Related papers: RNA matrix models with external interactions and t…

In this paper we study the problem of how resilient networks are to node faults. Specifically, we investigate the question of how many faults a network can sustain so that it still contains a large (i.e. linear-sized) connected component…

Growth-fragmentation processes describe the evolution of systems of cells which grow continuously and fragment suddenly; they are used in models of cell division and protein polymerisation. Typically, we may expect that in the long run, the…

We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…

We study the large-$N$ limit of adjoint fermion one-matrix models. We find one-cut solutions of the loop equations for the correlators of these models and show that they exhibit third order phase transitions associated with $m$-th order…

For a positive constant $\alpha$ a graph $G$ on $n$ vertices is called an $\alpha$-expander if every vertex set $U$ of size at most $n/2$ has an external neighborhood whose size is at least $\alpha\left|U\right|$. We study cycle lengths in…

Following the procedures by which O(N)-invariant real vector models and their large-N behavior have previously been solved, we extend similar techniques to the study of real symmetric N x N-matrix models with O(N)-invariant interactions.…

The evolution of open systems, subject to both Hamiltonian and dissipative forces, is studied by writing the $nm$ element of the time ($t$) dependent density matrix in the form \ber \rho_{nm}(t)&=& \frac {1}{A} \sum_{\alpha=1}^A \gamma…

Let $G$ be a compact Lie group, $N\geq 1$ and $L>0$. The random geometric graph on $G$ is the random graph $\Gamma(N,L)$ whose vertices are $N$ random points $g_1,\ldots,g_N$ chosen under the Haar measure of $G$, and whose edges are the…

Graphical models capture relations between entities in a wide range of applications including social networks, biology, and natural language processing, among others. Graph neural networks (GNN) are neural models that operate over graphs,…

Let $\xi_1,\xi_2,...$ be independent identically distributed random variables and $F:\bbR^\ell\to SL_d(\bbR)$ be a Borel measurable matrix-valued function. Set $X_n=F(\xi_{q_1(n)},\xi_{q_2(n)},...,\xi_{q_\ell(n)})$ where $0\leq…

In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…

The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…

Hill functions dominate gene regulatory network (GRN) modeling, but their fractional exponents create analytical pathologies when the Hill coefficient $n$ is non-integer -- a ubiquitous occurrence in experimental fits. We replace the Hill…

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…

We study the asymptotic spectral behavior of high-dimensional random Gram matrices with sparsity and a variance profile, motivated by applications in wireless communications. Specifically, we consider the Gram matrices $\mathbf S_n=\mathbf…

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…

In this paper we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the sub exponential factors for $k$-noncrossing RNA structures. Our…

We compute the beta-function and the anomalous dimension of all the non-derivative operators of the theory up to three-loops for the most general nearest-neighbour O(N)-invariant action together with some contributions to the four-loop…

We study the conformational properties of complex polymer macromolecules, consisting in general of $n$ subsequently connected chains (blocks) of different lengths and distinct chemical structure. Depending on the solvent conditions, the…

We consider the problem of detecting the presence of a submatrix with larger-than-usual values in a large data matrix. This problem was considered in (Butucea and Ingster, 2013) under a one-parameter exponential family, and one of the test…