Related papers: Statistical Physics of RNA-folding
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule…
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of…
It is shown that the enthalpy of any close packed structure for a given element can be characterised as a linear expansion in a set of continuous variables $\alpha_n$ which describe the stacking configuration. This enables us to represent…
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,…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight ~ l^{-c} for loops of length l in the recursion relation for the partition function, we show that the…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
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…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
Second-order structured deformations of continua provide an extension of the multiscale geometry of first-order structured deformations by taking into account the effects of submacroscopic bending and curving. We derive here an integral…