Discrete and Topological Models in Molecular Biology

Front Matter....Pages i-xiii
Front Matter....Pages 1-1
Perspectives in Computational Genome Analysis....Pages 3-22
The Sequence Reconstruction Problem....Pages 23-43
Extracting Coevolving Characters from a Tree of Species....Pages 45-65
When and How the Perfect Phylogeny Model Explains Evolution....Pages 67-83
An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques....Pages 85-107
Simplicial Models and Topological Inference in Biological Systems....Pages 109-141
Front Matter....Pages 143-143
Combinatorial Insights into RNA Secondary Structure....Pages 145-166
Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis....Pages 167-196
Modeling Autonomous Supramolecular Assembly....Pages 197-216
The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach....Pages 217-240
Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs....Pages 241-270
Front Matter....Pages 271-271
Programmed Genome Processing in Ciliates....Pages 273-287
The Algebra of Gene Assembly in Ciliates....Pages 289-307
Invariants of Graphs Modeling Nucleotide Rearrangements....Pages 309-323
Front Matter....Pages 325-325
Introduction to DNA Topology....Pages 327-345
Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations....Pages 347-361
Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links....Pages 363-386
Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination....Pages 387-401
Front Matter....Pages 403-403
Understanding DNA Looping Through Cre-Recombination Kinetics....Pages 405-418
The QSSA in Chemical Kinetics: As Taught and as Practiced....Pages 419-442
Front Matter....Pages 403-403
Algebraic Models and Their Use in Systems Biology....Pages 443-474
Deconstructing Complex Nonlinear Models in System Design Space....Pages 475-506
IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology....Pages 507-524