Accurate modeling of DNA damages resulting from ionizing radiation remains a challenge of today's radiobiology research. An original set of physics processes has been recently developed for modeling the detailed transport of protons and neutral hydrogen atoms in liquid water and in DNA nucleobases using the Geant4-DNA extension of the open source Geant4 Monte Carlo simulation toolkit. The theoretical cross sections as well as the mean energy transfers during the different ionizing processes were taken from recent works based on classical as well as quantum mechanical predictions. Furthermore, in order to compare energy deposition patterns in liquid water and DNA material, we here propose a simplified cellular nucleus model made of spherical voxels, each containing randomly oriented nanometer-size cylindrical targets filled with either liquid water or DNA material (DNA nucleobases) both with a density of 1 g/cm(3). These cylindrical volumes have dimensions comparable to genetic material units of mammalian cells, namely, 25 nm (diameter) x 25 nm (height) for chromatin fiber segments, 10 nm (d) x 5 nm (h) for nucleosomes and 2 nm (d) x 2 nm (h) for DNA segments. Frequencies of energy deposition in the cylindrical targets are presented and discussed. (C) 2013 Elsevier B.V. All rights reserved.306165168French Agence Nationale de la Recherche [ANR-09-BLAN-0135-01]European Space Agency [AO6041-22712/09/NL/AT]International Associated Laboratory "France Korea Particle Physics Laboratory" (FKPPL)France-Korea Partenariat Hubert Curien (PHC) STAR program ("PROTEUS" project)National Nuclear R&D Program through the National Research Foundation of Korea [2011-0020782]French Agence Nationale de la Recherche [ANR-09-BLAN-0135-01]European Space Agency [AO6041-22712/09/NL/AT]National Nuclear R&D Program through the National Research Foundation of Korea [2011-0020782]