Modelling DNA at the mesoscale: a challenge for nonlinear science?

Abstract

When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be used as a guide to improve them. There are nevertheless many open problems, particularly to describe DNA at the scale of a few tens of base pairs, which is relevant for many biological phenomena.

Invited paper, in the series "Open Problems" of Nonlinearity

References in corpus (9)

• Why is the DNA Denaturation Transition First Order?
• Thermostats for "slow" configurational modes
• Helicoidal model for DNA opening
• Order of the phase transition in models of DNA thermal denaturation
• Thermal denaturation of an helicoidal DNA model
• Can one predict DNA Transcription Start Sites by studying bubbles?
• Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system
• Local Cooperativity Mechanism in the DNA Melting Transition
• Modeling DNA beacons at the mesoscopic scale

Cited by in corpus (12)

• Thermodynamics of Twisted DNA with Solvent Interaction
• Driving denaturation: Nanoscale thermal transport as a probe of DNA melting
• Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
• Tunable Thermal Switching via DNA-Based Nano Devices
• Thermal and mechanical properties of a DNA model with solvation barrier
• Base pair fluctuations in helical models for nucleic acids
• LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA
• A three-state model with loop entropy for the over-stretching transition of DNA
• Mesoscopic helical models for DNA
• Energy Transfer in molecular devices
• Self-organised criticality in base-pair breathing in DNA with a defect
• Statistical method for A-RNA and B-DNA