Related papers: Minimal Models for RNA Simulations
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Since the Hadean era of Earth's history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
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…
A phase field model which describes the formation of protein-RNA complexes subject to phase segregation is analyzed. A single protein, two RNA species, and two complexes are considered. Protein and RNA species are governed by coupled…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
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…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…