Novel methods in soft matter simulations:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Berlin [u.a.]
Springer
2004
|
| Series: | Lecture notes in physics
640 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIV, 393 S. Ill., graph. Darst. |
| ISBN: | 3540209166 |
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| 245 | 1 | 0 | |a Novel methods in soft matter simulations |c M. Karttunen ... (eds.) |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2004 | |
| 300 | |a XIV, 393 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Lecture notes in physics |v 640 | |
| 490 | 0 | |a Physics and astronomy online library | |
| 650 | 4 | |a Soft condensed matter |x Computer simulation | |
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Record in the Search Index
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|---|---|
| adam_text | Contents
Introduction
....................................................... 1
Applications
of Dissipative Particle
Dynamics
Robert
D.
Groot
.................................................... 5
1
Why Mesoscopic Simulation?
........................................ 5
2
Introduction to DPD
................................................ 6
2.
1 Forces
....................................................... 7
2.2
Simulation Techniques
......................................... 9
2.3
Parameterisation
............................................... 10
2.4
Generalisations and Alternatives
................................. 12
3
Block Copolymer Mesophase Separation
............................... 14
3.1
Polymers in Melt
.............................................. 14
3.2
Expected and Simulated Phase Diagram
........................... 16
3.3
Evolution Pathways
............................................ 20
3.4
Importance of Hydrodynamics
................................... 21
4
Polymers and Membranes Interacting with Surfactant Solutions
............ 25
4.1
Polymers and Surfactants in Solution
............................. 25
4.2
Biomembrane
Morphology
...................................... 30
4.3
Biomembrane
Deformation and Rupture
........................... 34
5
Conclusions
....................................................... 36
Simulating the Dynamics of Mesoscopic Systems
Christopher P. Lowe and
Menno
W.
Dreischor............................. 39
1
Introduction
....................................................... 39
1.1
Renormalizing Static Properties
.................................. 40
1.2
Time-Scales
.................................................. 41
2
Absolutely Minimal Mesoscopic Dynamics
............................. 43
2.1
Modelling the Solvent with an Andersen Thermostat
................ 44
2.2
Langevin
Dynamics of a Gaussian Chain
.......................... 45
2.3
Brownian Dynamics
........................................... 47
2.4
The Dynamics of a Colloidal Suspension
.......................... 47
2.5
What Does Minimal Dynamics Teach Us
.......................... 52
3
More Realistic Solvent Dynamics
-
Hydrodynamics
..................... 52
3.1
The Importance of Hydrodynamics
............................... 52
3.2
Putting Back the Hydrodynamics
................................. 54
VIII Contents
3.3
Dissipative Partide Dynamics
and the Lowe-Andersen Thermostat
.............................. 55
3.4
Parametrically Correct
Solvent
Modelling
......................... 57
3.5
Concluding Remarks
........................................... 58
4
An Example Problem
-
A Long Polymer Chain in an External Potential
..... 59
4.1
Renormalizing the Static Properties of the Ideal Chain
............... 59
4.2
Long Polymer Dynamics from Short Model Polymers
............... 61
4.3
Results for the Test Problem
..................................... 64
4.4
What Do We Learn from This Example
............................ 66
5
General Conclusions
................................................ 66
Statistical Mechanics of Coarse-Graining
Pep
Español
....................................................... 69
1
Introduction
....................................................... 69
2
The Theory of Coarse-Graining in a Nutshell
............................ 70
3
Example: A Colloidal Suspension
..................................... 72
3.1
Microscopic Level: Classical Mechanics
.......................... 72
3.2
Mesoscopic Level
1 :
Hydrodynamics
............................. 74
3.3
Mesoscopic Level
2:
Fokker-Planck
.............................. 76
3.4
Mesoscopic Level
3:
Smoluchowski
.............................. 77
3.5
Mesoscopic Level
4:
Fick
....................................... 78
3.6
Macroscopic Level: Thermodynamics
............................. 78
4
The Mathematics of the Theory of Coarse-Graining
...................... 79
4.1
The Microscopic Level
......................................... 80
4.2
Liouville Theorem
............................................. 80
4.3
Equilibrium at the Microscopic Level
............................. 81
4.4
The Mesoscopic Level
.......................................... 82
4.5
Exact Equation for P(x, t)
...................................... 84
4.6
The Fokker-Planck Equation
.................................... 86
5
Example: Smoluchowski Level
....................................... 88
6
How to Compute the Objects in the FPE from a MD Simulation?
........... 89
7
GENERIC Structure of the Fokker-Planck Equation
..................... 92
7.1
Properties of
L
and
M
......................................... 94
7.2
GENERIC Stochastic Differential Equation
........................ 96
7.3
The Size of the Fluctuations and the Deterministic Equations
......... 97
8
Fluid Particle Models for Simulating Complex Fluids
.................... 99
8.1
Soft Fluid Particles
............................................102
8.2
Complex Fluids
...............................................111
9
Summary
.........................................................112
Mesoscopic Multi-particle Collision Model for Fluid Flow
and Molecular Dynamics
Anatoly Malevanets, Raymond
Kapral
..................................116
1
Introduction
.......................................................116
2
Multi-particle Collision Model for Fluid Flow
...........................117
2.1
Evolution Equation
............................................120
2.2
Н
-Theorem...................................................
121
Contents
IX
3 Hydrodynamic
Equations
and Transport Properties
.......................126
3.1
Evolution Equations for Mean Dynamical Variables
.................126
3.2
Kinetic Equations for Conserved Variables
.........................128
3.3
General Form of the Kinetic Equation
.............................132
3.4
Hydrodynamic Equations
.......................................133
4
Simulations of Fluid Flow
...........................................135
5
Mesoscopic Model for Solute Molecular Dynamics
......................136
6
Simulations of Hybrid Dynamics
......................................138
6.1
Brownian Motion
..............................................138
6.2
Cluster Dynamics
..............................................142
6.3
Polymer Dynamics
.............................................144
6.4
Complex Fluids
...............................................146
7
Conclusion and Perspectives
.........................................147
Molecular Dynamics of Complex Systems:
Non-Hamiltonian, Constrained, Quantum-Classical
Giovanni Ciccotti and
Galina
Kalibaeva
.................................150
1
Introduction
.......................................................150
2
Non-Hamiltonian Molecular Dynamics
................................150
2.1
Nosé-Hoover
Demonstration
..................................150
2.2
Invariant Measure for Non-Hamiltonian Dynamical Systems
..........152
2.3
Liouville Equation and Its Stationary Solutions
.....................154
2.4
The Correct Rules to Construct the Equilibrium Ensemble
of Extended Variables Dynamical Systems
.........................156
2.5
The True Statistics of the
Nosé-Hoover
Ensemble
..................157
2.6
New Atomic W-stats (NVT, NPT)
..............................159
2.7
Molecular NPT with Constraints
.................................162
3
Implementations
...................................................167
3.1
Reversible Integrators
..........................................167
3.2
Constraints (SHAKE)
..........................................172
3.3
Concluding Remarks for Non-Hamiltonian Molecular Dynamics
......177
4
Dynamics and (Some) Statistical Mechanics
of Quantum-Classical Systems
........................................177
4.1
Quantum-Classical Non-adiabatic Dynamics
.......................177
4.2
Quantum-Classical Statistical Mechanics
..........................184
4.3
Concluding Remarks for Quantum-Classical Systems
................188
Hybrid Models: Bridging Particle and Continuum Scales
in Hydrodynamic Flow Simulations
Eirik G. Flekk0y, Sean McNamara,
Knut J0rgen
МаЏу,
Jens Feder,
Geri
Wagner
.......................................................190
1
Introduction
.......................................................190
2
A HybridModel for Diffusion
........................................191
2.1
Simulations and Results
........................................193
2.2
Transport Properties and Continuity
of the Discrete-Continuous Interface
..............................194
2.3
Equilibrium Fluctuations
........................................196
X
Contents
3
A
Hybrid
Model for the Navier-Stokes Equation
.........................201
4
A Hybrid Model for the Coupling of Gas and Grains
.....................205
4.1
Gas Dynamics
................................................206
4.2
Particle Dynamics
.............................................208
4.3
Implementation
...............................................210
4.4
Sedimentation
.................................................211
4.5
Fluidized
Beds
................................................213
4.6
Experimental Verification
.......................................214
5
Conclusions
.......................................................215
On the Reduction of Molecular Degrees of Freedom
in Computer Simulations
Alexander P. Lyubartsev andAatto Laaksonen
.............................219
1
Introduction
.......................................................219
1.1
Atomistic Force Fields
..........................................220
1.2
Parameterization of Force Fields
.................................224
2
Reduction of Molecular Degrees of Freedom
............................225
2.1
Eliminating Fast Fluctuations
....................................226
2.2
Simplifying Molecular Models
...................................227
2.3
Elimination of Explicit Solvent Molecules
.........................227
3
Effective Potentials and the Inverse Monte Carlo Method
.................228
3.1
Inverse Problem in Statistical Mechanics
..........................228
3.2
The Method
..................................................229
3.3
How to Implement the Method for More General Systems
............231
4
Some Examples and Discussion
.......................................232
4.1
Ab-lnitio Effective Potentials
....................................232
4.2
Effective Solvent-Mediated Potentials
.............................236
4.3
Effective Potentials for Macromolecules
...........................241
5
Summary
.........................................................242
Computer Simulations of the Electric Double Layer
AndréG. Moreira
and Roland
R.
Netz...................................245
1
Introduction
.......................................................245
2
Numerics of the Coulomb Interaction
..................................246
2.1
Electrostatic Energy for Periodic Systems
.........................248
2.2
Precision of the Lekner Summation
...............................252
3
Counterions Close to a Single Charged Wall
............................253
3.1
Counterion
Density Profile
......................................257
3.2
Two-Dimensional Liquid and Crystal
.............................259
3.3
Finite-Size Effects
.............................................262
3.4
Other Boundary Conditions
.....................................263
4
Charge-Modulated Substrate
.........................................265
5
Interacting Double Layers
...........................................270
6
Concluding Remarks
................................................275
Contents
XI
Lattice Boltzmann Modeling of Complex Fluids: Colloidal Suspensions
and Fluid Mixtures
Ignacio Pagonabarraga
..............................................279
1
Introduction
.......................................................279
2
Lattice Boltzmann: The Model
........................................280
2.1
Elementary Variables
...........................................282
2.2
Time Evolution
................................................282
2.3
The Equilibrium Distribution
....................................283
2.4
Macroscopic Dynamics
.........................................284
3
Colloidal Suspensions
...............................................286
3.1
Modeling Solid Particles
........................................286
3.2
Colloidal Hydrodynamics
.......................................289
3.3
Colloids at High Confinement
...................................290
4
Non-ideal Fluids: A Binary Mixture
...................................298
4.1
The Model
....................................................299
4.2
Spinodal Decomposition
........................................301
5
Conclusions
.......................................................306
Reverse Non-equilibrium Molecular Dynamics
Florian Müller-Plathe,
Patrice
Bordât
...................................310
1
Introduction
.......................................................310
2
Introduction: Transport Coefficients
...................................310
3
Illustration of the RNEMD Method: Calculating Shear Viscosity
...........312
4
Modification of the RNEMD Method: Thermal Conductivity
..............317
5
Digression: Features of the RNEMD Method
............................319
6
The RNEMD and Higher-Order Transport Coefficients:
The Ludwig-Soret Effect as an Example
...............................320
7
Molecular Fluids and the RNEMD Method
.............................321
8
A Bibliography of Applications of the RNEMD Method
..................323
8.1
Shear Flow, Viscosity
..........................................323
8.2
Thermal Conductivity
..........................................323
8.3
Thermal Diffusion, Soret Coefficient
..............................324
9
Status and Future Potential of the RNEMD Method
......................324
Coarse-Graining in Polymer Simulations
Séverine Girard
and
Florian Müller-Plathe...............................327
1
Introduction
.......................................................327
2
From Quantum Chemistry to Atomistic Simulation
.......................329
2.1
The Bonded-Potential
..........................................330
2.2
The Non-bonded Potential
......................................331
2.3
Force Field Optimisation
........................................332
3
Coarse-Graining from Atomistic to Mesoscopic Models
..................335
3.1
The Super-Atoms
..............................................336
3.2
Definition and Optimisation of the Potential
........................339
4
Reverse Mapping
...................................................347
5
Relation to Other Coarse-Graining Procedures
..........................349
5.1
Lattice Models
................................................349
XII Contents
5.2
Coarse-Graining Further: From Super-Atoms to Blobs
...............354
6
Conclusions
.......................................................354
Phase-Field Modeling of Dynamical Interface Phenomena in Fluids
Tapio
Ala-Nissila,
Sami
Majaniemi, Ken Elder
............................357
1
Introduction to Coarse-Graining
......................................357
2
Phase-Field Modeling
...............................................359
2.1
Construction of Free Energy
.....................................360
2.2
The Phase-Field
...............................................361
3
Sharp Interface Limit
...............................................364
3.1
Droplets
......................................................364
3.2
Dynamics of Gently Curved Fronts
...............................366
3.3
Kinetic Roughening
............................................368
3.4
Universality
..................................................370
4
Advantages of the Phase-Field Approach
...............................371
5
Alphabet Soup of Models
............................................372
6
Application: Kinetic Roughening in Imbibition
..........................374
6.1
Background
..................................................374
6.2
Phase-Field Model of Imbibition
.................................375
6.3
Evaporation and Gravity
........................................379
6.4
Capillaries
....................................................381
7
Phase-Field Models and Hydrodynamics
...............................382
8
Summary and Conclusions
...........................................384
Index
.............................................................389
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| genre | (DE-588)1071861417 Konferenzschrift 2002 Espoo gnd-content |
| genre_facet | Konferenzschrift 2002 Espoo |
| id | DE-604.BV017797044 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:21:56Z |
| institution | BVB |
| isbn | 3540209166 |
| language | English |
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| series | Lecture notes in physics |
| series2 | Lecture notes in physics Physics and astronomy online library |
| spelling | Novel methods in soft matter simulations M. Karttunen ... (eds.) Berlin [u.a.] Springer 2004 XIV, 393 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Lecture notes in physics 640 Physics and astronomy online library Soft condensed matter Computer simulation Computersimulation (DE-588)4148259-1 gnd rswk-swf Weiche Materie (DE-588)4609142-7 gnd rswk-swf (DE-588)1071861417 Konferenzschrift 2002 Espoo gnd-content Weiche Materie (DE-588)4609142-7 s Computersimulation (DE-588)4148259-1 s DE-604 Karttunen, Mikko Sonstige oth Varttulainen, Ilpo Sonstige oth Lukkarinen, Ari Sonstige oth Lecture notes in physics 640 (DE-604)BV000003166 640 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010686250&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Novel methods in soft matter simulations Lecture notes in physics Soft condensed matter Computer simulation Computersimulation (DE-588)4148259-1 gnd Weiche Materie (DE-588)4609142-7 gnd |
| subject_GND | (DE-588)4148259-1 (DE-588)4609142-7 (DE-588)1071861417 |
| title | Novel methods in soft matter simulations |
| title_auth | Novel methods in soft matter simulations |
| title_exact_search | Novel methods in soft matter simulations |
| title_full | Novel methods in soft matter simulations M. Karttunen ... (eds.) |
| title_fullStr | Novel methods in soft matter simulations M. Karttunen ... (eds.) |
| title_full_unstemmed | Novel methods in soft matter simulations M. Karttunen ... (eds.) |
| title_short | Novel methods in soft matter simulations |
| title_sort | novel methods in soft matter simulations |
| topic | Soft condensed matter Computer simulation Computersimulation (DE-588)4148259-1 gnd Weiche Materie (DE-588)4609142-7 gnd |
| topic_facet | Soft condensed matter Computer simulation Computersimulation Weiche Materie Konferenzschrift 2002 Espoo |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010686250&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000003166 |
| work_keys_str_mv | AT karttunenmikko novelmethodsinsoftmattersimulations AT varttulainenilpo novelmethodsinsoftmattersimulations AT lukkarinenari novelmethodsinsoftmattersimulations |