Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.
Author(s): Giuditta Franco (auth.), Nataša Jonoska, Masahico Saito (eds.)
Series: Natural Computing Series
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2014
Language: English
Pages: 524
Tags: Theory of Computation; Mathematical and Computational Biology; Evolutionary Biology; Systems Biology; Cell Biology; Biological Networks, Systems 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
