Computational Studies of RNA and DNA

Chapter 1 Basics of Nucleic Acid Structure

Chapter 2 Using Amber to Simulate DNA and RNA

Chapter 3 Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm

Chapter 4 Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands

Chapter 5 Data Mining of Molecular Dynamic Trajectories of Nucleic Acids

Chapter 6 Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids

Chapter 7 Modeling DNA Deformation

Chapter 8 Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes

Chapter 9 DNA Simulation Benchmarks as Revealed by X-Ray Structures

Chapter 10 RNA: The Cousin Left Behind Becomes a Star

Chapter 11 Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions

Chapter 12 Molecular Dynamics Simulations of Nucleic Acids

Chapter 13 Using Computer Simulations to Study Decoding by the Ribosome

Chapter 14 Base Stacking and Base Pairing

Chapter 15 Interaction of Metal Cations with Nucleic Acids and their Building Units

Chapter 16 Proton Transfer in DNA Base Pairs

Chapter 17 Comparative Study of Quantum Mechanical Methods Related to Nucleic Acid Bases: Electronic Spectra, Excited State Structures and Interations

Chapter 19 Computational modeling of Charge Transfer in DNA

Chapter 20 Quantum Chemical Calculations of NMR Parameters

Chapter 21 The Importance of Entropic Factors in DNA Behaviour: Insights from Simulations

Chapter 22 Sequence-Dependent Harmonic Deformability of Nucleic Acids Inferred from Atomistic Molecular Dynamics

Chapter 23 Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules

Chapter 24 Chromatin Simulations