Discrete and Topological Models in Molecular Biology, 1st Edition

  • Published By:
  • ISBN-10: 3642401937
  • ISBN-13: 9783642401930
  • DDC: 570.285
  • Grade Level Range: College Freshman - College Senior
  • 524 Pages | eBook
  • Original Copyright 2014 | Published/Released June 2014
  • This publication's content originally published in print form: 2014

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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 kSMPics 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.

Table of Contents

Front Cover.
Other Frontmatter.
Title Page.
Copyright Page.
Other Frontmatter.
1: Discrete and Graph-Theoretic Models for Data Analysis.
2: Perspectives in Computational Genome Analysis.
3: The Sequence Reconstruction Problem.
4: Extracting Coevolving Characters from a Tree of Species.
5: When and How the Perfect Phylogeny Model Explains Evolution.
6: An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques.
7: Simplicial Models and Topological Inference in Biological Systems.
8: Molecular Arrangements and Structures.
9: Combinatorial Insights into RNA Secondary Structure.
10: Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis.
11: Modeling Autonomous Supramolecular Assembly.
12: The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach.
13: Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs.
14: Gene Rearrangements.
15: Programmed Genome Processing in Ciliates.
16: The Algebra of Gene Assembly in Ciliates.
17: Invariants of Graphs Modeling Nucleotide Rearrangements.
18: Topological Models and Spatial DNA Embeddings.
19: Introduction to DNA Topology.
20: Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations.
21: Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links.
22: Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination.
23: Dynamics and Kinetics of Molecular Interactions.
24: Understanding DNA Looping through Cre-Recombination Kinetics.
25: The QSSA in Chemical Kinetics: As Taught and as Practiced.
26: Algebraic Models and Their Use in Systems Biology.
27: Deconstructing Complex Nonlinear Models in System Design Space.
28: IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology.