Related papers: RNA Secondary Structures: Complex Statics and Glas…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
We study two dimensional frustrated but non-disordered systems applying a replica approach to a stripe forming model with competing interactions. The phenomenology of the model is representative of several well known systems, like high-Tc…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
The low-temperature quasi-universal behavior of amorphous solids has been attributed to the existence of spatially-localized tunneling defects found in the low-energy regions of the potential energy landscape. Computational models of…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
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…
We calculate the density of states of a binary Lennard-Jones glass using a recently proposed Monte Carlo algorithm. Unlike traditional molecular simulation approaches, the algorithm samples distinct configurations according to…
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,…
Recently, the use of mathematical methods and computer science applications have got significant response among biochemists and biologists to modeling the biological systems. The computational and mathematical methods have enormous…
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…
We characterize the low temperature phase of a simple model for RNA secondary structures by determining the typical energy scale E(l) of excitations involving l bases. At zero temperature, we find a scaling law E(l) \sim l^\theta with…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
We have analyzed a non-randomly frustrated spin model which exhibits behavior remarkably similar to the phenomenology of structural glasses. The high-temperature disordered phase undergoes a strong first-order transition to a long-range…
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…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
Monte Carlo simulations are widely employed to measure the physical properties of glass-forming liquids in thermal equilibrium. Combined with local Monte Carlo moves, the Metropolis algorithm can also be used to simulate the relaxation…
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…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
We use the swap Monte Carlo algorithm to analyse the glassy behaviour of sticky spheres in equilibrium conditions at densities where conventional simulations and experiments fail to reach equilibrium, beyond predicted phase transitions and…