Theoretical Concepts for
Chemical Energy Conversion
last updated:
October 2, 2014



List of topics:

1. Recapitulation of key concepts in thermodynamics and statistical mechanics.

Slides of this lecture (uploaded on April 17, 2014)

2. Introduction to importance sampling Metropolis Monte Carlo, canonical ensemble and more.

Slides of this lecture (uploaded on April 23, 2014)

3. Introduction to (classical) molecular dynamics, microcanonical ensemble and more.

Slides of this lecture (uploaded on May 7, 2014)

4. Ab initio molecular dynamics: Born-Oppenheimer molecular dynamics and beyond (state of the art).

Slides of this lecture (uploaded on June 3, 2014, updated and extended version)

5. Ab initio Path Integral Molecolar Dynamics. Theory and application to realistic materials.

Slides of this lecture (uploaded on June 3, 2014)

6. Ab initio atomistic thermodynamics: phase diagrams. Application to surface/cluster corrosion and reactivity of realistic materials. Neutral and charged defects in semiconductors.

Slides of this lecture (uploaded on June 12, 2014)

7. Sampling free energy I: (ab initio) phase diagrams. Thermodynamics integration, smart advanced techniques, and applications to realistic materials.

Slides of this lecture (uploaded on June 12, 2014)

8. Sampling free energy II: enhanced sampling (biased sampling, metadynamics, and more). Theory and application to realistic materials.

Slides of this lecture (uploaded on June 23, 2014)

9. Sampling free energy III: replica exchange, the problem of the choice of order parameters and reaction coordinates (from many to few "relevant" dimensions). Theory and application to realistic materials.

Slides of this lecture (uploaded on October 2, 2014)

10. Chemical reactions as rare events: transition state theory and beyond. Methods (transition path sampling, transition interface sampling, and more) and application to realistic materials.

Slides of this lecture (uploaded on October 2, 2014)
Slides of a lecture on TST, given at IPAM in LA, with focus on TS search (uploaded on Oct 2, 2014)

11. Stochastic sampling beyond equilibrium: (ab initio) kinetic Monte Carlo. Theory and application to realistic materials.

Slides of this lecture (uploaded on October 2, 2014)



Material: Textbooks and papers

D. Frenkel and B. Smit
"Understanding Molecular Simulations", 2nd edition.
Academic Press, London (2002)

M. E. Tuckerman
"Statistical Mechanics: Theory and Molecular Simulation"
Oxford University Press, NY (2010)

N. L. Doltsinis,
"Nonadiabatic Dynamics: Mean-Field and Surface Hopping."
In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, Lecture Notes,
J. Grotendorst, D. Marx, A. Muramatsu (Eds.), John von Neumann Institute for Computing,
Jülich, NIC Series, Vol. 10, ISBN 3-00-009057-6, pp. 377-397, 2002.
http://webarchiv.fz-juelich.de/nic-series/volume10/volume10.html

Mark E. Tuckerman
"Path Integration via Molecular Dynamics"
In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, Lecture Notes,
J. Grotendorst, D. Marx, A. Muramatsu (Eds.), John von Neumann Institute for Computing,
Jülich, NIC Series, Vol. 10, ISBN 3-00-009057-6, pp. 377-397, 2002.
http://webarchiv.fz-juelich.de/nic-series/volume10/volume10.html

C. Stampfl, M.V. Ganduglia-Pirovano, K. Reuter, and M. Scheffler
"Catalysis and corrosion: the theoretical surface-science context"
Surf. Sci. 500, 368-394 (2002).
http://th.fhi-berlin.mpg.de/site/uploads/Publications/SS-500-368-2002.pdf

K. Reuter C. Stampfl, and M. Scheffler
"Ab initio atomistic thermodynamics and statistical mechanics of surface properties and functions".
In: Handbook of Materials Modeling, Vol. 1. (Ed.) Sidney Yip. Springer Berlin Heidelberg 2005, 149-194. ISBN 1-4020-3287-0.
http://th.fhi-berlin.mpg.de/site/uploads/Publications/handbook_reprint.pdf

Daniele Moroni
"Efficient sampling of Rare Events Pathways"
University of Amsterdam, PhD thesis.
http://www-theor.ch.cam.ac.uk/people/moroni/thesis.html

K. Reuter
"First-principles kinetic Monte Carlo simulations for heterogeneous catalysis: Concepts, status and frontiers"
Modeling Heterogeneous Catalytic Reactions: From the Molecular Process to the Technical System. (Ed.) O. Deutschmann, Wiley-VCH, Weinberg (2009).
http://th.fhi-berlin.mpg.de/site/uploads/Publications/wiley_reuter.pdf

Other Interesting readings:

J. P. Sethna
"Statistical Mechanics Entropy, Order Parameters, and Complexity".
Clarendon Press, Oxford (2011)
Freely available: http://pages.physics.cornell.edu/~sethna/StatMech/

S.-K. Ma
"Statistical Mechanics"
World Scientific, Singapore (1985)

D. Marx and J. Hutter
"Ab initio molecular dynamics: Theory and Implementation"
In Modern Methods and Algorithms of Quantum Chemistry,
J. Grotendorst (Ed.), John von Neumann Institute for Computing,
Jülich, NIC Series, Vol. 1, ISBN 3-00-005618-1, pp. 301-449, 2000.
http://webarchiv.fz-juelich.de/nic-series/Volume3/Volume3.html

Mark E. Tuckerman
"Ab Initio Molecular Dynamics and Ab Initio Path Integrals"
In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms, Lecture Notes,
J. Grotendorst, D. Marx, A. Muramatsu (Eds.), John von Neumann Institute for Computing,
Jülich, NIC Series, Vol. 10, ISBN 3-00-009057-6, pp. 377-397, 2002.
http://webarchiv.fz-juelich.de/nic-series/volume10/volume10.html