M2 Molecular Nano Bio PHOTonics

Robert PANSU (DR CNRS), Pierre AUDEBERT (Pr ENS Cachan), Bianca SCLAVI (CR CNRS), Claude NOGUES (CR CNRS).

36 hours of lectures 12 hours practicals.

Introduction to DNA and protein biochemistry
•Biochemistry of macromolecular recognition and ligand binding
•Enzyme-based biosensors
•Surface functionalization
•Surface Plasmon resonance
•Detection concepts
•Fluorescence basic
•Analogical probing in fluorescence
•Digital probing in fluorescence
•DNA Chips
•Electrochemistry

•SPR Imaging
•Flux Cytometry
•Fluorescence Imaging.

Chemical equilibrium, thermochemistry and kinetics. Electrochemistry.

Molecular fluorescence principles and applications / Valeur Bernard / Wiley-VCH - Introduction to fluorescence sensing / Demchenko Alexander P. / Springer - 2009 Orellana, G. and Moreno-Bondi, M. C. (2005) "Frontiers in chemical sensors: novel principles and techniques" Birkha?user.

Septembre - Octobre - Novembre - Décembre - Janvier - Février.

GIF-SUR-YVETTE

Emmanuelle Deleporte, Isabelle Ledoux, Marc Guillon.

68 hours of lectures A 4 hours exam encompassing the 3 parts of the Course.

I. Nanostructures for photonics: description and fabrication methods
1. “Top-down” elaboration techniques of nanostructures : photolithography, etching techniques Electron and ion beam lithography
2. Nanolithography at atomic scales : STM, AFM
3. Nanoparticles: preparation and functionalization
II. Physics at the nanometric scale and applications to photonics
1. Definitions and Basics: state densities, 3D electron gases, bandgap structures, excitons, polaritons, strong coupling
2. 2D, 1D and 0D quantum confinement. Electron and photon behaviour. Illustrations in carbon nanotubes.
3. Interaction between nano-objects and light.
a. scattering, linear optical properties
b. non-linear optical properties: role of the interfaces
c. emission properties: fluorescence, lasing emission
III. Instrumentation in nanophotonics and applications
1. Structural microscopy techniques: electron microscopy (EM), atomic force microscopy (AFM), tunneling microscopy
2. Optical microscopy: luminescence, nonlinear effects (two-photon fluorescence, second and third harmonic generation, surface enhanced Raman scattering)
3. Nano-objects manipulation: AFM, optical tweezers
4. Application to Biology (in connection with the biophotonics I and II courses).

Basics in quantum mechanics and/or solid state physics, basics in spectroscopy.

Nanoscience: Nanotechnologies And Nanophysics : Claire Dupas, Philippe Houdy, Marcel Lahmani, Springer.

Septembre - Octobre - Novembre - Décembre - Janvier - Février.

GIF-SUR-YVETTE

Ngoc Diep LAI.

30 hours of lectures Written exam.

Sessions 1 to 8: Basic Maxwellian optics from the molecular to the macroscopic scale
Microscopic model of light-matter interaction: the elastically bound electrons and its implications. Radiating properties of an ensemble of oscillating dipoles with near-field and far-field emission.
Macroscopic level: the propagation of light in a dielectric medium, introduction to the index of refraction, Snell’s laws for the refraction and reflection of light at interfaces.
Elements of crystalline optics: Polarization states and the Fresnel equation. The dielectric tensor and the index ellipsoid. Eigen-polarization states and principal dielectric axis. Optical axis. The double-sheet dielectric surface. Ordinary and extraordinary waves.
Wave optics: Diffraction and interference.

Sessions 9 to 14: Introduction to Lasers
Resonant cavity: condition, type, Gaussian beam
Semi-classical model of light-matter interaction: the case of the two-level atom. Absorption, stimulated emission and spontaneous emission. Rate equations for three and four level systems.
Introducing the laser and its major concepts: pumping, population inversion, threshold, gain and its saturation, feedback and cavities. Examples of major classes of laser (gaz, liquid, solid state),
Properties of the laser beam: particularly ultra-short laser pulses will be introduced in view of applications to time-resolved spectroscopy, nonlinear optics and multi-photon microscopy.

Basic mathematics necessary for electromagnetism and ordinary differential equations.

Fundamental of Photonics», Saleh and Teich (John Wiley, last edition) « Laser Physics », Eberly and Millony (John Wiley, last edition).

Septembre - Octobre - Novembre - Décembre.

GIF-SUR-YVETTE

Catherine Colin, Fanny Domenec.

The course is taught in 10 lessons of 3 hours each. Students will have to give an oral presentation in groups, and take a written exam at the end of the course. Attendance and participation in class will also be assessed.

The course will focus on academic and scientific English. Students will become more familiar with academic talks and scientific writing.
The course will also provide learning strategies and resources to help students improve their English on their own.

At least B1 level in English.

Septembre - Octobre.

GIF-SUR-YVETTE

Marie Caroline JULLIEN (ESPCI) : Physics in microfluidics - Valérie GENOT (PPSM): Practical in microfluidics and chemistry - Rasta Ghasemi (IdA) : Elaboration of microfluidics circuitry - Abdel EL-ABED (LPQM) : Microtechnologies in Microfluidics and Digital microfluidics - Jean Pierre LEFEVRE (PPSM) : Microfluidics platform responsible.

28 hours for lecture, 12 hours for lab work.

I. Introduction
- Concept of Microsystems : case of BioMEMS and microfluidic
- Scaling laws in Microsystems
II. Microtechnologies and Microfluidic
- Clean room, Photolithography and Microelectronics technology
- Microfluidic technology : glass, silicon, polymer (moulding-casting)
- Case study : Micromixer and MicroPCR
III. Physics of microfluidic (12h MCJ)
- Microhydrodynamics : continues microfluidics
- Capillarity: digital microfluidcs - Droplet
- Electro-hydrodynamics (EHD)
- Mixing and sorting in microfluidics
V Practical training
- Lab1 : Microfluidic design with the help of Comsol ©
- Lab2 : Fabrication and testing of a micromixer in PDMS
- Lab3 : Droplet generator and phase diagram characterisation.

General background in physics or chemistry.

Fundamentals and applications of Microfluidics, Nguyen and Wereley, Artech House Introduction à la Microfluidique, P. Tabeling, Belin Theoretical Microfluidics, H. Bruus, Oxford University Press.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bruno Le Pioufle, Pamela Didier.

The course is organized in 28 hours of lectures and 12 hours of practical work.

1.DNA chip :concept of successive photoexposures to develop high throughput chips
2.Soluble protein chips- electrospray generation in a chip, 2D electrophoresis on a chip
3.Membrane protein biochips
Basics in electrophysiology, Huxley model of action potential propagation, Simulation of the Action potential (practicals), Main systems for ion channel recording, patch clamp, planar patch clamp, population patch clamp, artificial lipid bilayers Sructure and fabrication of membrane protein chip, physical properties, Membrane Protein insertion in LBM. Liposomes, Giant liposomes, electroformation.
4.Cell biochips –
use of electrical field or other means to handle, sort, or treat cells. Dielectrophoresis trapping, optical traps, fluidic aspects, cell arraying, electroporation on a chip.
5.Practicals – Laboratory
Simulation of the action potential (4h), Dielectrophoresis force simutation with finite element analysis (4h), Dielectrophoresis on a chip (4).

This course is open to multidisciplinar background students. There is thus no mandatory prerequisites.

Miller, C. Ion Channels Reconstitution; Plenum Press, 1986.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Ngoc Diep Lai; Bruno Palpant, Clément Lafargue.

30 hours lectures. Writing exam, based on scientific papers (duration: 3 hours).

PART ONE: Photonic crystals/nonlinear photonic crystals and applications
1D, 2D, and 3D photonic crystals: theory, simulation, photonic quasi-crystals
Photonic crystal with defect and applications
Nonlinear photonic crystals
Fabrication technologies and applications
PART TWO: Plasmonic effects
Electromagnetism and optics in bulk noble metals: Electromagnetism survival kit; Bulk noble metals: Electronic properties, optical response
Localised plasmon in metal nanoparticles: Mechanical analogy: driven damped linear oscillator; Dielectric confinement; Surface plasmon resonance; local field enhancement; applications for Surface-enhanced Raman scattering or fluorescence; bio-labelling; Effects of nanoparticle environment, size, shape and composition; Coupling between nanoparticles.Transient optical response and nanoscale light-heat conversion.
Selected applications: Light-heat conversion: Nanoscale hyperthermia against cancer, drug or DNA delivery, laser damage and laser shaping, photothermal imaging, optical limitation; Plasmonics for high-speed nanophotonics; Plasmonics for nonlinear optics
Part THREE : Laser physics.

Optical physics and electromagnetism (L3 level), basic mathematical physics notions in classical and quantum mechanics (L3 level), and Light-matter interactions course (M1 level).

Photonic Crystals: Molding the Flow of Light, second edition John D. Joannopoulos, Steven G. Johnson, Joshua N. Winn, and Robert D. Meade Published in 2008 by Princeton University Press.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bernard Journet.

22 hours lectures, 28 hours practicals Written exam.

Microwaves
Transmission lines in case of distributed element model, Smith chart
S parameters.
Impedance matching, amplifier design, simulation software ADS
Measurement techniques (network analyser)
Single conductor waveguides (TE and TM modes), dispersion
Optical telecommunications
1/ Optical fibres: determination of the different modes
Dispersion and absorption phenomena
Fabrication process
2/ Optical digital transmitters and receivers, optical amplification
Digital data transmission, different standards
Wavelength division multiplexing (WDM) technique, dispersion effects.

Basic knowledge about electrical and optical fundamentals; Maxwell's equations in vacuum. Complex numbers; Mathematical operators; Fourier analysis.

D. M. Pozar, "Microwave engineering", Wiley Ed. K. Zhang, D. Li, "Electromagnetic theory for microwaves and optoelectronics", Springer Ed.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Marco PASI.

14 hours for lectures, 16 hours of practical exercises.

CM:
1.Theoretical bases of molecular mechanics
Biomolecular empirical force fields : principles, approximations, common functional forms, the solvent, performance considerations, applications.
2.Sampling the potential energy surface
Algorithms and techniques (minimisation, Monte Carlo, molecular dynamics)
3.Simulating biological phenomena
Using simulation to compute ensemble properties, state-of-the-art applications in biology comparing simulation and experiment (NMR, AFM, cryo-EM, FRET, …)

TP:
4.Molecular visualization
Using molecular viewers to study the structure, interactions and dynamics of biomacromolecules
5. Molecular simulation software architecture
Configuration files and execution scripts, interacting with the software using the command line
6. Setting up your first MD simulation
From static structure to trajectory in physiological conditions ; study cases selected from examples in the "Nanophotonics" or "Biophotonics" courses ?
7. MD Trajectory analysis and comparison with experiment
Extracting useful information from the trajectory to evaluate simulation quality, compare with experiment and shed light on molecular mechanisms.

The four “Fundamentals” courses (or equivalent prior knowledge), “Molecules and Interactions”.

Molecular Modelling: Principles and Applications (Pearson Education, 2001), A. Leach; Understanding Molecular Simulation: From Algorithms to Applications (Academic Press, 1996) D. Frenkel & B. Smit.

Février - Mars.

ORSAY

Ngoc Diep Lai.

28 hours of lectures. Written exam (3 h).

Short overview of nonlinear optics
Introduction to nonlinear optics :a classical model for nonlinear effects
Nonlinear of bulk systems – coupled-wave theory, propagation equation
A fully treated useful example : non-resonant second-harmonic generation, phase matching and phase, mismatching
Second-order and third-order nonlinear optics
Second-harmonic and third harmonic generation, Parametric amplification, Pockel and Kerr effects, etc.
Nonlinear optics in micro- and nano-structures
Quasi-phase matching technique: structures 1D, 2D and 3D
Nonlinear photonic crystals: perfect phase matching.
Fabrication and applications of nonlinear photonic crystals
Nonlinear microscopies and nanoscopies
What does (or does not) matter from bulk to nanoscale
Multi-photon microscopies in nanophotonics and biosciences: SHG, TPFE, THG, T3FE, CARS, EO, STED, structured illumination, ...

Optical physics and electromagnetism, Laser (L3 level).

Nonlinear Optics » by R. Boyd.

Septembre - Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Chi Thanh Nguyen.

50 hours of lectures Homework reports (1/3 of weight of.

: This course, which is devoted to photonic devices for applications in the domains of optical communications and sensing, covers both theoretical and practical aspects of the physics of photonic devices, the fabrication and the characterization techniques of these devices, which are based on organic materials. It also introduce to the molecular photonics in some organic active materials. Applications of polymer-based photonic devices in optical communications and optofluidic devices in biochemical sensing will be finally presented.
Background of wave optics and photonics
Base of waveguide optics
Introduction to organic materials for photonic devices
Polymer-based electrooptic devices for optical communications
Polymer-based optofluidic devices for sensing.

Wave optics and electromagnetism in matter.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Ngoc Diep Lai.

Rotation of students to visit all experiments. Equivalent to a Practical in two groups.

1.Geometrical Optics: mirrors (concave, convex), lenses, microscope, light source, etc…

2.Interference and Diffraction: Fabry-Perot cavity, diffraction of different objects (grating, ball, etc.), interference of two beams, multiple beams, etc.

3.He-Ne Laser: build on a laser yourselfOptical physics and electromagnetism (L3 level). In order to choose this practical work, students should study two courses: Light-matter interactions (basics level) and Nonlinear Optics.

4.Nonlinear Optics: second-harmonic generation, one- and two-photon absorptions.

Optical physics and electromagnetism (L3 level). In order to choose this practical work, students should study two courses: Light-matter interactions (basics level) and Nonlinear Optics.

Janvier.

GIF-SUR-YVETTE

Marco PASI.

8 hours of lectures, 20 hours of practical work in a dedicated room in Paris Sud (Orsay).

1. Programming Python basics
Data types, control structures, lists, hashes, files
2. Good practices of collaborative scientific software development
The scientific development cycle in Jupyter notebooks, writing and distributing modular packages, Git and Github, documentation, testing, continuous integration
3. Analysing massive data using numpy, scipy and pandas
Representing, storing and sharing matrix data, indexing/slicing/iterating, vectorization, dataframe operations, basic statistics
4. Data visualisation using numpy, pandas and matplotlib
Visualising data for exploration and for publication, data science traceability and reproducibility, literate programming and executable papers
5. Personal/group project
Prepare a report about the statistical exploratory analysis of real dataset (chosen by students or proposed by the teacher).

Fundamentals in Mathematics” (or equivalent prior knowledge), some basic statistics.

Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython (O’Reilly, 2011) W. McKinney.

Décembre - Janvier - Février.

ORSAY

Jean-Pierre Barbot, Eric Vourc'h.

50 hours of lectures.

Signal processing fundamentals
- Introduction and definitions
- Classification
- Deterministic signals
- Random signals
- The signal processing for digital communications
- Introduction to digital communications
- The baseband transmission
- The source coding
- The in line coding
- The channel Coding
- The transmission over a carrier frequency
- The digital modulations and demodulations.

No special prerequisites.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bruno Le Pioufle, Cécile Legallais, Abdul Barakat, Olaf Mercier, Anne Dubart-Kupperschmitt, Ulysse Pereira, Emmanuel Martinod, Etienne Bur, Nicolas Ferry, Frédéric Worms.

The course is organized in the form of a 3-days workshop with sessions corresponding to the different aspects of the program as described above.

This module will cover the various aspects of tissue and organ bioengineering, a promising perspective to replace damaged human organs (e.g. liver) by natural organs elaborated using bio-engineering procedures starting from cell of the patient himself, then preventing from organic rejection of organs provided by other individuals, and bringing a valuable solution of the permanent lack of organs for grafting.
The module is organized in sessions devoted respectively to
-Cells : general presentation ; Spheroids : a first step for a bioengineered liver; Industrial production of mature cells
-Matrices and scaffolds : Natural and Artificial matrices; Fabrication of liver microtissues; Recellularization of biological scaffolds
-Bioprinting : Micropatterning ; Bioimpression techniques ; Modelling tissue and organ.
-On-chip strategies : Principes and introduction to organ on chips; Liver tissue on chip; : Vascular system on chip ; Predictive toxicology.
-Organogenesis and vascularisation of constructs
-Extracorporal systems : extracorporal Spleen ; Artificial lung; Encapsulation in extracorporeal system; Extracorporeal liver system
-Clinical applications : Vessels reconstruction using microfluidics ; Skin reconstruction ; Retinal reconstruction ; Tracheal reconstruction ; Biofabrication of fingers and hands ; Cardiac repair.
-Regulations/economics
-Ethics.

Basic notions in Biology.

Avril.

Eric Deprez, Sophie Brasselet, Olivier Delelis, Patrick Tauc.

28 hours of courses 22 hours of exercises and practical work.

Course (28 hours) :
oIntroduction to fluorescence in Biology. Principles of steady-state and time-resolved measurements. Influence of solvent polarity on emission spectra. Quenching of fluorescence…
oIntrinsic and extrinsic fluorophores, new photonic probes for Biology, quantum dots and applications in biology.
oIntroduction to Nonlinear Optics and lasers in Biological studies.
oFluorescence anisotropy and applications in studies of interactions between biological macromolecules.
oFluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy.
oTechniques of fluorescence imaging microscopy and confocal analysis. TIRF microscopy. Multiphotonic microscopy and analysis. Introduction to super-resolution microscopy (STED, PALM).
oFluorescence resonance energy transfer (FRET), principles and applications. Fluorescence lifetime imaging microscopy (FLIM), FRET/FLIM for studying protein-protein interactions in the cell context.
oOn the use of fluorescence in genomic studies: DNA technology, sequencing, quantitative PCR, FISH (Fluorescence In Situ Hybridization).
Instrumentation and analysis of research articles (22 hours) :
oInstrumentation for fluorescence spectroscopy / generalities. Example of a time-correlated single-photon counting experiment. FCS set-up (5H). Presentation of a confocal microscope and multiphoton microscopy (5H).
oAnalysis of research articles (Confocal imaging, FLIM, FRET, Fluorescence anisotropy,…).

A background in Biology is preferable (non-biologists have to take the “Fundamentals in Biology” course).

Joseph R. Lakowicz, Principles of fluorescence spectroscopy. Springer (2006).

Février - Mars.

GIF-SUR-YVETTE

Keitaro NAKATANI, Nicolas Bogliotti, Pierre Audebert, Luca Polacchi, Carine Julien-Rabant.

48 hours courses Written exam.

1.Molecules and Light Interactions, Photophysical Processes
Molecular orbitals and energy levels: Selection rules and phenomenological description: Electric dipole transitions.
Unimolecular photophysical processes: Introduction, relaxation processes, Radiationless and Radiative deactivation processes.
Experimental setups: Steady-state and Lifetime measurements. Quenching of excited states, Photoinduced energy transfer.
2.Complexation, Supra- and Inter-molecular Interactions
Inter-molecular interactions: Molecular dipoles, Ionic and Dipolar interactions, H-bond
Complexation: Lewis acids and bases, Complexation, d-orbitals and ligand field theory, Chelate and template, Examples and properties of complexes.
Examples of supramolecular assemblies involving complexation and/or inter-molecular interactions.
3.Interfacial chemistry, Electrochemical processes
Introduction to electrochemistry: Electrodes and electrolytes.
Thermodynamics of electrochemical reactions: Nernst equation, Galvanic vs. electrolytic cells.
Electrochemical kinetics: Rate of electrochemical reactions, the Butler-Volmer equation.
Fast vs. slow electrochemical systems, Morphology of the I(E) curve in steady-state conditions, Application to corrosion.
4.Polymers
Introduction: Basic definitions, Fundamental examples.
Properties: Molar mass, Glass transition, Mechanical properties.
Polymerization reactions: Step polymerization, Chain polymerization, Kinetics.
Examples: Photopolymers, Composites, Natural polymers.

For non-chemists, the “Fundamentals in Chemistry” course is required.

Molecular Interactions (Waterstone, 2012), D. Micha. Electrochemistry: Principles, Methods, and Applications (Oxford Science Publications, 1993), C. M. Brett, A. M. Oliveira Brett. Physical Chemistry (Oxford University Press, 2009), P. Atkins.

Février - Mars.

GIF-SUR-YVETTE

Clémence Richetta, Gérald Peyroche, Marie Regairaz.

30 hours of lecture, written exam (duration at least 2 hours).

Biochemistry of Proteins
Structure of other biomolecules
Internal organization of eukaryotic cells
DNA, the carrier of genetic information
How cells read the genome: from DNA to proteins
Diversity in the living world
Cells in their social context: example of the immune system
Tutorial: methods for working with proteins
Tutorial: methods for working with DNA
Tutorial: methods for working with antibodies
An introduction to single-molecule approaches.

This course is strongly recommended to students having no biology background.

Life: The Science of Biology, 7th Edition, William K. Purves, David Sadava, Gordon H. Orians, H. Craig Heller, W.H.Freeman & Co Ltd.

Septembre - Octobre.

GIF-SUR-YVETTE

Nicolas Bogliotti, Cédric Mongin.

30 hours of lecture, written exam (duration at least 2 hours).

1.Chemistry of the Elements
Models for atoms and electrons description. Electronic configuration. Periodic table and element properties.
2.Structural Chemistry
Chemical bonds. Structure and geometry. Quantum theories of molecular structure.
3.Organic Chemistry
Alkanes, alkenes and aromatic compounds. Alcohols and amines. Carboxylic acid, ester and amides. Structural organic chemistry.
4.Thermodynamics
First and second law. Application to chemical equilibrium.
5.General Chemistry in Aqueous Solution
Acid, bases and pH. Complexation. Solubility.
6.Kinetics
Reaction rate. Reaction mechanism.

This course is mandatory for students having a limited background in Chemistry, (e.g. electrical engineers, computer scientists, physicists).

“Physical Chemistry”, Peter Atkins “Physical Chemistry - Understanding our Chemical World”, Paul Monk “Chimie Physique - Cours et Applications”, Paul Arnaud “Manuel de Chimie Théorique”, Patrick Chaquin “Advanced Organic Chemistry”, Francis A. Carey and Richard J. Sundberg.

Septembre - Octobre.

GIF-SUR-YVETTE

Abdel EL ABED.

30 hours of lecture, written exam (duration at least 2 hours).

Ses 1: Differentiation
First-order derivative, second-order derivative, maximum, minimum, partial derivatives of a two-variable function, ...
Sess 2: Series and expansion of functions
Taylor series, and operations on Taylor series: ratio, composition, ...
Ses 3-4: Integration
Integration of simple functions, integration by parts, multiple integrals (surface, volume, ...), change of variables, ...
Ses 5: Complex numbers
Basic manipulation, hyperbolic functions, complex representation in wave physics (in particular in electromagnetism), ...
Ses 6-7: Fourier series and Fourier transform (2 sessions)
Applications to optics: spectrum of a temporal pulse, diffraction, damped oscillator, ...
Sess 8-9: Vector spaces and linear algebra (2 sessions)
Vectors: scalar product, vector product.
Vector spaces and linear operations: two dimensions
Matrices
Se 1 10: Differential equations
First-order, second-order, and third-order ordinary differential equations, with applications in physics.

This course is intended towards student in need of an update in basic math. It does not require any special prerequisite . Prior to the course, screening tests will be organized to check on the level of students and orient them to this course when needed.

Foundation Mathematics for the Physical Sciences, by Riley and Hobson, Cambridge University Press (2011).

Septembre - Octobre.

GIF-SUR-YVETTE

Abdel El Abed, Isabelle Ledoux-Rak.

30 hours of lecture, written exam (duration at least 2 hours).

I. Optical wave physics
Origin of light, waves, electromagnetism
II. Vibrations and phonons
Classical harmonic oscillator
Lagrangian/Hamiltonian Mechanics
III. Fundamentals in quantum mechanics
Light as particles and quantization of energy
The photoelectric effect
Wave-particle correspondence
Emission spectra of atoms
Quantum description of atoms
IV. Origin of light
Radiation from accelerated charges
Origin of electromagnetic waves
Properties of electromagnetic waves
Standing waves and quantification
V. Statistical Physics
Basic principles
Application to « hot » sources : relation between temperature and emission wavelength
Blackbody emission.

This course is strongly recommended for students having a limited background in Physics, (e.g. biologists or chemists).

Hugh D. Young and Roger A. Freedman, University Physics, 13th edition, Addison Wesley, Editor (2010).

Septembre - Octobre.

GIF-SUR-YVETTE

AVARVARI Narcis, YASSAR Abderahhim, ZUCCHI Gaël, AUDEBERT Pierre, NAKATANI Keitaro, MIOMANDRE Fabien.

Course organized in 3 parts (see above). 3 Written exams.

1- Conducting molecular materials (12H)
The “Conducting molecular materials” classes deal mainly with electroactive precursors providing stable radical species in the solid state as well as with corresponding crystalline conductors. In order to understand electron transport phenomena in such materials (insulators, semiconductors, metals) the formation of one-dimensional energy bands is investigated in detail, with applications towards organic conductors and transition metal complexes. An extension towards chiral materials is proposed as well.
2- From molecules to opto-electronic devices (12H)
This course will give an overview of organic semiconductors for organic field effect transistor applications (OFETs), organic light emitting diodes (OLEDs), and organic solar cells. It will also introduce pi-conjugated polymers as a unique class of materials for opto-electronic devices.
3-Switchable molecular materials (20H)
The aim of this course is to present molecular systems likely to undergo the control and the switch of their properties, mainly in the field of optics and electronics. These systems go from molecules to molecular materials (conjugated polymers, gels…) and functional surfaces. The course will include the description of the various synthetic routes, as well as the investigation of the properties, like photochromism, electrochromism and recent advances where the optical properties can be triggered by plasmon.

Background in Chemistry of “Fundamentals in Chemistry".

Novembre - Décembre - Janvier.

PALAISEAU - GIF-SUR-YVETTE

Van-Oanh Nguyen-Thi and Dominik Domin.

Lecture,Exercises Quizzs, practicals.

1- Fundamental concepts
Fundamental concepts of the domain of quantum mechanics : “microscopic word”
Properties of electromagnetic waves
Wave-particle duality : de Broglie’s wave for a free particle
Double slit experiment
Wave function
Time dependent and time independent Schrödinger equations
Superposition of states ; Postulates of quantum mechanics
2- Quantization
Quantization in an in?nite well (1D, 2D and 3D)
Tunnelling effects
Finite 1D well; Double well
3-Molecular vibrations
Born-Oppenheimer approximation; Separation of the center of mass in a two-body problem
Harmonic oscillators ; Vibration of a diatomic molecules
Vibrational normal modes
Franck-Condon principle
4-Rotations and Hydrogenic atoms
Particle on a sphere
Rigid diatomic rotor; Angular momentum and spin
Hydrogenic atom
5 - Electronic structure of molecules and nanoparticles
Molecular Hamiltonian and Born-Oppenheimer approximation Linear combination of atomic orbitals
Orthogonal and nonorthogonal basis sets, minimal basis set
Molecule orbitals : sigma/pi, overlap
Molecular orbital energies, Koopmans theorem
HOMO-LUMO gap
Mulliken charge, ionisation energy, electronegativity, electron af?nity
Molecular Orbital diagram
Walsh correlation diagram
Extended Hückel Theory
Introduction to Tight-Binding Density Functional Theory.

Elementary Linear Algebra, and Undergraduate Physical Chemistry.

Molecular Quantum mechanics, fourth edition 2005, Peter Atkins and Ronald Friedman, Oxford university press.

Septembre - Octobre - Novembre - Décembre - Janvier.

ORSAY

Heather McLean.

15h of English classes dealing with scientific writing and oral presentations will be dispensed during the first week of the course. These classes will be interspersed with lectures given by native or completely fluent English speakers. The second week of the course is reserved for student presentations and discussions- in English.

A portion of the teaching unit will take the form of formal English classes geared toward preparing students in scientific public speaking. The bulk of the teaching unit will be centered on research and teaching seminars that will be presented by native and fluent English speakers based upon their diverse fields of interest. Regular teaching faculty are supplemented by full-time researchers. Students attend lectures, and discuss the presentations with the lecturers, and write a short report on one of these above said lectures. Students will also present a 45 minute to one-hour seminar in English on a hypothesis-driven research article they select from the literature (in agreement with the course organizer). Discussion, held exclusively in English, will supplement the grades obtained in the formal english classes and the seminar presentation.

Basic knowledge in Biology, English level B1.

Janvier.

ORSAY

Etienne Delannoy (INRA, URGV); V. Brunaud; M(L. Martin-Magniette; Claire Lurin (INRA, URGV), Amin Madoui (CEA, Genoscope), Guillem Rigaill (UEVE, URGV), Jean Colcombet (INRA, URGV).

Lecture Exercises (TD) Quizzs, practicals.

Introduction to the module: From biology to modelling
Experimental functional genomics: ORFeome and interactome.
Transcriptome analysis
From data to knowledge in the framework of genome annotation.
Visit of the transcriptome platform of the Plant Genomics Research Unit.
Chromatin, chromosome and epigenetic
Proteome and phosphoproteome.

Basic notions of Biology.

Novembre - Décembre.

EVRY - JOUY-EN-JOSAS

Matthieu Jules (INRA/AgroParisTech, Micalis), Vincent Fromion (INRA, MIG), Anne Goelzer (INRA, MIG), Vincent Sauveplane (AgroParisTech, Micalis), Laurent Tournier (INRA, MIG).

Lecture Exercises (TD) Quizzs, practicals.

The diversity of biological issues requires the use of several types of mathematical modeling. In this course students will get to explore models enabling to handle in details the cellular network. The methods for the analysis of flux distribution, from constraint-based modeling (Flux Balance Analysis, Resource Balance Analysis, etc.) to dynamical modeling (Ordinary Differential Equations, etc.) are at the core of this course. We will also introduce tools and models enabling to integrate whole cell processes. Finally, we will enlighten the interest of models for metabolic engineering, i.e. in silico based strategy to improve bacterial or yeast cell factories.
Contents :
Introduction to global analysis (omics).
Introduction to the concept of resource allocation and cellular economics.
Lectures on data integration and mathematical modelling.
Tutorial classes in mathematical modeling of cellular metabolism.
Lectures on in silico based strategy of metabolic engineering.

Notions of Mathematics and modelling.

Systems Biology [Textbook], E. Klipp et al, Wiley-Blackwell, 2011. Metabolic engineering in the post genomic era, ed. B.N. Kholodenko, H.V. Westerhoff, Taylor & Francis, 2004.

Décembre.

JOUY-EN-JOSAS

Sébastien Bloyer (PU UPSay), Fabienne Malagnac (PU UPSay), Benoît Moindrot (MCU UPSay) and Pierre Grognet (MCU UPSay) + invited speakers (Université Paris-Saclay).

Lecture Exercises (TD) Quizzs, practicals.

Many biological processes involve epigenetic mechanisms: regulation of transcription (histone code, DNA methylation, non-coding RNAs ...) and translation (interfering RNA), splicing, maintenance of genome integrity, genomic imprinting, X-chromosome inactivation, embryonic development and cellular memory, pluripotency and differentiation of stem cells, etc.
This course will deepen the notions of epigenetic mechanisms and trans-generational transmission of epigenetic information discussed in the Core Courses, focusing on high-throughput and epigenomic aspects.
Students will also discover how epigenetic mechanisms structure and regulate three-dimensional compaction of the genome within the nucleus (3D genome); and the involvement of architecture and nuclear compartmentalization in the many processes of cellular regulation (nuclear foci of transcription or repression, compartments and genomic imprinting, differentiation and reprogramming of stem cells, etc.), in connection with human pathologies (progeria/Hutchinson-Gilford syndrome, metabolic diseases, neurological diseases, cancers, ...) and applications (epigenetic therapies, animal cloning, nutrition, ...).
Aspects of structural inheritances (prions, hysteresis, ...) will also be addressed. Some themes will be presented in the form of conferences by specialized researchers from the various institutes and laboratories.

Basic notions in Biology.

EpiGensSys European Network Website: http://www.epigenesys.eu/fr/ http://www.epigenesys.eu/fr/ Books available at the UPSay Library: Epigenetics, Second Edition – Cold Spring Harbor Laboratory Press - Edited by C. David Allis, Marie-Laure Caparros, Thomas Jenuwein and Danny Reinberg.

Février - Mars - Avril.

ORSAY

Oliver Nusse Hervé Le Stunff Marielle Valério Guillaume Lenoir.

Course : 13h Tutorial Sessions : 10 h Seminar : 2 h.

The plasma membrane is a barrier and a place of exchange between the cell and its environment. This teaching unit is focussed on the biochemical and biophysical properties of membranes and their role in cellular functions. It emphasizes the dynamics of membranes and processes of cell surface modification, secretion and cell signaling. The importance of this dynamic for physiological and pathological processes is illustrated by examples from neuroscience, immunology and endocrinology. Some examples of ongoing research will be presented as a lecture. The unit deals in particular with - The properties of membrane lipids and the organization of membranes into domains - The properties of membrane proteins - The mechanisms of membrane fusion and membrane fission in relation with exocytosis / endocytosis in the synapse, the pancreas as well as the entry / exit of a virus - Modification of membranes in cellular signaling, in particular through lipid kinases and phosphatases - Lipids as signaling molecules - Examples of pathologies concerning the cytoplasmic membrane - Specific methods for the analysis of membrane dynamics.

Basic Notions in Biology.

Molecular biology of the cell Alberts et al. 5th Edition or more recent Molecular cell biology Lodish et al. 5th Edition or more recent Biochemistry Berg et al 5th Edition or more recent.

Février - Mars - Avril.

ORSAY

Philippe Minard ; UPSay ; Karim Benihoud; UPSay Uriel Hazan ; PU ; ENS Paris Saclay Marie-Hélène Kryszke, ENS Paris Saclay.

50 h 20 h CM ; 10 h TD ; 20 h TP.

Environ 20 heures de cours dispensés par des chercheurs et enseignants- chercheurs travaillant dans ces domaines portent notamment sur une introduction générale
à la virologie suivie de conférences sur la vectorologie à visée thérapeutique (rétrovirus,
virus à ADN), la thérapie génique, et l’utilisation des virus procaryotes en génie génétique, illustrée par la technique de présentation phagique (phage display). Une vingtaine d’heures de travaux pratiques viennent compléter cette formation théorique. La première partie des travaux pratiques est une initiation à la rétrovectorologie au cours de laquelle des vecteurs rétroviraux sont produits et utilisés pour transduire le gène codant la GFP (green fluorescent protein) au sein de cellules cibles murines. Un roulement permettant aux étudiants d’effectuer les expériences en laboratoire de culture cellulaire par petits groupes est organisé. La deuxième partie des travaux pratiques illustre l'utilisation des bactériophages en génie génétique, avec la sélection et l'isolement de phages présentant des anticorps dirigés contre l'ubiquitine. Enfin, les étudiants présentent des articles de recherche portant sur des avancées récentes dans les domaines précédemment évoqués.

Formation de base en biologie. Connaissance de la langue francaise.

Principles of Virology », S.J. Flint et al., ASM Press.

Janvier.

GIF-SUR-YVETTE

Emilie Guillaume; Pascale Rialland-Lefèvre; Jean-Marc Ricort.

Cours (22h), TD (15 h) et TP (13h) Session 1 : Examen écrit 2h (2/5 de la note finale), présentation orale (3/10 de la note finale), TP (3/10 de la note finale) ; Session 2 : Examen écrit (2 h - coefficient 2/3) et TP (report de la note de contrôle continu de TP de première session, coefficient 1/3).

L’objectif de l’UE est de décrire les aspects structuraux et fonctionnels du cytosquelette. Les structures sont décrites au niveau moléculaire et supramoléculaire en insistant sur les aspects dynamiques. Les aspects fonctionnels intègrent entre autres la multiplication cellulaire ainsi que les processus d’adhérence et de motilité. La première partie des enseignements est consacrée à la description des différents éléments du cytosquelette, à leur dynamique et à leur implication dans les fonctions cellulaires clés impliquant le cytosquelette, ainsi qu’aux outils d’imagerie indispensables à l’étude du cytosquelette. La seconde partie des enseignements permet d’illustrer le rôle du cytosquelette et les modifications de sa dynamique dans le système immunitaire, l’infection virale et la transformation maligne. Le TP associé est l’illustration pratique de certains des éléments donnés dans le cadre des CM et permet de mettre en œuvre les méthodes d’analyse classiques en biologie cellulaire : marquages fluorescents et imagerie. Cette UE a pour objectif de fournir aux étudiants un socle de connaissances solide sur la structure et la dynamique des différents éléments du cytosquelette ainsi que sur l’implication du cytosquelette dans différentes situations physiologiques et pathologiques. La partie pratique a par ailleurs pour objectif de familiariser les étudiants avec les principales méthodes d’analyse du cytosquelette en imagerie ainsi qu’avec la culture de cellules animales.

Formation de base en biologie,. Connaissance de la langue française.

Ray. H. Gavin : Cytoskeleton : Methods and protocols, Humana Press.

Novembre - Décembre.

GIF-SUR-YVETTE

Clémence Richetta.

Il s'agit d'une série de travaux pratiques qui seront évalués comme suit : Première session : Présentation orale (1/2 de la note finale), TP (1/2 de la note finale) ; Deuxième session : Examen écrit (1h30).

Cette UE de travaux pratiques a pour objectif d’initier les étudiants à des techniques de biologie cellulaire et moléculaire couramment utilisées en virologie.
Dans une première partie, les étudiants étudieront les propriétés fusogèniques des protéines d’enveloppe du virus de la Rougeole par des techniques de biologie cellulaire et des techniques d’imagerie.Dans une seconde partie du TP, les étudiants travailleront sur un modèle de rétrovirus : le VIH. L’objectif sera d’étudier la régulation de la transcription à partir des LTR contenant le promoteur viral. Pour cela, des cellules seront transfectées avec des plasmides codant des gènes rapporteurs fluorescents sous le contrôle des LTR. Les étudiants analyseront l’impact de différentes mutations du LTR sur la transcription des gènes rapporteurs en suivant l’expression de ces derniers par cytométrie en flux. Les étudiants apprendront également à manipuler les VLP (Virus-Like-Particles). Par ailleurs, le travail sur les VLP permettra d’étudier les mécanismes d’assemblage du VIH. Les étudiants devront réaliser, en binôme, des exposés portant sur des techniques utilisées en virologie mais utilisées en biologie cellulaire et moléculaire, par exemple sur l’application des VLP en laboratoire, les méthodes d’imagerie des virus ; la méthode CRISPR/cas9. Des conférences pourront venir compléter cette formation.

Notions de base en biologie expérimentale Connaissance de la langue française.

Décembre.

GIF-SUR-YVETTE

Michel SIMONNEAU, ENS Paris Saclay; Jean Livet, Inserm; Jérôme Yelnik, INSERM; Laure Bally-Cuif, CNRS: C. Neri, Inserm ; Lydia Langlot, Inserm ; Marie-Claude Potier, CNRS; Cécile Martinat, Inserm.

CM : 25h, TD : 25h Mode de contrôle des connaissances: Examen écrit 2h (coefficient 0,7), présentation orale (coefficient 0,3) Deuxième session : Examen écrit (2h) Admission à l'UE après candidature sur dossier.

Ce cours de deux semaines sera axé sur la physiopathologie des maladies psychiatriques et neurodégenératives qui sont des maladies communes (prévalence> 1% de la population, pour chacune d’entre elles ; 50% pour la population âgée de plus de 85 ans dans le cas de la maladie d’Alzheimer). Ces dernières années ont vu de grandes avancées dans la compréhension des bases de leur physiopathologie, avec la mise au point de stratégies génétiques (étude sur génome entier ; GWAS pour Genome-Wide Association Study), de nouveaux modèles animaux, d’approches de biologie des systèmes et la mise au point de neurones humains dérivés des fibroblastes des patients (iPSC pour Induced Pluripotent Stem Cell).
Organisation de cet enseignement :
Seront présentés les bases physiopathologiques de ces maladies communes à partir des connaissances les plus actuelles en neurosciences moléculaires, cellulaires et intégrées ainsi que les méthodes d’étude de ces maladies.
Thématiques des cours :autisme, addiction, schizophrénie, troubles bipolaires, maladies neurodégénératives de type Parkinson et Alzheimer, modèles animaux, neurones dérivés des fibroblastes, génétiques des maladies complexes.

Formation de base en biologie Connaissance de la langue française.

Janvier.

GIF-SUR-YVETTE

Catherine Colin, Fanny Domenec.

The course is taught in 10 lessons of 3 hours each. Students will have to give an oral presentation in groups, and take a written exam at the end of the course. Attendance and participation in class will also be assessed.

The course will focus on academic and scientific English. Students will become more familiar with academic talks and scientific writing.
The course will also provide learning strategies and resources to help students improve their English on their own.

At least B1 level in English.

Septembre - Octobre.

GIF-SUR-YVETTE

Marie Caroline JULLIEN (ESPCI) : Physics in microfluidics - Valérie GENOT (PPSM): Practical in microfluidics and chemistry - Rasta Ghasemi (IdA) : Elaboration of microfluidics circuitry - Abdel EL-ABED (LPQM) : Microtechnologies in Microfluidics and Digital microfluidics - Jean Pierre LEFEVRE (PPSM) : Microfluidics platform responsible.

28 hours for lecture, 12 hours for lab work.

I. Introduction
- Concept of Microsystems : case of BioMEMS and microfluidic
- Scaling laws in Microsystems
II. Microtechnologies and Microfluidic
- Clean room, Photolithography and Microelectronics technology
- Microfluidic technology : glass, silicon, polymer (moulding-casting)
- Case study : Micromixer and MicroPCR
III. Physics of microfluidic (12h MCJ)
- Microhydrodynamics : continues microfluidics
- Capillarity: digital microfluidcs - Droplet
- Electro-hydrodynamics (EHD)
- Mixing and sorting in microfluidics
V Practical training
- Lab1 : Microfluidic design with the help of Comsol ©
- Lab2 : Fabrication and testing of a micromixer in PDMS
- Lab3 : Droplet generator and phase diagram characterisation.

General background in physics or chemistry.

Fundamentals and applications of Microfluidics, Nguyen and Wereley, Artech House Introduction à la Microfluidique, P. Tabeling, Belin Theoretical Microfluidics, H. Bruus, Oxford University Press.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bruno Le Pioufle, Pamela Didier.

The course is organized in 28 hours of lectures and 12 hours of practical work.

1.DNA chip :concept of successive photoexposures to develop high throughput chips
2.Soluble protein chips- electrospray generation in a chip, 2D electrophoresis on a chip
3.Membrane protein biochips
Basics in electrophysiology, Huxley model of action potential propagation, Simulation of the Action potential (practicals), Main systems for ion channel recording, patch clamp, planar patch clamp, population patch clamp, artificial lipid bilayers Sructure and fabrication of membrane protein chip, physical properties, Membrane Protein insertion in LBM. Liposomes, Giant liposomes, electroformation.
4.Cell biochips –
use of electrical field or other means to handle, sort, or treat cells. Dielectrophoresis trapping, optical traps, fluidic aspects, cell arraying, electroporation on a chip.
5.Practicals – Laboratory
Simulation of the action potential (4h), Dielectrophoresis force simutation with finite element analysis (4h), Dielectrophoresis on a chip (4).

This course is open to multidisciplinar background students. There is thus no mandatory prerequisites.

Miller, C. Ion Channels Reconstitution; Plenum Press, 1986.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Ngoc Diep Lai; Bruno Palpant, Clément Lafargue.

30 hours lectures. Writing exam, based on scientific papers (duration: 3 hours).

PART ONE: Photonic crystals/nonlinear photonic crystals and applications
1D, 2D, and 3D photonic crystals: theory, simulation, photonic quasi-crystals
Photonic crystal with defect and applications
Nonlinear photonic crystals
Fabrication technologies and applications
PART TWO: Plasmonic effects
Electromagnetism and optics in bulk noble metals: Electromagnetism survival kit; Bulk noble metals: Electronic properties, optical response
Localised plasmon in metal nanoparticles: Mechanical analogy: driven damped linear oscillator; Dielectric confinement; Surface plasmon resonance; local field enhancement; applications for Surface-enhanced Raman scattering or fluorescence; bio-labelling; Effects of nanoparticle environment, size, shape and composition; Coupling between nanoparticles.Transient optical response and nanoscale light-heat conversion.
Selected applications: Light-heat conversion: Nanoscale hyperthermia against cancer, drug or DNA delivery, laser damage and laser shaping, photothermal imaging, optical limitation; Plasmonics for high-speed nanophotonics; Plasmonics for nonlinear optics
Part THREE : Laser physics.

Optical physics and electromagnetism (L3 level), basic mathematical physics notions in classical and quantum mechanics (L3 level), and Light-matter interactions course (M1 level).

Photonic Crystals: Molding the Flow of Light, second edition John D. Joannopoulos, Steven G. Johnson, Joshua N. Winn, and Robert D. Meade Published in 2008 by Princeton University Press.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bernard Journet.

22 hours lectures, 28 hours practicals Written exam.

Microwaves
Transmission lines in case of distributed element model, Smith chart
S parameters.
Impedance matching, amplifier design, simulation software ADS
Measurement techniques (network analyser)
Single conductor waveguides (TE and TM modes), dispersion
Optical telecommunications
1/ Optical fibres: determination of the different modes
Dispersion and absorption phenomena
Fabrication process
2/ Optical digital transmitters and receivers, optical amplification
Digital data transmission, different standards
Wavelength division multiplexing (WDM) technique, dispersion effects.

Basic knowledge about electrical and optical fundamentals; Maxwell's equations in vacuum. Complex numbers; Mathematical operators; Fourier analysis.

D. M. Pozar, "Microwave engineering", Wiley Ed. K. Zhang, D. Li, "Electromagnetic theory for microwaves and optoelectronics", Springer Ed.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Marco PASI.

14 hours for lectures, 16 hours of practical exercises.

CM:
1.Theoretical bases of molecular mechanics
Biomolecular empirical force fields : principles, approximations, common functional forms, the solvent, performance considerations, applications.
2.Sampling the potential energy surface
Algorithms and techniques (minimisation, Monte Carlo, molecular dynamics)
3.Simulating biological phenomena
Using simulation to compute ensemble properties, state-of-the-art applications in biology comparing simulation and experiment (NMR, AFM, cryo-EM, FRET, …)

TP:
4.Molecular visualization
Using molecular viewers to study the structure, interactions and dynamics of biomacromolecules
5. Molecular simulation software architecture
Configuration files and execution scripts, interacting with the software using the command line
6. Setting up your first MD simulation
From static structure to trajectory in physiological conditions ; study cases selected from examples in the "Nanophotonics" or "Biophotonics" courses ?
7. MD Trajectory analysis and comparison with experiment
Extracting useful information from the trajectory to evaluate simulation quality, compare with experiment and shed light on molecular mechanisms.

The four “Fundamentals” courses (or equivalent prior knowledge), “Molecules and Interactions”.

Molecular Modelling: Principles and Applications (Pearson Education, 2001), A. Leach; Understanding Molecular Simulation: From Algorithms to Applications (Academic Press, 1996) D. Frenkel & B. Smit.

Février - Mars.

ORSAY

Ngoc Diep Lai.

28 hours of lectures. Written exam (3 h).

Short overview of nonlinear optics
Introduction to nonlinear optics :a classical model for nonlinear effects
Nonlinear of bulk systems – coupled-wave theory, propagation equation
A fully treated useful example : non-resonant second-harmonic generation, phase matching and phase, mismatching
Second-order and third-order nonlinear optics
Second-harmonic and third harmonic generation, Parametric amplification, Pockel and Kerr effects, etc.
Nonlinear optics in micro- and nano-structures
Quasi-phase matching technique: structures 1D, 2D and 3D
Nonlinear photonic crystals: perfect phase matching.
Fabrication and applications of nonlinear photonic crystals
Nonlinear microscopies and nanoscopies
What does (or does not) matter from bulk to nanoscale
Multi-photon microscopies in nanophotonics and biosciences: SHG, TPFE, THG, T3FE, CARS, EO, STED, structured illumination, ...

Optical physics and electromagnetism, Laser (L3 level).

Nonlinear Optics » by R. Boyd.

Septembre - Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Chi Thanh Nguyen.

50 hours of lectures Homework reports (1/3 of weight of.

: This course, which is devoted to photonic devices for applications in the domains of optical communications and sensing, covers both theoretical and practical aspects of the physics of photonic devices, the fabrication and the characterization techniques of these devices, which are based on organic materials. It also introduce to the molecular photonics in some organic active materials. Applications of polymer-based photonic devices in optical communications and optofluidic devices in biochemical sensing will be finally presented.
Background of wave optics and photonics
Base of waveguide optics
Introduction to organic materials for photonic devices
Polymer-based electrooptic devices for optical communications
Polymer-based optofluidic devices for sensing.

Wave optics and electromagnetism in matter.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Ngoc Diep Lai.

Rotation of students to visit all experiments. Equivalent to a Practical in two groups.

1.Geometrical Optics: mirrors (concave, convex), lenses, microscope, light source, etc…

2.Interference and Diffraction: Fabry-Perot cavity, diffraction of different objects (grating, ball, etc.), interference of two beams, multiple beams, etc.

3.He-Ne Laser: build on a laser yourselfOptical physics and electromagnetism (L3 level). In order to choose this practical work, students should study two courses: Light-matter interactions (basics level) and Nonlinear Optics.

4.Nonlinear Optics: second-harmonic generation, one- and two-photon absorptions.

Optical physics and electromagnetism (L3 level). In order to choose this practical work, students should study two courses: Light-matter interactions (basics level) and Nonlinear Optics.

Janvier.

GIF-SUR-YVETTE

Marco PASI.

8 hours of lectures, 20 hours of practical work in a dedicated room in Paris Sud (Orsay).

1. Programming Python basics
Data types, control structures, lists, hashes, files
2. Good practices of collaborative scientific software development
The scientific development cycle in Jupyter notebooks, writing and distributing modular packages, Git and Github, documentation, testing, continuous integration
3. Analysing massive data using numpy, scipy and pandas
Representing, storing and sharing matrix data, indexing/slicing/iterating, vectorization, dataframe operations, basic statistics
4. Data visualisation using numpy, pandas and matplotlib
Visualising data for exploration and for publication, data science traceability and reproducibility, literate programming and executable papers
5. Personal/group project
Prepare a report about the statistical exploratory analysis of real dataset (chosen by students or proposed by the teacher).

Fundamentals in Mathematics” (or equivalent prior knowledge), some basic statistics.

Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython (O’Reilly, 2011) W. McKinney.

Décembre - Janvier - Février.

ORSAY

Jean-Pierre Barbot, Eric Vourc'h.

50 hours of lectures.

Signal processing fundamentals
- Introduction and definitions
- Classification
- Deterministic signals
- Random signals
- The signal processing for digital communications
- Introduction to digital communications
- The baseband transmission
- The source coding
- The in line coding
- The channel Coding
- The transmission over a carrier frequency
- The digital modulations and demodulations.

No special prerequisites.

Octobre - Novembre - Décembre - Janvier.

GIF-SUR-YVETTE

Bruno Le Pioufle, Cécile Legallais, Abdul Barakat, Olaf Mercier, Anne Dubart-Kupperschmitt, Ulysse Pereira, Emmanuel Martinod, Etienne Bur, Nicolas Ferry, Frédéric Worms.

The course is organized in the form of a 3-days workshop with sessions corresponding to the different aspects of the program as described above.

This module will cover the various aspects of tissue and organ bioengineering, a promising perspective to replace damaged human organs (e.g. liver) by natural organs elaborated using bio-engineering procedures starting from cell of the patient himself, then preventing from organic rejection of organs provided by other individuals, and bringing a valuable solution of the permanent lack of organs for grafting.
The module is organized in sessions devoted respectively to
-Cells : general presentation ; Spheroids : a first step for a bioengineered liver; Industrial production of mature cells
-Matrices and scaffolds : Natural and Artificial matrices; Fabrication of liver microtissues; Recellularization of biological scaffolds
-Bioprinting : Micropatterning ; Bioimpression techniques ; Modelling tissue and organ.
-On-chip strategies : Principes and introduction to organ on chips; Liver tissue on chip; : Vascular system on chip ; Predictive toxicology.
-Organogenesis and vascularisation of constructs
-Extracorporal systems : extracorporal Spleen ; Artificial lung; Encapsulation in extracorporeal system; Extracorporeal liver system
-Clinical applications : Vessels reconstruction using microfluidics ; Skin reconstruction ; Retinal reconstruction ; Tracheal reconstruction ; Biofabrication of fingers and hands ; Cardiac repair.
-Regulations/economics
-Ethics.

Basic notions in Biology.

Avril.

Eric Deprez, Sophie Brasselet, Olivier Delelis, Patrick Tauc.

28 hours of courses 22 hours of exercises and practical work.

Course (28 hours) :
oIntroduction to fluorescence in Biology. Principles of steady-state and time-resolved measurements. Influence of solvent polarity on emission spectra. Quenching of fluorescence…
oIntrinsic and extrinsic fluorophores, new photonic probes for Biology, quantum dots and applications in biology.
oIntroduction to Nonlinear Optics and lasers in Biological studies.
oFluorescence anisotropy and applications in studies of interactions between biological macromolecules.
oFluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy.
oTechniques of fluorescence imaging microscopy and confocal analysis. TIRF microscopy. Multiphotonic microscopy and analysis. Introduction to super-resolution microscopy (STED, PALM).
oFluorescence resonance energy transfer (FRET), principles and applications. Fluorescence lifetime imaging microscopy (FLIM), FRET/FLIM for studying protein-protein interactions in the cell context.
oOn the use of fluorescence in genomic studies: DNA technology, sequencing, quantitative PCR, FISH (Fluorescence In Situ Hybridization).
Instrumentation and analysis of research articles (22 hours) :
oInstrumentation for fluorescence spectroscopy / generalities. Example of a time-correlated single-photon counting experiment. FCS set-up (5H). Presentation of a confocal microscope and multiphoton microscopy (5H).
oAnalysis of research articles (Confocal imaging, FLIM, FRET, Fluorescence anisotropy,…).

A background in Biology is preferable (non-biologists have to take the “Fundamentals in Biology” course).

Joseph R. Lakowicz, Principles of fluorescence spectroscopy. Springer (2006).

Février - Mars.

GIF-SUR-YVETTE

Keitaro NAKATANI, Nicolas Bogliotti, Pierre Audebert, Luca Polacchi, Carine Julien-Rabant.

48 hours courses Written exam.

1.Molecules and Light Interactions, Photophysical Processes
Molecular orbitals and energy levels: Selection rules and phenomenological description: Electric dipole transitions.
Unimolecular photophysical processes: Introduction, relaxation processes, Radiationless and Radiative deactivation processes.
Experimental setups: Steady-state and Lifetime measurements. Quenching of excited states, Photoinduced energy transfer.
2.Complexation, Supra- and Inter-molecular Interactions
Inter-molecular interactions: Molecular dipoles, Ionic and Dipolar interactions, H-bond
Complexation: Lewis acids and bases, Complexation, d-orbitals and ligand field theory, Chelate and template, Examples and properties of complexes.
Examples of supramolecular assemblies involving complexation and/or inter-molecular interactions.
3.Interfacial chemistry, Electrochemical processes
Introduction to electrochemistry: Electrodes and electrolytes.
Thermodynamics of electrochemical reactions: Nernst equation, Galvanic vs. electrolytic cells.
Electrochemical kinetics: Rate of electrochemical reactions, the Butler-Volmer equation.
Fast vs. slow electrochemical systems, Morphology of the I(E) curve in steady-state conditions, Application to corrosion.
4.Polymers
Introduction: Basic definitions, Fundamental examples.
Properties: Molar mass, Glass transition, Mechanical properties.
Polymerization reactions: Step polymerization, Chain polymerization, Kinetics.
Examples: Photopolymers, Composites, Natural polymers.

For non-chemists, the “Fundamentals in Chemistry” course is required.

Molecular Interactions (Waterstone, 2012), D. Micha. Electrochemistry: Principles, Methods, and Applications (Oxford Science Publications, 1993), C. M. Brett, A. M. Oliveira Brett. Physical Chemistry (Oxford University Press, 2009), P. Atkins.

Février - Mars.

GIF-SUR-YVETTE

Ngoc Diep LAI.

At least 20 weeks devoted to a research project in an research Laboratory. Choice of host laboratory must be approved by Prof. Lai. Authorized places to prepare Master Internship : - Students with a ENS Paris-Saclay scholarship : in a ENS Paris-Saclay laboratory ONLY - Students with a scholarship from Paris-Saclay : in a Paris-Saclay University laboratory - Students without scholarship : anywhere in the world ! Intermediate report: one page of summary of the middle internship, showing the progress of their work. Deadline for this middle report : April 26. Final thesis: deadline is 6 July (two weeks before defense). Length of the final Thesis : maximum 25 pages, including references and Table of contents. Size < 16 Mb in order to upload to the elearning website.

Defence is organized at the end of July. Duration of presentation : 25 minutes maximum (to be followed by 20 minutes of questions by the jury). The jury will be made of one expert in the field of the internship and at least two MONABIPHOT teachers.

Master Thesis on any topic related to the program of the MONABIPHOT Master course.

The student must have completed his First semester of the MONABIPHOT M2 Master course.

Février - Mars - Avril - Mai - Juin - Juillet.

ORSAY - EVRY - GIF-SUR-YVETTE - CHATENAY - VERSAILLES - PARIS - PALAISEAU - JOUY-EN-JOSAS

Heather McLean.

15h of English classes dealing with scientific writing and oral presentations will be dispensed during the first week of the course. These classes will be interspersed with lectures given by native or completely fluent English speakers. The second week of the course is reserved for student presentations and discussions- in English.

A portion of the teaching unit will take the form of formal English classes geared toward preparing students in scientific public speaking. The bulk of the teaching unit will be centered on research and teaching seminars that will be presented by native and fluent English speakers based upon their diverse fields of interest. Regular teaching faculty are supplemented by full-time researchers. Students attend lectures, and discuss the presentations with the lecturers, and write a short report on one of these above said lectures. Students will also present a 45 minute to one-hour seminar in English on a hypothesis-driven research article they select from the literature (in agreement with the course organizer). Discussion, held exclusively in English, will supplement the grades obtained in the formal english classes and the seminar presentation.

Basic knowledge in Biology, English level B1.

Janvier.

ORSAY

Etienne Delannoy (INRA, URGV); V. Brunaud; M(L. Martin-Magniette; Claire Lurin (INRA, URGV), Amin Madoui (CEA, Genoscope), Guillem Rigaill (UEVE, URGV), Jean Colcombet (INRA, URGV).

Lecture Exercises (TD) Quizzs, practicals.

Introduction to the module: From biology to modelling
Experimental functional genomics: ORFeome and interactome.
Transcriptome analysis
From data to knowledge in the framework of genome annotation.
Visit of the transcriptome platform of the Plant Genomics Research Unit.
Chromatin, chromosome and epigenetic
Proteome and phosphoproteome.

Basic notions of Biology.

Novembre - Décembre.

EVRY - JOUY-EN-JOSAS

Matthieu Jules (INRA/AgroParisTech, Micalis), Vincent Fromion (INRA, MIG), Anne Goelzer (INRA, MIG), Vincent Sauveplane (AgroParisTech, Micalis), Laurent Tournier (INRA, MIG).

Lecture Exercises (TD) Quizzs, practicals.

The diversity of biological issues requires the use of several types of mathematical modeling. In this course students will get to explore models enabling to handle in details the cellular network. The methods for the analysis of flux distribution, from constraint-based modeling (Flux Balance Analysis, Resource Balance Analysis, etc.) to dynamical modeling (Ordinary Differential Equations, etc.) are at the core of this course. We will also introduce tools and models enabling to integrate whole cell processes. Finally, we will enlighten the interest of models for metabolic engineering, i.e. in silico based strategy to improve bacterial or yeast cell factories.
Contents :
Introduction to global analysis (omics).
Introduction to the concept of resource allocation and cellular economics.
Lectures on data integration and mathematical modelling.
Tutorial classes in mathematical modeling of cellular metabolism.
Lectures on in silico based strategy of metabolic engineering.

Notions of Mathematics and modelling.

Systems Biology [Textbook], E. Klipp et al, Wiley-Blackwell, 2011. Metabolic engineering in the post genomic era, ed. B.N. Kholodenko, H.V. Westerhoff, Taylor & Francis, 2004.

Décembre.

JOUY-EN-JOSAS

Sébastien Bloyer (PU UPSay), Fabienne Malagnac (PU UPSay), Benoît Moindrot (MCU UPSay) and Pierre Grognet (MCU UPSay) + invited speakers (Université Paris-Saclay).

Lecture Exercises (TD) Quizzs, practicals.

Many biological processes involve epigenetic mechanisms: regulation of transcription (histone code, DNA methylation, non-coding RNAs ...) and translation (interfering RNA), splicing, maintenance of genome integrity, genomic imprinting, X-chromosome inactivation, embryonic development and cellular memory, pluripotency and differentiation of stem cells, etc.
This course will deepen the notions of epigenetic mechanisms and trans-generational transmission of epigenetic information discussed in the Core Courses, focusing on high-throughput and epigenomic aspects.
Students will also discover how epigenetic mechanisms structure and regulate three-dimensional compaction of the genome within the nucleus (3D genome); and the involvement of architecture and nuclear compartmentalization in the many processes of cellular regulation (nuclear foci of transcription or repression, compartments and genomic imprinting, differentiation and reprogramming of stem cells, etc.), in connection with human pathologies (progeria/Hutchinson-Gilford syndrome, metabolic diseases, neurological diseases, cancers, ...) and applications (epigenetic therapies, animal cloning, nutrition, ...).
Aspects of structural inheritances (prions, hysteresis, ...) will also be addressed. Some themes will be presented in the form of conferences by specialized researchers from the various institutes and laboratories.

Basic notions in Biology.

EpiGensSys European Network Website: http://www.epigenesys.eu/fr/ http://www.epigenesys.eu/fr/ Books available at the UPSay Library: Epigenetics, Second Edition – Cold Spring Harbor Laboratory Press - Edited by C. David Allis, Marie-Laure Caparros, Thomas Jenuwein and Danny Reinberg.

Février - Mars - Avril.

ORSAY

Oliver Nusse Hervé Le Stunff Marielle Valério Guillaume Lenoir.

Course : 13h Tutorial Sessions : 10 h Seminar : 2 h.

The plasma membrane is a barrier and a place of exchange between the cell and its environment. This teaching unit is focussed on the biochemical and biophysical properties of membranes and their role in cellular functions. It emphasizes the dynamics of membranes and processes of cell surface modification, secretion and cell signaling. The importance of this dynamic for physiological and pathological processes is illustrated by examples from neuroscience, immunology and endocrinology. Some examples of ongoing research will be presented as a lecture. The unit deals in particular with - The properties of membrane lipids and the organization of membranes into domains - The properties of membrane proteins - The mechanisms of membrane fusion and membrane fission in relation with exocytosis / endocytosis in the synapse, the pancreas as well as the entry / exit of a virus - Modification of membranes in cellular signaling, in particular through lipid kinases and phosphatases - Lipids as signaling molecules - Examples of pathologies concerning the cytoplasmic membrane - Specific methods for the analysis of membrane dynamics.

Basic Notions in Biology.

Molecular biology of the cell Alberts et al. 5th Edition or more recent Molecular cell biology Lodish et al. 5th Edition or more recent Biochemistry Berg et al 5th Edition or more recent.

Février - Mars - Avril.

ORSAY