RNA Secondary Structures: Complex Statics and Glassy Dynamics
| Autor: | Alexander K. Hartmann, Alexander Mann, S. Wolfsheimer, Bernd Burghardt |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Statistics and Probability
Physics Statistical Mechanics (cond-mat.stat-mech) Monte Carlo method Complex system FOS: Physical sciences Biomolecules (q-bio.BM) Statistical and Nonlinear Physics Disordered Systems and Neural Networks (cond-mat.dis-nn) Condensed Matter - Disordered Systems and Neural Networks 01 natural sciences Transfer matrix 010305 fluids & plasmas Quantitative Biology - Biomolecules FOS: Biological sciences Phase space Metastability 0103 physical sciences Density of states State space Statistical physics Statistics Probability and Uncertainty 010306 general physics Topology (chemistry) Condensed Matter - Statistical Mechanics |
| Popis: | Models for RNA secondary structures (the topology of folded RNA) without pseudo-knots are disordered systems with a complex state space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected when performing Monte Carlo simulations. Interestingly, in contrast to most other complex systems, the ground states and the density of states can be computed in polynomial time exactly using transfer matrix methods. Hence, the RNA secondary structure is an ideal model to study the relation between static/thermodynamic properties and dynamics of algorithms. Also they constitute an ideal benchmark system for new Monte Carlo methods. Here we considered three different recent Monte Carlo approaches: entropic sampling using flat histograms, optimized-weights ensembles and ParQ, which estimates the density of states from transition matrices. These methods were examined by comparing the obtained density of states with the exact results. We relate the complexity seen in the dynamics of the Monte Carlo algorithms to static properties of the phase space by studying the correlations between tunneling times, sampling errors, amount of metastable states and degree of ultrametricity at finite temperature. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|