Basics of Nucleic Acid Structure:Concepts, Tools, and Archives -- Using Amber to simulate DNA and RNA -- Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes Using CHARMM -- Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes With Ligands -- Data Mining of Molecular Dynamic Trajectories of Nucleic Acids -- Enhanced Sampling Methods for Atomistic Simulation Of Nucleic Acids -- Modeling DNA Deformation -- Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes -- DNA Simulation Benchmarks as Revealed by X-Ray Structures.-RNA: The Cousin Left Behind Becomes a Star -- Molecular dynamics simulations of RNA systems: importance of the initial conditions- RNA molecular dynamics -- Molecular dynamics simulations of nucleic acids: MD simulations of G-DNA and functional RNAs -- Using Computer Simulations to Study Decoding by the Ribosome -- Base stacking and base pairing: Advanced quantum chemical studies -- Interaction of Metal Cations With Nucleic Acids and their Building Units: A comprehensive view from quantum chemical calculations -- Proton transfer in DNA base pairs: Potential mutagenic processes -- Comparative Study of Quantum Mechanical Methods Related to Nucleic Acid Bases: Electronic Spectra, Excited State Structures and Interactions -- Substituent Effects on Hydrogen Bonds in DNA:A Kohn-Sham DFT approach -- Computational modeling of charge transfer in DNA -- Quantum chemical calculations of NMR parameters -- The Importance of Entropic Factors In DNA Behaviour: Insights From Simulations -- Sequence-dependent harmonic deformability of nucleic acids inferred from atomistic molecular dynamics -- Simulation of equilibrium and dynamic properties of large DNA molecules -- Chromatin Simulations: From DNA to chromatin fibers. .