Related papers: RNA Secondary Structures: Complex Statics and Glas…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
Multi-dimensional density of states provides a useful description of complex frustrated systems. Recent advances in Monte Carlo methods enable efficient calculation of the density of states and related quantities, which renew the interest…
We propose a new sensitivity analysis methodology for complex stochastic dynamics based on the Relative Entropy Rate. The method becomes computationally feasible at the stationary regime of the process and involves the calculation of…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
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…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
Monte Carlo techniques play a central role in statistical mechanics approaches for connecting macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo…
Dynamic Complexity is a phenomenon exhibited by a nonlinearly interacting system within which multitudes of different sizes of large scale coherent structures emerge, resulting in a globally nonlinear stochastic behavior vastly different…
The interrelation of dynamic processes active on separated time-scales in glasses and viscous liquids is investigated using a model displaying two time-scale bifurcations both between fast and secondary relaxation and between secondary and…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
Successful computer studies of glass-forming materials need to overcome both the natural tendency to structural ordering and the dramatic increase of relaxation times at low temperatures. We present a comprehensive analysis of eleven…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
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…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
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…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…