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Understanding Molecular Simulation: From Algorithms to Applications

Autor Daan Frenkel, Berend Smit
en Limba Engleză Paperback – 18 iul 2023
Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text.
Since the second edition’s publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed.


  • Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results
  • Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields
  • Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning
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Specificații

ISBN-13: 9780323902922
ISBN-10: 0323902928
Pagini: 679
Dimensiuni: 152 x 229 x 42 mm
Greutate: 1.18 kg
Ediția:3
Editura: ELSEVIER SCIENCE

Public țintă

Postgraduate students in physics and materials science departments studying molecular simulation techniques; scientists in the fields of polymers, materials science, and applied physics.

Cuprins

1. Introduction
Part I: Basics
2. Thermodynamics and Statistical Mechanics
3. Monte Carlo Simulations
4. Molecular Dynamics Simulations
5. Computer Experiments
Part II: Ensembles
6. Monte Carlo Simulations in Various Ensembles
7. Molecular Dynamics in Various Ensembles
Part III: Free -Energy Calculations
8. Free Energy Calculations
9. Free Energies of Solids
10. Free Energy of Chain Molecules
Part IV: Advanced Techniques
11. Long-Ranged Interactions
12. Configurational Bias Monte Carlo
13. Accelerating Monte Carlo Sampling
14. Time-Scale-separation Problems in MD
15. Rare Events
16. Mesoscopic Fluid Models
Part V: Appendices
A: Lagrangian and Hamiltonian
B: Non-Hamiltonian Dynamics
C: Non-equilibrium Thermodynamics
D: Smoothed Dissipative Particle Dynamics
E: Committor for 1-D diffusive barrier crossing
F: Linear Response Theory: examples
G: Statistical Errors
H: Integration Schemes
I: Saving CPU Time
J: Reference States
K: Statistical Mechanics of the Gibbs "Ensemble"
L: Overlapping Distribution for Polymers
M: Some General Purpose Algorithms

Recenzii

From the previous edition: "... this book brilliantly lays down the scientific foundations of the simulational approach ..." --Prof. Kurt Binder in Physics World, 1997
"... a treasure. The book is a marvellous mix of just enough formalism with an informal and readable style, sufficient detail to understand methodological advances, appropriate mathematics ..." --Prof. Mark A. Ratner in Physics Today, 1997

Descriere

Descriere de la o altă ediție sau format:

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.

Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on:

· Transition path sampling and diffusive barrier crossing to simulaterare events
· Dissipative particle dynamic as a course-grained simulation technique
· Novel schemes to compute the long-ranged forces
· Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations
· Multiple-time step algorithms as an alternative for constraints
· Defects in solids
· The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules
· Parallel tempering for glassy Hamiltonians

Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.