Related papers: On a barrier height problem for RNA branching
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However, for reasons not well…
Many biological systems and artificial structures are ramified, and present a high geometric complexity. In this work, we propose a space-averaged model of branched systems for conservation laws. From a one-dimensional description of the…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Branching random flights are key to describing the evolution of many physical and biological systems, ranging from neutron multiplication to gene mutations. When their paths evolve in bounded regions, we establish a relation between the…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
A configuration-interaction model is presented for the barrier region of induced fission. The configuration space is composed of seniority-zero configurations constructed from self-consistent mean-field wave functions. The Hamiltonian…
We derive a message passing method for computing the spectra of locally tree-like networks and an approximation to it that allows us to compute closed-form expressions or fast numerical approximates for the spectral density of random graphs…
The investigation of dynamical processes on networks has been one focus for the study of contagion processes. It has been demonstrated that contagions can be used to obtain information about the embedding of nodes in a Euclidean space.…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Rugged (or, rough) energy landscape (REL) with spatially distributed maxima and minima are often employed in applications of physics, chemistry and biology (enzyme kinetics, protein folding, diffusion in disordered solids, transport in…
Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
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…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…