Related papers: Combinatorics of RNA-RNA interaction
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
Many non-coding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is however a challenging task. On the other hand, thanks to the low cost of sequencing…
Interaction nets are a graphical model of computation, which has been used to define efficient evaluators for functional calculi, and specifically lambda calculi with patterns. However, the flat structure of interaction nets forces pattern…
We describe a basic correspondence between linear algebraic structures within vector embeddings in artificial neural networks and conditional independence constraints on the probability distributions modeled by these networks. Our framework…
An extended pairing plus QQ force model, which has been shown to successfully explain the nuclear binding energy and related quantities such as the symmetry energy, is applied to study the alpha-like four-nucleon correlations in 1f_{7/2}…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
An approach to obtain the structural properties of additive binary hard-sphere mixtures is presented. Such an approach, which is a nontrivial generalization of the one recently used for monocomponent hard-sphere fluids [S. Pieprzyk, A. C.…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
(Bi)multi-partite interaction patterns are commonly observed in real world systems which have inhibitory and excitatory couplings. We hypothesize these structural interaction pattern to be stable and naturally arising in the course of…
Using a break junction technique, we find a clear signature for the formation of conducting hybrid junctions composed of a single organic molecule (benzene, naphthalene or anthracene) connected to chains of platinum atoms. The hybrid…
Constructing gene regulatory networks is a fundamental task in systems biology. We introduce a Gaussian reciprocal graphical model for inference about gene regulatory relationships by integrating mRNA gene expression and DNA level…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…