Molecular Biology: Research Activities

Experimental research is carried out in the Molecular Biology Laboratory of the Scuola Normale Superiore in the research area of the National Research Council (CNR) of Pisa. Some projects are also carried out in collaboration with the International Centre for Genetic Engineering and Biotechnology (ICGEB) in Trieste.

Main research fields are:

•  Study of gene therapy methodology
•  Study of molecular properties of the HIV-1 virus
•  Study of regulation of the replication of human DNA
•  Use of computational graphics and three-dimensional animation for the visualization of biomolecular processes.

Molecular Biology: Teaching Activities

There are regular graduate courses and cycles of annual seminars on topics of advanced research in the field of molecular biology and its applications to biomedics.

Molecular Biophysics: Research activities
Experimental and theoretical research is carried out at NEST (National Enterprise for nanoScience and nanoTechnology) Laboratory of NEST-CNR INFM and Scuola Normale Superiore, and in collaboration with the Molecular Biology Laboratory, both at the Scuola Normale Superiore.

Main research fields are:

• Monitoring and modeling single molecule and single-bioevents in living cells
• Design and realization of active nanoprobes as magnetic or fluorescent intracellular reporters
• Analysis of vibrational and electronic spectral properties, modeling and optimization of green fluorescent protein (GFP) mutants
• New high-resolution fluorescence or magnetic in-vitro and in-vivo imaging strategies (e.g., two-photon, correlation spectroscopy, superparamagnetic compounds)
• Study of the interactions among proteins and their inter- and intra-cell dynamics using high-spatial-resolution spectroscopic techniques like Fluorescence Resonant Energy Transfer (FRET) and Fluorescence Recovery After Photobleaching (FRAP). Modeling through molecular recognition and multi-scale methods
• Scanning probe microscopy characterization
• Molecular motifs for targeted intracellular delivery of drugs and nanorobots
• Modeling, design and realization of active nanoprobes as intracellular nanorobots
• Development of portable micro-/nano-fluidic systems for ultra-high sensitivity diagnostics
• New strategies for biomolecule immobilization with high-spatial resolution onto biocompatible surfaces
• Nanotechnologies for guided cell culture and differentiation under highly controlled conditions
• Low resolution models for dynamical and structural studies of nucleic acids
• Identification of new computational strategies using DNA
• Software development for multi-scale modeling; application to GFP or selected biomolecular systems.

Molecular Biophysics: Teaching Activities
Courses and seminars are held both by Scuola Normale and external professors. First-year graduate students in Molecular Biophysics, in agreement with the Class Council, attend three full-year courses at either the Scuola Normale Superiore or the graduate program at the University of Pisa or at the Scuola Superiore Sant’Anna. These courses both deepen the students' knowledge of the field of Molecular Biophysics and assist them in choosing a specific research project.

Chemistry: Research Activities
The Scuola Normale, in collaboration with the professors of the Universities of Pisa and Bologna and with the Zurich Polytechnic, promotes research in the following fields of chemical science:
1. Computational Chemistry
- Development of methods for the numeric simulation of complex chemical processes.
-Classical molecular dynamics and quantum mechanics.
-Studies of biological systems.
-Numeric design of new drugs. Study of nanosystems and advanced materials.
2 . Physical Chemistry
-Quantum mechanics: methodological and computational developments.
-Study of electronic and structural properties of atoms, molecules and clusters.
-Radiation-matter interaction: applications to spectroscopic problems.
3. Inorganic Chemistry
- coordination compositions
- metalorganic compositions
- structural and electronic properties of the ligand-metal system and its reactivity.
4. Macromolecular Chemistry
Systems and catalysis in polymerization.
- New polymeric materials with special properties.
-Property-structure relation.
5. Organic Chemistry
-Molecular discrimination in chemical and biochemical problems
-Advanced methodologies in organic synthesis.
-Chemical and spectroscopic properties linked to supramolecular systems

Chemistry: Teaching Activities
Graduate students in Chemistry are required to attend three courses from among either the specialized courses of the Scuola Normale Superiore, or from the final three years of the Scuola Normale undergraduate courses, or from the final two years of the undergraduate/any graduate courses in the Department of Chemistry at the University of Pisa related to the research areas listed above.

Physics: Research Activities
Main research fields are:

•  Astrophysics and Plasmas
Astrophysics is divided into the following areas:
-Dynamics of normal galaxies and of globular masses
-Obscure material in spirals and elliptics
-X Emissions from galaxies and masses
-Astrophysical plasmas
There is growing interest in galaxy masses and cosmology.
Partnerships with many international institutions (in particular with MIT, Space Telescope Science Institute, European Southern Observatory, Groningen), with other Italian institutes (Arcetri, Bologna, Padova, Pisa) and participation in various observatory projects (with ESO and HST telescopes, among others).
For Plasma Physics, interest is primarily theoretical and based on collaboration with MIT, the Joint European Torus, Utrecht, General Physics Institute, Moscow and the University of Pisa.

•  Material Physics
Both theoretical and experimental research is carried out at the NEST-INFM centre of the Scuola Normal ( www.nest.sns.it ). Main research fields are:
-Excited states induced by electromagnetic radiation.
°Non-linear optics and quantum transport in semiconductors and heterostructures in reduced dimensions and in hybrid structures in organic-inorganic semiconductors.
°Quantum phase transitions in low dimensional electronic systems.
-Transport and magnetic transport in hybrid semiconductor-superconductor mesoscopic systems
°Confined atomic vapours: Bose Einstein condensation, fermionic vapours and boson-fermion mixtures, matter wave lasers.
°Calculus of classical and ab initio molecular dynamics of macromolecular systems, including biological systems.
°Molecular biophysics: intra and inter-cell dynamics of single biomolecules, biomolecular optical-electronic devices.
- Magnetism in gas of strongly correlated electrons.
- Superfluidity and condensation in quantum plasmas.
-Cohesion and structure of micro aggregates in gas, liquids and glasses.

•  Experimental Elementary Particle Physics
Graduate students interested in the field of Elementary Particle Physics can have access to research carried out in the most important laboratories in the world by groups where the professors of the Scuola Normale are working.
Main research areas are:
- Study of high energy proton-proton interactions, research on the Higgs boson and of super symmetry with the CMS experiment under construction at the LHC accelerator at the CERN of Geneva.
- Study of proton-antiproton physics at the Tevatron of Fermilab in the CDF experiment.
- Study of the nature of CP violations in neutral K decay at the SPS of CERN.
This experimental work is carried out with the equipment and funding provided by the INFN, Pisa at the Laboratory located in San Piero a Grado.

•  Theoretical Physics of elementary particles, astrophysics and cosmology
Research activities tend to the formulation of models of fundamental interactions and to the study of their phenomenological consequences on the basis of information derived from elementary particle physics, astrophysics and cosmology.

Specific areas are: Electro-weak breaking symmetry, supersymmetry, unification of strong and electro weak interactions, flavour physics and neutrino physics.

•  Theoretical physics and mathematics
- Systems with infinite degrees of freedom
- Field theories and multi body system theories
- Breaking symmetries

Physics: Teaching Activities
Courses and seminars are held by professors of the Scuola Normale and external experts. Graduate students are required to attend three courses from among either the specialized courses of the Scuola Normale Superiore, or from the graduate courses in the Department of Physics at the University of Pisa. These courses both deepen the graduate students' knowledge and assist them in choosing a specific research project.

Condensed Matter Physics: Research activities
Experimental and theoretical research is carried out at NEST (National Enterprise for nanoScience and nanoTechnology) of the INFM, recently set up at the Scuola Normale.
Main research areas are:
- Physics of coherent systems. Study of coherent processes in nanostructure semiconductors and semiconductor-superconductor hybrids. Electronic interferometer in quantum Hall effect regime. Study of the transport of fractional loads through confined geometries. Theories of quantum transport in nanostructures. Properties of superconductive nanostructures. Quantum computation in solid state systems.
-Nanostructured photonic devices. Radiation-matter interaction in confined electronic and photonic systems. Laser and heterostructure detectors . Nanostructured sources of single photons.
-Experimental physics of collective states in nanostructures. Phase transitions and critical points. Experimental analysis of instable collective modes through anelastic diffusion of light.
-Spin electronics. Spin filters based on semiconductor nanostructures as quantum points and quantum points contact.
- Theory of highly correlated electronic and bosonic systems. Property of fundamental state, excitation spectra and transport phenomena in quantum fluids (electron and charged boson plasmas in various dimensions; Bose-Einstein condensates and fermion atoms in harmonic traps and optical reticles).
- Molecular biophysics. Experimental and theoretical studies of the photophysical properties of single Green Fluorescent Protein (GFP). Computer-aided design and production of GFP mutants with optimized optical properties. Study of the interactions among proteins and their inter- and intra-cell dynamics using high-spatial-resolution spectroscopic.
- Biomolecular electronics. Production of single-molecule optical memory devices, optical commutators, single-photon emitters.
- Identification of new computational strategies using DNA.

Condensed Matter Physics: Teaching activities
Courses and seminars are held by professors of the Scuola Normale and external experts. Graduate students are required to attend three courses from among either the specialized courses of the Scuola Normale Superiore, or from the graduate courses in the Department of Physics at the University of Pisa. These courses both deepen the graduate students' knowledge and assist them in choosing a specific research project.

Mathematics: Research Activities
1. Calculus of variations (problems of semi continuity and G-convergence, geometric theory of measure, problems of geometric evolution).
2. Infinite dimension analysis, Stochastic Analysis, stochastic partial differential equations.
3. Harmonic analysis (convolution operators in Euclidian spaces and Lie groups; commutative and non Fourier analysis, applications of differential operators and complex analysis).
4. Dynamic systems and arithmetic (quasi periodic orbits, problems of small divisors, KAM theory, continued fractions, holomorphic dynamics).
5. Geometry and complex analysis (global analysis of foliation varieties, problems of non linear analysis involving the geometric theory of holomorphic functions of complex variables, cobordism for the CR varieties and symplectic filling, Levi form evolution of compact subsets of a Kaehler variety, Kaehler-Einstein variety and hyperkaehler metrics, minimal subvariety and special Lagrangian subvariety in Calabi-Yau spaces.
6. Diophantine geometry (whole points on curves and algebraic varieties of superior dimension, diophantine equations of function fields, height of algebraic points on subvarieties of varieties of group and intersections of algebraic subvarieties which vary in families, e.g., of fixed dimension).

Mathematics: Teaching Activities
Courses and seminars are held by professors of the Scuola Normale and external experts. Graduate students are required to attend three courses from among either the specialized courses of the Scuola Normale Superiore, or from the graduate courses in the Department of Mathematics at the University of Pisa. These courses both deepen the graduate students' knowledge and assist them in choosing a specific research project.

Mathematics for Technology and Industry: Research Activities
Graduate work in this department is organized around the different areas of applications of this field in technology. In particular, at least the follow research fields are available:
- Continuous Mechanics: Theory and applications
Research activity will develop in the following directions: fundamental questions of fluid and solid theory like, e.g., the existence, uniqueness and asyntotic behavior of solutions of Euler and Navier-Stokes equations; models and development of advanced computational techniques for complex flow; methodology for the analysis of signals from turbulent flow; analysis of fluid dynamic instability; problems of best form of relatively rigid bodies, like aerodynamic profiles, or very deformable, like biologic and synthetic materials, and problems of fluid-wall interaction.
- Mathematical models of semiconductor transport
Principally research on transport in advanced submicrometer devices where the usual approximations of derive-diffusion are no longer valid and detailed kinetic descriptions are needed. Alternative methods to the Monte Carlo technique have been developed, based on the system of moments of the semiclassical Boltzmann equation, which are computationally more efficient than the stochastic simulation of the Monte Carlo type. Problems of electromagnetic propagation in submicrometer devices are being studied, consistent in the coupled system of the Maxwell equation and in the equations of the transport of the devices. The analytic and numeric methodologies used are the same used for the systems of the laws of conservation of the hyperbolic type.
- Mathematics for Telecommunications and Information
Probabilistic questions like the following will be investigated: theory of the codification and transmission of information through channels with disturbances, e.g., codes; analysis and treatment of images; problems of network theory in information transmission and code theory.
- Mathematical models for Geophysics and Volcanology
The study of the Earth using geophysical instruments and the production of models for understanding processes which take place in the atmosphere, on the surfaces and inside our planet: This is the challenge in identifying and facing global changes, managing and lessening natural risks like earthquakes, volcanic eruptions, tsunami, etc., and locating and better using natural resources. The problems are usually multiphase, with large space-time variability in the processes, presence of free frontiers, sub/super critical transitions giving rise to shock waves, hysteresis phenomena, non-linear effects of the butterfly type. The quantitative description of a varied universe, in which chaotic behavior often prevails over determinism, requires adequate mathematical instruments. This is the reason why the Scuola Normale collaborates with the National Institute of Geophysics and Volcanology in the field of Computational and Applied Mathematics. Research areas, all of which revolve around “mathematical simulation” of geophysical phenomena, are: Methods of resolving partial differential equations, Lagrangian SPH and Cellular Automata, Stochastic and Probabilistic Analysis, Geodetic measures of precision.

More information can be found on the graduate web page ( http://www.sns.it ). Moreover, if there is interest among graduate students, other research activities in mathematics for technology and industry (like mathematics in materials science, mathematics for biology, medicine and the environment, etc.) can be planned. In their research program, candidates can refer to one of the areas above or to other areas where they have already worked; such references are for information only and are considered non-binding.

Mathematics for Technology and Industry: Teaching Activities
Work is carried out in traditional courses, laboratories and lesson series. Courses and laboratory work cover basic topics like technological modeling and computational technique as well as specific research areas. Among courses there are: numerical methods for resolving partial derivative equations, mathematical modeling of industrial processes, mathematical modeling and numeric simulation for semiconductor devices, continuous mechanics, computational fluid dynamics, probabilistic methods in information and telecommunication theory. Periods of internship in European industries or research centers are foreseen.

Financial Mathematics: Research Activities
Research and training is carried out in the following areas:

- Mathematical models for financial markets;

- General theory of stochastic processes, statistic models and application to microeconomic models.

If there is interest among graduate students, other research activities in mathematics for finance can be planned (statistical methods for analysis and modelling empirical data, techniques of stochastic control. In their research program, candidates can refer to one of the areas above or to other areas where they have already worked; such references are for information only and are considered non-binding.

Financial Mathematics: Teaching Activities
Study and research is organized in traditional courses, laboratory courses and work-study internships in the research centres of financial and insurance institutions. The course includes specific courses like “Applications of Stochastic Calculus to Financial Mathematics” and “Differential Stochastic Equations” as well as more typically mathematical courses (like “Differential Equations with Partial Derivatives” or “Probabilistic Models and Statistic Methods”); an introduction to Microeconomics will be provided by the Scuola Superiore di Studi Universitari e Perfezionamento S.Anna. Laboratory work will also include statistical and empirical analysis on real financial data. An internship at a research centre of a bank or an insurance industry represents an important part of the training activity.

Neurobiology: Research Activity
Research is carried out at the Neurobiology Laboratory of the Scuola Normale. Main research areas are:

• Study of the factors that regulate the development and the plasticity of the nervous system. Plasticity here means the modifiability of nervous systems in response to experience. Experience, through the modulation of electric activity, leaves profound signs in our neural circuits, in a particular way during the developmental years but, in a lesser way, in the adult as well. Experiences during a brief period of childhood (critical period) definitively model what our behaviour will be for the rest of our lives. Lack of correct interaction with the environment during the critical period can lead to permanent modifications in the way the cortical is organized, and consequently damage nervous functions. Our research aims to understand how experience models and modifies the nervous circuits by using advanced techniques of neuroanatomy, in vivo and in vitro electrophysiology, neurochemistry, imaging and behavioural techniques. The areas are:
  • Study of the role and mechanisms of neurotrophines in the regulation of the plasticity of the visual cortical.
  • Study of the mechanisms which determine the timing of the critical period.
  • Study of transduction pathway of signals, at the heart of synaptic plasticity in the developing visual cortical.
    
• Degeneration and regeneration of the Central Nervous System (CNS):
  • Study of the mechanisms of cell death after traumatic lesions of the CNS. Study of gene expression in the degenerating neurons.
  • Study of the mechanisms which regulate the reaction to traumas using advanced techniques of electrophysiology and imaging.
  • Model to study molecular mechanisms of neurodegenerative diseases (particularly Alzheimer Disease)
  • Development and expression of new therapeutic strategies to promote the survival and regeneration after cerebral lesions:
    • administration of neurotrophic factors
    • administration of recombinant antibodies
      
  • Molecular biochemical and biophysical studies to characterize recombinant neurotrophic factors engineered to optimaze therapeutical applications
  • Develop and application of intracellular expression of intracellular antibodies (intrabodies) to interfere in a localized way with specific protein functions in neurons
    
    A characteristic element of this line is to evaluate the therapeutic efficacy of the strategies adopted in terms of repair of the damaged function.

Neurobiology: Teaching Activity
Graduate courses are offered by the Scuola Normale, along with seminar series concerning cutting edge topics in the field of Neurobiology.