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ОбложкаBachmann M. Thermodynamics and statistical mechanics of macromolecular systems. - Cambridge: Cambridge university press, 2014. - xv, 342 p.: ill. - Bibliogr.: p.323-335. - Ind.: p.337-342. - ISBN 078-1-107-01447-3
Шифр: (И/Е0-В12) 02
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
Preface and outline .......................................... xiii

1    Introduction ............................................... 1
1.1  Relevance of biomolecular research ......................... 1
1.2  Proteins ................................................... 3
     1.2.1  The trinity of amino acid sequence, structure, and
            function ............................................ 3
     1.2.2  Ribosomal synthesis of proteins ..................... 6
     1.2.3  From sequence to function: The protein folding
            process ............................................. 7
1.3  Molecular modeling ......................................... 9
     1.3.1  Covalent bonds ...................................... 9
     1.3.2  Effective noncovalent interactions and nanoscopic
            modeling: Toward a semiclassical all-atom
            representation ..................................... 11
1.4  All-atom peptide modeling ................................. 12
1.5  The mesoscopic perspective ................................ 14
     1.5.1  Why coarse-graining...? The origin of the
            hydrophobic force .................................. 15
     1.5.2  Coarse-grained hydrophobic-polar modeling .......... 17
1.6  Polymers .................................................. 20
     1.6.1  DNA and RNA ........................................ 20
     1.6.2  Modeling free DNA .................................. 22
     1.6.3  Flexible, attractively self-interacting polymers ... 23
     1.6.4  Elastic polymers ................................... 27

2    Statistical mechanics: A modern review .................... 31
2.1  The theory of everything .................................. 31
2.2  Thermodynamics and statistical mechanics .................. 33
     2.2.1  The thermodynamic limit ............................ 33
     2.2.2  Thermodynamics of closed systems: The canonical
            ensemble ........................................... 34
     2.2.3  Thermodynamic equilibrium and the statistical
            nature of entropy .................................. 36
2.3  Thermal fluctuations and the statistical path integral .... 43
2.4  Phase and pseudophase transitions ......................... 46
2.5  Relevant degrees of freedom ............................... 48
     2.5.1  Coarse-grained modeling on mesoscopic scales ....... 48
     2.5.2  Macroscopic relevant degrees of freedom: The
            free-energy landscape .............................. 49
2.6  Kinetic free-energy barrier and transition state .......... 51
2.7   Microcanonical statistical analysis ...................... 53
     2.7.1  Temperature as a derived quantity .................. 54
     2.7.2  Identification of first-order transitions by
            Maxwell construction ............................... 55
     2.7.3  Systematic classification of transitions by
            inflection-point analysis .......................... 62

3    The complexity of minimalistic lattice models for
     protein folding ........................................... 67
3.1  Evolutionary aspects ...................................... 67
3.2  Self-avoiding walks and contact matrices .................. 68
3.3  Exact statistical analysis of designing sequences ......... 69
3.4  Exact density of states and thermodynamics ................ 76

4    Monte Carlo and chain growth methods for molecular
     simulations ............................................... 81
4.1  Introduction .............................................. 81
4.2  Conventional Markov-chain Monte Carlo sampling ............ 82
     4.2.1  Ergodicity and finite time series .................. 82
     4.2.2  Statistical error and bias ......................... 84
     4.2.3  Binning-jackknife error analysis ................... 88
4.3  Systematic data smoothing by using Bezier curves .......... 93
     4.3.1  Construction of a Bezier curve ..................... 93
     4.3.2  Smooth Bezier functions for discrete noisy data
            sets ............................................... 96
4.4  Markov processes and stochastic sampling strategies ...... 100
     4.4.1  Master equation ................................... 100
     4.4.2  Selection and acceptance probabilities ............ 101
     4.4.3  Simple sampling ................................... 102
     4.4.4  Metropolis sampling ............................... 103
4.5  Reweighting methods ...................................... 104
     4.5.1  Single-histogram reweighting ...................... 104
     4.5.2  Multiple-histogram reweighting .................... 105
4.6  Generalized-ensemble Monte Carlo methods ................. 108
     4.6.1  Replica-exchange Monte Carlo method: Parallel
            tempering ......................................... 108
     4.6.2  Simulated tempering ............................... 109
     4.6.3  Multicanonical sampling ........................... 109
     4.6.4  Wang-Landau method ................................ 117
4.7  Elementary Monte Carlo updates ........................... 118
4.8  Lattice polymers: Monte Carlo sampling vs. Rosenbluth
     chain growth ............................................. 123
4.9  Pruned-enriched Rosenbluth method: Go with the winners ... 126
4.10 Canonical chain growth with PERM ......................... 127
4.11 Multicanonical chain-growth algorithm .................... 129
     4.11.1 Multicanonical sampling of Rosenbluth-weighted
            chains ............................................ 129
     4.11.2 Iterative determination of the density of states .. 130
4.12 Random number generators ................................. 133
4.13 Molecular dynamics ....................................... 134

5    First insights to freezing and collapse of flexible
     polymers ................................................. 137
5.1  Conformational transitions of flexible homopolymers ...... 137
5.2  Energetic fluctuations of finite-length polymers ......... 138
     5.2.1  Peak structure of the specific heat ............... 138
     5.2.2  Simple-cubic lattice polymers ..................... 139
     5.2.3  Polymers on the face-centered cubic lattice ....... 141
5.3  The 0 transition ......................................... 144
5.4  Freezing and collapse in the thermodynamic limit ......... 147

6    Crystallization of elastic polymers ...................... 149
6.1  Lennard-Jones clusters ................................... 149
6.2  Perfect icosahedra ....................................... 150
6.3  Liquid-solid transitions of elastic flexible polymers .... 152
     6.3.1  Finitely extensible nonlinear elastic Lennard-
            Jones polymers .................................... 152
     6.3.2  Classification of geometries ...................... 153
     6.3.3  Ground states ..................................... 155
     6.3.4  Thermodynamics of liquid-solid transitions
            toward complete icosahedra ........................ 156
     6.3.5  Liquid-solid transitions of elastic polymers ...... 158
     6.3.6  Long-range effects ................................ 162
6.4  Systematic analysis of compact phases .................... 164
6.5  Dependence of structural phases on the range of
     nonbonded interactions ................................... 165

7    Structural phases of semiflexible polymers ............... 175
7.1  Structural hyperphase diagram ............................ 175
7.2  Variation of chain length ................................ 180

8    Generic tertiary folding properties of proteins on
     mesoscopic scales ........................................ 181
8.1  A simple model for a parallel β helix lattice protein .... 181
8.2  Protein folding as a finite-size effect .................. 184
8.3  Hydrophobic-polar off-lattice heteropolymers ............. 185

9    Protein folding channels and kinetics of two-state
     folding .................................................. 191
9.1  Similarity measure and order parameter ................... 192
9.2  Identification of characteristic folding channels ........ 195
9.3  Go kinetics of folding transitions ....................... 198
     9.3.1  Coarse-grained Go modeling ........................ 199
     9.3.2  Thermodynamics .................................... 201
     9.3.3  Kinetics .......................................... 204
     9.3.4  Mesoscopic heteropolymers vs. real proteins ....... 208
9.4  Microcanonical effects ................................... 209
9.5  Two-state cooperativity in helix-coil transitions ........ 213

10   Inducing generic secondary structures by constraints ..... 217
10.1 The intrinsic nature of secondary structures ............. 217
10.2 Polymers with thickness constraint ....................... 218
     10.2.1 Global radius of curvature ........................ 218
     10.2.2 Modeling flexible polymers with constraints ....... 219
     10.2.3 Thickness-dependent ground-state properties ....... 220
     10.2.4 Structural phase diagram of tube-like polymers .... 222
10.3 Secondary-structure phases of a hydrophobic-polar
     heteropolymer model ...................................... 223

11   Statistical analyses of aggregation processes ............ 227
11.1 Pseudophase separation in nucleation processes of
     polymers ................................................. 227
11.2 Mesoscopic hydrophobic-polar aggregation model ........... 228
11.3 Order parameter of aggregation and fluctuations .......... 229
11.4 Statistical analysis in various ensembles ................ 230
     11.4.1 Multicanonical results ............................ 230
     11.4.2 Canonical perspective ............................. 233
     11.4.3 Microcanonical interpretation: The backbending
            effect ............................................ 235
11.5 Aggregation transition in larger heteropolymer systems ... 239

12   Hierarchical nature of phase transitions ................. 243
12.1 Aggregation of semiflexible polymers ..................... 243
12.2 Structural transitions of semiflexible polymers with
     different bending rigidities ............................. 244
12.3 Hierarchies of subphase transitions ...................... 247
12.4 Hierarchical peptide aggregation processes ............... 249
12.5 Hierarchical aggregation of GNNQQNY ...................... 252

13    Adsorption of polymers at solid substrates .............. 255
13.1 Structure formation at hybrid interfaces of soft and
     solid matter ............................................. 255
13.2 Minimalistic modeling and simulation of hybrid
     interfaces ............................................... 256
13.3 Contact-density chain-growth algorithm ................... 258
13.4 Pseudophase diagram of a flexible polymer near an
     attractive substrate ..................................... 259
     13.4.1 Solubility-temperature pseudophase diagram ........ 260
     13.4.2 Contact-number fluctuations ....................... 261
     13.4.3 Anisotropic behavior of gyration tensor
            components ........................................ 263
13.5 Alternative view: The free-energy landscape .............. 264
13.6 Continuum model of adsorption ............................ 269
     13.6.1 Off-lattice modeling .............................. 269
     13.6.2 Energetic and structural quantities for phase
            characterization by canonical statistical
            analysis .......................................... 270
     13.6.3 Comparative discussion of structural
            fluctuations ...................................... 271
     13.6.4 Adsorption parameters ............................. 273
     13.6.5 The pseudophase diagram of the hybrid system in
            continuum ......................................... 274
13.7 Comparison with lattice results .......................... 277
13.8 Systematic microcanonical analysis of adsorption
     transitions .............................................. 279
     13.8.1 Dependence on the surface attraction strength ..... 280
     13.8.2 Chain-length dependence ........................... 282
     13.8.3 Translational entropy ............................. 284
13.9 Polymer adsorption at a nanowire ......................... 286
     13.9.1 Modeling the polymer-nanowire complex ............. 287
     13.9.2 Structural phase diagram .......................... 288

14   Hybrid protein-substrate interfaces ...................... 293
14.1 Steps toward bionanotechnology ........................... 293
14.2 Substrate-specific peptide adsorption .................... 294
     14.2.1 Hybrid lattice model .............................. 294
     14.2.2 Influence of temperature and solubility on
            substrate-specific peptide adsorption ............. 295
14.3 Semiconductor-binding synthetic peptides ................. 301
14.4 Thermodynamics of semiconductor-binding peptides in
     solution ................................................. 303
14.5 Modeling a hybrid peptide-silicon interface .............. 307
     14.5.1 Introduction ...................................... 307
     14.5.2 Si(100), oxidation, and the role of water ......... 308
     14.5.3 The hybrid model .................................. 309
14.6 Sequence-specific peptide adsorption at silicon (100)
     surface .................................................. 312
     14.6.1 Thermal fluctuations and deformations upon
            binding ........................................... 312
     14.6.2 Secondary-structure contents of the peptides ...... 313
     14.6.3 Order parameter of adsorption and nature of
            adsorption transition ............................. 315

15   Concluding remarks and outlook ........................... 319

References .................................................... 323

Index ......................................................... 337

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