Computational Approaches in Molecular Radiation Biology

1. Front Matter

   Pages i-ix

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2. Significance of Computational Biology

   1. Computational Biology Opportunity and Challenges for the Future

      • John C. Wooley, Matesh N. Varma

      Pages 1-9

   2. Overview of Significant Challenges in Molecular Biology Amenable to Computational Methods

      • Robert M. Glaeser

      Pages 11-19

3. Initial Physical and Chemical Studies

   1. Basic Physical and Chemical Information Needed for Development of Monte Carlo Codes

      • Mitio Inokuti

      Pages 21-31

   2. Interactions of Low-Energy Electrons with Condensed Matter: Relevance for Track Structure

      • R. H. Ritchie, R. N. Hamm, J. E. Turner, W. E. Bolch

      Pages 33-47

   3. Electron Emission Resulting from Fast Ion Impact on Thin Metal Foils: Implications of These Data for Development of Track Structure Models

      • R. D. DuBois, C. G. Drexler

      Pages 49-63

   4. Direct Ionization of DNA in Solution

      • J. H. Miller, W. E. Wilson, R. H. Ritchie

      Pages 65-76

4. Track Structure Code Development

   1. Charged-Particle Transport in Biomolecular Media: The Third Generation

      • M. Zaider, A. Fung, M. Bardash

      Pages 77-92

   2. Track Structure, Chromosome Geometry and Chromosome Aberrations

      • David J. Brenner, John F. Ward, Rainer K. Sachs

      Pages 93-113

   3. Monte Carlo and Analytic Methods in the Transport of Electrons, Neutrons, and Alpha Particles

      • Randall S. Caswell, Stephen M. Seltzer

      Pages 115-136

   4. PITS: A Code Set for Positive Ion Track Structure

      • W. E. Wilson, J. H. Miller, H. Nikjoo

      Pages 137-153

   5. Monte Carlo Track-Structure Calculations for Aqueous Solutions Containing Biomolecules

      • J. E. Turner, R. N. Hamm, R. H. Ritchie, W. E. Bolch

      Pages 155-166

5. Comparison of Track Structure Codes

   1. Comparison of Various Monte Carlo Track Structure Codes for Energetic Electrons in Gaseous and Liquid Water

      • Hooshang Nikjoo, Shuzo Uehara

      Pages 167-185

   2. A Comparison between Two Monte Carlo Codes on Determination of Transient Chemical Yields

      • R. N. Hamm, J. E. Turner, A. Chatterjee

      Pages 187-193

   3. An Attempt to Modify the MOCA Water-Vapor-Ion Code to Simulate Liquid Phase

      • S. B. Curtis, J. B. Schmidt, W. E. Wilson

      Pages 195-198

6. Modeling of Biological Effects

   1. Three Statistical Technologies with High Potential in Biological Imaging and Modeling

      • Moshe Fridman, J. Michael Steele

      Pages 199-224

   2. Monte Carlo Approach in Assessing Damage in Higher Order Structures of DNA

      • Aloke Chatterjee, James B. Schmidt, William R. Holley

      Pages 225-241

   3. A Nucleosome Model for the Simulation of DNA Strand Break Experiments

      • Michel Terrissol, Ekkehard Pomplun

      Pages 243-250

   4. A Computational Approach to the Relationship between Radiation Induced Double Strand Breaks and Translocations

      • William R. Holley, Aloke Chatterjee

      Pages 251-259

7. Back Matter

   Pages 261-263

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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.

• DNA
• Termination
• biological effects
• development
• imaging
• liquid water
• molecular biology

• U.S. Department of Energy, Gaithersburg, USA

  Matesh N. Varma

• Lawrence Berkeley Laboratory, Berkeley, USA

  Aloke Chatterjee

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