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Chapter 1. Introduction, perspectives, and aims.
On the science of simulation and modelling.
Modelling at bulk, meso, and nano scale. (2
hours). Chapter 2. Experimental Techniques in
Nanotechnology. Theory and Experiment Two faces
of the same coin (2 hours). Chapter 3.
Introduction to Methods of the Classic and
Quantum Mechanics. Force Fields, Semiempirical,
Plane-Wave pseudpotential calculations. (2
hours) Chapter 4. Intoduction to Methods and
Techniques of Quantum Chemistry, Ab initio
methods, and Methods based on Density Functional
Theory (DFT). (4 hours) Chapter 5. Visualization
codes, algorithms and programs. GAUSSIAN
CRYSTAL, and VASP. (6 hours).
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Chapter 6. Calculation of physical and chemical
properties of nanomaterials. (2 hours). Chapter
7. Calculation of optical properties.
Photoluminescence. (3 hours). Chapter 8.
Modelization of the growth mechanism of
nanomaterials. Surface Energy and Wullf
architecture (3 hours) Chapter 9.
Heterostructures Modeling. Simple and complex
metal oxides. (2 hours) Chapter 10. Modelization
of chemical reaction at surfaces. Heterogeneous
catalysis. Towards an undertanding of the
Nanocatalysis. (4 hours)º
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In the past years, theoretical and technological
advancements have produced an impressive
improvement of computational facilities providing
a wide range of methodologies, economically and
conceptually accessible for a huge number of
researchers in different fields of molecular
sciences. Electronic structure calculations
represent nowadays one of the most commonly used
approaches by the physical-chemical community,
allowing highly accurate description of systems
with a large number of atoms, i.e., systems with
an order of atoms of 102-103 and more. Martin,
R. Electronic Structure Basic Theory and
Practical Methods Cambridge University Press
Cambridge, UK, 2004. Hung, L. Carter, E. A.
Chem. Phys. Lett. 2009, 475, 163.
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However, there is still a lot of work to do. As a
matter of fact, modeling at the electronic level
of systems with high configurational complexity
is still challenging. In this case, the main
problem is either practical and conceptual as the
different observables to be modeled depend on
processes occurring at different length, energy,
and time scales. Computational tools typically
employed for systems of such dimensions are
classical simulations which, however, produce
reliable results as far as transitions in quantum
degrees of freedom do not take place. On the
other hand, when the observables of interest
explicitly involve quantum degrees of freedom,
e.g., chemical reactions or spectral transitions,
their modeling should be derived from statistical
averages of genuine quantum states interacting
with fluctuating perturbing environments.
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Our ability to model physical and chemical
processes at the atomic and sub-atomic levels has
progressed rapidly over the last three decades,
due to development of theoretical methods based
on statistical mechanics and quantum mechanics,
rapid increases in computer speed and memory,
more efficient algorithms and a steady
improvement in force field development. Among the
most useful theoretical methods for surface
science are ab initio and classical density
functional theories and molecular simulation
methods, that is the numerical solution of the
equations of statistical mechanics using Monte
Carlo or molecular dynamics techniques.
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Theory and simulation can provide fundamental
understanding of observed phenomena, and can be
used to make predictions for systems that are
difficult or impossible to study experimentally,
for example adsorption of toxic or biological
agents, or behavior at very high temperature or
pressure. In addition, theory and simulation can
give detailed molecular level information that is
difficult or impossible to determine from
laboratory experiments. Examples are the
molecular structure of adsorbed phases, detailed
mapping of diffusion of guest molecules in highly
disordered microporous materials, the pressure
tensor in a pore and the wave function of the
electrons. These methods also find important
applications in determining the limits of well
known macroscopic laws, which may break down for
nano-scale systems. Examples are the concept of
surface tension1 and Gibbs surface
thermodynamics in general, related equations such
as those of Kelvin,2 Young and Laplace,1 Ficks
Law of diffusion36 and the Second Law of
Thermodynamics
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Theory and experiment each have different
strengths and limitations, but these are
complementary to a large extent and there is much
to be gained by constructing research
programs that combine the two. Significant
difficulties in experimental studies of
adsorption and confinement effects include
identifying the nature and composition of the
host adsorbate phase, longlived metastable
states, and preferential adsorption of trace
impurities on the pore walls, while in
theoretical and simulation studies the main
difficulties are uncertainties about the pore
morphology and topology of the real materials (in
the case of non-crystalline materials), and about
the force fields involved.
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A further limitation for simulation at present
is that current computers are not yet powerful
enough to carry out molecular dynamics
simulations for longer than about a microsecond
of real time. While this is sufficient for
studies of relatively small adsorbate molecules,
the self-assembly of larger surfactant or protein
molecules on solid surfaces and in pores requires
longer times. Such studies are likely to become
possible in the next decade, when more powerful
machines are available. While metastability also
occurs in theoretical calculations, free energy
calculations enable this to be detected and the
true equilibrium state determined moreover, the
nature and composition of the host phase is
readily determined.
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Chapter 3. Introduction to Methods of the
Classic and Quantum Mechanics. Force Fields,
Semiempirical, Plane-Wave pseudpotential
calculations. (2 hours)
Juan Andrés y Lourdes Gracia Departamento de
Química-Física y Analítica Universitat Jaume
I Spain CMDCM, Sao Carlos Brazil
Sao Carlos, Novembro 2010
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1) Force Fields
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2) Semi-empirical
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3) Plane-Wave pseudopotential calculations
In the Plane-Wave method, the single electron
(pseudo-) wave function is explanded using a
plane-wave basis set