Parcours Physics of Complex Matter Parcours International 2e année

This course is an introduction to complex interacting systems. It provides the theoretical tools for the stochastic and deterministic descriptions of the time evolution of interacting systems, and the understanding of the dynamical response of systems in microscopic terms.

Content:

• Introduction: Equilibrium and non-equilibrium statistical mechanics with
  some examples, general overview;
• Stochastic variables;
• Brownian motion and Langevin equation;
• The Fokker-Planck equation;
• The Master equation;
• Introduction to stochastic thermodynamics;
• Linear response theory and correlation functions;
• Non equilibrium thermodynamics and Onsager relations.

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Goal

Complex fluids are mixtures of different materials and fluids. Usually, we consider the coexistence between two phases: solid–liquid (like suspensions or solutions of polymers, proteins or DNA), solid–gas (like granular materials), liquid–gas (like foams) or liquid–liquid (like emulsions). Complex fluids exhibit unusual mechanical responses to applied stress or deformation. The mechanical response includes non-linear behaviors such as shear thinning or shear thickening as well as large fluctuations (elastic turbulence). The mechanical properties of complex fluids can be attributed to characteristics such as polymer unfolding, caging, or clustering on multiple length scales. The course deals mainly with two kinds of complex fluids: polymer fluids and suspensions.

Content:

1. Introduction to Complex fluids in nature and in industry
2. Conservation laws. Matter, Momentum and Energy
3. Standard flows (Poiseuille flow, Couette flow).
4. Dissipation
5. Polymer fluids

• Non-linear fluids and shear dependent viscosity
• Normal stresses and Weissenberg experiment
• From nano to macro: starting from a polymer chain to macroscopic properties

6. Suspensions

• Rheology
• Homogenization
• Taylor dispersion
• Active suspension (natural and artificial nano and micro-swimmers)

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Goal: The aim of the lecture is to give an overview of the neutrons based and X-ray based techniques suitable for the study of soft matter at the nanoscale.

Content: The first part of the lecture will go into details of the dynamical structure factor S(Q,w), its relations with the properties of the materials, and how it can be extracted from short length scale radiation scattering.

The second part will focus on more specific techniques such as small angle scattering and reflectometry for structural investigations, inelastic and quasi-elastic scattering for the study of the dynamics, and the complementarity between the different radiations. Instrumental aspects of the last generation of instruments developed at large scale facilities will be presented.

The last part will describe the most advanced X-ray techniques based on absorption (ASAXS, EXAFS, GISAXS….) and coherent imaging (CXDI, pychography…).

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Goal: Nanomechanics is an important part of applied nanotechnology, This course will provide a working knowledge of nano-mechanics and nano-tribology emphasizing the role of surfaces,  interfaces, defects, roughness, and quantum effects. Nano-mechanical measurements techniques and applications in micro-electronic technologies and nano-manufactoring will be developped.

I. Overview and preliminaries.
     Surface interactions ; Van der Waals long range forces ; Derjaguin approximation, measuring surfaces forces  SFA AFM.

II. Mechanics of solid contacts.
     Single contact: Herz contact ; mechanics of adhesive contacts.
     Statistics of contacts: Greenwood-Williamson model ; elasto-plastic contact 

III. Friction an lubrication
     Amonton's law and Coulomb friction ;  Tabor 's model of friction. Static and dynamic friction ; stick-slip ; Rice and Ruina law's of friction.  Lubrication regimes, Reynolds equation, squeeze film lubrication. Exercice class.

IV. Applications in micro-electronics 
     MEMS & NEMS applications                                                                                            Direct bonding, wetting ;  bonding wave dynamics
     Mechanics of fracture ; smartcut process

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From 2004, ESONN is a two-week course aimed at providing training for graduate students, postdoctoral and junior scientists from universities and laboratories, all around the world, in the field of Nanosciences and Nanotechnologies.    https://www.esonn.fr

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Introduction to the statistical learning theory and prediction (regression/classification)

• Review of Models/Algorithms for supervised/unsupervised learning
• Illustration de ces algorithmes sur différents jeux de données on different dataset
  (intelligence artificielle, Bioinformatics, vision, etc ...)

Content:

• General introduction to the statistical learning theory and prediction (regression/classification)
• Generative approaches: Gaussian discriminant analysis, naïve Bayes hypothesis
• Discriminative approaches: logistic regression
• Prototype approaches: support vector machines (SVM)
• Unsupervised classification (kmeans and mixture model)
• Dictionnary learning / Sparse reconstruction
• Source separation

This course is given at Phelma-INP.

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The aim of this course is to cover numerical methods that are widely used in soft matter. The course will focus in particular on molecular dynamics, and a small numerical project (Python, C or C++) will be required on this theme. 
Students wishing to take this course are required to have some knowledge of Python, C or C++.

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The Second year Research Training can take two different forms:

- 10 half-days spent in identified labs on recurrent subjects proposed by the coordinator of the teaching unit ;

- a part-time internship in a lab of the Grenoble area, representing more or less 1 day each week during a semester. In can be on the same subject as the M1 internships and/or of the future M2 internships, allowing a continuous immersion in a laboratory on a given for the whole duration of the master program. Students joining the program in M2 can also follow this program but they must readily find a welcoming lab by themselves prior to their arrival in Grenoble or at the very beginning of the academic year.

In both cases, the module is evaluated through a short report followed by an oral examination, in which students expose their research objectives, implementation, and results, and answer to the questions of the jury.

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This course will be focused on the main nanofabrication and characterization techniques used in clean-rooms in research laboratory and semi-industrial environments for the fabrication of current and future semiconductor devices. It will combine regular lectures and a practical training on nanobiotechnology in clean room facilities.

Outline
This course will include a first part covering the main nanofabrication and characterization techniques used in clean-rooms and
a second part dedicated to a practical training.

• The first part will be taught as regular lectures. The principles of these techniques will be presented and illustrated through concrete examples obtained in the clean-rooms of the Minatech Campus in Grenoble. This course will provide you with the basics of technological steps, thin film deposition techniques, lithography processes, and advanced characterization used during the fabrication of single devices up to their large-scale integration.
• The practical training (second part) will consist in the construction of a micro-patterned device using state-of-the art microfabrication techniques. Fluorescently marked cells will be deposited on the constructed micropatterns and different cell.

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This course will be dedicated to advanced characterization techniques of nanostructures. It will cover electron microscopy techniques (electron diffraction, loss spectroscopy, imaging), X ray spectroscopy and scattering techniques and Synchrotron radiation measurements.

Content

X-ray scattering (from single electron to periodic material, anomalous scattering)
Reciprocal space (reminder +
Surface sensitive X-ray scattering
X-ray absorption fine structure
Examples of application : strain and composition determination, in situ studies of growth
Introduction to the X-ray synchrotron radiation production (including the forth generation source like the ESRF Extremely Brilliant Source)
Coherent X-ray scattering and X-ray photon correlation spectroscopy
The basis of electron microscopy
Electron diffraction and Electron loss Spectroscopy
Imaging and chemical sensitivity (Transmission Electron Microscopy and Scanning Transmission Electron Microscopy)
Case studies

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This course is a series of lectures that could be given in a thematic research school, ie at the intersection of training in a field and the presentation of the latest advances in it.

It consists in a weekly seminar on subjects related to condensed matter studied at the nanometer scale, highlighting fields of active research in soft condensed matter. 

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Goal: From the sequencing and electronic analysis of single molecules, to waste water treatment, desalinisation, or osmotic energy harvesting, , nanopores and membranes technologies are a rapidly growing area of nanosciences with increasing applications in the fields of sustainable energy, environment, and nanobiotechnologies. The aim of the course is to provide the theoretical concepts governing the transport of fluids, ions and molecules in nanochannels and confined spaces.  It will highlight the new properties and functionnalities which arise from the interplay of surface interactions in solutions,  flow and transport.

 Content:
1. A general overview of nanopores and membrane technologies.
2. The basics of surface transport in fluids
     . Flow and diffusion at a nano-scale
     . Ions and molecule surface interactions in fluids
3. Coupled transport at surfaces and in nano-channels.
      Electro-osmosis, diffusio-osmosis and beyond
      Weak out-of-equilibrium limit and Onsager relations
      From nano properties to macroscopic efficiency
      Example of application: energy harvesting/conversion     
4. Non-linear and rectification effects.
     Nano-fluidic diodes, osmotic diode, and transistor.
5. Nano-pores for single molecules transport and detection
6. Membranes for fuel cells.

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The active material is made up of a large number of active living or artificial agents, each of which consumes energy to move and exert forces on other agents. The most important example is the plankton which represents the largest biomass on earth. Such systems are inherently out of thermodynamic equilibrium. The examples of active ingredient are very numerous and cover a wide range of length scales. At the nanoscale, important examples are biopolymers and microtubules in biology as well as synthetic janus nanoparticles and microparticles. On a larger scale, active systems are micro-organisms (plankton, bacteria), schools of fish, crowds of pedestrians and swarms of birds. Active matter is a relatively new material classification of soft matter: the most studied model, the Vicsek model, dates from 1995.

Active matter research includes hydrodynamics, kinetic theory and non-equilibrium statistical physics.

This course will present current research with illustrations at all the length scales mentioned above, emphasizing main relevant theoretical models. Within this course, a Python based programming for numerical and experimental study of active matter is proposed to the students at the LIPhy lab.


Content:

I. Microscopic phenomena:

• Self-propelled particles
• Biological and synthetic active particles
• Brownian motion
• Persistence Random walk.
• Interaction with environment (fluid/ particles/ walls)
• Dry active matter. Social interaction models: Vicsek model, Helbing model

II. Hydrodynamics

• Stokes equation
• Dipoles of forces and hydrodynamic interaction
• Pullers/pushers
• Interaction with a wall (Black green function)
• The squirmer model
• Singular solution of Stokes eq.

III. Macroscopic phenomena:

• Kinetic theory
• Rheology
• Bio-convection

IV. Python based programming for numerical and experimental study of active matter

V. Journal club:  Each student studies a published paper and presents it to the class.

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Nanotechnologies give access to new and interesting properties of materials. Applications or potential applications of nanomaterials are today very numerous in research, industrial processes but also everyday life. As a consequence, impact on health and safety of those new substances becomes important. Indeed, assessment on life cycle analysis is a key element of development. This course presents the current knowledge and research regarding the potential risks associated to the development of nanotechnologies, organized around 3 axes:

• Toxicology and ecotoxicology current knowledge, thanks to presentation of latest scientific studies on the subject,
• occupationnal potential risks : how to manage an emerging risk ? what’s mandatory ? what kind of metrology can we use ? what are the best practices in order to prevent impact on health and environment ?
• social perception of nanotechnologies over the world and over different cultures.

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Introduction to biology (components and structure of the cells, genetic information, metabolism, regulation of gene expression), stochastic processes and diffusion in biological systems (with applications in population mobility patterns or in molecular motor processes), introduction to evolution (historical perspectives, the modern synthesis, genetic drifts), genetic circuits (transcription regulation, genetic logic gates, oscillatory or bistable circuits, synthetic biology), optimality in biological systems (evolution of genetic circuits, cost-benefit issues, game theory in evolving biological systems).

After each chapter, the newly introduced concepts will be illustrated through the analysis and discussion of scientific articles, either by the teacher or by the students. Each student will be required to present at least one article to the group during the overall lectures.

Introduction à la biologie (composants et structure des cellules, information génétique, métabolisme, régulation de l’expression génétique), processus stochastiques et diffusion dans les systèmes biologiques (applications à la mobilité des populations ou aux moteurs moléculaires), introduction à l’évolution (perspectives historiques, synthèse moderne, dérives génétique), circuits génétiques (régulation transcriptionnelle, portes logiques génétiques, circuits oscillateurs ou bistables, biologie synthétique), optimalité dans les systèmes biologiques (évolution des circuits génétiques, problèmes coût-bénéfice, théorie des jeux dans l’évolution des systèmes biologiques). 

Après chaque chapitre, les concepts nouvellement introduits seront illustrés à travers l’analyse et la discussion d’articles scientifiques, soit par l’enseignant soit par les étudiants. Chaque étudiant devra présenter au moins un article au groupe sur l’ensemble du cours.)

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Introduction à la biologie structurale, Introduction à différentes techniques de microscopie électronique et préparation des échantillons, diffusion aux rayons X des macromolécules, cristallographie macromoléculaire, Principes de la Résonance Magnétique Nucléaire et détermination de la structure biomoléculaire.

Introduction to structural biology, Introduction to different electron microscopy (EM) techniques to study cells (TEM/SEM) and sample preparation, X-ray scattering by macromolecules, Macromolecular crystallography, Nuclear Magnetic Resonance principles and key steps for structure determination of biomacromolecules

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