Related papers: Loops in canonical RNA pseudoknot structures
The central limit theorem for Markov chains generated by iterated function systems consisting of orientation preserving homeomorphisms of the interval is proved. We study also ergodicity of such systems.
The hyperon-nucleon interaction is investigated through the final-state interaction in the $K^-d\to\pi^-\Lambda p$ reaction. We focus on the $\Lambda N$-$\Sigma N$ coupled-channel interaction, which produces characteristic structures around…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and…
Ropelength and embedding thickness are related measures of geometric complexity of classical knots and links in Euclidean space. In their recent work, Freedman and Krushkal posed a question regarding lower bounds for embedding thickness of…
We investigate the emergence of spanning structures in sparse pseudo-random $k$-uniform hypergraphs, using the following comparatively weak notion of pseudo-randomness. A $k$-uniform hypergraph $H$ on $n$ vertices is called…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…
We continue the work of a series of previous studies of a mathematical model that describes the mean-field limit behavior of a homogeneous network of excitatory point spiking neurons. Contrary to other models, here noise is intrinsic to the…
The virtual corrections to the production cross section of a Standard Model Higgs boson are computed up to order \alpha_s^4. Using an effective Lagrangian for the limit M_t -> \infty, we evaluate the relevant massless two-loop vertex…
The weights of a neural network are typically initialized at random, and one can think of the functions produced by such a network as having been generated by a prior over some function space. Studying random networks, then, is useful for a…
In this paper, we study the restricted isometry property of partial random circulant matrices. For a bounded subgaussian generator with independent entries, we prove that the partial random circulant matrices satisfy $s$-order RIP with high…
We continue our consideration of a class of models describing the reversible dynamics of $N$ Boolean variables, each with $K$ inputs. We investigate in detail the behavior of the Hamming distance as well as of the distribution of orbit…
C-loops are loops satisfying the identity $x(y\cdot yz) = (xy\cdot y)z$. We develop the theory of extensions of C-loops, and characterize all nuclear extensions provided the nucleus is an abelian group. C-loops with central squares have…
We investigate the limit behavior of supercritical multitype branching processes in random environments with linear fractional offspring distributions and show that there exists a phase transition in the behavior of local probabilites of…
Canalization of genetic regulatory networks has been argued to be favored by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial…
We construct non-perturbative inputs for the elastic gluon-hadron scattering amplitudes in the forward kinematic region for both polarized and non-polarized hadrons. We use the optical theorem to relate invariant scattering amplitudes to…
The open problem of calculating the limiting spectrum (or its Shannon transform) of increasingly large random Hermitian finite-band matrices is described. In general, these matrices include a finite number of non-zero diagonals around their…
We describe the fluctuations of the overlap between two replicas in the 2-spin spherical SK model about its limiting value in the low temperature phase. We show that the fluctuations are of order $N^{-1/3}$ and are given by a simple,…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
We consider two types of random networks grown in blocks. Hooking networks are grown from a set of graphs as blocks, each with a labelled vertex called a hook. At each step in the growth of the network, a vertex called a latch is chosen…