DNA viewed as an out-of-equilibrium structure

The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to $r=6$. Although detailed balance seems to hold at the level of purine-pyrimidine notation it fails when all four basepairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain we study the exit distances from a specific symbol, the distribution of recurrence distances and the Hurst exponent, all of which show power law tails and long range characteristics. These results suggest that human DNA can be viewed as a non-equilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method we construct a model DNA sequence. This method allows to keep all long range and short range statistical characteristics of the original sequence. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture point-to-point details

Supersymmetric probability distributions

We use anticommuting variables to study probability distributions of random variables, that are solutions of Langevin's equation. We show that the probability density always enjoys "worldpoint supersymmetry". The partition function, however, may not. We find that the domain of integration can acquire a boundary, that implies that the auxiliary field has a non-zero expectation value, signalling spontaneous supersymmetry breaking. This is due to the presence of "fermionic" zeromodes, whose contribution cannot be cancelled by a surface term. This we prove by an explicit calculation of the regularized partition function, as well as by computing the moments of the auxiliary field and checking whether they satisfy the identities implied by Wick's theorem. Nevertheless, supersymmetry manifests itself in the identities that are satisfied by the moments of the scalar, whose expressions we can calculate,for all values of the coupling constant. We also provide some quantitative estimates concerning the visibility of supersymmetry breaking effects in the identities for the moments and remark that the shape of the distribution of the auxiliary field can influence quite strongly how easy it would be to mask them, since the expectation value of the auxiliary field doesn't coincide with its typical value.Comment: LaTeX2e: 24 pages, 7 figure

Derrick's theorem beyond a potential

Scalar field theories with derivative interactions are known to possess solitonic excitations, but such solitons are generally unsatisfactory because the effective theory fails precisely where nonlinearities responsible for the solitons are important. A new class of theories possessing (internal) galilean invariance can in principle bypass this difficulty. Here, we show that these galileon theories do not possess stable solitonic solutions. As a by-product, we show that no stable solitons exist for a different class of derivatively coupled theories, describing for instance the infrared dynamics of superfluids, fluids, solids and some k-essence models.Comment: 4 page

Superluminality in DGP

We reconsider the issue of superluminal propagation in the DGP model of infrared modified gravity. Superluminality was argued to exist in certain otherwise physical backgrounds by using a particular, physically relevant scaling limit of the theory. In this paper, we exhibit explicit five-dimensional solutions of the full theory that are stable against small fluctuations and that indeed support superluminal excitations. The scaling limit is neither needed nor invoked in deriving the solutions or in the analysis of its small fluctuations. To be certain that the superluminality found here is physical, we analyze the retarded Green's function of the scalar excitations, finding that it is causal and stable, but has support on a widened light-cone. We propose to use absence of superluminal propagation as a method to constrain the parameters of the DGP model. As a first application of the method, we find that whenever the 4D energy density is a pure cosmological constant and a hierarchy of scales exists between the 4D and 5D Planck masses, superluminal propagation unavoidably occurs.Comment: 23 pages. Minor corrections. Version to appear in JHE

Model error and sequential data assimilation. A deterministic formulation

Data assimilation schemes are confronted with the presence of model errors arising from the imperfect description of atmospheric dynamics. These errors are usually modeled on the basis of simple assumptions such as bias, white noise, first order Markov process. In the present work, a formulation of the sequential extended Kalman filter is proposed, based on recent findings on the universal deterministic behavior of model errors in deep contrast with previous approaches (Nicolis, 2004). This new scheme is applied in the context of a spatially distributed system proposed by Lorenz (1996). It is found that (i) for short times, the estimation error is accurately approximated by an evolution law in which the variance of the model error (assumed to be a deterministic process) evolves according to a quadratic law, in agreement with the theory. Moreover, the correlation with the initial condition error appears to play a secondary role in the short time dynamics of the estimation error covariance. (ii) The deterministic description of the model error evolution, incorporated into the classical extended Kalman filter equations, reveals that substantial improvements of the filter accuracy can be gained as compared with the classical white noise assumption. The universal, short time, quadratic law for the evolution of the model error covariance matrix seems very promising for modeling estimation error dynamics in sequential data assimilation

Energy's and amplitudes' positivity

In QFT, the null energy condition (NEC) for a classical field configuration is usually associated with that configuration's stability against small perturbations, and with the sub-luminality of these. Here, we exhibit an effective field theory that allows for stable NEC-violating solutions with exactly luminal excitations only. The model is the recently introduced `galileon', or more precisely its conformally invariant version. We show that the theory's low-energy S-matrix obeys standard positivity as implied by dispersion relations. However we also show that if the relevant NEC-violating solution is inside the effective theory, then other (generic) solutions allow for superluminal signal propagation. While the usual association between sub-luminality and positivity is not obeyed by our example, that between NEC and sub-luminality is, albeit in a less direct way than usual.Comment: 21 pages. v2: Typos in eq. (2.41) and (2.41) corrected; discussion of section 2.3 modified accordingly. Other sections and conclusions unchanged. Matches the Erratum published in JHE

Reactive dynamics on fractal sets: anomalous fluctuations and memory effects

We study the effect of fractal initial conditions in closed reactive systems in the cases of both mobile and immobile reactants. For the reaction $A+A\to A$, in the absence of diffusion, the mean number of particles $A$ is shown to decay exponentially to a steady state which depends on the details of the initial conditions. The nature of this dependence is demonstrated both analytically and numerically. In contrast, when diffusion is incorporated, it is shown that the mean number of particles $$ decays asymptotically as $t^{-d_f/2}$, the memory of the initial conditions being now carried by the dynamical power law exponent. The latter is fully determined by the fractal dimension $d_f$ of the initial conditions.Comment: 7 pages, 2 figures, uses epl.cl

More on gapped Goldstones at finite density: More gapped Goldstones

It was recently argued that certain relativistic theories at finite density can exhibit an unconventional spectrum of Goldstone excitations, with gapped Goldstones whose gap is exactly calculable in terms of the symmetry algebra. We confirm this result as well as previous ones concerning gapless Goldstones for non-relativistic systems via a coset construction of the low-energy effective field theory. Moreover, our analysis unveils additional gapped Goldstones, naturally as light as the others, but this time with a model-dependent gap. Their exact number cannot be inferred solely from the symmetry breaking pattern either, but rather depends on the details of the symmetry breaking mechanism--a statement that we explicitly verify with a number of examples. Along the way we provide what we believe to be a particularly transparent interpretation of the so-called inverse-Higgs constraints for spontaneously broken spacetime symmetries.Comment: 50 pages. v2: Fixed several typos in equations. Minor modifications to the counting rule. Acknowledgements and references added. Matches JHEP versio