1. A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
- Author
-
Modesto Orozco, Genís Bayarri, Adam Hospital, Alexandra Balaceanu, Pablo D Dans, and Jürgen Walther
- Subjects
Current (mathematics) ,Field (physics) ,Base pair ,Monte Carlo method ,Parameterized complexity ,Biology ,Molecular Dynamics Simulation ,01 natural sciences ,03 medical and health sciences ,Molecular dynamics ,0103 physical sciences ,Genetics ,030304 developmental biology ,0303 health sciences ,Mesoscopic physics ,Quantitative Biology::Biomolecules ,Internet ,010304 chemical physics ,Modal ,Methods Online ,Thermodynamics ,Biological system ,DNA, B-Form ,Monte Carlo Method ,Algorithms ,Software ,Microsatellite Repeats - Abstract
We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.
- Published
- 2020