Related papers: A Graph Grammar for Modelling RNA Folding
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
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…
We introduce bonding grammars, a graph grammar formalism developed to model DNA computation by means of graph transformations. It is a modification of fusion grammars introduced by Kreowski, Kuske and Lye in 2017. Bonding is a graph…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
We propose a hierarchical normalizing flow model for generating molecular graphs. The model produces new molecular structures from a single-node graph by recursively splitting every node into two. All operations are invertible and can be…
I introduce a formalism for representing the syntax of recursively structured graph-like patterns. It does not use production rules, like a conventional graph grammar, but represents the syntactic structure in a more direct and declarative…
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…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
In past work (Onokpasa, Wild, Wong, DCC 2023), we showed that (a) for joint compression of RNA sequence and structure, stochastic context-free grammars are the best known compressors and (b) that grammars which have better compression…
The study of evolution of networks has received increased interest with the recent discovery that many real-world networks possess many things in common, in particular the manner of evolution of such networks. By adding a dimension of time…
Given graphs as input, Graph Neural Networks (GNNs) support the inference of nodes, edges, attributes, or graph properties. Graph Rewriting investigates the rule-based manipulation of graphs to model complex graph transformations. We…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
The branching of an RNA molecule is an important structural characteristic yet difficult to predict correctly, especially for longer sequences. Using plane trees as a combinatorial model for RNA folding, we consider the thermodynamic cost,…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…