Verfügbarkeit: Nonlinear excitations in biomolecules

Nonlinear excitations in biomolecules: Les Houches School, May 30 to June 4, 1994

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Format:	Buch
Sprache:	German
Veröffentlicht:	Berlin [u.a.] Springer [u.a.] 1995
Schlagworte:	Biomolecules > Congresses Biophysics > Congresses DNA > Congresses Energy Transfer > Congresses Excited state chemistry > Congresses Molecular Biology > Congresses Nonlinear Dynamics > Congresses Proteins > Congresses Solitons > Congresses Nichtlineares Phänomen Soliton Molekularbiologie Biomolekül Angeregter Zustand Konferenzschrift > 1994 > Les Houches
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	XV, 426 S. Ill., graph. Darst.
ISBN:	3540592504 2868832474

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adam_text	CONTENTS LECTURE 1 The intersection of nonlinear science, molecular biology, and condensed matter physics. Viewpoints by JA. Krumhansl 1. Introduction ................................................................................................................... 1 2. Viewpoints .................................................................................................................... 2 2.1. Scientific objectives differ intrinsically .................................................................... 2 2.2. Differentiation ........................................................................................................ 3 2 3. Biomolecules as polymers are treated realistically these days .................................. 4 2.4 Models play an important role in Science ................................................................ 6 2.5 Towards more and finer measurements ................................................................... 7 2.6. Some paradigms in current nonlinear science .......................................................... 8 3 Concluding remarks ....................................................................................................... 9 LECTURE 2 Introduction to solitons and their applications in physics and biology by M. Peyrard 1. The specificity of nonlinear systems ............................................................................... 11 2. The concept of solitoti ................................................................................................... 12 3. Conditions to have solitons ............................................................................................ 15 4 The different classes of solitons ...................................................................................... 16 5. Solitons are everywhere! ................................................................................................ 18 6. The formation of solitons nonlinear energy localization ................................................. 21 7. Conclusion ..................................................................................................................... 24 CHAPTER I DNA, structure and function ..... 27 LECTURE 3 Selected topics in molecular biology, in need of hard science by C. Reiss 1. DNA Structure .............................................................................................................. 29 2. Gene expression ............................................................................................................. 36 3. Control and regulation of gene expression: physical aspects ........................................... 46 4. The protein folding problem ........................................................................................... 50 5. Conclusion ..................................................................................................................... 54 VI LECTURE 4 Modelling the DNA double helix: techniques and results by R. Lavery 1. Introduction ................................................................................................................... 57 2. Modelling techniques ..................................................................................................... 58 2.1. Modelling nucleic acids using adapted coordinate systems ...................................... 60 2.2. Conformational analysis .......................................................................................... 62 3. DNA fine structure ........................................................................................................ 62 3.1. Energy surface mapping ......................................................................................... 65 3.2. Combinatorial searches ........................................................................................... 66 3.3. Building long sequences by superposition ............................................................... 71 4. Flexibility and structural transitions ................................................................................ 72 4.1. Base pair opening ................................................................................................... 72 4.2. Backbone transitions .............................................................................................. 75 4.3. Transitions between allomorphic forms ................................................................... 77 5. DNA dynamics and large scale simulations ..................................................................... 79 6. Conclusions ................................................................................................................... 79 LECTURE 5 Potential-of-mean-force description of ionic interactions and structural hyd ration in biomolecular systems by G. Hummer, D.M. Soumpasis and A.E. Garcia 1. Introduction ................................................................................................................... 83 2. The statistical-mechanical foundation of the potential-of-mean-force formalism .............. 84 3. Interactions of nucleic acids with ionic solutions ............................................................ 86 4 A statistical-mechanical theory of biomolecular hydration .............................................. 87 4.1. Introductory remarks .............................................................................................. 87 4.2. Density expansion in inhomogeneous liquid systems ............................................... 88 4.3. The water-density profile at the interface of ice and water ...................................... 89 4.4. Hydration of biological macromolecules: Results for DNA..................................... 92 5. Conclusions ................................................................................................................... 96 LECTURE 6 Inelastic neutron scattering studies of oriented DNA by H. Grimm and A. Rupprecht 1. Introduction ................................................................................................................... 101 2. Self correlation .............................................................................................................. 103 2.1. Time-of-flight spectra ............................................................................................. 103 2.2. Scattering function ................................................................................................. 105 2.3. Eigenvalue density .................................................................................................. 106 2.4. Analysis of self correlation spectra .......................................................................... 107 VII 3. Distinct correlation ........................................................................................................ ПО 4. Central component ......................................................................................................... 112 5. Conclusions ................................................................................................................... 113 LECTURE 7 Model simulations of base pair motion in B-DNA by M.A. Collins and F. Zhang 1. Introduction ................................................................................................................... 117 2. What sort of model? ...................................................................................................... 118 3. The model ..................................................................................................................... 118 3.1. Model potential surface .......................................................................................... 120 4. Some dynamical averages of this model DNA motion .................................................... 121 4.1. Hydrogen bond breaking ........................................................................................ 122 4.2. RMS atomic displacements ................................................................................. 123 4.3. Large amplitude excitations .................................................................................... 124 4.4. Correlations ........................................................................................................... 124 5. Concluding remarks ....................................................................................................... 124 LECTURE 8 A nonlinear model for DNA melting by T. Dauxois and M. Peyrard 1. Introduction ................................................................................................................... 127 2. The nonlinear dynamical model ...................................................................................... 129 3. Dynamics of the melting ................................................................................................. 130 4. Formation of denaturation bubbles ................................................................................. 133 5. Statistical mechanics ...................................................................................................... 134 5.1. Melting transition ................................................................................................... 134 5.2. Entropy driven DNA denaturation .......................................................................... 134 6. Conclusion ..................................................................................................................... 136 LECTURE 9 Dynamics of conformational excitations in the DNA macromolecule by A.M. Kosevich and S.N. Volkov 1. Introduction ............................................................................................................... 137 2. The model constructing ................................................................................................ 138 3. The conformational vibrations ...................................................................................... 140 4. The conformational solitons ......................................................................................... 142 VIII LECTURE 10 Nonlinear dynamics of plasmid pBR322 promoters by M. Salerno 1. Introduction ................................................................................................................... 147 2. The model ..................................................................................................................... 148 3. Numerical experiment and analysis ................................................................................. 149 4. Conclusions ................................................................................................................... 153 LECTURE 11 Helical geometry and DNA models by G. Gaeta 1. Introduction ................................................................................................................... 155 2. Selection of relevant degrees of freedom ........................................................................ 156 3. Description of the interactions ....................................................................................... 157 4. DNA hamiltonians......................................................................................................... 159 5. DNA dynamics .............................................................................................................. 160 6. Dispersion relations, and breather solutions .................................................................... 160 7. Soliton solutions ............................................................................................................ 161 8. Ising model approach ..................................................................................................... 162 9. Conclusions ................................................................................................................... 163 LECTURE 12 Nonlinear localized excitations and the dynamics of Н -bonds in DNA by S. Flach and C.R. Willis 1. Introduction ............................................................................................................ 2. Н -bond dynamics .................................................................................................... 2.1. Model classes .................................................................................................. 2.2. Nonlinear localized excitations ........................................................................ 3 Functioning with NLEs - phonon scattering ............................................................ IX CHAPTER II Proteins, conformation and dynamics ..... 175 LECTURE 13 Proteins and the physics of complexity by H. Frauenfelder 1. Proteins ......................................................................................................................... 177 2. The approach ................................................................................................................. 179 3. The structure of proteins ................................................................................................ 179 4. The energy landscape ..................................................................................................... 180 4.1. The experimental evidence for conformational substates ......................................... 181 4.1.1. Ligand binding to myoglobin ........................................................................... 181 4.1.2. Spectroscopic hole burning ............................................................................. 184 4.2. The hierarchy of conformational substates .............................................................. 184 4.2.1. Taxonomie conformational substates ............................................................... 185 4.2.2. Statistical substates ......................................................................................... 185 4.3. Conformational excitations ..................................................................................... 186 4.4. Theoretical and computational studies .................................................................... 186 5. Some remarks ................................................................................................................ 186 LECTURE 14 Multi-basin dynamics of a protein in aqueous solution by A.E. Garcia 1. Introduction ................................................................................................................... 191 2. Description of the system ............................................................................................... 192 3. Results and discussion ................................................................................................... 193 3.1. Localized non-linear motions .................................................................................. 193 3.2. Delocalized non-linear motions ............................................................................... 196 3.2.1. Tree analysis ................................................................................................... 197 3.3 Molecule optimal dynamical coordinates (MODC) ................................................. 199 4. Conclusions ................................................................................................................... 206 LECTURE 15 Nonlinear excitations in molecular crystals with chains of peptide bonds by M. Barthes 1. Introduction .......................................................................................................... 209 2 Acetanilide and derivatives ........................................................................ 209 2.1 Infrared results ........................................................................................ 211 χ 2.2. Raman scattering .................................................................................................... 213 2 3 Low temperature neutron diffraction ...................................................................... 213 2.4. Discussion .............................................................................................................. 215 3. N-methylacetamide ........................................................................................................ 215 4. L-alanine and polyalanines ............................................................................................. 219 5. Nucleotides, polypeptides and proteins .......................................................................... 219 6. Conclusion ..................................................................................................................... 220 LECTURE 16 Low temperature Raman spectra of acetanilide and its deuterated derivatives: comparison with normal mode analysis by G. De Nunzio 1. Introduction ................................................................................................................... 223 1.1. Bioenergetics ......................................................................................................... 223 1.1.1. Davydov s soliton ........................................................................................... 224 1.2. Where ACN comes in ............................................................................................. 224 1.3. Optical anomalies in ACN ...................................................................................... 225 1.4. Theories and experiments ....................................................................................... 225 2. Normal mode analysis .................................................................................................... 226 2.1 The program CHARMm ......................................................................................... 226 2.2. Results ................................................................................................................... 227 2.2.1. The range 1400-1700 cm 1 .............................................................................. 227 2.2.2. Some other frequency range ............................................................................ 230 LECTURE 17 Conformational dynamics of proteins: beyond the nanosecond time scale by H. Grubmüller, N. Ehrenhofer and P. Tavan 1. Introduction ................................................................................................................... 231 2. A simplified protein model ............................................................................................. 232 3 Configurational space and conformational substates ....................................................... 233 4 Conformational coordinates from neural clustering ......................................................... 235 5 Conformational coordinates from principal component analysis ...................................... 237 6 Summary and conclusion ............................................................................................... 239 XI LECTURE 18 Motions and correlations of the transmembrane domain of a protein receptor studied by molecular dynamics simulation by N. Gamier, D. Genest and M. Genest 1. Introduction ................................................................................................................... 241 2. Materials and methods .................................................................................................. 241 2.1. Molecular dynamics simulation ............................................................................... 24 1 2.2. Correlations ........................................................................................................... 242 2.3. Propagation of a local perturbation ......................................................................... 242 3. Results ........................................................................................................................... 243 4. Discussion and conclusion ............................................................................................. 246 CHAPTER III Energy and charge transport ..... 247 LECTURE 19 Solitary waves in biology by A.C. Scott 1. Introduction ................................................................................................................... 249 2. The nerve impulse .......................................................................................................... 250 2.1. Linear and nonlinear diffusion ................................................................................. 250 2.2. The Hodgkin-Huxley equations .............................................................................. 250 3. Soiitons in protein .......................................................................................................... 254 3.1. Polarons and conformons ....................................................................................... 254 3.2. Vibrational energy transport ................................................................................... 255 3.3. Quantum theory ..................................................................................................... 257 3.4. Thermal effects ....................................................................................................... 258 3.5. Crystalline acetanilide ............................................................................................. 260 3.6. Transport of electronic charge ................................................................................ 261 3.7. Protonic soiitons.................................................................................................... 262 3.8. Biological applications ............................................................................................ 262 4. Conclusions ................................................................................................................... 265 LECTURE 20 Exact two-quantum states of the seniiclassical Davydov model and their thermal stability by L. Cruzeiro-Hansson and V.M. Kenkre 1 Introduction .......................................................................................................... 269 2. The Davydov model .......................................................................................... 270 хи 3. Two-quantum states and their thermal stability ............................................................... 271 4. General remarks ............................................................................................................. 274 LECTURE 21 Post-soliton quantum mechanics by D.W. Brown The inverse problem .......................................................................................................... 280 General properties of Wannier states .................................................................................. 281 Weak coupling limits ......................................................................................................... 283 Conclusion ........................................................................................................................ 286 LECTURE 22 Dynamic form factor for the Yomosa model for the energy transport in proteins by A. Neuper and F.G. Mertens 1. Solitons in muscle fibers ................................................................................................. 287 2 Form factors in the Toda lattice ..................................................................................... 287 2.1. Simulation results ................................................................................................... 289 2.2. Cnoidal-wave approach .......................................................................................... 290 2.3. The soliton limit ..................................................................................................... 292 3. Summary ....................................................................................................................... 293 LECTURE 23 Energy and charge transfer in photosynthesis by W. Mantele 1. Introduction. Photosynthesis: a physico-chemo-biologist s view ..................................... 295 2. The lipid bilayer membrane as a structural basis ............................................................. 296 3 Pigments used for light absorption in photosynthesis ...................................................... 298 4. Pigments and proteins form pigment-protein-complexes ................................................. 300 5. Antenna systems of plants and bacteria .......................................................................... 302 6 From antennae to reaction centers: converting and stabilizing light energy ...................... 304 7. Information on structure and composition of reaction centers ......................................... 306 8. Characteristics of a quinone type reaction center ......................................................... 307 9 Primary processes, forward, and reverse electron transfer and the corresponding rates in the reaction center ......................................................................................................... 308 10 Why do reaction centers use quiñones as electron acceptors? ....................................... 310 11 What is the molecular basis for external reorganization energy in the reaction center? .. 312 12. Concluding remarks ..................................................................................................... 314 XIII LECTURE 24 The role of nonlinea rity in modelling energy transfer in Scheibe aggregates by O. Bang, P.L. Christiansen, K..0. Rasmussen and Y.B. Gaididei 1. Introduction ................................................................................................................... 317 2. Scheibe aggregates ........................................................................................................ 318 2.1. Langmuir-Blodgett films and Scheibe aggregates .................................................... 318 2.2. Experiments on Langmuir-Blodgett Scheibe aggregates .......................................... 319 2.3. Applications, and the connection with photosynthesis ............................................. 321 2.4. Physical models ...................................................................................................... 324 3. The nonlinear model ...................................................................................................... 325 3.1. Derivation .............................................................................................................. 325 3.2. Parameter values fora monolayer oxacyanine LB Scheibe aggregate ...................... 327 3.3. Approximations of the colored noise ...................................................................... 329 3.4. Choosing the initial condition ................................................................................. 330 3.5. Nonlinear coherence time for the ground state solitary wave solution ..................... 331 3.6. The role of collapse ................................................................................................ 333 4. Conclusion ..................................................................................................................... 335 LECTURE 25 Protons in hydrated protein powders by G. Careri, F. Bruni and G. Consolini 1. Abstract ......................................................................................................................... 337 2. Proton percolation and emergence of biological function in nearly dry biosystems .......... 338 3. Likely detection of protonie polarons in percolative water clusters adsorbed on lysozyme powders ............................................................................................................................. 341 LECTURE 26 Nonlinear models of collective proton transport in hydrogen-bonded systems by M. Peyrard 1. Introduction ................................................................................................................... 349 2. The physical problem and the first answers ..................................................................... 350 3. The A-D-Z soliton model for proton transport ............................................................... 351 4. Is there an experimental evidence of the soliton0 ........................................................... 354 5. Conclusion ..................................................................................................................... 359 XIV LECTURE 27 Proton-solitons bridge physics with biology by G.P. Tsironis 1. Introduction ................................................................................................................... 361 2. Proton-soliton mobility .................................................................................................. 363 3. Quantum tunnelling ........................................................................................................ 364 4. Conclusions ................................................................................................................... 365 Appendix. Calculation of the classical solitonmass ............................................................ 365 Semiclassical correction .................................................................................... 366 LECTURE 28 Neutron scattering studies of biopolymer-water systems: solvent mobility and collective excitations by H.D. Middendorf 1. Introduction ................................................................................................................... 369 2. Basic relations and scattering properties ......................................................................... 370 3. Globular proteins at low hydration ................................................................................. 372 3.1. Hydration dynamics of phycocyanin in the sorption regime ..................................... 372 3.2 High-resolution quasi-elastic scattering, Λω< 100 цеУ........................................... 373 3.3 Quasi-elastic and inelastic scattering with/ttû > 100 μεν ........................................ 376 4. Highly hydrated systems: polymer and biopolymer gels .................................................. 377 4.1. Structure and dynamics of aqueous gels .................................................................. 377 4.2. Quasi-elastic scattering ........................................................................................... 378 4.3. Inelastic scattering .................................................................................................. 380 5. Conclusions ................................................................................................................... 381 CHAPTER IV Beyond biological molecules ..... 385 LECTURE 29 The cell s microtubules: self-organization and information processing properties by JA. Tuszynski, B. Trpisová, D. Sept, M.V. Satane and S. Hameroff 1. Background information ................................................................................................ 387 2. Assembly/disassembly modelling .................................................................................. 389 3 The dipolar lattice and its phases .................................................................................... 390 4 Dynamics in the ferroelectric phase ............................................................................. 393 XV 5. Stability of the spin-glass phase ...................................................................................... 3 98 6 Information capacity in various phases ........................................................................... 400 7. Summary ...................................................................................................................... 403 LECTURE 30 Translation optimization in bacteria: statistical models by F. Bagnoli, G. Guasti and P. Lió 1. Introduction ................................................................................................................... 405 2. A dynamical model ........................................................................................................ 406 3. Statistical mechanics ...................................................................................................... 408 4. Concluding remarks ....................................................................................................... 410 LECTURE 31 Dynamics of vibrational dissociation of a pseudo-cluster by D. Hennig and H. Gabriel 1. Introduction ................................................................................................................... 413 2. The model hamiltonian ................................................................................................... 413 3. Dynamics of the model .................................................................................................. 415 3.1. Whisker map .......................................................................................................... 415 3.2. Resonance overlap ................................................................................................. 416 LECTURE 32 The step-potential model for π -electrons in hydrocarbon-systems by С Kuhn 1. Introduction ................................................................................................................... 42 1 2. Non-linear optics ........................................................................................................... 423 3. Kinks in polyacetylene: statics and dynamics .................................................................. 423 4. The Сю molecule ........................................................................................................... 425 CONCLUSION ..... 427
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genre	(DE-588)1071861417 Konferenzschrift 1994 Les Houches gnd-content
genre_facet	Konferenzschrift 1994 Les Houches
id	DE-604.BV010409871
illustrated	Illustrated
indexdate	2024-07-09T17:52:01Z
institution	BVB
isbn	3540592504 2868832474
language	German
oai_aleph_id	oai:aleph.bib-bvb.de:BVB01-006932555
oclc_num	34411850
open_access_boolean
owner	DE-355 DE-BY-UBR DE-91 DE-BY-TUM DE-703 DE-29T
owner_facet	DE-355 DE-BY-UBR DE-91 DE-BY-TUM DE-703 DE-29T
physical	XV, 426 S. Ill., graph. Darst.
publishDate	1995
publishDateSearch	1995
publishDateSort	1995
publisher	Springer [u.a.]
record_format	marc
spelling	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994 ed. M. Peyrard Berlin [u.a.] Springer [u.a.] 1995 XV, 426 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biomolecules Congresses Biophysics Congresses DNA Congresses Energy Transfer Congresses Excited state chemistry Congresses Molecular Biology Congresses Nonlinear Dynamics Congresses Proteins Congresses Solitons Congresses Nichtlineares Phänomen (DE-588)4136065-5 gnd rswk-swf Soliton (DE-588)4135213-0 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Biomolekül (DE-588)4135124-1 gnd rswk-swf Angeregter Zustand (DE-588)4142423-2 gnd rswk-swf (DE-588)1071861417 Konferenzschrift 1994 Les Houches gnd-content Molekularbiologie (DE-588)4039983-7 s Soliton (DE-588)4135213-0 s DE-604 Biomolekül (DE-588)4135124-1 s Angeregter Zustand (DE-588)4142423-2 s Nichtlineares Phänomen (DE-588)4136065-5 s Peyrard, Michel Sonstige oth Digitalisierung TU Muenchen application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006932555&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994 Biomolecules Congresses Biophysics Congresses DNA Congresses Energy Transfer Congresses Excited state chemistry Congresses Molecular Biology Congresses Nonlinear Dynamics Congresses Proteins Congresses Solitons Congresses Nichtlineares Phänomen (DE-588)4136065-5 gnd Soliton (DE-588)4135213-0 gnd Molekularbiologie (DE-588)4039983-7 gnd Biomolekül (DE-588)4135124-1 gnd Angeregter Zustand (DE-588)4142423-2 gnd
subject_GND	(DE-588)4136065-5 (DE-588)4135213-0 (DE-588)4039983-7 (DE-588)4135124-1 (DE-588)4142423-2 (DE-588)1071861417
title	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994
title_auth	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994
title_exact_search	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994
title_full	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994 ed. M. Peyrard
title_fullStr	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994 ed. M. Peyrard
title_full_unstemmed	Nonlinear excitations in biomolecules Les Houches School, May 30 to June 4, 1994 ed. M. Peyrard
title_short	Nonlinear excitations in biomolecules
title_sort	nonlinear excitations in biomolecules les houches school may 30 to june 4 1994
title_sub	Les Houches School, May 30 to June 4, 1994
topic	Biomolecules Congresses Biophysics Congresses DNA Congresses Energy Transfer Congresses Excited state chemistry Congresses Molecular Biology Congresses Nonlinear Dynamics Congresses Proteins Congresses Solitons Congresses Nichtlineares Phänomen (DE-588)4136065-5 gnd Soliton (DE-588)4135213-0 gnd Molekularbiologie (DE-588)4039983-7 gnd Biomolekül (DE-588)4135124-1 gnd Angeregter Zustand (DE-588)4142423-2 gnd
topic_facet	Biomolecules Congresses Biophysics Congresses DNA Congresses Energy Transfer Congresses Excited state chemistry Congresses Molecular Biology Congresses Nonlinear Dynamics Congresses Proteins Congresses Solitons Congresses Nichtlineares Phänomen Soliton Molekularbiologie Biomolekül Angeregter Zustand Konferenzschrift 1994 Les Houches
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006932555&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT peyrardmichel nonlinearexcitationsinbiomoleculesleshouchesschoolmay30tojune41994

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