Related papers: Combinatorics of RNA-RNA interaction
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant,…
We study the pairing of fermions in a one-dimensional lattice of tunable double-well potentials using radio-frequency spectroscopy. The spectra reveal the coexistence of two types of atom pairs with different symmetries. Our measurements…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
It is shown that the combination of the structure functions $F_2$ predicted by the CKMT model at low and moderate values of $Q^2$ and MRS99 parton distribution functions at high $Q^2$ gives a good description of the data over complete…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The structural properties of additive binary hard-sphere mixtures are addressed as a follow-up of a previous paper [S. Pieprzyk et al., Phys. Rev. E 101, 012117 (2020)]. The so-called rational-function approximation method and an approach…
The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…
Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. However, current computational methods often struggle with suboptimal performance due to…
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,…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…