Page 297 - 2014 Printable Abstract Book
P. 297
(PS5-18) A radiation chemistry code based on the green's functions of the diffusion equation. Ianik
1
2
1
2
Plante and Honglu Wu , USRA/DSLS, Houston, TX and NASA Johnson Space Center, Houston, TX
Ionizing radiation produces radiolytic species such as .OH, e-aq, and H. when they interact with
biological matter. Following their creation, these species diffuse and chemically react with biological
molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing
radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the
radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-
step radiation chemistry code based on the Green’s functions of the diffusion equation (GFDE), which is
able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations
based on the GFDE have been used to simulate biochemical networks in time and space [1, 2] and are
often used as the “gold standard” to validate diffusion-reaction theories. The exact GFDE for partially
diffusion-controlled reactions is complex and difficult to use for simulations. Therefore, the much simpler
radial Green’s function is often used [3]. Recently, we have developed a sampling algorithm for the radial
Green’s function [4]. This algorithm yields the inter-particle distance vector length after a time step; the
deviation angles of the inter-particle vector are not taken into consideration. In this work, we have
developed an algorithm to fully characterize the inter-particle vector after a time step, using the radial
Green’s function and a technique developed by Clifford et al. [5] to generate the vector deviation angles,
knowing the inter-particle vector length before and after a time step. The results are compared with those
predicted by the exact GFDE and by the analytical angular functions for free diffusion. This is another step
in the creation of the radiation chemistry code that should help understanding the contribution of the
indirect effect in the formation of DNA damage and double-strand breaks. [1] Agmon, N., Popov, A.V., J.
Chem. Phys. 119, 6680-6690 (2003) [2] van Zon, J.S. and ten Wolde, P.R. J. Chem. Phys. 123, 234910 (2005)
[3] Krissinel, E.B., Agmon, N. J. Comput. Chem. 17, 1085-1098 (1995) [4] Plante, I., Devroye, L., Cucinotta,
F.A., J. Comput. Phys. 242, 531-543 (2013) [5] Clifford, P. et al. J. Chem. Soc., Faraday Trans. I, 82, 2673-
2689 (1986)
(PS5-19) PARTRAC modelling of proton bunches focused to submicrometer scales: Low-LET radiation
1;2
1;2
damage in high-LET-like spatial structure. Werner Friedland, PhD ; Pavel Kundrát, PhD ; and Elke
1
1;2
Schmitt, PhD ; Institute of Radiation Protection, Neuherberg, Germany and Helmholtz Zentrum
2
München, German Research Center of Environmental Health, Neuherberg, Germany
PARTRAC is a state-of-the-art tool for Monte Carlo simulations of radiation track structures,
damage induction in cellular DNA, and double-strand break (DSB) repair via the non-homologous end-
joining (NHEJ) pathway. Dedicated modules describe in an event-by-event manner the energy depositions
by ionizing particles in the traversed medium as well as the production and mutual reactions of reactive
species. DNA damage is assessed by overlapping the track structures, namely energy deposition events
for direct effects and distributions of radicals for indirect effects of radiation, with multi-scale chromatin
models. The implemented DNA and chromatin structures range from atomic models of base pairs over
nucleosomes, chromatin fibre, loops and domains to chromosome territories in eukaryotic cell nuclei. The
NHEJ module represents the spatial mobility of individual DNA ends from the induced DSB and their
enzymatic processing. Recently this module has been extended to simulate chromosomal aberrations.
PARTRAC calculations have been thoroughly tested against physical, chemical and biological data. In
recent and ongoing microbeam experiments (Schmid et al 2012 Phys Med Biol 57, 5889), protons and Li
295 | P a g e
1
2
1
2
Plante and Honglu Wu , USRA/DSLS, Houston, TX and NASA Johnson Space Center, Houston, TX
Ionizing radiation produces radiolytic species such as .OH, e-aq, and H. when they interact with
biological matter. Following their creation, these species diffuse and chemically react with biological
molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing
radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the
radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-
step radiation chemistry code based on the Green’s functions of the diffusion equation (GFDE), which is
able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations
based on the GFDE have been used to simulate biochemical networks in time and space [1, 2] and are
often used as the “gold standard” to validate diffusion-reaction theories. The exact GFDE for partially
diffusion-controlled reactions is complex and difficult to use for simulations. Therefore, the much simpler
radial Green’s function is often used [3]. Recently, we have developed a sampling algorithm for the radial
Green’s function [4]. This algorithm yields the inter-particle distance vector length after a time step; the
deviation angles of the inter-particle vector are not taken into consideration. In this work, we have
developed an algorithm to fully characterize the inter-particle vector after a time step, using the radial
Green’s function and a technique developed by Clifford et al. [5] to generate the vector deviation angles,
knowing the inter-particle vector length before and after a time step. The results are compared with those
predicted by the exact GFDE and by the analytical angular functions for free diffusion. This is another step
in the creation of the radiation chemistry code that should help understanding the contribution of the
indirect effect in the formation of DNA damage and double-strand breaks. [1] Agmon, N., Popov, A.V., J.
Chem. Phys. 119, 6680-6690 (2003) [2] van Zon, J.S. and ten Wolde, P.R. J. Chem. Phys. 123, 234910 (2005)
[3] Krissinel, E.B., Agmon, N. J. Comput. Chem. 17, 1085-1098 (1995) [4] Plante, I., Devroye, L., Cucinotta,
F.A., J. Comput. Phys. 242, 531-543 (2013) [5] Clifford, P. et al. J. Chem. Soc., Faraday Trans. I, 82, 2673-
2689 (1986)
(PS5-19) PARTRAC modelling of proton bunches focused to submicrometer scales: Low-LET radiation
1;2
1;2
damage in high-LET-like spatial structure. Werner Friedland, PhD ; Pavel Kundrát, PhD ; and Elke
1
1;2
Schmitt, PhD ; Institute of Radiation Protection, Neuherberg, Germany and Helmholtz Zentrum
2
München, German Research Center of Environmental Health, Neuherberg, Germany
PARTRAC is a state-of-the-art tool for Monte Carlo simulations of radiation track structures,
damage induction in cellular DNA, and double-strand break (DSB) repair via the non-homologous end-
joining (NHEJ) pathway. Dedicated modules describe in an event-by-event manner the energy depositions
by ionizing particles in the traversed medium as well as the production and mutual reactions of reactive
species. DNA damage is assessed by overlapping the track structures, namely energy deposition events
for direct effects and distributions of radicals for indirect effects of radiation, with multi-scale chromatin
models. The implemented DNA and chromatin structures range from atomic models of base pairs over
nucleosomes, chromatin fibre, loops and domains to chromosome territories in eukaryotic cell nuclei. The
NHEJ module represents the spatial mobility of individual DNA ends from the induced DSB and their
enzymatic processing. Recently this module has been extended to simulate chromosomal aberrations.
PARTRAC calculations have been thoroughly tested against physical, chemical and biological data. In
recent and ongoing microbeam experiments (Schmid et al 2012 Phys Med Biol 57, 5889), protons and Li
295 | P a g e
