Model for Folding and Aggregation in RNA Secondary Structures

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the secondary structure and the energy gained by pairing drives the RNA to undergo a `temperature independent' second order phase transition from a molten to an aggregated phase'. The aggregated phase thus obtained has a macroscopically large number of contacts between different RNAs. The partition function scaling exponent for this phase is \theta ~ 1/2 and the crossover exponent of the phase transition is \nu ~ 5/3. The relevance of these calculations to the aggregation of biological molecules is discussed.Comment: Revtex, 4 pages; 3 Figures; Final published versio

Inclinations of small quiet-Sun magnetic features based on a new geometric approach

High levels of horizontal magnetic flux have been reported in the quiet-Sun internetwork, often based on Stokes profile inversions. Here we introduce a new method for deducing the inclination of magnetic elements and use it to test magnetic field inclinations from inversions. We determine accurate positions of a set of small, bright magnetic elements in high spatial resolution images sampling different photospheric heights obtained by the Sunrise balloon-borne solar observatory. Together with estimates of the formation heights of the employed spectral bands, these provide us with the inclinations of the magnetic features. We also compute the magnetic inclination angle of the same magnetic features from the inversion of simultaneously recorded Stokes parameters. Our new, geometric method returns nearly vertical fields (average inclination of around 14 deg with a relatively narrow distribution having a standard deviation of 6 deg). In strong contrast to this, the traditionally used inversions give almost horizontal fields (average inclination of 75+-8 deg) for the same small magnetic features, whose linearly polarised Stokes profiles are adversely affected by noise. The almost vertical field of bright magnetic features from our geometric method is clearly incompatible with the nearly horizontal magnetic fields obtained from the inversions. This indicates that the amount of magnetic flux in horizontal fields deduced from inversions is overestimated in the presence of weak Stokes signals, in particular if Stokes Q and U are close to or under the noise level. By combining the proposed method with inversions we are not just improving the inclination, but also the field strength. This technique allows us to analyse features that are not reliably treated by inversions, thus greatly extending our capability to study the complete magnetic field of the quiet Sun.Comment: 12 pages, 9 figures, 1 table; Accepted for publication in Astronomy & Astrophysic

Green's Relations in Finite Transformation Semigroups

We consider the complexity of Green's relations when the semigroup is given by transformations on a finite set. Green's relations can be defined by reachability in the (right/left/two-sided) Cayley graph. The equivalence classes then correspond to the strongly connected components. It is not difficult to show that, in the worst case, the number of equivalence classes is in the same order of magnitude as the number of elements. Another important parameter is the maximal length of a chain of components. Our main contribution is an exponential lower bound for this parameter. There is a simple construction for an arbitrary set of generators. However, the proof for constant alphabet is rather involved. Our results also apply to automata and their syntactic semigroups.Comment: Full version of a paper submitted to CSR 2017 on 2016-12-1

The delayed uncoupled continuous-time random walks do not provide a model for the telegraph equation

It has been alleged in several papers that the so called delayed continuous-time random walks (DCTRWs) provide a model for the one-dimensional telegraph equation at microscopic level. This conclusion, being widespread now, is strange, since the telegraph equation describes phenomena with finite propagation speed, while the velocity of the motion of particles in the DCTRWs is infinite. In this paper we investigate how accurate are the approximations to the DCTRWs provided by the telegraph equation. We show that the diffusion equation, being the correct limit of the DCTRWs, gives better approximations in $L_2$ norm to the DCTRWs than the telegraph equation. We conclude therefore that, first, the DCTRWs do not provide any correct microscopic interpretation of the one-dimensional telegraph equation, and second, the kinetic (exact) model of the telegraph equation is different from the model based on the DCTRWs.Comment: 12 pages, 9 figure

Work probability distribution and tossing a biased coin

We show that the rare events present in dissipated work that enters Jarzynski equality, when mapped appropriately to the phenomenon of large deviations found in a biased coin toss, are enough to yield a quantitative work probability distribution for Jarzynski equality. This allows us to propose a recipe for constructing work probability distribution independent of the details of any relevant system. The underlying framework, developed herein, is expected to be of use in modelling other physical phenomena where rare events play an important role.Comment: 6 pages, 4 figures

Equilibrium of anchored interfaces with quenched disordered growth

The roughening behavior of a one-dimensional interface fluctuating under quenched disorder growth is examined while keeping an anchored boundary. The latter introduces detailed balance conditions which allows for a thorough analysis of equilibrium aspects at both macroscopic and microscopic scales. It is found that the interface roughens linearly with the substrate size only in the vicinity of special disorder realizations. Otherwise, it remains stiff and tilted.Comment: 6 pages, 3 postscript figure

Comparison of solar photospheric bright points between SUNRISE observations and MHD simulations

Bright points (BPs) in the solar photosphere are radiative signatures of magnetic elements described by slender flux tubes located in the darker intergranular lanes. They contribute to the ultraviolet (UV) flux variations over the solar cycle and hence may influence the Earth's climate. Here we combine high-resolution UV and spectro-polarimetric observations of BPs by the SUNRISE observatory with 3D radiation MHD simulations. Full spectral line syntheses are performed with the MHD data and a careful degradation is applied to take into account all relevant instrumental effects of the observations. It is demonstrated that the MHD simulations reproduce the measured distributions of intensity at multiple wavelengths, line-of-sight velocity, spectral line width, and polarization degree rather well. Furthermore, the properties of observed BPs are compared with synthetic ones. These match also relatively well, except that the observations display a tail of large and strongly polarized BPs not found in the simulations. The higher spatial resolution of the simulations has a significant effect, leading to smaller and more numerous BPs. The observation that most BPs are weakly polarized is explained mainly by the spatial degradation, the stray light contamination, and the temperature sensitivity of the Fe I line at 5250.2 \AA{}. The Stokes $V$ asymmetries of the BPs increase with the distance to their center in both observations and simulations, consistent with the classical picture of a production of the asymmetry in the canopy. This is the first time that this has been found also in the internetwork. Almost vertical kilo-Gauss fields are found for 98 % of the synthetic BPs. At the continuum formation height, the simulated BPs are on average 190 K hotter than the mean quiet Sun, their mean BP field strength is 1750 G, supporting the flux-tube paradigm to describe BPs.Comment: Accepted for publication in Astronomy & Astrophysics on May 30 201

Condensation phase transitions of symmetric conserved-mass aggregation model on complex networks

We investigate condensation phase transitions of symmetric conserved-mass aggregation (SCA) model on random networks (RNs) and scale-free networks (SFNs) with degree distribution $P(k) \sim k^{-\gamma}$. In SCA model, masses diffuse with unite rate, and unit mass chips off from mass with rate $\omega$. The dynamics conserves total mass density $\rho$. In the steady state, on RNs and SFNs with $\gamma>3$ for $\omega \neq \infty$, we numerically show that SCA model undergoes the same type condensation transitions as those on regular lattices. However the critical line $\rho_c (\omega)$ depends on network structures. On SFNs with $\gamma \leq 3$, the fluid phase of exponential mass distribution completely disappears and no phase transitions occurs. Instead, the condensation with exponentially decaying background mass distribution always takes place for any non-zero density. For the existence of the condensed phase for $\gamma \leq 3$ at the zero density limit, we investigate one lamb-lion problem on RNs and SFNs. We numerically show that a lamb survives indefinitely with finite survival probability on RNs and SFNs with $\gamma >3$, and dies out exponentially on SFNs with $\gamma \leq 3$. The finite life time of a lamb on SFNs with $\gamma \leq 3$ ensures the existence of the condensation at the zero density limit on SFNs with $\gamma \leq 3$ at which direct numerical simulations are practically impossible. At $\omega = \infty$, we numerically confirm that complete condensation takes place for any $\rho > 0$ on RNs. Together with the recent study on SFNs, the complete condensation always occurs on both RNs and SFNs in zero range process with constant hopping rate.Comment: 6 pages, 6 figure

Dephasing by a nonstationary classical intermittent noise

We consider a new phenomenological model for a $1/f^{\mu}$ classical intermittent noise and study its effects on the dephasing of a two-level system. Within this model, the evolution of the relative phase between the $|\pm>$ states is described as a continuous time random walk (CTRW). Using renewal theory, we find exact expressions for the dephasing factor and identify the physically relevant various regimes in terms of the coupling to the noise. In particular, we point out the consequences of the non-stationarity and pronounced non-Gaussian features of this noise, including some new anomalous and aging dephasing scenarii.Comment: Submitted to Phys. Rev.

Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion

In many biological and small scale technological applications particles may transiently bind to a cylindrical surface. In between two binding events the particles diffuse in the bulk, thus producing an effective translation on the cylinder surface. We here derive the effective motion on the surface, allowing for additional diffusion on the cylinder surface itself. We find explicit solutions for the number of adsorbed particles at one given instant, the effective surface displacement, as well as the surface propagator. In particular sub- and superdiffusive regimes are found, as well as an effective stalling of diffusion visible as a plateau in the mean squared displacement. We also investigate the corresponding first passage and first return problems.Comment: 26 pages, 5 figure