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Applied Biophysics: A Molecular Approach for Physical Scientists

Applied Biophysics: A Molecular Approach for Physical Scientists

Thomas Andrew Waigh

ISBN: 978-0-470-51316-3

Sep 2007

436 pages



This book presents the fundamentals of molecular biophysics, and highlights the connection between molecules and biological phenomena, making it an important text across a variety of science disciplines.

The topics covered in the book include:

  • Phase transitions that occur in biosystems (protein crystallisation, globule-coil transition etc)
  • Liquid crystallinity as an example of the delicate range of partially ordered phases found with biological molecules
  • How molecules move and propel themselves at the cellular level
  • The general features of self-assembly with examples from proteins
  • The phase behaviour of DNA

The physical toolbox presented within this text will form a basis for students to enter into a wide range of pure and applied bioengineering fields in medical, food and pharmaceutical areas.



1 The Building Blocks.

1.1 Proteins.

1.2 Lipids.

1.3 Nucleic Acids.

1.4 Carbohydrates.

1.5 Water.

1.6 Proteoglycans and Glycoproteins.

1.7 Cells (Complex Constructs of Biomolecules).

1.8 Viruses (Complex Constructs of Biomolecules).

1.9 Bacteria (Complex Constructs of Biomolecules).

1.10 Other Molecules.

Further Reading.

Tutorial Questions.

2 Mesoscopic Forces.

2.1 Cohesive Forces.

2.2 Hydrogen Bonding.

2.3 Electrostatics.

2.3.1 Unscreened Electrostatic Interactions.

2.3.2 Screened Electrostatic Interactions.

2.3.3 The Force Between Charged Spheres in Solution.

2.4 Steric and Fluctuation Forces.

2.5 Depletion Forces.

2.6 Hydrodynamic Interactions.

2.7 Direct Experimental Measurements of Intermolecular and Surface Forces.

Further Reading.

Tutorial Questions.

3 Phase Transitions.

3.1 The Basics.

3.2 Helix–Coil Transition.

3.3 Globule–Coil Transition.

3.4 Crystallisation.

3.5 Liquid–Liquid Demixing (Phase Separation).

Further Reading.

Tutorial Questions.

4 Liquid Crystallinity.

4.1 The Basics.

4.2 Liquid–Nematic–Smectic Transitions.

4.3 Defects.

4.4 More Exotic Possibilities for Liquid Crystalline Phases.

Further Reading.

Tutorial Questions.

5 Motility.

5.1 Diffusion.

5.2 Low Reynold’s Number Dynamics.

5.3 Motility.

5.4 First Passage Problem.

5.5 Rate Theories of Chemical Reactions.

Further Reading.

Tutorial Questions.

6 Aggregating Self-Assembly.

6.1 Surfactants.

6.2 Viruses.

6.3 Self-Assembly of Proteins.

6.4 Polymerisation of Cytoskeletal Filaments (Motility).

Further Reading.

Tutorial Questions.

7 Surface Phenomena.

7.1 Surface Tension.

7.2 Adhesion.

7.3 Wetting.

7.4 Capillarity.

7.5 Experimental Techniques.

7.6 Friction.

7.7 Other Surface Phenomena.

Further Reading.

Tutorial Question.

8 Biomacromolecules.

8.1 Flexibility of Macromolecules.

8.2 Good/Bad Solvents and the Size of Polymers.

8.3 Elasticity.

8.4 Damped Motion of Soft Molecules.

8.5 Dynamics of Polymer Chains.

8.6 Topology of Polymer Chains – Super Coiling.

Further Reading.

Tutorial Questions.

9 Charged Ions and Polymers.

9.1 Electrostatics.

9.2 Debye–Huckel Theory.

9.3 Ionic Radius.

9.4 The Behaviour of Polyelectrolytes.

9.5 Donnan Equilibria.

9.6 Titration Curves.

9.7 Poisson–Boltzmann Theory for Cylindrical Charge Distributions.

9.8 Charge Condensation.

9.9 Other Polyelectrolyte Phenomena.

Further Reading.

Tutorial Questions.

10 Membranes.

10.1 Undulations.

10.2 Bending Resistance.

10.3 Elasticity.

10.4 Intermembrane Forces.

Further Reading.

Tutorial Questions.

11 Continuum Mechanics.

11.1 Structural Mechanics.

11.2 Composites.

11.3 Foams.

11.4 Fracture.

11.5 Morphology.

Further Reading.

Tutorial Questions.

12 Biorheology.

12.1 Storage and Loss Moduli.

12.2 Rheological Functions.

12.3 Examples from Biology.

12.3.1 Neutral Polymer Solutions.

12.3.2 Polyelectrolytes.

12.3.3 Gels.

12.3.4 Colloids.

12.3.5 Liquid Crystalline Polymers.

12.3.6 Glassy Materials.

12.3.7 Microfluidics in Channels.

Further Reading.

Tutorial Questions.

13 Experimental Techniques.

13.1 Static Scattering Techniques.

13.2 Dynamic Scattering Techniques.

13.3 Osmotic Pressure.

13.4 Force Measurement.

13.5 Electrophoresis.

13.6 Sedimentation.

13.7 Rheology.

13.8 Tribology.

13.9 Solid Properties.

Further Reading.

Tutorial Questions.

14 Motors.

14.1 Self-assembling Motility – Polymerisation of Actin and Tubulin.

14.2 Parallelised Linear Stepper Motors – Striated Muscle.

14.3 Rotatory Motors.

14.4 Ratchet Models.

14.5 Other Systems.

Further Reading.

Tutorial Question.

15 Structural Biomaterials.

15.1 Cartilage – Tough Shock Absorber in Human Joints.

15.2 Spider Silk.

15.3 Elastin and Resilin.

15.4 Bone.

15.5 Adhesive Proteins.

15.6 Nacre and Mineral Composites.

Further Reading.

Tutorial Questions.

16 Phase Behaviour of DNA.

16.1 Chromatin – Naturally Packaged DNA Chains.

16.2 DNA Compaction – An Example of Polyelectrolyte Complexation.

16.3 Facilitated Diffusion.

Further Reading.


Answers to Tutorial Questions.


"Given the significant breadth and depth of this rapidly growing subject, Tom Waigh does a good job in providing a valuable bridge between physics and biology." (The Higher Education Academy Physical Sciences Centre, June 2008)