Thermodynamics and statistical mechanics of macromolecular systems:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge
Cambridge Univ. Press
2014
|
| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Klappentext Inhaltsverzeichnis |
| Beschreibung: | XV, 342 S. graph. Darst. |
| ISBN: | 9781107014473 |
Internformat
MARC
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| 100 | 1 | |a Bachmann, Michael |d 1973- |e Verfasser |0 (DE-588)123274117 |4 aut | |
| 245 | 1 | 0 | |a Thermodynamics and statistical mechanics of macromolecular systems |c Michael Bachmann |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Cambridge |b Cambridge Univ. Press |c 2014 | |
| 300 | |a XV, 342 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Macromolecules |x Thermodynamics | |
| 650 | 4 | |a Biomolecules |x Structure | |
| 650 | 4 | |a DNA |x Structure | |
| 650 | 4 | |a Statistical mechanics | |
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Datensatz im Suchindex
| _version_ | 1804152201007857664 |
|---|---|
| adam_text | Contents
li
Preface
and outline page
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
η
m Contents
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 Cario
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
Bézier
curves
93
4.3.1
Construction of
a Bézier
curve
93
4.3.2
Smooth
Bézier
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.И.2
Iterative determination of the density of states
130
4.12
Random number generators
133
4.13
Molecular dynamics
134
Contents
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
Θ
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
Thennodynamics 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 Hydrophobie-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
Microcanooical effects
209
9.5
Two-state cooperativity in helix-coil transitions
213
Contents
W
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
Π
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
1
2.
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 Anisotropie
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
sì
Contents
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
The structural mechanics of proteins that fold into
functional shapes, polymers that aggregate and form
clusters, and organic macromolecules that bind to
inorganic matter can be understood only through
statistical physics and thermodynamics.
This book reviews the statistical mechanics concepts
and tools necessary for the study of structure formation
processes in macromolecular systems that are essentially
influenced by finite-size and surface effects. Readers
are introduced to molecular modeling approaches, advanced
Monte Carlo simulation techniques, and systematic statistical
analyses of numerical data. Applications to folding, aggregation,
and substrate adsorption processes of polymers and proteins
are discussed in great detail. Particular emphasis is placed on
the reduction of complexity by coarse-grained modeling, which
allows for the efficient, systematic investigation of structural
phases and transitions.
Providing insight into modern research at this interface
between physics, chemistry, biology, and nanotechnology,
this book is an excellent reference for graduate students and
researchers.
Michael Bachmann
is Associate Professor in the Department of
Physics and Astronomy at the University of
Georg».
His major fields
of interest include theoretical physics, computational physics, statistical
physics, biophysics, and chemical physics.
|
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| discipline | Chemie / Pharmazie Physik Biologie |
| edition | 1. publ. |
| format | Book |
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| id | DE-604.BV041853322 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T01:06:56Z |
| institution | BVB |
| isbn | 9781107014473 |
| language | English |
| lccn | 013032171 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-027297727 |
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| physical | XV, 342 S. graph. Darst. |
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| publisher | Cambridge Univ. Press |
| record_format | marc |
| spelling | Bachmann, Michael 1973- Verfasser (DE-588)123274117 aut Thermodynamics and statistical mechanics of macromolecular systems Michael Bachmann 1. publ. Cambridge Cambridge Univ. Press 2014 XV, 342 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Macromolecules Thermodynamics Biomolecules Structure DNA Structure Statistical mechanics Thermodynamik (DE-588)4059827-5 gnd rswk-swf Makromolekül (DE-588)4037172-4 gnd rswk-swf Makromolekül (DE-588)4037172-4 s Thermodynamik (DE-588)4059827-5 s DE-604 Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027297727&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Klappentext Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027297727&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bachmann, Michael 1973- Thermodynamics and statistical mechanics of macromolecular systems Macromolecules Thermodynamics Biomolecules Structure DNA Structure Statistical mechanics Thermodynamik (DE-588)4059827-5 gnd Makromolekül (DE-588)4037172-4 gnd |
| subject_GND | (DE-588)4059827-5 (DE-588)4037172-4 |
| title | Thermodynamics and statistical mechanics of macromolecular systems |
| title_auth | Thermodynamics and statistical mechanics of macromolecular systems |
| title_exact_search | Thermodynamics and statistical mechanics of macromolecular systems |
| title_full | Thermodynamics and statistical mechanics of macromolecular systems Michael Bachmann |
| title_fullStr | Thermodynamics and statistical mechanics of macromolecular systems Michael Bachmann |
| title_full_unstemmed | Thermodynamics and statistical mechanics of macromolecular systems Michael Bachmann |
| title_short | Thermodynamics and statistical mechanics of macromolecular systems |
| title_sort | thermodynamics and statistical mechanics of macromolecular systems |
| topic | Macromolecules Thermodynamics Biomolecules Structure DNA Structure Statistical mechanics Thermodynamik (DE-588)4059827-5 gnd Makromolekül (DE-588)4037172-4 gnd |
| topic_facet | Macromolecules Thermodynamics Biomolecules Structure DNA Structure Statistical mechanics Thermodynamik Makromolekül |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027297727&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027297727&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT bachmannmichael thermodynamicsandstatisticalmechanicsofmacromolecularsystems |