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Abstract: PHITS (Particle and Heavy-Ion Transport code System) is a general-purpose three-dimensional Monte Carlo code, developed and maintained by RIST, JAEA and KEK in Japan together with Sihver et al. at Chalmers in Sweden. PHITS can deal with the transports of all varieties of hadrons and heavy ions with energies up to around 100GeV/nucleon, and in this paper the current status of PHITS is presented. We introduce a relativistically covariant version of JQMD, called R-JQMD, that features an improved ground state initialization algorithm, and we will present the introduction of electron and photon transport in PHITS using EGS5, which have increased the energy region for the photon and energy transport from up to around 3GeV to up to several hundred GeV depending on the atomic number of the target. We show how the accuracy in dose and fluence calculations can be improved by using tabulated cross sections. Benchmarking of shielding and irradiation effects of high energy protons in different materials relevant for shielding of accelerator facilities is also presented. In particular, we show that PHITS can be used for estimating the dose received by aircrews and personnel in space. In recent years, many countries have issued regulations or recommendations to set annual dose limitations for aircrews. Since estimation of cosmic-ray spectra in the atmosphere is an essential issue for the evaluation of aviation doses, we have calculated these spectra using PHITS. The accuracy of the atmospheric propagation simulation of cosmic-ray performed by PHITS has been well verified by experimental cosmic-ray spectra taken under various conditions. Based on a comprehensive analysis of the simulation results, an analytical model called “PARMA” has been proposed for instantaneously estimating the atmospheric cosmic-ray spectra below the altitude of 20km. We have also performed preliminary simulations of long-term dose distribution measurements at the ISS performed with the joint ESA-FSA experiment MATROSHKA-R (MTR-R) led by the Russian Federation Institute of Biomedical Problems (IMBP) and the ESA supported experiment MATROSHKA (MTR), led by the German Aerospace Center (DLR). For the purpose of examining the applicability of PHITS to the shielding design in space, the absorbed doses in a tissue equivalent water phantom inside an imaginary space vessel has been estimated for different shielding materials of different thicknesses. The results confirm previous results which indicate that PHITS is a suitable tool when performing shielding design studies of spacecrafts. [Copyright &y& Elsevier]