RNA folding kinetics using Monte Carlo and Gillespie algorithms

DOI10.1007/S00285-017-1169-7zbMATH Open1392.92066arXiv1707.03922OpenAlexW2963996765WikidataQ47737296 ScholiaQ47737296MaRDI QIDQ1741906FDOQ1741906

Authors: Peter Clote, Amir H. Bayegan 

Publication date: 10 April 2018

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny (~ 20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to <N> times that of the Gillespie algorithm, where <N> denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by <N>; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gille- spie algorithms is publicly available, as is our software to compute the expected degree of the net- work of secondary structures of a given RNA sequence { see http://bioinformatics.bc.edu/clote/ RNAexpNumNbors.

Full work available at URL: https://arxiv.org/abs/1707.03922

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zbMATH Keywords

Metropolis algorithmGillespie algorithmRNA secondary structuremean first passage timemean recurrence timeexpected network degreerefolding kinetics

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Monte Carlo methods (65C05) Protein sequences, DNA sequences (92D20) Other programming paradigms (object-oriented, sequential, concurrent, automatic, etc.) (68N19)

Cites Work

• Title not available (Why is that?)
• Monte Carlo sampling methods using Markov chains and their applications
• Equation of state calculations by fast computing machines
• The Role of the Group Generalized Inverse in the Theory of Finite Markov Chains
• Title not available (Why is that?)
• On some new sequences generalizing the Catalan and Motzkin numbers
• Efficient computation of RNA folding dynamics
• RNA secondary structures and their prediction
• Funnels in energy landscapes
• RNA folding pathways and kinetics using 2D energy landscapes
• Combinatorics of locally optimal RNA secondary structures

Cited In (7)

• A continuous analogue for RNA folding
• RNA folding pathways and kinetics using 2D energy landscapes
• RNAexpNumNbors
• Title not available (Why is that?)
• Title not available (Why is that?)
• Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure
• An IP algorithm for RNA folding trajectories

Uses Software

• Rfam
• ViennaRNA
• FFTbor2D
• KFOLD
• ERD
• MSMBuilder
• FFTbor
• MODENA
• NNDB

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