Computational Approaches in Molecular Radiation Biology, 1994
Monte Carlo Methods
Basic Life Sciences Series, Vol. 63

The Office of Health and Environmental Research (OHER) has supported and continues to support development of computational approaches in biology and medicine. OHER's Radiological and Chemical Physics Program initiated development of computational approaches to determine the effects produced by radiation of different quality (such as high energy electrons, protons, helium and other heavy ions, etc. ) in a variety of materials of biological interest-such as water, polymers and DNA; these include molecular excitations and sub-excitations and the production of ionization and their spatial and temporal distribution. In the past several years, significant advances have been made in computational methods for this purpose. In particular, codes based on Monte Carlo techniques have ·been developed that provide a realistic description of track-structure produced by charged particles. In addition, the codes have become sufficiently sophisticated so that it is now possible to calculate the spatial and temporal distribution of energy deposition patterns in small volumes of subnanometer and nanometer dimensions. These dimensions or resolution levels are relevant for our understanding of mechanisms at the molecular level by which radiations affect biological systems. Since the Monte Carlo track structure codes for use in radiation chemistry and radiation biology are still in the developmental stage, a number of investigators have been exploring different strategies for improving these codes.

Significance of Computational Biology.- Computational Biology Opportunity and Challenges for the Future.- Overview of Significant Challenges in Molecular Biology Amenable to Computational Methods.- Initial Physical and Chemical Studies.- Basic Physical and Chemical Information Needed for Development of Monte Carlo Codes.- Interactions of Low-Energy Electrons with Condensed Matter: Relevance for Track Structure.- Electron Emission Resulting from Fast Ion Impact on Thin Metal Foils: Implications of These Data for Development of Track Structure Models.- Direct Ionization of DNA in Solution.- Track Structure Code Development.- Charged-Particle Transport in Biomolecular Media: The Third Generation.- Track Structure, Chromosome Geometry, and Chromosome Aberrations.- Monte Carlo and Analytic Methods in the Transport of Electrons, Neutrons, and Alpha Particles.- PITS: A Code Set for Positive Ion Track Structure.- Monte Carlo Track-Structure Calculations for Aqueous Solutions Containing Biomolecules.- Comparison of Track Structure Codes.- Comparison of Various Monte Carlo Track Structure Codes for Energetic Electrons in Gaseous and Liquid Water.- A Comparison between Two Monte Carlo Codes on Determination of Transient Chemical Yields.- An Attempt to Modify the MOCA Water-Vapor-Ion Code to Simulate Liquid Phase.- Modeling of Biological Effects.- Three Statistical Technologies with High Potential in Biological Imaging and Modeling.- Monte Carlo Approach in Assessing Damage in Higher Order Structures of DNA.- A Nucleosome Model for the Simulation of DNA Strand Break Experiments.- A Computational Approach to the Relationship between Radiation Induced Double Strand Breaks and Translocations.