Polymer translocation:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Boca Raton [u.a.]
CRC Press
2011
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVII, 354 S. Ill., graph. Darst. |
| ISBN: | 9781420075168 |
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| adam_text | Titel: Polymer translocation
Autor: Muthukumar, Murugappan
Jahr: 2011
CONTENTS Preface xiii Acknowledgments XV Author xvii 1 General Premise 1 1.1 Biological Contexts 1 1.2 Single-Molecule Experiments 4 1.3 Nomenclature 7 1.4 Entropie Barrier Idea 7 1.5 Physics of Translocation 9 1.5.1 Drift-Diffusion 9 1.5.2 Capture 9 1.5.3 Translocation 11 1.6 Outlook 12 2 Size, Shape, and Structure of Macromolecules 13 2.1 Measures of Polymer Conformations 13 2.2 Universal Behavior 21 2.3 Excluded Volume Interaction 23 2.4 Coarse-Grained Models of Chain Connectivity 24 2.4.1 Freely Jointed Chain 24 2.4.2 Kuhn Chain Model 25 2.4.3 Gaussian Chain 27 2.4.4 Wormlike Chain 32 2.5 Chain Swelling by Excluded Volume Effect 34 2.6 Coil-Globule Transition 39 2.7 Concentration Effects 40 2.8 Summary 44 3 Electrolyte Solutions, Interfaces, and Geometric Objects 45 3.1 Electrolyte Solutions 45 3.1.1 Coulomb Interaction and Bjerrum Length 46 3.1.2 Poisson-Boltzmann Equation 48 3.1.3 Debye-Hückel Theory 49
vin Contents 3.1.3.1 Electrostatic Screening Length 50 3.1.3.2 Effect of Ion Size 52 3.1.3.3 Charge Distribution around an Ion 54 3.1.3.4 Free Energy 56 3.2 Charged Interfaces 57 3.2.1 Charged Spherical Particles 58 3.2.2 Planar Interfaces 60 3.2.2.1 Salt-Free Solutions 61 3.2.2.2 Salty Solutions 62 3.2.3 Cylindrical Pore 65 3.2.4 Charged Cylinder 69 3.2.5 Charged Line 72 3.2.6 Dielectric Mismatch 74 3.3 Summary 77 4 Flexible and Semiflexible Polyelectrolytes 79 4.1 Concepts 80 4.1.1 Coulomb Strength 81 4.1.2 Debye Length for Polyelectrolyte Solutions 81 4.1.3 Chain Connectivity 82 4.1.4 Counterion Worm 84 4.1.5 Dielectric Mismatch 85 4.1.6 Electrostatic Excluded Volume 87 4.1.7 Electrostatic Persistence Length 88 4.1.8 Hydrophobic Interaction 90 4.2 Experimental Results 90 4.3 Simulation Results 92 4.3.1 Radius of Gyration 94 4.3.2 Counterion Adsorption and Effective Charge 95 4.4 Electrostatic Swelling with Fixed Polymer Charge 100 4.4.1 High Salt Limit 100 4.4.2 Low Salt Limit 102 4.4.3 Electrostatic Blob 104 4.4.4 Crossover Formula 106 4.5 Self-Regularization of Polymer Charge 107 4.6 Concentration Effects 1 11 4.7 Summary 113 5 Confinement, Entropie Barrier, and Free Energy Landscape 115 5.1 Hole in a Wall 116 5.2 Spherical Cavities 121 5.2.1 Gaussian Chain 122 5.2.2 Uncharged Polymer with Excluded Volume 128 5.2.3 Polyelectrolyte Chain 132 5.3 Cylindrical Pores 134 5.3.1 Flexible Chain 135 5.3.2 Semiflexible Chain 138
Contents ix 5.4 Infinitely Wide Channels 141 5.5 Summary 142 6 Random Walks, Brownian Motion, and Drift 145 6.1 Biased Random Walk 146 6.1.1 Gaussian Chain Statistics 148 6.1.2 Drift-Diffusion 149 6.2 Brownian Motion and Langevin Equation 152 6.2.1 Brownian Particle without External Force 153 6.2.2 Brownian Particle under an External Force 156 6.2.3 General Form of Langevin Equation 156 6.3 Fokker-Planck-Smoluchowski Equation 157 6.4 Collection of Brownian Particles 159 6.5 Equilibrium versus Steady State 160 6.5.1 Equilibrium 161 6.5.2 Steady State 161 6.6 Finite Boundaries and First Passage Time 162 6.6.1 General Equations 163 6.6.2 General Solutions 165 6.7 Properties of Drift-Diffusion Process 167 6.7.1 One Absorbing Barrier 168 6.7.2 Two Absorbing Barriers 169 6.7.3 Reflecting Boundary 172 6.7.4 Radiation Boundary Condition 173 6.8 Summary 174 7 Polyelectrolyte Dynamics 177 7.1 Solvent Continuum and Hydrodynamic Interaction 178 7.2 Uncharged Polymer 181 7.2.1 General Expectations 181 7.2.2 Rouse Model 183 7.2.3 Zimm Dynamics 186 7.2.4 Semidilute Solutions and Hydrodynamic Screening 189 7.2.5 Entanglement Regime 193 7.3 Diffusion of Polyelectrolyte Chains 194 7.4 Electrophoretic Mobility 198 7.5 Coil Stretch under Flow 204 7.6 Summary 206 8 Ion Flow in Single Pores 209 8.1 A General Scenario 209 8.2 Equilibrium 212 8.3 Steady State without Diffusion 213 8.3.1 Ionic Current and Ohm s Law 214 8.3.2 Relaxation of Charge Density 215 8.4 Steady State with Drift and Diffusion 216 8.4.1 Analogy to Electrical Circuits 217 8.4.2 Solutions of PNP Equations 218
x Contents 8.4.3 Constant Field Approximation 219 8.4.3.1 GHK Current Equation 220 8.4.3.2 Concentration Profile 221 8.4.3.3 Resting Potential 221 8.5 Effect of Barriers 223 8.6 Ionic Current through Protein Pores 224 8.6.1 Gramicidin A Channel 225 8.6.2 a-Hemolysin Pore 226 8.7 Fluctuations in Ionic Current 230 8.8 Electroosmotic Flow 234 8.8.1 EOF near Planar Interfaces 234 8.8.2 EOF inside Cylindrical Pores 236 8.9 Summary 238 9 Polymer Capture 241 9.1 Representative Experimental Results 241 9.2 General Considerations 244 9.3 Diffusion-Limited Capture 247 9.4 Drift-Limited Regime 250 9.5 Effect of Convective Flow 251 9.6 Polymer Capture with Electroosmotic Flow 252 9.7 Effect of Barriers on Capture Rate 256 9.7.1 Capture Rate 259 9.7.2 Probability of Successful Translocation 262 9.7.3 Phenomenological Chemical Kinetics Model 265 9.8 Summary 268 10 Translocation Kinetics: Nucleation and Threading 271 10.1 Representative Experimental Results 271 10.1.1 Translocation through a-Hemolysin Pore 272 10.1.2 Translocation through Solid-State Nanopores 276 10.1.3 Translocation through Channels 278 10.2 Insights from Simulations 279 10.3 Theory of Translocation Kinetics 284 10.3.1 Nucleation Time 288 10.3.2 Translocation Time 289 10.3.2.1 Two Absorbing Barriers 291 10.3.2.2 One Absorbing Barrier and One Reflecting Barrier 293 10.3.3 Effect of Pore-Polymer Interactions 295 10.3.3.1 Escape from a Spherical Cavity 296 10.3.3.2 Translocation between Two Spherical Cavities 297 10.3.3.3 Two Spherical Cavities Connected by a Pore 297 10.3.3.4 Translocation with a Membrane Potential 300 10.4 Comparison between Experimental Data and Theory 302 10.4.1 Translocation through a-Hemolysin Pore 302
Contents xi 10.4.2 Translocation through Solid-State Nanopores 304 10.4.3 Translocation through Channels 306 10.5 Summary 31 1 11 Further Issues 313 11.1 Nonequilibrium Conformations during Threading 313 11.2 Amplification of Chemical Details 315 11.2.1 Chemical Decoration of the Pore 316 11.2.2 Secondary Structures of the Translocating Polymer 31 8 11.3 Biological Examples 320 11.3.1 Mitochondrial Transport 320 11.3.2 Bacterial Conjugation 322 11.3.3 Transport through Nuclear Pore 322 11.3.4 Genome Packing in Bacteriophages 323 11.4 Summary 325 References 327 Index 343
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| discipline | Chemie / Pharmazie |
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| spelling | Muthukumar, Murugappan Verfasser aut Polymer translocation Murugappan Muthukumar Boca Raton [u.a.] CRC Press 2011 XVII, 354 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Translokation (DE-588)4185910-8 gnd rswk-swf Polyelektrolyt (DE-588)4175165-6 gnd rswk-swf Polyelektrolyt (DE-588)4175165-6 s Translokation (DE-588)4185910-8 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=022544942&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Muthukumar, Murugappan Polymer translocation Translokation (DE-588)4185910-8 gnd Polyelektrolyt (DE-588)4175165-6 gnd |
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| title | Polymer translocation |
| title_auth | Polymer translocation |
| title_exact_search | Polymer translocation |
| title_full | Polymer translocation Murugappan Muthukumar |
| title_fullStr | Polymer translocation Murugappan Muthukumar |
| title_full_unstemmed | Polymer translocation Murugappan Muthukumar |
| title_short | Polymer translocation |
| title_sort | polymer translocation |
| topic | Translokation (DE-588)4185910-8 gnd Polyelektrolyt (DE-588)4175165-6 gnd |
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