This paper is published as part of a PCCP Themed Issue on: Nucleic Acid Simulations Guest Editors: Modesto Orozco and Charles Laughton Editorial Nucleic Acid Simulations Modesto Orozco and Charles Laughton, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b921472k Perspectives Viral assembly: a molecular modeling perspective Stephen C. Harvey, Anton S. Petrov, Batsal Devkota and Mustafa Burak Boz, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b912884k Simulation of DNA catenanes Alexander Vologodskii and Valentin V. Rybenkov, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910812b Papers Stabilization of radical anion states of nucleobases in DNA Alexander A. Voityuk, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910690a Effects of the biological backbone on DNA–protein stacking interactions Cassandra D. M. Churchill, Lex Navarro-Whyte, Lesley R. Rutledge and Stacey D. Wetmore, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910747a The impact of monovalent ion force field model in nucleic acids simulations Agnes Noy, Ignacio Soteras, F. Javier Luque and Modesto Orozco, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b912067j Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration Milo M. Lin, Dmitry Shorokhov and Ahmed H. Zewail, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910794k Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations Srinivasaraghavan Kannan and Martin Zacharias, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910792b Sensors for DNA detection: theoretical investigation of the conformational properties of immobilized single-strand DNA Vincenzo Barone, Ivo Cacelli, Alessandro Ferretti, Susanna Monti and Giacomo Prampolini, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b914386f Relaxation dynamics of nucleosomal DNA Sergei Y. Ponomarev, Vakhtang Putkaradze and Thomas C. Bishop, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910937b Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by Brownian dynamics Tomasz Wocjan, Jan Krieger, Oleg Krichevsky and Jörg Langowski, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b911857h A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation Witcha Treesuwan, Kitiyaporn Wittayanarakul, Nahoum G. Anthony, Guillaume Huchet, Hasan Alniss, Supa Hannongbua, Abedawn I. Khalaf, Colin J. Suckling, John A. Parkinson and Simon P. Mackay, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910574c Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory Giuseppe de Marco and Péter Várnai, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b917109f Dependence of A-RNA simulations on the choice of the force field and salt strength Ivana Beššeová, Michal Otyepka, Kamila Réblová and Jiří Šponer, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b911169g Protein–DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies Krystyna Zakrzewska, Benjamin Bouvier, Alexis Michon, Christophe Blanchet and Richard Lavery, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b910888m Evaluation of molecular modelling methods to predict the sequence-selectivity of DNA minor groove binding ligands Hao Wang and Charles A. Laughton, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b911702d Mesoscale simulations of two nucleosome-repeat length oligonucleosomes Tamar Schlick and Ognjen Perišić, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b918629h On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations F. Lankaš, O. Gonzalez, L. M. Heffler, G. Stoll, M. Moakher and J. H. Maddocks, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b919565n Charge transfer equilibria of aqueous single stranded DNA Marco D’Abramo, Massimiliano Aschi and Andrea Amadei, Phys. Chem. Chem. Phys., 2009 DOI: 10.1039/b915312h