages. An old paper posted for archival purposes

We introduce an extension of hamiltonian dynamics, defined on hyperkahler manifolds, which we call ``hyperhamiltonian dynamics''. We show that this has many of the attractive features of standard hamiltonian dynamics. We also discuss the prototypical integrable hyperhamiltonian systems, i.e. quaternionic oscillators., Comment: 24 pages; to appear in J. Phys. A

We give a detailed and mainly geometric proof of a theorem by N.N. Nekhoroshev for hamiltonian systems in $n$ degrees of freedom with $k$ constants of motion in involution, where $1 \le k \le n$. This states persistence of $k$-dimensional invariant tori, and local existence of partial action-angle coordinates, under suitable nondegeneracy conditions. Thus it admits as special cases the Poincar\'e-Lyapounov theorem (corresponding to $k=1$) and the Liouville-Arnold one (corresponding to $k = n$), and interpolates between them. The crucial tool for the proof is a generalization of the Poincar\'e map, also introduced by Nekhoroshev., Comment: 21 pages, no figures

We briefly review the main aspects of (Poincar\'e-Dulac) normal forms; we have a look at the non-uniqueness problem, and discuss one of the proposed ways to ``further reduce'' the normal forms. We also mention some convergence results., Comment: standard LaTeX, 20 pages

We give criteria for finite dimensionality or infinite dimensionality of the polynomial centralizer of the Lie algebra of a linear Lie group, in terms of invariants and relative invariants of the group. In the finite dimensional scenario some applications to normal forms and to certain equations with fundamental solutions are presented., Comment: 10 pages; revised version to appear in J. Math. Anal. Appl

The Poincare'-Dulac normal form of a given resonant system is in general non unique; given a specific normal form, one would like to further reduce it to a simplest normal form. In this note we give an algorithm, based on the Lie algebraic structure of the set of normal forms, to obtain this. The algorithm can be applied under some condition, non generic but often met in applications; when applicable, it only requires to solve linear equations, and is more powerful than the one proposed in previous work by the same author [Lett. Math. Phys. 42, 103-114; and Ann. I.H.P. 70, 461-514]., Comment: 20 pages, no figures