Soft matter and biophysics 1st year

Goal:  Mechanics plays a forefront role at the nanoscale,  from the generation of nano-structures by growth instabilities to the properties of nano-composite materials, the design of micro and nano-mechanical devices, the nano-imaging techniques, the control of biologic functions.  This course introduces the mechanics of continuous media and its main applications to nanosciences and nano-technologies.  

Content:
- Simple deformations, definition of elastic modulii E, G, K, nu
- Flexion of beams, static, dynamics and waves. Example: the AFM cantilever.
- 3D linear elasticity of isotropic media: strain tensor ;  elasticity as a field theory (expression of the free energy) ; stress tensor ; general equilibrium equation
- elastic instabilities in thin films
- elasticity of membranes, ADN coil.

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Goal: Microfluidics studies the transport of liquids at the scale of some micrometer to the hundred of micrometer, such as the flow of red blood cells in a blood vessel, the transport of polymer chains in a porous medium, or the locomotion of micro-organisms. Nanofluidics studies the flow of liquids at the colloidal scale, that is at distance of the nanometer to the micrometer from a surface. This course introduces the concepts of low Reynolds number flows and surface-driven flows and describes the main properties of flows and transport at the sub-millimeter scale.

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Goal: Introduce the basic statistical physics concepts to address the equilibrium and evolution properties of nano-scale systems.

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Goal: As the size of systems decreases, surface effects become more important. The nano- scale is also the scale at which surface effects dominate over bulk effects. This course introduces the main notions to adress the specific properties and the organization of matter at surfaces from a physical, chemical and biological point of view.

Content:
- notions on molecular and surface interactions. The hydrophobic effect
- thermodynamics of surfaces ; surface tension
- capillarity, wetting, contact angle
- surfactants,  micelles, self-assemblies and lyotropic phases
- Gibbs monolayers, Langmuir-Blodgett films
- introduction to biologic membranes

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This course is open and mandatory only for students taking part to the Thematic Program (PT) Soft Nano (Graduate School).

Students undertake a research project in soft nanosciences, starting by an appropriation phase. The goal of the course is to learn how to plan, set-up, and write, a research proposal.

Content

Students spend 1+1/2 day per week in their research team. In addition the group meets on a weekly basis, and works on the following topics:

• reading and synthetizing the scientific literature
• understanding the novelty of the approach to be developed
• defining the research objectives
• defining the new tools /techniques/ know-how needed for the project, starting to acquire them
• elaborating a tentative schedule for implementation of the 2-year research work, with milestones

Students take turns in presenting their progress to the promotion.
In addition to this continous activity, they are evaluated at the end of the term through:
- the submission of a research proposal (about 15 pages, including a state-of-the-art, novelty and objectives of approach, new  instrumentation/ elaboration/ numerics/ methodology to be developed, expected outcomes, scheme and schedule of implementation)
- an oral public presentation and defense of their proposal,  in presence of all the promotion and of a unique pluridisciplinary jury for all students.

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Goal: This course is a deepening of the quantum mechanics concepts introduced in the undergraduate courses. The fundamental principle of quantum mechanics are illustrated by applications to nanoscale condensed-matter systems taken from recent research works and by discussing prospects for quantum information technologies. The concepts presented in this course are prerequisites for many second-year courses related to nanophysics and quantum engineering. A good knowledge in quantum mechanics is indeed more and more essential for technological research and development of nanoscale quantum devices.

Content

• Chapter 1: Introduction and recalls on the quantum mechanics postulates and formalism (Dirac notation, Hilbert space). Two-level system, Zeeman effect, spin Hamiltonian. Tensorial product notation for states and operators. Many-body quantum states (bosons and fermions).
  Exercices: Basics of quantum mechanics formalism.
• Chapter 2: Recalls on confinement problem. Electron bound states in a potential.
  Exercises: Example of 1D confinement problems, quantum harmonic oscillator.
• Chapter 3: Introduction to atomic physics. Spherical symmetry, angular and spin kinetic momenta. Mean field approximation, central potential, many electrons atoms, Hund rules, spin-orbit coupling, optical transitions.
  Exercises: Grotrian diagrams, spin-orbit coupling, fine and hyperfine structure.
• Chapter 4: Approximation methods for eigenstate calculations, perturbation theory, variational method.
  Exercises: Application to electronic systems.
• Chapter 5: Time evolution. General equation for the time evolution, two-level systems, perturbation theory, Fermi golden rules.
  Exercises: Application to Rabi oscillations.

Prerequisites: Basics of quantum mechanics.

Bibliography: Quantum mechanics, C. Cohen-Tannoudji, Vol. 1, ISBN-13: 978-0471164333, Vol. 2, ISBN-13: 978-0471569527.

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Goal: This solid-state physics class aims at providing the basics theories that allow to understand the properties of materials, and in particular their electronic and vibrational properties. Why are some solids metallic and other semiconducting ?  How can we describe their electrical and thermal properties ?  Applications to low-dimensional systems (including graphene and nanotubes) will serve as a bridge to nanosciences.

Content: Presentation of simple models and calculations of solids properties:

• Free electrons : classical Drude model.
• Quantum model: Sommerfeld model.
• Metals and insulators : nearly-free quantum model, tight-binding model, Bloch therorem.
• Vibrations in solids: acoustic and optical phonons, sound velocity.

Prerequisites: Electromagnetism, waves and vibrations, basic quantum mechanics.

Bibliography:
Introduction to solid state physics, 8th edition, Charles Kittel.
Solid state physics, Neil Ashcroft and David Mermin.

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Laser and nonlinear optics - 20h
The laser aspects will focus on the study of the gain medium and the resonator including the notions of oscillation threshold, Gaussian optics, stability, cavity modes and the different temporal regimes. Concerning nonlinear optics, it will deal with laser frequency synthesis and mixing like second harmonic generation, optical parametric amplification and optical parametric oscillation. Notions of crystal optics will be given in this framework.
 
Optical spectroscopy – 20h
This lecture concerns itself with the interaction between light and matter. In this part, we present a theoretical framework to discuss the absorption, emission, and luminescence properties of, principally, gas phase molecular systems. Experimental techniques will be discussed, including modern and state-of-the-art techniques used in the environmental (e.g., infrared trace gas detection) and life sciences (such as Raman non-linear spectroscopies).

Guided optics – 10h
The objective of this part of the course is to give an insight into guided wave optics. Starting from Maxwell's equations, guided waves in planar (1d) structures will be presented. The notions of effective index and modal distribution will be explained and practical tools to compute them will be given. An overview of guided modes in bidimensionnal structures will also be given. The effective index method will be used to obtain a first approximation of the modes supported by these structures.

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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.

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SpectrumThis course is organized in two parts, each made of nine sessions of 1.5 hours. In each part, five sessions are devoted to lectures, and four sessions are exercice classes devoted to problem-set solving.

The first part encompasses optical spectroscopies and focuses on the interaction of the electrical field component of light with matter. It deals with infrared and UV-visible spectroscopies, based on vibrational and electronic motions in the molecules. Some elements of group theory are presented to explain the occurence of the transitions and the aspect of the spectra related to the molecular structures.

The second part of the course focuses on the interaction of the magnetic field component of light with matter. This part aims at illustrating the principle of magnetic resonance spectroscopies, both nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR), and their use for structure determination, for chemical kinetics and thermodynamics, as well as for molecular dynamics characterization in solution and in the solid state of organic and inorganic molecules and nanomaterials.

Assessments takes place as two written exams of 1 hour each for each part of the course.

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This course gives an overview of the polymer field from the synthesis of polymers to characterization, properties, and applications of synthetic and natural polymers. All major polymerization methods, their reaction mechanisms and kinetic aspects are considered: step growth polymerization, chain growth polymerization with ionic and radical variations, insertion polymerization. A lecture portion is integrated with a laboratory component, in which experiments are conducted that are directly connected to the class work. Analysis of  polymer solution properties and caracterization techniques are presented :  thermodynamics, polymer/solvent interactions, average molecular weight determination via osmometry, ligth scattering, viscosimetry and SEC.

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Objectives : Aquire some knowledges about electrochemisty methods as Cyclic Voltammetry (CV) , Electrochemical Impedance Spectroscopy (EIS) to characterize electrochemical reactions in solution and immobilized on the surfaces of electrodes.
Examples taken from litterature illustrate the lectures for a better understanding to characterize, investigate electrochemical systems, to elucidate different electrochemical reactions.

Content :

• Lectures + tutorials :13.5 H

- Reminders (1H 30)

- Cyclic Voltammetry (6 H): -Experimental and theoretical basis of voltammetry
Characterization in solution of reversible redox systems, irreversible redox systems,
quasi-reversible redox systems, consecutive redox systems, coupled homogeneous
chemical reactions EC reaction, CE reaction, EC reaction (catalytic) , ECE reactions,′
Characterization of immobilized systems on electrode

- Electrochemical Impedance Spectroscopy (6 H): -Measurement: principle, experimental conditions
Impedance of circuit elements in an electrochemical system, Impedance of electrochemical systems,
Modeling utilizing electric and dielectric parameters

• Lab works : 3 experimental work sessions (3 X 4 H) illustrate topics of lectures

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An overview of discrete element simulations, force transmission in granular packings,  another vision of soil mechanics, microscopic origins of some constitutive laws, role of the geometry,  numerical homogenization,  "Tools" for characterizing the microstructure, complex systems and strong coupling. 

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This course gives a general overview of some of the most common techniques used in image and signal processing, with a special focus in Fluid Mechanics. It starts with a review of the basic concepts of both signals and image processing (systems, block diagrams, Fourier series, 1 and 2D Fourier Transforms, basic image manipulation, filters…). In a second stage, the course focalises in more complex statistical techniques like, for the case of signals, spectral analysis, correlation and structure functions. For the case of images, it covers the reconstruction of particle trajectories and the basics of PIV (Particle Image Velocimetry) analysis.  

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The Research Intensive Training is a trademark of the Master N². It is specifically dedicated to intensify the formation through research, allowing students to the be continuously immersed in their laboratories in parallel to their courses, during the 2 years of the program.

For this purpose, students can choose up to 3 optional RIT modules of 3 credits each, one in each semester of the program, except for the last semester which is already fully devoted to the master thesis.

A RIT module consists in a part-time internship in a lab of the Grenoble area, representing 1 day each week during a semester. RIT modules are thought to be performed in the same research teams on the same research project, allowing students to achieve a substantial research contribution with possibly a publication during their master.  However students can also change lab, project or research team, with the agreement of their program coordinator, in order to get a broader scientific experience. Students can then discover ongoing research in nanosciences not only in their specialization but also in sister disciplines. It also offers them an opportunity to initiate connections in view of finding their master thesis subject.

RIT modules are 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. RIT performed in the second semester of the first year can be evaluated together with the compulsory M1 research internship.

Admission to Research Intensive Training modules requires the agreement of the school-year coordinator.  In M1, the training is fully appropriate to students having completed a 4-years bachelor of science, or engineering, however 3-year's bachelors who have excellent academic results can also be admitted to the RIT.

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Ce cours se concentrera sur la formation aux étudiants à l’élaboration de curriculum vitae et lettre de motivation, à la préparation aux entretiens d’embauche dans le monde industriel. Une large partie de cet enseignement sera aussi consacrée à la gestion de projets et à la notion d’innovation.

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The internship is a key step of the M1 since in many cases it is the first long stay in a Research lab to develop an original scientific topics. The internship lasts a minimum of 8 weeks between April to June, on a subject related to nanosciences or nanotechnologies.
The internship can be a performed in a research institute of the Grenoble area or abroad, or in a company.
Students conduct a research project under the guidance of their supervisor. The internship can be extended during the summer up a to length of 4 months.

At the end of June students have to produce a report of about 20 pages including the bibliography. The report introduces their subject, the state of the art, and their objectives. It describes the methods they have used, their realizations, and discusses the results obtained during the internship. The reports concludes by giving perspectives of the performed work.
The students have then an oral defense based on a presentation of 15mn followed by 10mn of questions.

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• To address multidisciplinary approaches in nanosciences through a set of practical work.
• To train on high-tech platforms in nanosciences and in nanotechnology.
• To understand chemical methods of nanomaterials synthesis by a bottom-up approach.
• To learn the physical principles and practice of nanomaterials characterization techniques

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The Nanosciences course offers high level experimental training and labwork performed in the nano-facilities and technology centers of UGA: CIME-Nanotech, CUBE, Chemistry platform.

Nanosciences Labwork

This course addresses the pluridisciplinar aspect of nanosciences and in nanotechnologies. The goal is to train students at the interface between the different sciences: chemistry and physics (Part I), physics and biology (Part II), and show the importance of a collaborative approach to the production and the characterization of nanoscale objects. Courses are in support for understand the great principles of the bottom-up approach in nanochemistry, the physical principle of different methods of characterization in nanosciences (AFM, SEM, TEM) and the elementary principles in biophysics. The pedagogical team is composed of teachers working in the field of nanochemistry, nanophysics and biophysics. The different practical work taking place on various practical teachings platforms located in Grenoble allowing the use of characterizations equipment at the forefront of nanoscience research.

Nano-biophysics

This course  is devoted to the Morphological and the Mechanical studies of biological cells fixed on a micro-functionalized pattern, by Atomic Force and Fluorescence Microscopies techniques. It consists of 14h of lectures addressing  biochemical and physical concepts at the nanoscale, and 12h of labwork taking place at the CUBE and CIME-Nanotech.

• To address multidisciplinary approaches in nanosciences through a set of practical work.
• To train on high-tech platforms in nanosciences and in nanotechnology.
• To understand chemical methods of nanomaterials synthesis by a bottom-up approach.
• To learn the biophysical principles of the interface between nanomaterials and animal cells.

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Goal: This course will give a general view on the topic of photon or wave interactions with matter at various energy scales and length scales.

Content
In the first part, we will focus on the problem of the propagation of an electromagnetic wave when the wavelength is large (UV, optical, etc.) compared to the interatomic distances. The problem of polarization of the medium in metals and in semiconductors (Drude, Lorentz, interband, etc.) will be discussed and surface plasmons which are longitudinal excitations at the SC-metal interface will be treated. Finally, we will discuss how we can localize light on length scales smaller than the wavelength (e.g. nanoparticles). This part will be completed by a section on the Kramers-Kronig relations that link reflectance to absorption. The second part of the course will focus on phenomena where the incident wavelength is much smaller, such that matter can be resolved to atomic scales. The problem of structure factors and their interpretation in terms of correlation functions (neutrons, X, etc.) will be discussed.

References

1. Zangwill, Modern Electrodynamics, Cambridge University Press.
2. D. Tanner, Optical Effects in Solids, Cambridge University Press.
3. P. Chaikin and T. Lubensky, Principles of Condensed Matter Physics, Cambridge University Press.

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Goal: This course proposes an introduction to soft matter physics. The physics of soft matter is governed by weak interactions which are at the source of the generic characteristics of soft matter systems: nanoscale self-organisation at room temperature, importance of entropy and fluctuations, high susceptibility and response to stimulii, specific structures at surfaces and interfaces, slow dynamics. The course is organized in two parts. The first part describes the interactions at work in soft matter systems and their measurements. The second part develops on the particular system of polymer melts and solutions, the generic characteristics of soft matter systems and the physical tools needed to modelize them.

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Goal: To introduce the basic thermodynamics concepts to address the equilibrium and evolution properties of nano-scale systems.

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Goal: Introduction to local probes techniques in the field of nanosciences and nanotechnologies.

Content

1. Introduction to Scanning Probes Microscopy (1h30)

• Comparison between surface analysis techniques: SEM/TEM, SFA
• Presentation of the SPM sub-families: STM / SFM / SNOM via examples of applications

2. The Scanning Tunneling Microscope (7h)

• The tunneling effect
  • STM relevant parameters
  • Expression of the tunneling current
• The STM instrument
  • Tip fabrication methods
  • Electronic and instrumental chain to measure and control tunnelling current in the pico/nano-ampere range ADC/DAC, I/V converter, lock-in amplifier
  • Source of noises and detection limit
  • Vibration isolation (tutorial on transfer function and damping)
  • Measurement at low temperature : how to operate an STM in a cryostat>
• Operating STM modes and associated measurements
  • Local density of states (LDOS) and I/V spectroscopy
  • Constant current mode versus constant height mode

3. The Atomic Force Microscope (12h)

• Why mechanical oscillators
  • Introduction and history
  • Mechanical susceptibility
  • Limits of sensitivity (readout noise and Brownian motion)
  • Working at resonance, decrease the size/mass
• How to build an AFM
  • Micro fabrication of cantilever and tips
  • Nano positioning (piezo material and issues with them as hysteresis…)
  • Precision position measurements (optical and capacitive)
  • Signal analysis (Homodyne detection, PLL and PID)
• Operating AFMs
  • Calibration process (cantilever stiffness, position detection)
  • What physical values are accessible (van der Waals, electrical, magnetic, friction forces)
  • Different modes of operation
• Maps analysis and image processing
  • Surface analysis parameters: rms, ra, skewness, kurtosis, etc
  • Artefacts, tip dilation effect
  • Tilt correction via polynomial subtraction and color scale
  • Tutorial on processing of the images and spectroscopy curves obtained in PW via Gwyddion software

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Mandatory course for the students of the Soft Nano Thematic program (PT) of the Graduate School.

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The Research Intensive Training is a trademark of the Master N². It is specifically dedicated to intensify the formation through research, allowing students to the be continuously immersed in their laboratories in parallel to their courses, during the 2 years of the program.

For this purpose, students can choose up to 3 optional RIT modules of 3 credits each, one in each semester of the program, except for the last semester which is already fully devoted to the master thesis.

A RIT module consists in a part-time internship in a lab of the Grenoble area, representing 1 day each week during a semester. RIT modules are thought to be performed in the same research teams on the same research project, allowing students to achieve a substantial research contribution with possibly a publication during their master.  However students can also change lab, project or research team, with the agreement of their program coordinator, in order to get a broader scientific experience. Students can then discover ongoing research in nanosciences not only in their specialization but also in sister disciplines. It also offers them an opportunity to initiate connections in view of finding their master thesis subject.

RIT modules are 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. RIT performed in the second semester of the first year can be evaluated together with the compulsory M1 research internship.

Admission to Research Intensive Training modules requires the agreement of the school-year coordinator.  In M1, the training is fully appropriate to students having completed a 4-years bachelor of science, or engineering, however 3-year's bachelors who have excellent academic results can also be admitted to the RIT.

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Goal: Because numerical tools in nowadays science research has become unavoidable, this course aims in familiarizing with methodologies, Python language and algorithms, ranging from classical to quantum physics, when the use of the numerics is inevitable to get answers to a problem.

Content: Based on independent projects starting on day one and possibly related to the different topics encountered during their master, the students will have to do an A to Z study, developing their own model, implementing it in Python with an appropriate approach, benchmarking it by understanding pros and cons and eventually doing the physical analysis.

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This course gives an overview of the polymer field from the synthesis of polymers to characterization, properties, and applications of synthetic and natural polymers. All major polymerization methods, their reaction mechanisms and kinetic aspects are considered: step growth polymerization, chain growth polymerization with ionic and radical variations, insertion polymerization. A lecture portion is integrated with a laboratory component, in which experiments are conducted that are directly connected to the class work. Analysis of  polymer solution properties and caracterization techniques are presented :  thermodynamics, polymer/solvent interactions, average molecular weight determination via osmometry, ligth scattering, viscosimetry and SEC.

This course is divided in two parts covering selected aspects of polymer chemistry and physical chemistry. The chemistry part aims to help students better understand contemporary polymer science focusing on syntheses and materials properties of polymers. It covers copolymer synthesis, discussing control of copolymer composition and relevant recent research such as controlled radical polymerization, supramolecular polymers and bio-based polymers. The course will also provide detailed information for polymerization techniques and polymer characterization tools.

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The applications of surface functionalization are multiple and cover large fields at the interface between chemistry and biology. The aim of this course is to focus on two challenging applications: surface functionalization for biosensors and for (electro)catalysis. The course is structured into two modules differentiated by the nature of the functionalized material which (mineral/inorganic or biological).

Contents:

I. Short introduction on biomolecules (DNA, proteins, enzymes, sugars…)

II. Functionalization of mineral and inorganic based-materials and related characterization techniques (fluorescence microscopy, AFM, SEM, ellipsometry…)

  DNA, sugars and proteins

• Physisorption, chemisorption
• Self-assembly on conducting and semi-conducting surfaces (silanization, thiol self assembly)
• Electrofunctionnalization: conducting polymers, diazonium salts
• Auto-organization of biomolecules : origami, DNA wires, protein auto-assembly, protein organized around organizing structure (Metals…)
•  Applications: biosensors, stimulating electrodes and anti-fouling surfaces

Catalysts

• Functionnalization
• Applications: (photo)electrocatalytic water splitting (reduction of protons, water oxidation), CO2 reduction

Enzymes

• Functionnalization
• Applications: hydrogenases, CO2 reductase …

III. Functionnalization of bio-based nanomaterials
DNA

•  Functionnalization with catalysts
•  Applications

Proteins

•  Functionnalization (bioconjugation) with catalysts (artificial enzymes) and nanoparticles
•  Applications

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