RNA secondary structure design

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called designable. We implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer whether such a sequence exists. The bound required by the branch-and-bound algorithm are calculated by a dynamic programming algorithm. We consider different alphabet sizes and an ensemble of random structures, which we want to design. We find that for two letters almost none of these structures are designable. The designability improves for the three-letter case, but still a significant fraction of structures is undesignable. This changes when we look at the natural four-letter case with two pairs of complementary bases: undesignable structures are the exception, although they still exist. Finally, we also study the relation between designability and the algorithmic complexity of the branch-and-bound algorithm. Within the ensemble of structures, a high average degree of undesignability is correlated to a long time to prove that a given structure is (un-)designable. In the four-letter case, where the designability is high everywhere, the algorithmic complexity is highest in the region of naturally occurring RNA.Comment: 11 pages, 10 figure

Density Matrix Renormalization Group in the Heisenberg Picture

In some cases the state of a quantum system with a large number of subsystems can be approximated efficiently by the density matrix renormalization group, which makes use of redundancies in the description of the state. Here we show that the achievable efficiency can be much better when performing density matrix renormalization group calculations in the Heisenberg picture, as only the observable of interest but not the entire state is considered. In some non-trivial cases, this approach can even be exact for finite bond dimensions.Comment: version to appear in PRL, acronyms in title and abstract expanded, new improved numerical example

Ground-State and Domain-Wall Energies in the Spin-Glass Region of the 2D ±J\pm J Random-Bond Ising Model

The statistics of the ground-state and domain-wall energies for the two-dimensional random-bond Ising model on square lattices with independent, identically distributed bonds of probability $p$ of $J_{ij}= -1$ and $(1-p)$ of $J_{ij}= +1$ are studied. We are able to consider large samples of up to $320^2$ spins by using sophisticated matching algorithms. We study $L \times L$ systems, but we also consider $L \times M$ samples, for different aspect ratios $R = L / M$. We find that the scaling behavior of the ground-state energy and its sample-to-sample fluctuations inside the spin-glass region ($p_c \le p \le 1 - p_c$) are characterized by simple scaling functions. In particular, the fluctuations exhibit a cusp-like singularity at $p_c$. Inside the spin-glass region the average domain-wall energy converges to a finite nonzero value as the sample size becomes infinite, holding $R$ fixed. Here, large finite-size effects are visible, which can be explained for all $p$ by a single exponent $\omega\approx 2/3$, provided higher-order corrections to scaling are included. Finally, we confirm the validity of aspect-ratio scaling for $R \to 0$: the distribution of the domain-wall energies converges to a Gaussian for $R \to 0$, although the domain walls of neighboring subsystems of size $L \times L$ are not independent.Comment: 11 pages with 15 figures, extensively revise

Renormalization algorithm with graph enhancement

We introduce a class of variational states to describe quantum many-body systems. This class generalizes matrix product states which underly the density-matrix renormalization group approach by combining them with weighted graph states. States within this class may (i) possess arbitrarily long-ranged two-point correlations, (ii) exhibit an arbitrary degree of block entanglement entropy up to a volume law, (iii) may be taken translationally invariant, while at the same time (iv) local properties and two-point correlations can be computed efficiently. This new variational class of states can be thought of as being prepared from matrix product states, followed by commuting unitaries on arbitrary constituents, hence truly generalizing both matrix product and weighted graph states. We use this class of states to formulate a renormalization algorithm with graph enhancement (RAGE) and present numerical examples demonstrating that improvements over density-matrix renormalization group simulations can be achieved in the simulation of ground states and quantum algorithms. Further generalizations, e.g., to higher spatial dimensions, are outlined.Comment: 4 pages, 1 figur

Interpolation and harmonic majorants in big Hardy-Orlicz spaces

Free interpolation in Hardy spaces is caracterized by the well-known Carleson condition. The result extends to Hardy-Orlicz spaces contained in the scale of classical Hardy spaces $H^p$, $p>0$. For the Smirnov and the Nevanlinna classes, interpolating sequences have been characterized in a recent paper in terms of the existence of harmonic majorants (quasi-bounded in the case of the Smirnov class). Since the Smirnov class can be regarded as the union over all Hardy-Orlicz spaces associated with a so-called strongly convex function, it is natural to ask how the condition changes from the Carleson condition in classical Hardy spaces to harmonic majorants in the Smirnov class. The aim of this paper is to narrow down this gap from the Smirnov class to ``big'' Hardy-Orlicz spaces. More precisely, we characterize interpolating sequences for a class of Hardy-Orlicz spaces that carry an algebraic structure and that are strictly bigger than $\bigcup_{p>0} H^p$. It turns out that the interpolating sequences are again characterized by the existence of quasi-bounded majorants, but now the weights of the majorants have to be in suitable Orlicz spaces. The existence of harmonic majorants in such Orlicz spaces will also be discussed in the general situation. We finish the paper with an example of a separated Blaschke sequence that is interpolating for certain Hardy-Orlicz spaces without being interpolating for slightly smaller ones.Comment: 19 pages, 2 figure

Flows, Fragmentation, and Star Formation. I. Low-mass Stars in Taurus

The remarkably filamentary spatial distribution of young stars in the Taurus molecular cloud has significant implications for understanding low-mass star formation in relatively quiescent conditions. The large scale and regular spacing of the filaments suggests that small-scale turbulence is of limited importance, which could be consistent with driving on large scales by flows which produced the cloud. The small spatial dispersion of stars from gaseous filaments indicates that the low-mass stars are generally born with small velocity dispersions relative to their natal gas, of order the sound speed or less. The spatial distribution of the stars exhibits a mean separation of about 0.25 pc, comparable to the estimated Jeans length in the densest gaseous filaments, and is consistent with roughly uniform density along the filaments. The efficiency of star formation in filaments is much higher than elsewhere, with an associated higher frequency of protostars and accreting T Tauri stars. The protostellar cores generally are aligned with the filaments, suggesting that they are produced by gravitational fragmentation, resulting in initially quasi-prolate cores. Given the absence of massive stars which could strongly dominate cloud dynamics, Taurus provides important tests of theories of dispersed low-mass star formation and numerical simulations of molecular cloud structure and evolution.Comment: 32 pages, 9 figures: to appear in Ap

Reduction of Two-Dimensional Dilute Ising Spin Glasses

The recently proposed reduction method is applied to the Edwards-Anderson model on bond-diluted square lattices. This allows, in combination with a graph-theoretical matching algorithm, to calculate numerically exact ground states of large systems. Low-temperature domain-wall excitations are studied to determine the stiffness exponent y_2. A value of y_2=-0.281(3) is found, consistent with previous results obtained on undiluted lattices. This comparison demonstrates the validity of the reduction method for bond-diluted spin systems and provides strong support for similar studies proclaiming accurate results for stiffness exponents in dimensions d=3,...,7.Comment: 7 pages, RevTex4, 6 ps-figures included, for related information, see http://www.physics.emory.edu/faculty/boettcher

Spontaneous scalarization of self-gravitating magnetic fields

In this paper, we study the spontaneous scalarization of an extended, self-gravitating system which is static, cylindrically symmetric and possesses electromagnetic fields. We demonstrate that a real massive scalar field condenses on this Melvin magnetic universe solution when introducing a nonminimal coupling between the scalar field and (a) the magnetic field and (b) the curvature of the space-time, respectively. We find that in both cases, the solutions exist on a finite interval of the coupling constant and that solutions with a number of nodes k in the scalar field are present. For case (a) we observe that the intervals of existence are mutually exclusive for different k