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Polymer Physics and Molecular Biophysics Himadri B Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Jawaharlal Nehru University © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information Cambridge House, 4381/4 Ansari Road, Daryaganj, Delhi 110002, India Cambridge University Press is part of the University of Cambridge. It furthers the University’s mission by disseminating knowledge in the pursuit of education, learning and research at the highest international levels of excellence. www.cambridge.org Information on this title: www.cambridge.org/9781107058705 © Himadri B. Bohidar 2015 This publication is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 2015 Printed in India A catalogue record for this publication is available from the British Library Library of Congress Cataloging-in-Publication Data Bohidar, Himadri B. Fundamentals of polymer physics and molecular biophysics / Himadri B. Bohidar. pages cm Includes bibliographical references and index. Summary: “Provides a physical interpretation of the data obtained in macromolecular transport phenomena in a given system and also addresses some important issues and concepts related to biopolymers such as proteins and nucleic acids”-- Provided by publisher. ISBN 978-1-107-05870-5 (hardback) 1. Polymers. 2. Physics. 3. Biophysics. I. Title. QD281.P6B62 2014 530.4’13--dc23 2014007362 ISBN 978-1-107-05870-5 Hardback Cambridge University Press has no responsibility for the persistence or accuracy of URLs for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information Contents List of Figures xi List of Tables xvii Preface xix 1. Essential Thermodynamic and Statistical Concepts 1.1. Irreversible thermodynamics 1 1.2. Postulates in irreversible thermodynamics 4 1.3. Phenomenological forces and fluxes 4 1.4. Gibbs–Duhem equation 5 1.5. Statistical parameters 8 1.6. Probability distributions 9 1.6.1. Binomial distribution 10 1.6.2. Gaussian distribution 12 1.6.3. Poisson distribution 13 1.6.4. Multi-variable distributions 15 Bibliography 17 Exercises 17 2. Polymer Structure and Nomenclature 2.1. Basic structures 18 2.2. Some common polymers 21 2.3. Molecular weight and polydispersity 27 2.4. Forces and interactions 31 2.4.1. Covalent bond 31 2.4.2. Ionic bond 31 2.4.3. Coulomb forces 31 2.4.4. Charge–dipole force 31 2.4.5. Lennard–Jones potential 32 2.4.6. Hydrogen bond 32 2.5. Polymer gels and networks 33 Summary 37 References 37 Exercises 38 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information iv | Contents 3. Polymer Solutions 3.1. Basic concepts 40 3.2. Ideal solution model 41 3.3. Real polymer solutions 42 3.4. Flory–Huggins model 44 3.5. Change in Gibbs free energy 47 3.6. Determination of X1 from osmotic pressure 49 3.7. Dilute polymer solutions 50 Summary 53 References 53 Bibliography 53 Exercises 54 4. Phase Stability and Phase Transitions 4.1. Phase transitions 56 4.2. Thermodynamic stability 57 4.3. Entropy of mixing 59 4.4. Internal energy of mixing 60 4.5. UCST and LCST 61 Summary 64 Bibliography 65 Exercises 65 5. Static Properties of Single Chains 5.1. Radius of gyration and hydrodynamic radius 66 5.2. Freely jointed chain model 68 5.3. Random flight chain model 70 5.4. Concept of segments and persistence length 72 5.5. Distribution of end-to-end length 76 5.6. Ideal chain behaviour 79 5.7. Good solvent behaviour 80 5.8. Excluded volume effect 80 5.9. Gaussian chain 86 Summary 87 References 88 Bibliography 89 Exercises 89 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information Contents | v 6. Diffusion 6.1. Diffusion and irreversible thermodynamics 92 6.2. Fick’s laws 99 6.3. Osmotic pressure 102 6.4. Diffusion in different solvents 104 6.5. Concentration dependence 108 6.6. Diffusion in three component systems 111 6.7. Temperature dependence 112 6.8. Langevin equation of diffusion 113 6.9. Smoluchowski equation of diffusion 115 6.10. Determination of molecular structure 117 Summary 118 References 119 Bibliography 119 Exercises 119 7. Viscosity of Polymer Solutions 7.1. Einstein relation 121 7.2. Brinkman relation 123 7.3. Einstein–Simha relation 124 7.4. Staudinger–Mark–Houwink relation 126 7.5. Intrinsic viscosity of polymer chains 126 7.6. Free-draining chain 128 7.7. Impermeable chain 131 7.8. Huggins equation 132 7.9. Kraemer equation 132 7.10. Flory–Fox equation 133 7.11. Krigbaum equation 134 7.12. Stockmayer–Fixman equation 134 7.13. Peterlin equations 135 7.14. Scheraga–Mandelkern relation 136 Summary 136 References 136 Bibliography 137 Exercises 137 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information vi | Contents 8. Sedimentation 8.1. Svedberg equation 139 8.2. Irreversible thermodynamic and sedimentation 141 8.3. Mark–Houwink–Kuhn–Sakurada equation 146 8.4. Wales–van Holde ratio 146 8.5. Scaling in dilute solutions 147 Summary 148 References 148 Bibliography 148 Exercises 148 9. Concentration Regimes and Scaling 9.1. General description 151 9.1.1. Dilute solutions 151 9.1.2. Semi-dilute solutions 151 9.1.3. Concentrated solutions 152 9.2. Dilute solution regime 153 9.2.1. Semi-dilute solutions 153 9.2.2. Sedimentation coefficient 156 9.2.3. Intrinsic viscosity 157 9.3. Semi-dilute solution regime 158 9.3.1. Good solvents 158 9.3.2. Theta solvents 159 9.3.3. Osmotic pressure 159 9.3.4. Analysis of dynamic phenomena 160 9.3.5. Cooperative sedimentation 163 9.3.6. Sedimentation: Theta solutions 164 9.3.7. Cooperative diffusion 164 9.3.8. Dynamic regions in diffusion 166 Summary 167 References 167 Bibliography 167 Exercises 168 10. Internal Dynamics 10.1. Rouse model: Theta solvent 170 10.2. Zimm model: Theta solvent 173 10.3. Zimm model: Good solvent 174 10.4. Reptation model 175 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information Contents | vii Summary 176 References 177 Exercises 177 11. Dynamics in Polymer Gels 11.1. Dynamics in networks 179 11.2. Renewal time 179 11.3. Experimental data 181 11.4. Swelling of gels 182 11.5. Kinetics of swelling 183 11.6. Swelling of polyelectrolyte gels 184 11.7. Density fluctuations in gels 186 11.8. Scaling and phase diagram in Q Gels 188 Summary 190 References 190 Bibliography 191 Exercises 191 12. Molecular Biophysics 12.1. Chirality of biomolecules 193 12.2. Polyelectrolytes and polyampholytes 196 12.3. Debye–Hückel theory 197 Summary 204 References 205 Bibliography 205 Exercises 205 13. Structure of Biopolymers 13.1. Nucleic acids 206 13.2. Proteins and amino acids 212 13.3. Peptide bond 216 13.4. Structure of proteins 217 13.5. Carbohydrates 220 13.5.1. Monosaccharides 221 13.5.2. Oligosaccharides 224 13.5.3. Disaccharides 224 13.5.4. Polysaccharides 224 Summary 229 Bibliography 230 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B. Bohidar Frontmatter More information viii | Contents 14. Physics of Proteins 14.1. Charge on protein molecules 231 14.2. Protein folding: Helix–coil transition 238 14.2.1. Thermodynamic treatment 238 14.3. Kinetics of protein folding 248 14.3.1. Presence of intermediate states 248 14.3.2. Three step process 253 14.4. Polymerization of amino acids 255 14.4.1. Linear growth 256 14.4.2. Helical growth 258 14.5. Energetic of ligand binding 260 14.6. Enzymatic reactions 262 14.6.1. Single intermediate step process 262 14.6.2. Two intermediate step process 265 Summary 268 References 268 Bibliography 269 Exercises 269 15. Physics of Nucleic Acids 15.1. DNA stacking 272 15.2. Misfolding and loop formation 275 15.3. Tertiary structures of DNA 277 15.4. Stoichiometry of stacking 279 15.5. Ligand binding 283 15.5.1 Scatchard equation 284 15.5.2. Hill constant 288 15.6. Genetic code and protein biosynthesis 293 15.6.1. What is a genetic code? 293 15.6.2. Universality of the genetic code 295 15.6.3. Transfer of information via codons 295 15.6.4. Steps involved in information transfer 295 15.6.5. Protein biosynthesis summary 298 15.6.6. Mutations 299 Summary 300 References 300 Bibliography 301 Exercises 301 © in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-05870-5 - Fundamentals of Polymer Physics and Molecular Biophysics Himadri B.
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