Related papers: On a barrier height problem for RNA branching

We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the unfolded states is Gaussian, which follows from central…

Branching architecture characterizes numerous systems, ranging from synthetic (hyper)branched polymers and biomolecules such as lignin, amylopectin, and nucleic acids to tracheal and neuronal networks. Its ubiquity reflects the many…

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…

Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…

RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…

In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…

Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…

Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…

A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…

We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the…

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

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…

We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component,…