Forced-unfolding and force-quench refolding of RNA hairpins [PDF]
, 2006 Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of $f_S$ and the loading rate ($r_f$). The simulations and theoretical analysis have been done without and with the handles that are explicitly modeled by ...
Barsegov +54 more
core +3 more sources
On the Hairpin Incompletion [PDF]
Fundamenta Informaticae 110 (2011) 255--269, 2011 Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and studied on the closure properties and algorithmic problems concerning several families of languages.
arxiv +1 more source
Extract and Characterize Hairpin Vortices in Turbulent Flows [PDF]
, 2023 Hairpin vortices are one of the most important vortical structures in turbulent flows. Extracting and characterizing hairpin vortices provides useful insight into many behaviors in turbulent flows. However, hairpin vortices have complex configurations and might be entangled with other vortices, making their extraction difficult.
arxiv +1 more source
Lipid vesicles chaperone an encapsulated RNA aptamer. [PDF]
, 2018 The organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids.
Chen, Irene A +2 more
core +1 more source
How RNA acts as a nuclease:some mechanistic comparisons in the nucleolytic ribozymes [PDF]
, 2017 Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. The discovery of several new ribozymes in this class has now allowed comparisons to be made, and the beginnings of mechanistic ...
Lilley, David M. J.
core +2 more sources
Interference and heat transfer between hairpin vortices in wakes behind staggered hills [PDF]
arXiv, 2022 The present study performs a numerical simulation of the interference and heat transfer between hairpin vortices formed in wakes behind staggered hills in a laminar boundary layer. Hairpin vortices are periodically shed in the wake of a row of hills, causing interference between the hairpin vortices. As the spanwise distance between the hills decreases,
arxiv
RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity
, 2012 Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail.
Hyeon, Changbong +2 more
core +1 more source
NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site [PDF]
The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme.
Alam +85 more
core +2 more sources
Force for ancient and recent life: viral and stem-loop RNA consortia promote life. [PDF]
, 2014 Lytic viruses were thought to kill the most numerous host (i.e., kill the winner). But persisting viruses/defectives can also protect against viruses, especially in a ubiquitous virosphere. In 1991, Yarmolinsky et al.
Villarreal, Luis P
core +1 more source
Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot [PDF]
, 2017 The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms.
arxiv +1 more source