Hierarchical Methods for Dynamics in Complex Molecular Systems

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Johannes Grotendorst
Forschungszentrum Jülich, 2012 - 540 Seiten
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Inhalt

Hard and Soft Materials
1
Multiparticle Collision Dynamics
2
Embedded Objects and Boundary Conditions
3
CellLevel Canonical Thermostat
4
Transport Coefficients
5
MPC without Hydrodynamics
6
External Fields
7
Hydrodynamic Simulations of Polymers in Flow Fields
8
5
321
Introduction
328
Identifying States
349
Calculating Rate Constants
351
Kinetic Monte Carlo Simulation
361
Analytical Solution of the Master Equation
362
Diffusion of Xenon in Silicalite
365
Diffusion of CO2 in Polyamide imide
371

Conclusions
9
Biomolecular Systems
39
Transition Path Sampling of Phase Transitions Nucleation and Growth
47
Dissipative Particle Dynamics Pep Espanol 1 Introduction
58
The Simulation of Simple Fluids 4 Two Technical Points Integrators and Boundary Conditions 5 Microscopic Foundation of DPD 6 Conclusion
75
Neural Network Potentials for Efficient LargeScale Molecular Dynamics
81
LargeScale Molecular Dynamics Studies and ScaleBridging Models
107
Exploration of MultiDimensional Free Energy Landscapes in Molecular
115
Long TimeStep Molecular Dynamics
126
Algorithmic Rethinking and Code Reengineering for Truly Massively Parallel
134
Methods on TDDFTBased Nonadiabatic Dynamics with Applications
139
Hybrid CarParrinello Molecular Dynamics Molecular Mechanics
163
4
175
6
177
Simulation Techniques for Studying the Impact of Force on Biochemical
183
Coarse Grained Models for Multiscale Simulations of Biomolecular Systems
195
ParticleBased Dynamics Simulations of MultiProtein Systems and Cellular
219
NonEquilibrium Molecular Dynamics for Biomolecular Systems Using Fluc
269
Multigrid QMMM Approaches in ab initio Molecular Dynamics
279
7
303
Accelerated Molecular Dynamics Methods
312
8
313
10
317
Dynamic Integration of a Markovian Web and its Application to Structural Relaxation in Glasses
376
Lumping
382
Summary
384
Extension to Quantum Problems Luigi Delle Site 1 2 3 4 5 6 Introduction
391
The AdResS Method
392
The Conceptual Problem
394
Path Integral Molecular Dynamics
395
QuantumClassical Adaptive Resolution Simulation via PIMD
398
Conclusions and Perspectives
400
Flow Simulation and Transport Coupling Molecular Dynamics and Lattice Boltzmann to Simulate Brownian Motion with Hydrodynamic Interactions...
403
Coupling Scheme
405
Statistical Mechanics
407
Stochastic Collisions 6 Lattice Boltzmann 3 ChapmanEnskog Expansion
410
A Polymer Chain in Solvent
412
417
417
431
431
349
441
445
445
412
466
489
489
Parallel Computing and Numerical Methods
511
Scalability of µϕ and the Parallel Algebraic Multigrid Solver of DUNEISTL
527

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