Minho Aveiro Porto
  • Courses 2012-2013
Universidade do Minho
Universidade de Aveiro
Universidade do Porto

MAPFis Courses 2012/2013

(1st Semester)

Advanced Topics in Physics I

Modules with three and more students will have normal classes, whose timetable is given in the following.  Modules with one to two students will function in a tutorial format.



Contacts:alf@fis.ua.pt;orfeu.bertolami@fc.up.pt;antonio.onofre@cern.ch; ypogorel@fc.up.pt;martin.andritschky@fisica.uminho.pt; lanceros@fisica.uminho.pt;peter.schellenberg@fisica.uminho.pt; alfredo.rocha@ua.pt;carmelo@fisica.uminho.pt;mikhail@fisica.uminho.pt; peres@fisica.uminho.pt;apleite@fc.up.pt;belsley@fisica.uminho.pt


Module 1: Computational Physics (normal classes)

Lecturer:  António Luís Ferreira

(total 18h,in 6 weeks, classes Friday 14h-17h)

Parallel Programming

Manuel Barroso, total 6h, 1st class19/10/2012, 2nd class 26/10/2012

(Students are advised to bring their laptops/notebooks for practical exercises)

1.     Introduction

   a.     Motivations and actual state of development

   b.     Advantages and disadvantages

   c.     Parallel computation models

           i.      Message passing

           ii.      Shared memory

          iii.      Combination of different models

   d.     Present status and future trends

2.     OpenMP

   a.     Introduction and basic concepts

   b.     Compiler Directives

   c.     Parallel loops

   d.     Data sharing

   e.     Parallel regions

   f.       Auto-parallelization

   g.     Parallel libraries

   h.     Runtime options

3.     MPI

   a.     Introduction and basic concepts

   b.     MPI functions

   c.     Point-to-point communication

   d.     Datatypes

   e.     Compiling and running programs

   f.       Collective communication

   g.     Communicators

   h.     Parallel libraries

   i.       Implementations


“Parallel Programming in OpenMP”, R. Chandra, L. Dagum, D. Kohr, D. Maydan, J. McDonald, R. Menon, 2001, Academic Press.

“Parallel Programming in C with MPI and OpenMP”, Michel J. Quinn, 2004, McGraw-Hill.

“Parallel Programming with MPI”, Peter S. Pacheco, 1997, Morgan Kaufmann.

“Using MPI – second edition”, W. Gropp, E. Lusk, A. Skjellum, 1999, MIT Press.


Monte Carlo Methods

6h,  António Luís Ferreira, 1st class 2/11/2012, 2nd class 9/11/2012

1.     MarkovChains

   a.     Chapman-Kolmogorovequation

   b.     Transientandstationary regimes

   c.     Detailed balance

2.     Monte-CarloIntegration

   a.      Hit or Miss Monte-Carlo

   b.     Integration as an averagecalculation

   c.     RandomSampling

   d.     ImportanceSampling

   e.     MarkovChain Monte-Carlo;

   f.       MetropolisAlgorithm

3.     Applications toStatisticalPhysics

   a.     Ergodicity

   b.     Detailed balance

   c.     Equilibration

   d.     Estimating errors

4.     Advanced MC Techniques

   a.     Histogramreweighting

   b.     NVT, NPT and Grand-Canonical Simulations

   c.     Paralell Tempering

   d.     Transition matrix MC

            i.      Projeted dynamics

           ii.      N-fold algorithm

   e.     Flat Histogram Ensemble

   f.       Wang-Landau algorithm

   g.     Umbrella Sampling

   h.     Simulated Tempering

   i.       Bennet acceptance ratio

   j.       Gibbs Ensemble Method



Understanding Molecular Simulations,DaanFrenkel and BerendSmit

Computer Simulation of Liquids, M P Allen and D J Tildesley

Monte Carlo Methods in Statistical Physicsby Mark Newman, G T Barkema


Lanczos Method

6h, Jaime Santos,  1st class 16/11/2012 2nd class 23/11/2012

Exact diagonalisation of Many-Body Hamiltonians through the Lanczos method.

Spectral density of Many-Body Systems.

Implementation of the algorithms in C++.

A detailed description of this module, including bibliography, will be
provided in due course. 


Module 2: General Relativity (normal classes)

Lecturer:  Orfeu Bertolami

1. Special Relativity 

- Lorentz group and transformations
- Vectors e Tensors 
- Electrodynamics

2. Einstein's Equivalence Principle 
- Clock Postulate and the Universality of the gravitational redshift and the geodesic deviation
- Weak Equivalence Principle
- Covariance under local Lorentz transformations
- Covariance under position transformations
- Schiff's conjecture 
-  Strong Equivalence Principle

3. Generalized Covariance Principle 

4. Introduction to Differential Geometry 
- Manifolds
- Exterior derivative and Lie derivative
- Covariant derivative
- Curvature tensor
- Metric

5. Einstein's General Relativity
- Energy-Momentum tensor
- Einstein's field equations
- Newtonian limit, linear approximation of Einstein's field equations and gravitational waves
- Matter fields
-  Lagrange formulation (Einstein-Hilbert action,  bosonic string action and corrections to the Einstein-Hilbert action) 
- Classic tests: Deflection of light and radar eco delay in the vicinity of the sun, and advance precession of Mercury's perihelion

6. Exact Solutions of  Einstein's field equations
- Minkowski, De Sitter e anti-De Sitter space-time
- Schwarzschild's black hole solution 
- Robertson-Walker space-time


- S. Weinberg, ``Gravitation and Cosmology: Principles and Applications of the General Theory of Relativity'' (John Wiley and Sons, New York 1972). Chapters: 1, 2, 3, 4, 7, 8.

- S.W. Hawking and G.F.R. Ellis, ``The Large Scale Structure of Space-Time'' (Cambridge University Press, Cambridge 1973). Chapters: 1, 2, 3.

- C.W. Misner, K.S. Thorne and J.A. Wheeler, ``Gravitation'' (Freeman, San Francisco, 1974).

- ``300 Years of Gravitation'', Eds. S.W. Hawking and W. Israel (Cambridge University Press, Cambridge 1987). Capítulos: 4 e 5.

- R.M. Wald, ``General Relativity'', (The University of Chicago Press, Chicago 1984). Chapters: 1, 2, 3, 
4, 5, 6.

- C.M. Will, ``Theory and experiment in gravitational physics'' (Cambridge University Press, Cambridge 1993). Capítulos: 1, 2, 3 e 14.

- G.G. Ross, ``Grand Unified Theories''  (Benjamin/Cummings, Menlo Park, California 1984).  
Chapters: 2, 3, 4 and 12.

- M.B. Green, J.H. Schwarz and E. Witten, ``Superstring Theory  Vol. 1 Introduction''  
(Cambridge University Press, 1987). Chapters: 2.

- E.W. Kolb e M.S. Turner, ``The Early Universe''  (Addison-Wesley P. C., 1990). Chapters: 1, 3, 4, 5 and 8.

- P.J.E. Peebles, D.N. Schramm, E.L. Turner e R.G. Kron, Nature, 352 (1991) 769.

- O. Bertolami, ``Modelo Cosmológico Padrão: uma breve introdução'',  "Agregação" lecture, Instituto Superior Técnico, July 1996.


Module 3: Experimental Particle and Astroparticle Physics (normal classes)

Lecturers: António Onofre/ Nuno Castro

- Introduction to the Standard Model (AO+NC)
•Introduction: matter and forces
•Non relativistic quantum mechanics and special relativity
•Electromagnetic interactions of spin-0 particles
•Electromagnetic interactions of spin 1/2 particles

- Introduction to the Standard Model (NC)
•Weak interactions of quarks and leptons
•Introduction to Quantum Chromodynamics
•Experimental tests of the Standard Model

- Neutrino Physics and Astroparticles (AO)
Neutrino Physics and Astroparticles:
•Neutrino Physics
•Atmospheric and solar neutrinos
•Phenomenology of Neutrino Oscillations
•Neutrino Oscillation Experiments
•Neutrino puzzles: LSND anomaly and MiniBoone results
•Neutrino mass
•The futur: super-beams and neutrino-factories
Cosmic Rays
•The cosmic ray spectrum and cosmological sources
•Ultra-high-energy (UHECR) cosmic rays
•The GZK cut-off
•Experiments and detectors of UHECR

- Hadron Collider Physics (AO+NC)
•History of hadron colliders
•Hadron collider observables and differential distributions
•Cross sections and decay rates
•Elastic and inelastic collisions of hadrons
•Minimum bias and soft underlying events
•PDF and heavy flavour production (top and bottom quarks)
•Vector boson production at hadron colliders
•Special probes of the Standard Model: why is the top quark so interesting?
•The Higgs search

- Final Remarks and Evaluation

1.Provide basic knowledge on the Standard Model and its experimental tests
2.Make a brief introduction to Collider Physics and explore examples of colliders (the LHC)
3.Introduce the students to Neutrino Physics and compare different experimental techniques for detection of neutrino oscillations
4.Explore the Cosmic Ray spectra with special focus to the ultra high energy region.

Evaluation: Project research work (based also on IDPASC material)

1.I.J.R. Aitchison and A.J.G Hey, “Gauge theories in particle physics”, Vols. I and II, IoP publishing, 3rd Ed. (2003).
2.F. Halzen and A.D. Martin, “Quarks and leptons: an introductory course in modern particle physics”, Wiley (1984).
3.D.M. Gingrich, “Practical Quantum Electrodynamics”, Taylor and Francis (2006).
4.David J. Griffiths, “Introduction to Electrodynamics”, 3rd Edition, Prentice Hall, Upper Saddle River, New Jersey 07458

Additional usefull text books:

1. R.K. Ellis, W.J. Stirling and B.R. Webber, “QCD and collider physics”, Cambridge (1996).

2. E.A. Paschos, “Electroweak Theory”, Cambridge (2007).
3. B.R. Martin and G. Shaw, “Particle physics”, Wiley (1992).
4. W.S.C. Williams, “Nuclear and particle physics”, Oxford (1991).
5. S. Eidelman et al., “Review of particle physics”, Physics Letters B 592 (2004) 1.
6. J.D. Bjorken and S.D. Drell, “Relativistic Quantum Mechanics”, McGraw (1964). e.g. G. Arfken, “Mathematical Methods for Physicists”, Academic Press (1985).

All lectures will have their own material (pdf documents)

Module 4: Magnetism of nanostructured systems (normal classes)

Lecturer: Yuri Pogorelov

1. Effects of low dimensionality and of nanoscopic size in formation of equilibrium magnetic states and their dynamics in nanostructured systems.
2. Reduction of the order parameter and of critical temperature.
3. Spatial quantization of excitation states.
4. Specific effects of surface (Nèel anisotropy) in ultrafine magnetic films.
5. Indirect interactions (of the RKKY type) in multilayered systems.
6. Anisotropy and interaction effects in magnetic resonance and in magneto-optics (including Brillouin light scattering).
7. Effects of dipolar interactions for magnetic states and magnetic excitations in nanostructured systems.
8. Specific degeneracy (of Luttinger-Tisza type) of magnetic ground state and its lifting.
9. Numerical methods of studies for nanostructured magnetic systems.
10. OOMMF and multiscale methods.
11. Numerical simulations of equilibrium states and magnetic domains dynamics.

D.L. Mills, J.A.C. Bland, NANOMAGNETISM, 1. Ultrathin Films, Multilayers
and Nanostructures. Elsevier, 2006.
A.P. Guimarães, Principles of Nanomagnetism, Springer, 2009

Module 5: Experimental techniques of nanomaterial

Lecturer:  Martin Andritschky 


  1. Introduction
  2. Vacuumtechnology
  3. Nano-structure of thin films grown by PECVD (example a-Si and mc-Si thin films)
  4. Synthesis and deposition of nano-clusters
  5. Fabrication of nanostructured thin films by PVD methods
    1. Nano-structure (example super-hard materials)
    2. Multilayer and superlattices
  6. Fabrication of quantum dots
  7. X-ray diffraction of nano particles


Experimental: (growth of a-Si and mc-Si thin films by PECVD and subsequent optical and electrical caracterization)


To be provided later


Module 6: Sensors and electronic devices

Lecturer:  Professor Senentxu Lanceros-Mendez 

The miniaturization based on silicon devices allowed the fabrication of electronic products that have strongly influenced our lives. Nanotechnology allowed a further level of complexity that will allow further miniaturization. The new paradigm will be based on different materials, nanostructures and in the physical principles governing interactions at that size and time scales.

The present course gives information of some of those materials, fabrication techniques and devices based both in silicon and in novel inorganic and organic materials.



1)      Introduction to sensors

a.      Introduction

b.      Physical principles

c.      Characteristics

d.      Examples

e.      Fabrication techniques

2)      Sensors and actuators

a.      Electroactive

b.      Magnetoactive

3)      Signal acquisition, control and transmission electronic



To be provided later


Module 7: Selected Topics in Biophysics (normal classes)

Lecturer: Peter Schellenberg


Brief introduction into the molecular basis of life
DNA, RNA, Proteins
Protein structure, folding, dynamics and function
Structure visualization, structure databanks (if possible with computer excercise)

Structure Determination of Biomolecules
Diffraction methods -determining the coordinates of the system
Protein crystallisation techniques
X-ray scattering,
Electron scattering and electron microscopy
Spectroscopic methods -probing chemical environments
Nuclear Magnetic Resonance
Mössbauer Spectroscopy
Method comparison

Biology and Light
Spectroscopy of molecules
Electronic structure and quantum mechanics of molecules
Steady-state and time-resolved absorption and fluorescence spectroscopy
Infrared-spectroscopy of biological systems
The physics of the primary processes of photosynthesis
Structure and function of photosynthetic systems
Energy -and electron -transfer
Excitonic coupling, coherent excitation
Physical and molecular basis of vision
Structure and function of light detection proteins
Selected systems: Rhodopsin, Photoactive Yellow Protein, Phytochrome, Phototropin

Optical Microscopy
Theory and applications of optical microscopes
classical microscopy, resolution limit, phase contrast microscopy
confocal microscopy, Laser scanning microscopy, two-photon microscopy,
Fluorescence lifetime imaging microscopy
Micromanipulation by laser
Optical tweezer
Laser microdissection
Fluorescent markers and proteins
Green Fluorescent Protein and its variants
Applications of Foerster Resonance Energy Transfer (FRET)
beyond Abbe: Stimulated Emission Depletion and Ground State Depletion Microscopy

Single molecule techniques and applications
Near-field microscopy, Atomic-Force Microscopy (AFM)
Single molecule/protein spectroscopy
Homogeneous and inhomogeneous lines
excitonic coupling in a single molecule
single molecule fluorescence spectroscopy
Nanomechanics of biological systems
direct observation of molecular dynamics by FRET
ATPase -a single enzym molecule in motion
direct observation of DNA -repair and cutting enzymes
The molecular machinery: microtubules

Nanobiotechnology (tentative)
Nanointegration of molecular structures in technical environments
Nuclear Acid based nanostructuring
Protein immobilization on surfaces
Protein -and DNA -Chips


Module 8: Climate variability and change (normal classes)

Lecturer: Alfredo Rocha


1. The climate system.
2. Interaction amongst climate sub-systems.
3. Feedbacks in the climate system.
4. Forcing agents of climate.
5. Climate variability and change simulations due to external forcing.

National Research Council, 2003. Understanding climate change feedbacks. The National Academies Press. 152 p.
Peixoto and Oort, 1992. Physics of climate. American Institute of Physics. 520 p.
Solomon, Qin, Manning, Chen, Marquis, Averyt, Tignor and Miller (eds.), 2007. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, 2007. Cambridge Uni. Press. Cambridge, United Kingdom and New York, NY, USA
Santos and Miranda, 2006. Alterações climáticas em Portugal. Cenários, impactos e medidas de adaptação. Gradiva. 503 p.


Module 9: Numerical simulation of the atmosphere and ocean normal classes)

Lecturers: Alfredo Rocha/João Miguel Dias


1. History of numerical modelling in atmospheric/oceanic sciences
2. Conservation equations
3. Methods to solve the equations
4. Vertical coordinates
5. Initial conditions
6. Data assimilation
7. Boundary conditions
8. Ensemble forecasting
9. Physic parametrizations

McGuffie and Henderson-Sellers, 2005. A modelling climate primer. Wiley. 280 p.
Washington and Parkinson, 2005. An introduction to climate modeling. Uni. Sci. Books. 353 p.
Krishnamurti, Bedi and Hardiker, 1998. An introduction to global spectral modelling. Oxford Uni. Press. 251 p.
Pielke, 2002. Mesoscale meteorological modelling. Academic Press. 676 p.
Dynamics of meteorology – Holton
Physics of climate – Peixoto and Oort
Lorenz, 1993. The essence of chaos. Uni. Washington Press. 227 p.

Modules 10: Exotic Physics of Low-Dimensional Materials (tutorial classes)


Module 10-A: Correlation Effects in Low-Dimensional Materials and Systems

Lecturer: José M. P. Carmelo


1.      Why are the effects of many-body interactions more important in lower dimensions?

2.      The Fermi liquid versus non-perturbative low-dimensional electronic problems.

3.      The Luttinger liquid and beyond it.

4.      Solvable 1D electronic models.

5.      Different properties of integrable and non-integrable 1D quantum problems.


To be provided later


Module 10-B: Quantum dots

Lecturer: Mikhail Vasilevskiy


The aim of this module is to give the student an understanding of the basic electronic and optical properties of these “zero-dimensional” structures. 


1.      Introduction: semiconductos

2.      Different types of quantum dots (QDs)

2.1  Electrostatic confinement and lithography

2.2  Nanocrystal QDs

2.3  Self-assembled QDs (SAQDs)

3.      Electronic spectra: quantum confinement effect

3.1  Spherical QDs

3.2  SAQDs

4.      Absorption and emission spectra

5.      Phonons and electron-phonon interaction in nanocrystals

6.      Applications and challenges


J. H. Davies, “The physical properties of low-dimensional semiconductors”, Cambridge University Press, 1998.

M. I. Vasilevskiy, M. I. C. Ferreira, “Física dos semicondutores: fundamentos, aplicações e nanoestruturas”, Edições Almedina, S.A., Portugal, 2005

D. Bimberg, M. Grundmann, N. N. Ledentsov “Quantum Dot Heterostructures”, Wiley, 1999

A. L. Rogach (ed.) Semiconductor Nanocrystal Quantum Dots, Springer, 2008

L. Jasak, P. Hawrylak, A. Wojs “Quantum dots”, Springer, 1998


Module 10-C:  Two-Dimensional Quantum Systems

Lecturer: Nuno M. R. Peres


1.) The 2D electron-gas: density of states and landau levels


2.) Graphene: direct lattice, reciprocal lattice, tight-binding, and the Dirac equation


3.) Landau levels in graphene


4.) The transparency of graphene


5.) Transport problems in graphene


Module 11: Guided Optics

Lecturer: António Pereira Leite


1. Introduction
Optical communication technology and optical information processing. Guided propagation, dielectric waveguides. Optical fibers, optical fiber devices, integrated optical devices. Fiber optics transmission systems evolution. Basic elements of a transmission system by optical fiber.

2. Waveguides in planar geometry.
TE and TM guided modes in parallel plane guides. Guided modes and total reflection. Dispersion relation. Cutoff of modes, limits of high and low frequency, number of guided modes. Normalized parameters and normalized dispersion relation of TE and TM modes. Intermodal and intramodal dispersion. Guided power and power and power confinement. Radiation modes of the substrate and of the substrate-superstrate. Characterization of planar guides with a prism. Orthogonality and normalization of the modes. Expansion of an arbitrary field in normal modes. Reference the loss-gain, and surface plasmons. Three-dimensional waveguides. Method of effective indices. MMI devices. Radiation from a three-dimensional waveguide; Gaussian approximation to the fundamental mode.

3. Propagation in optical fibers
Propagation in fibers with step index profile (SI). HE, EH, TE and TM modes. Dispersion relation. Propagation cutoff. Normalized parameters. Dispersion. Groups of modes in the limit of weak guidance; LP pseudo modes. Single mode operation. Guided power and modal power confinement. Dispersion in single mode fibers. Control of dispersion, and US, DS and DF fibers. Modal diameter (MFD) and equivalent step index profile (ESI). Polarization dispersion and birefringence in optical fibers. Multimode optical fibers. Propagation in graded index profile fibers (GI) according to Geometric Optics; optical ray dispersion and optimization of the index profile. WKB approach; dispersion and its optimization. Micro structured optical fibers, photonic crystal fibers.

4. Fiber-fiber and fiber-emitter coupling
Coupling between single mode fibers, tolerances, connectors and joints; optical reflections. Coupling between a Gaussian beam and a single-mode fiber. Coupling between multimode fibers, and between an extended emitter and a multimode fiber.

5. Coupled mode theory
Lorentz reciprocity theorem, orthogonality of modes, expansion of an arbitrary field in eigenmodes of the unperturbed guide. System of coupled equations in the modal amplitudes; coupling coefficients. Directional coupler; phase synchronism; power transfer; spectral behavior. Optical tunable filter and optical switch. Analysis of directional coupling in terms of super modes of the structure; arrays of coupled guides. Contra directional coupling in a guide with a periodic grating; phase synchronism; reflection coefficient; spectral response of the reflector.

6. Nonlinear effects in optical fibers
Optical Kerr effect; phase self-modulation; nonlinear Schrodinger equation. Optical solitons. Pulse compression. Raman and Brillouin scattering. Second harmonic generation. Four-wave mixing in optical fibers.

7. "Beam propagation method" and "Staircase concatenation method"
Fundamentals of FFT-BPM; application examples. Fundamentals of FD-BPM. Fundamentals of "staircase concatenation method"; examples: WDM couplers.

K. Okamoto, Fundamentals of Optical Waveguides, 2nd. ed., Academic Press 2006.
G.P. Agrawal, Lightwave Technology: Components and Devices, Wiley 2004.


Module 12: Conformal field theory (tutorial classes)

Lecturer: João Penedones


1. Scaling and renormalization - phase transitions, critical exponents,
renormalization group, quantum critical points, effective field theory;

2. Conformal field theory - conformal transformations, primary operators,
correlation functions, operator product expansion, state-operator map, Weyl
anomaly, Cardy formula;

3. Conformal field theory in two dimensions - Virasoro algebra, minimal