Chaire d'Analyse Appliquée

DNA reading list for DNA modelling


 

Understanding DNA, The molecule & how it work

C. R. Calladine & H. R. Drew, 1992 Academic Press, ISBN 0-12-155086-9

summary: Understanding DNA explains, step by step, why DNA forms specific structures, the form of these structures and how they fundamentally affect the biological processes of transcription and replication.

Unravelling DNA

M. D. Frank-Kamenetskii 1993 VCH Publishers, ISBN 1-56-081617-1

summary: A curious blend of history, biographical details to cover the development of molecular biology from the influence of physicists earlier in the century, through the central dogma of molecular biology to discussion of social issues raised by genetic engineering.

DNA topology

A. D. Bates & A. Maxwell, 1993 Oxford University Press, IRL Press, In Focus Series, ISBN 0-19-963349-5

summary: A clear, concise explanation of the relevance of supercoiling and catenation in the context of biological activity of the DNA molecule.

DNA structure and Function

R. R. Sinden, 1994 Academic Press, ISBN 0-12-645750-6

summary: a timely and comprehensive resource, that provides a simple yet comprehensive introduction to nearly all aspects of DNA structure. It also explains current ideas on the biological significance of classic and alternative DNA conformations.
 

Statistical Physics of Macromolecules

A. Y. Grosberg & A. R. Khokhlov, 1994, American Institute of Physics Press, ISBN 1-56-396071-0

summary: A contemporary textbook on statistics of chain models of polymer solutions and melts, liquid crystals, polyelectrolyte chains, also featuring dynamic viscoelasticity behavior of polymer systems, with some specific attention towards biopolymers DNA and proteins. Some recent advances in statistical theory of DNA gel electrophoresis, polymers at interfaces, and dynamics of concentrated solutions of branched polymers, are also covered.

Dynamics of proteins and nucleic acids

J. A. McCammon & S. C. Harvey, 1987, Cambridge University Press, ISBN 0-52-135652-0 (paperback) ISBN 0-52-130750 (hardback)

summary: a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plaus a crucially important role in biological activity. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function.

Mathematical Approaches to Biomolecular Structure and Dynamics

The IMA volumes in mathematics and its applications vol. 82

1996 Springer, ISBN 0-38-794838-4

summary: Interdisciplinary research in mathematics and molecular biology is driven by ever-growing experimental, theoretical and computational power. This volume consists of a representative sample of papers presented during the month-long IMA Summer Program in Molecular Biology and covers the spectrum from experiment to computation to simulation to theory.

Calculating the Secrets of Life

E. S. Lander & M. S. Waterman, Editors 1995, National Academy Press, NRC, ISBN 0-30-904886-9

summary: explores how differential geometry, topology, and differential mechanics have allowed researchers to wind and unwind DNA's double helix to understand the phenomenon of supercoiling. The book describes the role of mathematics in researching the origin, structure and function of life by applying stochastic and statistical theory to the study of DNA sequences.

The theory of Polymer Dynamics

M. Doi & S. F. Edwards, 1986, Oxford University Press, ISBN 0-19-852033-6

summary: a comprehensive account of the modern theory for the dynamical properties of polymer solutions, including viscoelasticity(non linear too, based on molecular dynamical models), diffusion, dynamic light scattering, flow, and electric birefringence.

Nonlinear Problems of Elasticity

S. S. Antman, 1995, Applied Mathematical Sciences 107, Springer, ISBN 0-38-794199-1

summary: a manual which covers the equations of motion for extensible and elastic strings and rods, bifurcation theory, variational methods, the special Cosserat theory of rods, 3D continuum mechanics, general theories of rods and shells, non-linear plasticity, and dynamical problems as well. The bible of rodlike continuum approaches.

Modeling Superhelical DNA: Recent Analytical and Dynamical Approaches

T. Schlick, 1995, in Current Opinion in Structural Biology vol 5.2 on "Theory and Simulation", B. Honig Eds

summary: a review paper about analytical and kinetic approaches spanning molecular, Langevin and Brownian dynamics, as well as dynamical theories of elastic rods.

Simulating DNA at low resolution

W. Olson, 1996, in Current Opinion in Structural Biology vol 6, pp 242-256

summary: another review paper about the modeling of local and global structural changes induced by the binding of various proteins to DNA, sequence-specific and environmental (salt) effects.
 



 


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last update : PF, october 26, 1998