CONTENTS -- Introduction -- Methylation of DNA may be Useful as a Computational Tool: Experimental Evidence Susannah Gal, Nancy Monteith, Sara Shkalim, Hu Huang and Tom Head -- 1. Introduction -- 2. Materials and Methods -- 3. Results -- 3.1. Explanation of the system set-up and approach -- 3.2. Testing available methylases and restriction enzymes -- 3.3. 3-variable SAT computation with plasmid DNA and PCR product -- 4. Discussion -- References -- Dynamics of Random Boolean Networks James F. Lynch -- 1. Introduction -- 2. Definitions -- 3. Local Structure of Networks -- 4. Branching Processes -- 5. Ineffective Gates -- 6. Frozen Gates -- 7. Networks of 2-Input Gates -- 8. Future Work and Open Problems -- References -- Unknots and DNA Louis H. Kauffman and S. Lambropoulou -- 0. Introduction -- 1. Culprits -- 2. Rational Tangles, Rational Knots and Continued Fractions -- 2.1. Rational Tangles and their Invariant Fractions -- 2.2. Rational Knots and Continued Fractions -- 3. Sums of Two Rational Tangles -- 4. Continued Fractions, Convergents and Lots of Unknots -- 5. Constructing Hard Unknots -- 6. The Smallest Hard Unknots -- 7. The Goeritz Unknot -- 8. Stability in Processive DNA Recombination -- Acknowledgements -- References -- Developing a Mathematical Model of Phagocytosis: A Learning Process Nataˇsa Macura, Tong Zhang and Arturo Casadevall -- 1. Introduction -- 2. Efficacy of Phagocytosis -- 3. Modeling phagocytosis -- 4. Modeling Goals -- References -- An Age Structured Model of T Cell Populations Brynja Kohler -- 1. Biological Background -- 2. The Model and Analysis -- 2.1. Derivation of the age-structured PDE system -- 2.2. Age independent ODE problem -- 2.3. Simplified case: No net population change -- 2.4. Formulation of the Cauchy problem -- 2.5. Solution using Laplace transforms.

2.6. Extending the solution: Allowing population growth -- 3. Simulation Results -- 3.1. Parameter selection and assumptions -- 3.2. Single clone results -- 3.3. Scarcity of antigen -- 3.4. Memory -- 3.5. Two clones competing for antigen sites -- References -- Modeling and Simulation of Age- and Space-Structured Biological Systems Bruce P. Ayati -- 1. Introduction -- 2. General Problem -- 3. Computational Methods -- 3.1. Moving-grid Galerkin method in age -- 3.2. Relationship to Leslie matrix models -- 3.3. Time and space integration -- 3.4. Convergence results -- 4. Example Systems -- 4.1. Proteus mirabilis swarm-colony development -- 4.2. Tumor invasion -- 5. Conclusions -- References -- Nutrient-Plankton Interaction with a Toxin in a Variable Input Nutrient Environment Sophia R.-J. Jang and James Baglama -- 1. Introduction -- 2. The Nutrient-Phytoplankton-Zooplankton Model -- 3. A Nutrient-Plankton-Toxin Model with Inhibition of the Phytoplankton -- 4. Discussion -- References -- On the Mechanism of Strain Replacement in Epidemic Models with Vaccination Maia Martcheva -- 1. Introduction -- 2. The Mechanism of Strain Replacement -- 3. Differential Effectiveness of the Vaccine and Strain Replacement -- 4. Coinfection, Perfect Vaccination and Strain Replacement -- 5. Cross-Immunity and Strain Replacement -- 6. Discussion -- Acknowledgments -- References.