Related Experiment Video
Updated: Dec 24, 2025
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
Published on: July 19, 2024
Technical Note: Taking EGSnrc to new lows: Development of egs++ lattice geometry and testing with microscopic
Martin P Martinov1, Rowan M Thomson1
1Laboratory for Radiotherapy Physics, Department of Physics, Carleton University, Ottawa, ON, K1S 5B6, Canada.
Purpose:
This work introduces a new lattice geometry library, egs_lattice, into the EGSnrc Monte Carlo code, which can be used for both modeling very large (previously unfeasible) quantities of geometries (e.g., cells or gold nanoparticles (GNPs)) and establishing recursive boundary conditions. The reliability of egs_lattice, as well as EGSnrc in general, is cross-validated and tested at short length scales and low energies.
Methods:
New Bravais, cubic, and hexagonal lattice geometries are defined in egs_lattice and their transport algorithms are described. Simulations of cells and GNP-containing cavities are implemented to compare to independent, published Geant4-DNA and PENELOPE results. Recursive boundary conditions, implemented through a cubic lattice, are used to perform electron Fano cavity tests. The Fano test is performed on three different-sized cells containing GNPs in the region around the nucleus for three source energies.
Results:
Lattices are successfully implemented in EGSnrc, and are used for validation. EGSnrc calculated the dose to cell cytoplasm and nucleus when irradiated by an internal electron source with a median difference of 0.6% compared to published Geant4-DNA results. EGSnrc calculated the ratio of dose to a microscopic cavity containing GNPs over dose to a cavity containing a homogeneous mixture of gold, and results generally agree (within 1%) with published PENELOPE results. The electron Fano cavity test is passed for all energies and cells considered, with sub-0.1% discrepancies between EGSnrc-calculated and expected values. Additionally, the recursive boundary conditions used for the Fano test provided a factor of over a million increase in efficiency in some cases.
Conclusions:
The egs_lattice geometry library, currently available as a pull request on the EGSnrc GitHub "develop" branch, is now freely accessible as open-source code. Lattice geometry implementations cross-validated with independent simulations in other MC codes and verified with the electron Fano cavity test demonstrate not only the reliability of egs_lattice, but also, by extension, EGSnrc's ability to simulate transport in nanometer geometries and score in microscopic cavities.
Related Concept Videos
02:33Lattice Centering and Coordination Number
Types of Unit Cells
Imagine taking a large number of identical...
02:54Trends in Lattice Energy: Ion Size and Charge
02:46Crystal Field Theory - Tetrahedral and Square Planar Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...