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These files contain cell models for TOPAS/Geant4 and the inclusion of nano particles in particle scattering simulations. A simple spherical cell with nanoparticles can be generated in a fast manner. The user has the option to include the following organelles: nucleus, mitochondria, cell membrane. Additionally nanoparticles can be included in the cytosol and at the surface of the nucleus and/or the mitochondria.
The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org). The sourcecode together with examples and scorers are provided.
"If you use this extension please cite the following literature:
Hahn, M.B., Zutta Villate, J.M. "Combined cell and nanoparticle models for TOPAS to study radiation dose enhancement in cell organelles." Sci Rep 11, 6721 (2021).
https://doi.org/10.1038/s41598-021-85964-2 "
To simulate the movement of the macroscopic magnetic moment in ferromagnetic systems under the influence of elevated temperatures, the stochastic version of the Landau-Lifshitz (LL) or the Landau-Lifshitz-Gilbert equation with a spin density of one per unit cell has to be used.
To apply the stochastic LL to micromagnetic simulations, where the spin density per unit cell is generally higher, a conversion has to be performed. OOMMF sample files MIF) are provided which can be used to determine the Curie temperature for the classical bulk magnets, iron, nickel and cobalt.
Raman spectroscopic signature of ectoine conformations in bulk solution and crystalline state
(2020)
Recent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further Shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules.
Ectoine is a small zwitterionic osmolyte and compatible solute, which does not interfere with cell metabolism even at molar concentrations. Plasmid DNA (pUC19) was irradiated with ultraviolet radiation (UV-C at 266 nm) under quasi physiological conditions (PBS) and in pure water in the presence and absence of ectoine (THP(B)) and hydroxyectoine (THP(A)). Different types of UV induced DNA damage were analysed: DNA single-strand breaks (SSBs), abasic sites and cyclobutane pyrimidine dimers (CPDs). A complex interplay between these factors was observed with respect to the nature and occurrence of DNA damage with 266 nm photons. In PBS, the cosolutes showed efficient protection against base damage, whilst in pure water, a dramatic shift from SSB damage to base damage was observed when cosolutes were added. To test whether these effects are caused by ectoine binding to DNA, further experiments were conducted: small-angle X-ray scattering (SAXS), surface-plasmon resonance (SPR) measurements and Raman spectroscopy. The results show, for the first time, a close interaction between ectoine and DNA. This is in stark contrast to the assumption made by preferential exclusion models, which are often used to interpret the behaviour of compatible solutes within cells and with biomolecules. It is tentatively proposed that the alterations of UV damage to DNA are attributed to ectoine influence on nucleobases through the direct interaction between ectoine and DNA.
DNA basierte Dosimetrie
(2020)
We propose the development of a standardized DNA based dosimeter. This dosimeter will improve the comparability between the results of different laboratories in radiation research. Compared to conventional methods in dosimetry, this Approach provides direct access to the relation between radiation interaction and biological damage. Moreover, it enables the systematic investigation of the relation between the microscopic characteristics of radiation and DNA damage over a wide dose range.
The image designed by Natalia Cano Murillo and colleagues shows the cross section of a ternary composite (boehmite/polycarbonate/epoxy, 80μm x 80μm). The surface was measured by AFM kelvin probe microscopy, yielding the surface potential which is shown as 3D‐surface and contour lines. The sample was further subjected to AFM force spectroscopy with a lateral resolution of 1μm², yielding the local Young's modulus, projected in false colors on the 3D surface. The ternary system, containing boehmite nanoparticles, shows a broad distribution of modulus, desirable for optimized macroscopic mechanical properties, such as high stiffness as well as toughness.