Verfügbarkeit: Theoretical molecular biophysics

Theoretical molecular biophysics:

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Hauptverfasser:	Scherer, Philipp O. J. (VerfasserIn), Fischer, Sighart F. 1938- (VerfasserIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Berlin Springer [2017]
Ausgabe:	Second edition
Schriftenreihe:	Biological and medical physics, biomedical engineering
Schlagworte:	Theoretische Biophysik Molekulare Biophysik PDE TC Elementary Processes in Biophysics Molecular Biophysics Explained Theoretical Biophysics textbook Molecular Biophysics Textbook Photosynthetic System Statistical Mechanics of Biopolymers Reaction Kinetics Photoinduced Processes
Online-Zugang:	Inhaltstext Inhaltsverzeichnis
Beschreibung:	XVI, 513 Seiten Illustrationen, Diagramme (teilweise farbig)
ISBN:	9783662556702 3662556707

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Datensatz im Suchindex

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adam_text	CONTENTS PART I STATISTICAL MECHANICS OF BIOPOLYMERS 1 RANDOM WALK MODELS FOR THE CONFORMATION ...................................... 3 1.1 THE FREELY JOINTED C H AIN ............................................................... 3 1.1.1 ENTROPIE ELASTICITY ............................................................ 5 1.1.2 FORCE-EXTENSION R ELATION ............................................... 6 1.2 TWO COMPONENT M O D EL................................................................. 9 1.2.1 FORCE-EXTENSION RELATION ................................................. 10 1.2.2 TWO COMPONENT MODEL WITH INTERACTIONS...................... 12 2 FLORY-HUGGINS THEORY FOR BIOPOLYMER SOLUTIONS ................................ 21 2.1 MONOMERIC SOLUTION........................................................................ 21 2.2 POLYMERIC SOLUTION.......................................................................... 24 2.3 PHASE TRANSITIONS............................................................................ 30 2.3.1 STABILITY C RITERION ............................................................ 30 2.3.2 CRITICAL COUPLING............................................................... 32 2.3.3 PHASE DIAGRAM................................................................... 34 PROBLEMS......................................................................................................... 37 PART II PROTEIN ELECTROSTATICS AND SOLVATION 3 IMPLICIT CONTINUUM SOLVENT MODELS........................................................ 41 3.1 POTENTIAL OF MEAN F ORCE................................................................. 41 3.2 DIELECTRIC CONTINUUM MODEL .......................................................... 42 3.3 BOM M O D E L..................................................................................... 44 3.4 CHARGES IN A PROTEIN........................................................................ 45 3.5 TIME DEPENDENT REACTION F IE LD ................................................... 48 3.6 GENERALIZED BOM M ODELS............................................................... 50 4 DEBYE-HUECKEL T HEORY................................................................................. 53 4.1 ELECTROSTATIC SHIELDING BY MOBILE C HARGES.................................. 53 4.2 1-1 ELECTROLYTES................................................................................. 55 4.3 CHARGED SPHERE................................................................................. 55 4.4 CHARGED C YLINDER ............................................................................ 58 4.5 CHARGED MEMBRANE (GOUEY-CHAPMAN DOUBLE LAYER) ................ 61 4.6 STEM MODIFICATION OF THE DOUBLE L AYER ...................................... 67 PROBLEMS.......................................................................................................... 68 5 PROTONATION E Q U ILIB R IA ............................................................................... 71 5.1 PROTONATION EQUILIBRIA IN SOLUTION ................................................. 71 5.2 PROTONATION EQUILIBRIA IN PROTEINS ................................................. 75 5.2.1 APPARENT PKA VALUES ........................................................ 75 5.2.2 PROTONATION ENTHALPY ........................................................ 76 5.2.3 PROTONATION ENTHALPY RELATIVE TO THE UNCHARGED S TA TE ................................................................................... 78 5.2.4 STATISTICAL MECHANICS OF PROTONATION ............................. 79 5.3 ABNORMAL TITRATION CURVES OF COUPLED R ESIDUES ...................... 80 PROBLEMS.......................................................................................................... 81 P A RT III REACTION KINETICS 6 FORM AL K INETICS............................................................................................ 85 6.1 ELEMENTARY CHEMICAL R EACTIONS.................................................... 85 6.2 REACTION VARIABLE AND REACTION R A TE ........................................... 85 6.3 REACTION O RDER................................................................................. 87 6.3.1 ZERO-ORDER REACTIONS ........................................................ 87 6.3.2 FIRST-ORDER REACTIONS ........................................................ 87 6.3.3 SECOND-ORDER REACTIONS.................................................... 88 6.4 DYNAMICAL EQUILIBRIUM ................................................................... 89 6.5 COMPETING R EACTIONS...................................................................... 90 6.6 CONSECUTIVE R EACTIONS ................................................................... 90 6.7 ENZYMATIC C ATALYSIS........................................................................ 91 6.8 REACTIONS IN S OLUTIO NS ................................................................... 93 6.8.1 DIFFUSION CONTROLLED LIMIT ............................................... 94 6.8.2 REACTION CONTROLLED L IM IT........................................... .. . 95 PROBLEMS.......................................................................................................... 95 7 KINETIC THEORY - FOKKER-PLANCK E Q U A TIO N ........................................... 97 7.1 STOCHASTIC DIFFERENTIAL EQUATION FOR BROWNIAN M OTION.............. 97 7.2 PROBABILITY DISTRIBUTION ................................................................... 99 7.3 DIFFUSION............................................................................................ 101 7.3.1 SHARP INITIAL DISTRIBUTION ................................................. 102 7.3.2 ABSORBING BOUNDARY ........................................................ 103 7.4 FOKKER-PLANCK EQUATION FOR BROWNIAN MOTION ........................... 104 7.5 STATIONARY SOLUTION TO THE FOKKER-PLANCK E QUATION .................. 105 7.6 DIFFUSION IN AN EXTERNAL POTENTIAL ................................................. 107 7.7 LARGE FRICTION LIMIT - SMOLUCHOWSKI EQUATION......................... 109 7.8 MASTER EQUATION .............................................................................. 110 PROBLEMS......................................................................................................... 110 8 K RAM ERS T H E O RY .......................................................................................... 113 8.1 KRAMERS* M ODEL .............................................................................. 113 8.2 KRAMERS* CALCULATION OF THE REACTION R ATE.................................. 115 9 DISPERSIVE K IN E TIC S..................................................................................... 119 9.1 DICHOTOMOUS M ODEL........................................................................ 120 9.1.1 FAST SOLVENT FLUCTUATIONS ................................................. 123 9.1.2 SLOW SOLVENT FLUCTUATIONS............................................... 124 9.1.3 NUMERICAL EXAMPLE .......................................................... 125 9.2 CONTINUOUS TIME RANDOM WALK PROCESSES.................................. 126 9.2.1 FORMULATION OF THE M ODEL ............................................... 126 9.2.2 EXPONENTIAL WAITING TIME DISTRIBUTION......................... 127 9.2.3 COUPLED EQUATIONS ............................................................ 129 9.3 POWERTIME LAW KINETICS................................................................. 134 PROBLEMS......................................................................................................... 136 P ART IV T RANSPORT PROCESSES 10 NON-EQUILIBRIUM THERM ODYNAM ICS .......................................................... 139 10.1 CONTINUITY EQUATION FOR THE MASS D EN SITY .................................. 140 10.2 ENERGY CONSERVATION........................................................................ 141 10.3 ENTROPY PRODUCTION.......................................................................... 142 10.4 PHENOMENOLOGICAL RELATIONS .......................................................... 145 10.5 STATIONARY STATES .............................................................................. 145 PROBLEMS......................................................................................................... 147 11 SIMPLE TRANSPORT P ROCESSES...................................................................... 149 11.1 HEAT T RANSPORT ................................................................................ 149 11.2 DIFFUSION IN AN EXTERNAL ELECTRIC F IE LD ........................................ 150 PROBLEMS......................................................................................................... 153 12 ION T RANSPORT THROUGH A M E M B RA N E ..................................................... 155 12.1 DIFFUSIVE TRANSPORT.......................................................................... 155 12.2 GOLDMAN-HODGKIN-KATZ M ODEL.................................................... 158 12.3 HODGKIN-HUXLEY M ODEL................................................................. 161 12.4 COOPERATIVELY IN ION CHANNEL K INETICS ........................................ 163 12.4.1 MWC M ODEL ..................................................................... 164 12.4.2 KNF M ODEL........................................................................ 167 XII CONTENTS 13 REACTION-DIFFUSION S Y STE M S...................................................................... 173 13.1 DERIVATION.......................................................................................... 173 13.2 LINEARIZATION..................................................................................... 174 13.3 FITZHUGH-NAGUMO M ODEL............................................................... 175 P A RT V REACTION RATE THEORY 14 EQUILIBRIUM REACTIONS................................................................................. 183 14.1 ARRHENIUS L A W ................................................................................. 183 14.2 STATISTICAL INTERPRETATION OF THE EQUILIBRIUM CONSTANT ................. 185 15 CALCULATION OF REACTION R ATES ................................................................... 187 15.1 COLLISION THEORY............................................................................... 187 15.2 TRANSITION STATE THEORY ................................................................... 190 15.3 COMPARISON BETWEEN COLLISION THEORY AND TRANSITION STATE THEORY ..................................................................................... 192 15.4 THERMODYNAMICAL FORMULATION OF TST ........................................ 194 15.5 KINETIC ISOTOPE E FFECTS ................................................................... 195 15.6 GENERAL RATE EXPRESSIONS............................................................... 196 15.6.1 THE FLUX OPERATOR............................................................. 197 PROBLEMS.......................................................................................................... 199 16 M ARCUS THEORY OF ELECTRON TRAN SFER........................................................ 201 16.1 PHENOMENOLOGICAL DESCRIPTION OF E T ........................................... 201 16.2 SIMPLE EXPLANATION OF MARCUS T HEORY ........................................ 204 16.3 FREE ENERGY CONTRIBUTION OF THE NONEQUILIBRIUM POLARIZATION........................................................................................ 205 16.4 ACTIVATION ENERGY ............................................................................ 209 16.5 SIMPLE MODEL SYSTEM S ................................................................... 213 16.5.1 CHARGE SEPARATION............................................................. 215 16.5.2 CHARGE S H IF T...................................................................... 216 16.6 THE ENERGY GAP AS THE REACTION C OORDINATE ............................. 216 16.7 INNER SHELL REORGANIZATION............................................................. 218 16.8 THE TRANSMISSION COEFFICIENT FOR NONADIABATIC ELECTRON T RA N SFER............................................................................................ 219 16.9 CHARGE DELOCALIZATION AND SELF-TRAPPING .................................... 220 PROBLEMS.......................................................................................................... 223 P A RT VI ELEM ENTARY PHOTOPHYSICS 17 M OLECULAR S TA TE S .......................................................................................... 227 17.1 BOM-OPPENHEIMER SEPARATION...................................................... 227 17.2 HARMONIC APPROXIMATION TO THE NUCLEAR M OTION ...................... 229 17.3 NONADIABATIC INTERACTION ................................................................. 232 17.4 TRUE MOLECULAR EIGENSTATES ........................................................ 235 18 INTRAM OLECULAR ELECTRONIC T RANSITIONS ................................................... 237 18.1 COUPLING TO THE RADIATION F IE LD ................................................... 238 18.2 OPTICAL TRANSITIONS.......................................................................... 242 18.3 DIPOLE TRANSITIONS IN THE CONDON APPROXIMATION ...................... 244 18.4 TIME-CORRELATION FUNCTION (TCF) FORM ALISM ............................. 245 18.5 EXCITATION BY A SHORT PULSE ............................................ 246 18.6 RADIATIONLESS TRANSITIONS................................................................. 247 18.6.1 INTERNAL CONVERSION .......................................................... 248 18.6.2 INTERSYSTEM CROSSING........................................................ 249 PROBLEMS......................................................................................................... 249 19 THE DISPLACED HARM ONIC O SCILLATOR........................................................ 251 19.1 THE TIME-CORRELATION FUNCTION IN THE DISPLACED HARMONIC OSCILLATOR APPROXIMATION............................................................... 251 19.2 HIGH FREQUENCY MODES ................................................................... 254 19.3 LOW FREQUENCY M ODES ................................................................... 255 20 SPECTRAL D IFFUSION....................................................................................... 257 20.1 DEPHASING.......................................................................................... 257 20.2 GAUSSIAN FLUCTUATIONS ..................................................................... 260 20.2.1 LONG CORRELATION T IM E .................................................... 262 20.2.2 SHORT CORRELATION T IM E .................................................... 262 20.3 MARKOVIAN M ODULATION ................................................................... 263 PROBLEMS......................................................................................................... 267 21 CROSSING OF TWO ELECTRONIC S TA TE S .......................................................... 269 21.1 WAVEPACKET M OTION........................................................................ 269 21.1.1 FREE PARTICLE M O TIO N ........................................................ 270 21.1.2 HARMONIC OSCILLATOR .......................................................... 272 21.2 THE ADIABATIC TO DIABATIC TRANSFORM ATION.................................. 273 21.3 QUASIDIABATIC S TA TES........................................................................ 278 21.4 CROSSING BETWEEN TWO STATES........................................................ 280 21.5 AVOIDED CROSSING ALONG ONE COORDINATE.................................... 281 21.6 SEMICLASSICAL APPROXIM ATION........................................................ 284 21.7 LANDAU-ZENER M O D EL ..................................................................... 285 21.8 APPLICATION TO DIABATIC E T ............................................................ 287 21.9 CONICAL INTERSECTIONS........................................................................ 288 21.10 LINEAR VIBRONIC COUPLING M O D EL ................................................. 290 PROBLEMS......................................................................................................... 293 22 DYNAMICS OF AN EXCITED S TATE................................................................... 295 22.1 COUPLING TO A QUASI-CONTINUUM.................................................... 295 22.2 GREEN*S FORMALISM.......................................................................... 296 22.2.1 RESOLVENT AND PROPAGATOR ............................................... 297 22.2.2 DYSON EQUATION................................................................. 300 XIV CONTENTS 22.2.3 TRANSITION O PERATOR .......................................................... 301 22.2.4 LEVEL SHIFT.......................................................................... 301 22.3 LADDER M ODEL................................................................................... 303 22.4 DESCRIPTION WITHIN THE SADDLE POINT M ETHOD ............................. 308 22.5 THE ENERGY GAP L A W ...................................................................... 313 PROBLEMS.......................................................................................................... 317 P A RT VII ELEM ENTARY PHOTOINDUCED PROCESSES 23 PHOTOPHYSICS OF CHLOROPHYLLS AND CAROTENOIDS...................................... 321 23.1 MO MODEL FOR THE ELECTRONIC STATES ............................................. 321 23.2 THE FREE ELECTRON MODEL FOR POLYENES ........................................ 322 23.3 THE LCAO APPROXIMATION............................................................. 324 23.4 HUECKEL APPROXIMATION ................................................................... 325 23.5 SIMPLIFIED CL MODEL FOR POLYENES ................................................. 327 23.6 CYCLIC POLYENE AS A MODEL FOR PORPHYRINS.................................. 328 23.7 THE FOUR ORBITAL MODEL FOR PORPHYRINS ...................................... 329 23.8 ENERGY TRANSFER P ROCESSES............................................................. 331 PROBLEMS.......................................................................................................... 332 24 INCOHERENT ENERGY T RA N SFE R...................................................................... 335 24.1 EXCITED STATES................................................................................... 335 24.2 ENERGY TRANSFER MECHANISM .......................................................... 337 24.3 INTERACTION MATRIX ELEM ENT............................................................. 338 24.4 MULTIPOLE EXPANSION OF THE EXCITONIC INTERACTION ...................... 339 24.5 ENERGY TRANSFER R A TE ...................................................................... 341 24.6 SPECTRAL OVERLAP............................................................................... 342 24.7 ENERGY TRANSFER IN THE TRIPLET S TA TE ............................................. 346 25 COHERENT EXCITATIONS IN PHOTOSYNTHETIC SYSTEM S ................................... 349 25.1 COHERENT EXCITATIONS......................................................................... 350 25.1.1 STRONGLY COUPLED D IM E RS ............................................... 350 25.1.2 EXCITONIC STRUCTURE OF THE REACTION C EN TER .................. 355 25.1.3 CIRCULAR MOLECULAR A GGREGATES ...................................... 356 25.1.4 DIMERIZED SYSTEMS OF LHII............................................. 362 25.2 INFLUENCE OF D ISORDER...................................................................... 367 25.2.1 SYMMETRY BREAKING LOCAL PERTURBATION ......................... 367 25.2.2 PERIODIC M ODULATION ........................................................ 369 25.2.3 DIAGONAL DISORDER............................................................. 372 25.2.4 OFF-DIAGONAL DISORDER...................................................... 374 PROBLEMS.......................................................................................................... 376 26 CHARGE TRANSFER IN D N A .......................................................................... 379 26.1 DIFFUSIVE HOLE TRANSFER................................................................... 380 26.2 TUNNELING OVER BRIDGE S TATES........................................................ 382 26.3 COMBINED TRANSFER M ECHANISM ................................................... 383 27 PROTON T RANSFER IN BIOM OLECULES ............................................................ 385 27.1 THE PROTON PUMP BACTERIORHODOPSIN............................................. 386 27.2 BORN-OPPENHEIMER SEPARATION...................................................... 388 27.3 NONADIABATIC PROTON TRANSFER (SMALL COUPLING)......................... 390 27.4 STRONGLY BOUND P ROTONS................................................................. 391 27.5 ADIABATIC PROTON TRANSFER............................................................... 393 28 PROTON COUPLED COHERENT CHARGE T R A N S FE R ......................................... 395 28.1 THE NONADIABATIC ELECTRONIC INCOHERENT STEP TRANSFER M ODEL........................................................................ 395 28.1.1 THE RATE EXPRESSION........................................................ 396 28.1.2 APPLICATION OF THE SADDLE POINT M ETHOD ........................ 398 28.2 HETEROGENEOUS SUPEREXCHANGE COUPLING ...................................... 402 28.3 PROTON COUPLED SUPEREXCHANGE ................................................... 409 28.4 COHERENT DYNAMICS.......................................................................... 411 28.5 COHERENT O SCILLATIONS ..................................................................... 412 P A RT V M MOLECULAR M OTOR MODELS 29 CONTINUOUS RATCHET M O D ELS ..................................................................... 417 29.1 TRANSPORT E QUATIONS........................................................................ 418 29.2 A SIMPLE SAWTOOTH R ATCHET.......................................................... 423 29.3 RATCHETS IN THE LOW TEMPERATURE L IM IT ...................................... 426 29.4 CHEMICAL TRANSITIONS ..................................................................... 429 29.5 THE TWO-STATE M ODEL ..................................................................... 435 29.5.1 THE CHEMICAL C Y C LE ........................................................ 436 29.5.2 THE FAST REACTION L IM IT ................................................. 441 29.5.3 THE FAST DIFFUSION LIM IT ................................................. 441 29.5.4 OPERATION CLOSE TO THERMAL EQUILIBRIUM....................... 443 29.6 RATCHET WITH LOCALIZED REACTIONS ................................................. 445 PROBLEMS......................................................................................................... 448 30 DISCRETE RATCHET M ODELS............................................................................ 449 30.1 LINEAR DISCRETE RATCHETS................................................................. 449 30.2 LINEAR MODEL WITH TWO INTERNAL STATES ........................................ 449 P ART IX APPENDIX APPENDIX A: THE G RAND CANONICAL E NSEM BLE............................................. 455 A .L GRAND CANONICAL DISTRIBUTION........................................... 456 A.2 CONNECTION TO THERMODYNAMICS ...................................... 457 XVI CONTENTS APPENDIX B: CLASSICAL APPROXIM ATION OF QUANTUM M O TIO N .................... 459 APPENDIX C: TIME CORRELATION FUNCTION OF THE DISPLACED HARM ONIE OSCILLATOR M ODEL.......................................................................... 463 C.L EVALUATION OF THE TIME CORRELATION FUNCTION .................... 463 C.2 BOSON ALGEBRA.................................................................. 465 C.2.1 DERIVATION OF THEOREM 1 ..................................... 465 C.2.2 DERIVATION OF THEOREM 2 ..................................... 466 C.2.3 DERIVATION OF THEOREM 3 ................................... 466 C.2.4 DERIVATION OF THEOREM 4 ..................................... 467 APPENDIX D: COMPLEX COTANGENT F U N C TIO N ................................................ 469 APPENDIX E: THE SADDLE POINT M ETHOD......................................................... 471 S O LU TIO N S................................................................................................................ 475 R EFERENCES.............................................................................................................. 503 I N D E X ....................................................................................................................... 509
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author	Scherer, Philipp O. J. Fischer, Sighart F. 1938-
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author_facet	Scherer, Philipp O. J. Fischer, Sighart F. 1938-
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language	English
oai_aleph_id	oai:aleph.bib-bvb.de:BVB01-030134416
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physical	XVI, 513 Seiten Illustrationen, Diagramme (teilweise farbig)
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spelling	Scherer, Philipp O. J. Verfasser (DE-588)110745108 aut Theoretical molecular biophysics Philipp O.J. Scherer, Sighart F. Fischer Second edition Berlin Springer [2017] © 2017 XVI, 513 Seiten Illustrationen, Diagramme (teilweise farbig) txt rdacontent n rdamedia nc rdacarrier Biological and medical physics, biomedical engineering Theoretische Biophysik (DE-588)4185096-8 gnd rswk-swf Molekulare Biophysik (DE-588)4170391-1 gnd rswk-swf PDE TC Elementary Processes in Biophysics Molecular Biophysics Explained Theoretical Biophysics textbook Molecular Biophysics Textbook Photosynthetic System Statistical Mechanics of Biopolymers Reaction Kinetics Photoinduced Processes Molekulare Biophysik (DE-588)4170391-1 s Theoretische Biophysik (DE-588)4185096-8 s DE-604 Fischer, Sighart F. 1938- Verfasser (DE-588)1089786549 aut Springer-Verlag GmbH (DE-588)1065168780 pbl Erscheint auch als Online-Ausgabe Scherer, Philipp O.J. Theoretical Molecular Biophysics 978-3-662-55671-9 Berlin, Heidelberg : Springer Berlin Heidelberg, 2017 Online-Ressourcen Vorangegangen ist 9783540856092 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=d33b254531584b21ade346da1f05250f&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030134416&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Scherer, Philipp O. J. Fischer, Sighart F. 1938- Theoretical molecular biophysics Theoretische Biophysik (DE-588)4185096-8 gnd Molekulare Biophysik (DE-588)4170391-1 gnd
subject_GND	(DE-588)4185096-8 (DE-588)4170391-1
title	Theoretical molecular biophysics
title_auth	Theoretical molecular biophysics
title_exact_search	Theoretical molecular biophysics
title_full	Theoretical molecular biophysics Philipp O.J. Scherer, Sighart F. Fischer
title_fullStr	Theoretical molecular biophysics Philipp O.J. Scherer, Sighart F. Fischer
title_full_unstemmed	Theoretical molecular biophysics Philipp O.J. Scherer, Sighart F. Fischer
title_short	Theoretical molecular biophysics
title_sort	theoretical molecular biophysics
topic	Theoretische Biophysik (DE-588)4185096-8 gnd Molekulare Biophysik (DE-588)4170391-1 gnd
topic_facet	Theoretische Biophysik Molekulare Biophysik
url	http://deposit.dnb.de/cgi-bin/dokserv?id=d33b254531584b21ade346da1f05250f&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030134416&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
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