Atjaunināt sīkdatņu piekrišanu

E-grāmata: Molecular Kinetics in Condensed Phases: Theory, Simulation, and Analysis

4.00/5 (2 ratings by Goodreads)
, , (University of Illinois at Urbana-Champaign)
  • Formāts: PDF+DRM
  • Izdošanas datums: 25-Nov-2019
  • Izdevniecība: John Wiley & Sons Inc
  • Valoda: eng
  • ISBN-13: 9781119176787
Citas grāmatas par šo tēmu:
  • Formāts - PDF+DRM
  • Cena: 98,68 €*
  • * ši ir gala cena, t.i., netiek piemērotas nekādas papildus atlaides
  • Ielikt grozā
  • Pievienot vēlmju sarakstam
  • Šī e-grāmata paredzēta tikai personīgai lietošanai. E-grāmatas nav iespējams atgriezt un nauda par iegādātajām e-grāmatām netiek atmaksāta.
  • Bibliotēkām
Molecular Kinetics in Condensed Phases: Theory, Simulation, and AnalysisPalielināt
  • Formāts: PDF+DRM
  • Izdošanas datums: 25-Nov-2019
  • Izdevniecība: John Wiley & Sons Inc
  • Valoda: eng
  • ISBN-13: 9781119176787
Citas grāmatas par šo tēmu:

DRM restrictions

  • Kopēšana (kopēt/ievietot):

    nav atļauts

  • Drukāšana:

    nav atļauts

  • Lietošana:

    Digitālo tiesību pārvaldība (Digital Rights Management (DRM))
    Izdevējs ir piegādājis šo grāmatu šifrētā veidā, kas nozīmē, ka jums ir jāinstalē bezmaksas programmatūra, lai to atbloķētu un lasītu. Lai lasītu šo e-grāmatu, jums ir jāizveido Adobe ID. Vairāk informācijas šeit. E-grāmatu var lasīt un lejupielādēt līdz 6 ierīcēm (vienam lietotājam ar vienu un to pašu Adobe ID).

    Nepieciešamā programmatūra
    Lai lasītu šo e-grāmatu mobilajā ierīcē (tālrunī vai planšetdatorā), jums būs jāinstalē šī bezmaksas lietotne: PocketBook Reader (iOS / Android)

    Lai lejupielādētu un lasītu šo e-grāmatu datorā vai Mac datorā, jums ir nepieciešamid Adobe Digital Editions (šī ir bezmaksas lietotne, kas īpaši izstrādāta e-grāmatām. Tā nav tas pats, kas Adobe Reader, kas, iespējams, jau ir jūsu datorā.)

    Jūs nevarat lasīt šo e-grāmatu, izmantojot Amazon Kindle.

A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases

Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times.

The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book:

  • Offers an introduction to the topic that combines theory, simulation and analysis
  • Presents a guide written by authors that are well-known and highly regarded leaders in their fields
  • Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed.
  • Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics

Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.

Acknowledgments xiii
Introduction: Historical Background and Recent Developments that Motivate this Book xv
1 The Langevin Equation and Stochastic Processes
1(28)
1.1 General Framework
1(4)
1.2 The Ornstein-Uhlenbeck (OU) Process
5(3)
1.3 The Overdamped Limit
8(3)
1.4 The Overdamped Harmonic Oscillator: An Ornstein--Uhlenbeck process
11(1)
1.5 Differential Form and Discretization
12(7)
1.5.1 Euler-Maruyama Discretization (EMD) and Ito Processes
15(2)
1.5.2 Stratonovich Discretization (SD)
17(2)
1.6 Relation Between Ito and Stratonovich Integrals
19(2)
1.7 Space Varying Diffusion Constant
21(2)
1.8 Ito vs Stratonovich
23(1)
1.9 Detailed Balance
23(2)
1.10 Memory Kernel
25(1)
1.11 The Many Particle Case
26(3)
References
26(3)
2 The Fokker--Planck Equation
29(12)
2.1 The Chapman--Kolmogorov Equation
29(1)
2.2 The Overdamped Case
30(4)
2.2.1 Derivation of the Smoluchowski (Fokker--Planck) Equation using the Chapman--Kolmogorov Equation
30(3)
2.2.2 Alternative Derivation of the Smoluchowski (Fokker--Planck) Equation
33(1)
2.2.3 The Adjoint (or Reverse or Backward) Fokker--Planck Equation
34(1)
2.3 The Underdamped Case
34(1)
2.4 The Free Case
35(2)
2.4.1 Overdamped Case
35(1)
2.4.2 Underdamped Case
36(1)
2.5 Averages and Observables
37(4)
References
39(2)
3 The Schrodinger Representation
41(8)
3.1 The Schrodinger Equation
41(2)
3.2 Spectral Representation
43(1)
3.3 Ground State and Convergence to the Boltzmann Distribution
44(5)
References
47(2)
4 Discrete Systems: The Master Equation and Kinetic Monte Carlo
49(14)
4.1 The Master Equation
49(4)
4.1.1 Discrete-Time Markov Chains
49(2)
4.1.2 Continuous-Time Markov Chains, Markov Processes
51(2)
4.2 Detailed Balance
53(5)
4.2.1 Final State Only
54(1)
4.2.2 Initial State Only
54(1)
4.2.3 Initial and Final State
55(1)
4.2.4 Metropolis Scheme
55(1)
4.2.5 Symmetrization
55(3)
4.3 Kinetic Monte Carlo (KMC)
58(5)
References
61(2)
5 Path Integrals
63(6)
5.1 The Ito Path Integral
63(3)
5.2 The Stratonovich Path Integral
66(3)
References
67(2)
6 Barrier Crossing
69(20)
6.1 First Passage Time and Transition Rate
69(8)
6.1.1 Average Mean First Passage Time
71(2)
6.1.2 Distribution of First Passage Time
73(1)
6.1.3 The Free Particle Case
74(1)
6.1.4 Conservative Force
75(2)
6.2 Kramers Transition Time: Average and Distribution
77(4)
6.2.1 Kramers Derivation
78(2)
6.2.2 Mean First Passage Time Derivation
80(1)
6.3 Transition Path Time: Average and Distribution
81(8)
6.3.1 Transition Path Time Distribution
82(2)
6.3.2 Mean Transition Path Time
84(2)
References
86(3)
7 Sampling Transition Paths
89(28)
7.1 Dominant Paths and Instantons
92(6)
7.1.1 Saddle-Point Method
92(1)
7.1.2 The Euler-Lagrange Equation: Dominant Paths
92(4)
7.1.3 Steepest Descent Method
96(1)
7.1.4 Gradient Descent Method
97(1)
7.2 Path Sampling
98(1)
7.2.1 Metropolis Scheme
98(1)
7.2.2 Langevin Scheme
99(1)
7.3 Bridge and Conditioning
99(18)
7.3.1 Free Particle
102(1)
7.3.2 The Ornstein-Uhlenbeck Bridge
102(2)
7.3.3 Exact Diagonalization
104(1)
7.3.4 Cumulant Expansion
105(6)
References
111(1)
Appendix A Gaussian Variables
111(2)
Appendix B
113(4)
8 The Rate of Conformational Change: Definition and Computation
117(16)
8.1 First-order Chemical Kinetics
117(2)
8.2 Rate Coefficients from Microscopic Dynamics
119(14)
8.2.1 Validity of First Order Kinetics
120(3)
8.2.2 Mapping Continuous Trajectories onto Discrete Kinetics and Computing Exact Rates
123(3)
8.2.3 Computing the Rate More Efficiently
126(2)
8.2.4 Transmission Coefficient and Variational Transition State Theory
128(1)
8.2.5 Harmonic Transition-State Theory
129(2)
References
131(2)
9 Zwanzig-Caldeiga-Leggett Model for Low-Dimensional Dynamics
133(14)
9.1 Low-Dimensional Models of Reaction Dynamics From a Microscopic Hamiltonian
133(4)
9.2 Statistical Properties of the Noise and the Fluctuation-dissipation Theorem
137(605)
9.2.1 Ensemble Approach
138(1)
9.2.2 Single-Trajectory Approach
139(3)
9.3 Time-Reversibility of the Langevin Equation
142(3)
References
145(2)
10 Escape from a Potential Well in the Case of Dynamics Obeying the Generalized Langevin Equation: General Solution Based on the Zwanzig-Caldeira-Leggett Hamiltonian
147(10)
10.1 Derivation of the Escape Rate
147(3)
10.2 The Limit of Kramers Theory
150(2)
10.3 Significance of Memory Effects
152(1)
10.4 Applications of the Kramers Theory to Chemical Kinetics in Condensed Phases, Particularly in Biomolecular Systems
153(2)
10.5 A Comment on the Use of the Term "Free Energy" in Application to Chemical Kinetics and Equilibrium
155(2)
References
156(1)
11 Diffusive Dynamics on a Multidimensional Energy Landscape
157(16)
11.1 Generalized Langevin Equation with Exponential Memory can be Derived from a 2D Markov Model
157(4)
11.2 Theory of Multidimensional Barrier Crossing
161(6)
11.3 Breakdown of the Langer Theory in the Case of Anisotropic Diffusion: the Berezhkovskii-Zitserman Case
167(6)
References
171(2)
12 Quantum Effects in Chemical Kinetics
173(20)
12.1 When is a Quantum Mechanical Description Necessary?
173(1)
12.2 How Do the Laws of Quantum Mechanics Affect the Observed Transition Rates?
174(3)
12.3 Semiclassical Approximation and the Deep Tunneling Regime
177(7)
12.4 Path Integrals, Ring-Polymer Quantum Transition-State Theory, Instantons and Centroids
184(9)
References
191(2)
13 Computer Simulations of Molecular Kinetics: Foundation
193(10)
13.1 Computer Simulations: Statement of Goals
193(2)
13.2 The Empirical Energy
195(2)
13.3 Molecular States
197(2)
13.4 Mean First Passage Time
199(1)
13.5 Coarse Variables
199(1)
13.6 Equilibrium, Stable, and Metastable States
200(3)
References
202(1)
14 The Master Equation as a Model for Transitions Between Macrostates
203(10)
References
211(2)
15 Direct Calculation of Rate Coefficients with Computer Simulations
213(10)
15.1 Computer Simulations of Trajectories
213(6)
15.2 Calculating Rate with Trajectories
219(4)
References
221(2)
16 A Simple Numerical Example of Rate Calculations
223(10)
References
231(2)
17 Rare Events and Reaction Coordinates
233(8)
References
240(1)
18 Celling
241(14)
References
252(3)
19 An Example of the Use of Cells: Alanine Dipeptide
255(4)
References
257(2)
Index 259
Ron Elber is Professor of Chemistry at the University of Texas at Austin and W. A. "Tex" Moncrief, Jr. Endowed Chair in Computational Life Sciences and Biology in the Oden Institute for Computational Engineering and Sciences.

Dmitrii E. Makarov is Professor of Chemistry at the University of Texas at Austin. His research is in the field of computational and theoretical chemical physics.

Henri Orland is Directeur de Recherches at the Institut de Physique Théorique, the French Alternative Energies and Atomic Energy Commission, CEA, France.
Biežāk uzdotie jautājumi par e-grāmatām Biežāk uzdotie jautājumi par e-grāmatām
Permanent link: https://www.kriso.lv/db/97811191767872e.html
Keywords: