Universality of Long-Range Correlations in Expansion-Randomization Systems

We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of non-equilibrium 1D expansion-randomization systems with generic stationary long-range correlations in a regime of growing sequence length. We obtain explicitly the two-point correlation function of the sequence composition and the distribution function of the composition bias in sequences of finite length. The characteristic exponent $\chi$ of these quantities is determined by the ratio of two effective rates, which are explicitly calculated for several specific sequence evolution dynamics of the universality class. Depending on the value of $\chi$, we find two different scaling regimes, which are distinguished by the detectability of the initial composition bias. All analytic results are accurately verified by numerical simulations. We also discuss the non-stationary build-up and decay of correlations, as well as more complex evolutionary scenarios, where the rates of the processes vary in time. Our findings provide a possible example for the emergence of universality in molecular biology.Comment: 23 pages, 15 figure

Stochastic stability of viscoelastic systems under Gaussian and Poisson white noise excitations

As the use of viscoelastic materials becomes increasingly popular, stability of viscoelastic structures under random loads becomes increasingly important. This paper aims at studying the asymptotic stability of viscoelastic systems under Gaussian and Poisson white noise excitations with Lyapunov functions. The viscoelastic force is approximated as equivalent stiffness and damping terms. A stochastic differential equation is set up to represent randomly excited viscoelastic systems, from which a Lyapunov function is determined by intuition. The time derivative of this Lyapunov function is then obtained by stochastic averaging. Approximate conditions are derived for asymptotic Lyapunov stability with probability one of the viscoelastic system. Validity and utility of this approach are illustrated by a Duffing-type oscillator possessing viscoelastic forces, and the influence of different parameters on the stability region is delineated

Probing the high-density behavior of symmetry energy with gravitational waves

Gravitational wave (GW) astronomy opens up an entirely new window on the Universe to probe the equations of state (EOS) of neutron-rich matter. With the advent of next generation GW detectors, measuring the gravitational radiation from coalescing binary neutron star systems, mountains on rotating neutron stars, and stellar oscillation modes may become possible in the near future. Using a set of model EOSs satisfying the latest constraints from terrestrial nuclear experiments, state of the art nuclear many-body calculations of the pure neutron matter EOS, and astrophysical observations consistently, we study various GW signatures of the high-density behavior of the nuclear symmetry energy, which is considered among the most uncertain properties of dense neutron-rich nucleonic matter. In particular, we find the tidal polarizability of neutron stars, potentially measurable in binary systems just prior to merger, is more sensitive to the high density component of the nuclear symmetry energy than the symmetry energy at nuclear saturation density. We also find that the upper limit on the GW strain amplitude from elliptically deformed stars is very sensitive to the density dependence of the symmetry energy. This suggests that future developments in modeling of the neutron star crust, and direct gravitational wave signals from accreting binaries will provide a wealth of information on the EOS of neutron-rich matter. We also review the sensitivity of the $r$-mode instability window to the density dependence of the symmetry energy. Whereas models with larger values of the density slope of the symmetry energy at saturation seem to be disfavored by the current observational data, within a simple $r$-mode model, we point out that a subsequent softer behavior of the symmetry energy at high densities (hinted at by recent observational interpretations) could rule them in.Comment: 14 pages, 11 figures, 3 tables; submitted to EPJA Special Volume on Nuclear Symmetry Energ

A Solvable Sequence Evolution Model and Genomic Correlations

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations in the composition of letters as long as the sequence length is growing, i.e., the combined rates of duplications and insertions are higher than the deletion rate. For constant sequence length, on the other hand, all initial correlations decay exponentially. These results are obtained analytically and by simulations. They are compared with the long-range correlations observed in genomic DNA, and the implications for genome evolution are discussed.Comment: 4 pages, 4 figure