This book integrates modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.

1. Basics of Nucleic Acid Structure, Bohdan Schneider and Helen M. Berman 2. Using Amber to Simulate DNA and RNA, Thomas E. Cheatham, III and David A. Case 3. Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm, Alexander D. MacKerell, Jr. and Lennart Nilsson 4. Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands, Martin Zacharias 5. Data Mining of Molecular Dynamic Trajectories of Nucleic Acids, Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda, Carles Ferrer, Antonio Valencia, Alberto Perez, Oliver Carrillo, Juan Fernandez-Recio, Xavier de la Cruz and F. Javier Luque 6. Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids, Catherine Kelso and Carlos Simmerling 7. Modeling DNA Deformation, Peter Varnai and Richard Lavery 8. Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes, David L. Beveridge, Surjit B. Dixit, Bethany L. Kormos, Anne M. Baranger and B. Jayaram 9. DNA Simulation Benchmarks as Revealed by X-Ray Structures, Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge, Guohui Zheng, and Victor B. Zhurkin 10. RNA: The Cousin Left Behind Becomes a Star, Tamar Schlick 11. Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions, Pascal Auffinger 12. Molecular Dynamics Simulations of Nucleic Acids, Nada¿¿a Å paþkova, Thomas E. Cheatham, III and Jirí Å poner 13. Using Computer Simulations to Study Decoding by the Ribosome, Kevin Y. Sanbonmatsu 14. Base Stacking and Base Pairing, Jirí Å poner, Petr Jureþka and Pavel Hobza 15. Interaction of Metal Cations with Nucleic Acids and their Building Units, Judit E. Å poner, Jaroslav V. Burda, Jerzy Leszczynki, and Jirí Å poner 16. Proton Transfer in DNA Base Pairs, J. Bertran, L. Blancafort, M. Noguera, M. Sodupe 17. Comparative Study of Quantum Mechanical Methods Related to Nucleic Acid Bases: Electronic Spectra, Excited State Structures and Interactions, M.K. Shukla and Jerzy Leszczynski 18. Substituent Effects on Hydrogen Bonds in DNA, Celia Fonseca Guerra and F. Matthias Bickelhaupt 19. Computational modeling of Charge Transfer in DNA, Alexander A. Voityuk 20. Quantum Chemical Calculations of NMR Parameters, Wolfgang Schöfberger, Vladimír Sychrovsky and LukaÅ¡ Trantírek 21. The Importance of Entropic Factors in DNA Behaviour: Insights from Simulations, Sarah A. Harris and Charles A. Laughton 22. Sequence-Dependent Harmonic Deformability of Nucleic Acids Inferred from Atomistic Molecular Dynamics, Filip LankaÅ¡ 23. Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules, Alexander Vologodskii 24. Chromatin Simulations, J. Langowski and H. Schiessel