M2 Physics, Engineering and Chemistry for Biology

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

• Structural biology methods
• Introduction to classical genetics/ mitosis and meiosis
• DNA replication and DNA repair
• DNA Transcription and translation
• Molecular biology methods
• Internal organization of eukaryotic cells and functions of organelles
• Cell signaling
• Eukaryotic Cell death and differentiation
• Diversity of the living world
• Cells in their social context: example of the immune system
• Introduction to microbiology: host-interaction (viruses, bacteria)
• Cellular biology methods
• Neurone: synaptic communication- electrophysiology
• Main functions of the brain and neurotransmitters

To provide a basic training to non-biologists and to offer them a quick initiation to the various fields of life sciences. This training will allow students to choose biology-oriented modules of the Erasmus Mundus Master at the interface of physical sciences and molecular/cell biology.

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

This course is open to multidisciplinar background students.

1. Electrical monitoring of cells

• Single cell electrical characterization using bioimpedance Maxwell-Garnett mixing theory, multishell model, single shell model, thick membrane simplified model, complex permittivity of the cell and the mixture, double layer capacitance of the electrodes, estimation of the cell parameters
• Cell tissue characterization using impedance Frike Model, Cole-cole model, phase constant element, estimation of the cell tissue parameters
• Electromechanical characterization of cells : electrorotation of cells and vesicules, Clausius- Mossotti factor, fitting to a model,
• parameter estimation, from bioimpedance or electrorotation measurements
• Case of study cell impedance measurement on a chip (paper reading exercices)

2. Cell handling and sorting with the electrical field

• Polarization of cells, principle of the dielectrophoresis
• Cell trapping/sorting using the dieletrophoresis
• Cases of study of single cell sorting on a chip (paper reading exercices)

3. cell treatment with the electric field

• concepts of electroporation and nanoporation
• towards the electrochemotherapy
• Case of study of single cell electroporation on a chip (paper reading exercices)

4. Organ on chip

Practicals – Laboratory (possible choice possible for students)

Dielectrophoresis on a chip (4h), Bioimpedance measurement of a Tissue (4h) MODULE TPàElectrorotation experiment (4h) MODULE TPàDielectrophoresis force simutation with finite element analysis (4h),

The basics of electrical engineering for the biology will be provided to students during this course. This course proposes to review the most recent research and technologies developed in academy and industries for the electrical handling, sensing and treatment of cells. The cases of single cell analyses on a chip, as well as cell tissue reconstitution on a chip (organ on chips) will be addressed. Practical course, where the student will experiment the handling and treatment of cells within microfluidic devices, and compare to the theory and finite element simulation are part of this teaching.

This course browses the main electrical engineering aspects for the living cell monitoring and treatment, and introduces the latest research and industrial developments in micro and nanotechnology devoted these biological applications. Firstly, the course will give the principles of the electrical impedance measurement of cells, in order to estimate the electrical properties of membrane and cytoplasm. Such measurement is crucial for instance for cancer detection. Single cells as well as cell tissues will be considered. Secondly the principle of dielectrophoresis, broadly used for the handling and sorting of cells within microfluidic devices will be introduced. The possibility of electrical cell treatment using the electrical field pulses will then be presented. Finally, the course will introduce the concept of organ on chips.

This course is mandatory for students having a limited background in Chemistry

Part I: Molecular Chemistry

1. Chemistry of the Elements Models for atoms and electrons description. Electronic configuration. Periodic table and element properties.
2. Organic molecules Chemical bonds. Molecular structure and geometry. Aromaticity. Functional groups. Conformation and configuration.
3. Non-covalent interactions Ion-ion, ion-dipole, dipole-dipole, hydrogen bond, halogen bond, aromatic interaction, cation-π, anion-π, van der Waals

Part II: Physical Chemistry

1. Thermodynamics Enthalpy, Gibbs energy and entropy. Chemical equilibrium.
2. General Chemistry in Solution Acid, bases and pH. Complexation. Solubility and polarity effects.
3. Kinetics Reaction rate. Reaction mechanism. Catalysis
4. Basics of Surface Chemistry

This course is an overview of important and fundamental aspects of chemistry. Basic principles, necessary to understand chemistry and contiguous scientific fields, are given

“Chemistry3 - Introducing Inorganic, Organic and Physical Chemistry” A. Burrows, J. Holman, A. Parsons, G. Piling, G. Price. “Physical Chemistry”, P. Atkins. “Physical Chemistry - Understanding our Chemical World” P Monk. “Introduction to Organic Chemistry » W. H. Brown, T. Poon

Fundamental in biology

• Introduction to fluorescence / photoreactivity
• Time-resolved fluorescence analysis
• Fluorescent probes in biology
• Intrinsic fluorescence (e.g. protein fluorescence) & fluorescence quenching
• Steady state & time-resolved fluorescence anisotropy
• Fluorescence (cross)correlation spectroscopy
• Introduction to FRET (fluorescence resonance energy transfer) / FRET-FLIM
• Single molecule FRET – Introduction to TIRF microscopy
• Quantitative PCR
• Flow cytometry

This course will provide theoretical knowledge required to understand experimental methods underlying fluorescence-based assays for biology at the molecular level: (i) photoluminescence & photoreactivity (excited state, (non)radiative relaxation pathways, photoisomerization…), (ii) steady-state & time-resolved parameters/methods, (iii) main intrinsic/extrinsic fluorescent probes used in biology and (iv) biological applications (quantitative PCR, flow cytometry). The students must have understood the principle of these techniques and to be able to master them quickly in an experimental environment

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

Quantum physics, hydrogen atom, introduction to condensed matter (band structure of solids), Schrödinger equation, molecular orbitals, chemical kinetics

Introduction: overview on the conceptual tools and phenomena From Schrödinger equation to ... Molecules: Molecular orbitals - Energy levels - Jablonski-Perrin diagram Solids: Band structure of semiconductors - Different dimensionalities: quantum well, quantum wire, quantum dot - Phonons in a solid Ground to excited states: light absorption Molecules: Selection rules - Transition moment - Molecular physicochemical properties at excited states Solids: Absorption coefficient: interband optical transitions, selection rules, density of states -Properties at excited states: excitons Excited to ground states: light emission and other mechanisms Molecules: Non-radiative relaxation mechanisms: vibrational relaxation, internal conversion, inter-system crossing - Photoluminescence (fluorescence and phosphorescence): quantum yield, lifetime, emission and excitation spectra Solids: Intraband non-radiative relaxation (electron phonon interaction) - Photoluminescence (electron-hole recombination): quantum yield, lifetime, emission and excitation spectra Complex processes Molecules: Fluorescence quenching - Energy transfer (FRET: Förster resonance energy transfer) Solids: Energy transfers - Charge transfers

Exercise sessions Seminars - Examples from research Molecules: Photochemical reactions and photo-active molecule Solids: Optical properties of hybrid halide perovskites Lab visit - Instrumentation

In the context of light-matter interaction, this course focuses on the effect of light on molecules and solids: what happens to them?: formation of excited states, what are the outcomes? non-radiative and radiative relaxation phenomena from the excited states. Concepts and models to describe such interactions and resulting phenomena (absorption, emission) will be introduced and developed in parallel for molecules and solids, highlighting the analogies, similarities and specificities between these two systems. An objective of the course is then to connect worlds at different scales and have a complete and general overview on the optical properties in matter. The experimental means to observe the optical properties will be described and the introduced concepts and models will be illustrated by current research subjects, beyond textbook cases.

• Physical Chemistry, P. Atkins et al., Oxford University Press • Photochemistry of Organic Compounds: From Concepts to Practice", P. Klan and J. Wirz, Wiley-Blackwell • Molecular Fluorescence, B. Valeur and M.N. Berberan-Santos, Wiley-VCH • Optical Properties of Solids Mark Fox, Oxford Master Series in Physics, Mark Fox, Oxford Series in Physic

bases in fluorescence, ray optics, wave optics

1: Fundamentals of optical microscopy Structure of an optical microscope, Köhler configuration, phase contrast imaging, depth of field, spatial resolution. 2: Fluorescence microscopy and super-resolution techniques: imaging with nanometer-scale resolution Based on examples with biological applications. 3: Deeper in tissue Use of multi-photon microscopy and adaptive optics. Examples from neurosciences. 4: Faster: how to image in real-time living samples Tracking methods, resonant 2-photon imaging, functional imaging.

The aim of this course is to present different optical microscopy methods useful for studying biological samples at the cell and tissue scales. We will start by introducing the basics of optical microscopy (characteristics of a microscope objective, illumination configurations, notions of depth of field, resolution limits…). We will then turn our attention to fluorescence microscopy, and in particular to super-resolution techniques. Different techniques, such as STED, PALM or STORM will be presented. Compromises between spatial and time resolution will be discussed (structured illumination microscopy) as well as super-resolution in the optical-axis direction (PSF engineering). We will then see how multi-photon microscopy and adaptive optics provide a way to image deeper in the biological tissues. We will finally focus on fast imaging, to study live biological samples. Techniques as single-particle tracking and resonant two-photon imaging will be introduced.

“Introduction to Optical Microscopy”, Jérôme MERTZ, Cambridge University Press, 2nd edition (2019)

This course requires a good knowledge of Statistical Mechanics.

Part I: Statistical Mechanics of Interacting Systems: Appl

1. Review of Stastical Mechanics Postulates of Statistical Mechanics, Gibbs Ensembles, from micro to macro. Ideal systems.
2. Non-Ideal Systems and Virial expansion Ideal systems and they role in soft matter. Complexity and phase transition. A first treatment introducing the virial expansion.
3. Density Distribution Theory Introduction to the liquid state theory. Density distribution and radial distribution function (RDF). Connection of the RDF to thermodynamics properties. Stati structure factor. Brief introduction to computer simulations.
4. Scattering Theory Formal connection of the static structure factor with the scattering properties. Form factor. Performing scattering function in real life: SALS, SAXS, SANS. A brief introduction to Dynamic Light scattering (DLS)

Part II: Intermolecular interactions

1. Introduction Enthalpy, Gibbs energy and entropy. Chemical equilibrium.
2. van Der Waals interactions Origin, simple derivation, from microscopic to macroscopic interactions.
3. Electrostatic Interaction Poisson-Boltzman equation, Debye-Huckel Theory, DLVO interactions and aggregation

TDs: Applications

Ideal statistical mechanics and absorption of Oxygen by Haemoglobin. Dense solution of proteins as non-ideal systems. Osmotic Pressure. Depletion interaction.

This course is a general introduction to the world of soft matter. In particular, we will use the tools of Statistical Mechanics to discuss the equilibrium, the dynamical and mechanical properties of soft matter systems and we will explore different applications ranging from Material Science to Biophysics.

Any introductory Statistical Mechanics book. Good reference for Part I and II: David L. Goodstein - States of matter Notes of course

Basic Python programming; basic statistics.

1. Programming Python basics 00 (Homework: 6h) Data types, control structures, lists, hashes, files
2. Data Manipulation using pandas Reading, storing and sharing large datasets, indexing/slicing/iterating, vectorization, dataframe operations.
3. Data Visualisation using matplotlib and seaborn Visualising data for exploration and for publication, data science traceability and reproducibility.
4. Exploratory Data Analysis using pandas and seaborn Finding relationships between variables, formulating hypotheses and devising models.
5. Basic statistical modelling using scikit-learn Constructing and training simple models to make predictions based on the data.
6. Personal/group project 8 Prepare a report about the exploratory analysis and statistical modelling of a real dataset (chosen by the students or proposed by the teacher)

Python is a simple, multi-purpose language that is a reference in data science (statistical analysis of data and machine learning). This course focuses on the Python tools and libraries needed for high-performance manipulation, visualization and exploratory statistical analysis of large experimental datasets, as well as constructing and training statistical models to make predictions based on the data. The course is fully hands-on, and uses effective teaching techniques (e.g. live coding, active learning) to tackle modern problems in data science and emerging practices to solve them.

Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython (O’Reilly, 2011) W. McKinney; Introduction to Machine Learning with Python (O′Reilly, 2016) A. Mueller and S. Guido.

Fundamentals in Biology, or equivalent prior knowledge

CM:

1. Elements of quantum chemistry
2. The space of biological sequences and structures Multiple sequence alignments, conservation and (co-)evolution.
3. Protein structure prediction: physics and statistics The protein folding problem: approaches from physics (Anton) and statistics (AlphaFold).
4. Theoretical bases of molecular mechanics Biomolecular empirical force fields: principles, approximations, common functional forms, the solvent, performance considerations, applications.
5. Sampling the potential energy surface Algorithms and techniques (minimisation, Monte Carlo, molecular dynamics, Normal modes)

Lab Work 5. Quantum chemistry using Gaussian 6. Modelling structure From sequence to structure using machine learning; evaluating quality and limitations of models; using molecular viewers to study biomolecular structure and interactions and gain physical insight into the biological phenomena 7. Modelling dynamics From static structure to trajectory in physiological conditions; extracting useful information from the trajectory to evaluate simulation quality, compare with experiment and shed light on molecular mechanisms

Biomolecules adopt a dynamic ensemble of conformations to perform a multitude of cellular functions. In only a few years, structural biology, the study of the 3D structure or shape of proteins and other biomolecules, has been transformed by breakthroughs from machine learning algorithms. Despite all this progress, there are still many active and open challenges for the field, at the interface of Physics, Biology and Mathematics. This course will present recent advances and future perspectives, focusing on the complementarity of physical and statistical approaches

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

This course is open to multidisciplinar background students.

1. Super resolution for bio-microscopy
2. Cell detection : MorphoMat, image aspect, thresholding, segmentation (K-MEANS), De-noising
3. Cell tracking : Estimation movement, optical flow
4. Introduction to AI: ResNet Practicals – Laboratory Introduction to image processing, application to a case study (cell detection and counting)

The objective of the course is to acquire the basic notions of signal and image processing in order to be able to solve imaging problems of biological structures. We will study the principles of obtaining super-resolved imaging approaches and partially overcoming light diffraction problems. But we will also study the problem of image processing in order to create automatic image processing. Finally, we will study sequences in order to solve cell tracking problems.

The course will present the necessary aspects of information theory to understand the different existing super-resolved microscopy systems. The main image processing methods allowing the detection and identification of biological objects will be presented and manipulated (for example automatic thresholding methods, mathematical morphology approaches, Hough transform parametric approaches, segmentation approaches' K-means'...). Finally we will tackle cell tracking. To do this, we will study global or local motion estimation approaches (block matching algorithms, optical flow, Kalman filter). And we will be introduced to the new artificial intelligence algorithm, based on deep neural networks (ResNet).

Optical physics and electromagnetism, Laser (Bachelor level)

• Review of lasers  working principle  main properties, intensity  different kinds of laser  main applications • Introduction to nonlinear optics  general idea  reminder of linear 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, ...

First to give basics of nonlinear optics and its applications to laser technology and applications. Second, to explore the relatively recent domain of nonlinear optics from to micro towards the nanoscale, including nonlinear effect in micro and nanostructures, nonlinear photonic crystals, as well as some far-field nonlinear microscopies and nanoscopies. Applications in physics and biology will be discussed.

books “Lasers” – A. E. Siegman; “Nonlinear Optics” – R. Boyd

Quantum mechanics and basics of light-matter interaction

General Introduction Light-Matter Interaction reminders: Optical Bloch equations and Bloch sphere: how to manipulate a Qubit? Notion of decoherence and decoherence in a quantum sensing experiment Introduction to classical noises in measurements Noise in a quantum sensing experiment • NV centers in diamond basics and optically detected magnetic resonance (ODMR) • Applications of ODMR to magnetometry and thermometry: continuous wave regime and pulsed regime (Ramsey interferometry) • Some physical and biomedical applications of NV-diamond magnetometry and thermometry • Decoherence in NV-center in diamond and application to sensing of biophysical parameters

Understand how quantum states can improve the sensing of properties of different systems, and what are the limitations of quantum measurements. The concepts will be illustrated by examples of applications in physics and biology mostly based on nitrogen-vacancy centers in diamond.

Each time slot is separated into a concept introduction and tutorials, often illustrated by scientific papers. The aim of the course is to highlight classical limits that can be overcome by a quantum approach of the measurements. The first part of the course will be dedicated to the notion of quantum bit and how to use it to measure an external parameter such as temperature, electric or magnetic field… We will see how the decoherence mechanisms limit the quantum measurement. Among the quantum sensors, we will particularly focus on negatively charged nitrogen-vacancy (NV) centers in diamond, a solid-state quantum sensor relying on an electron spin resonance that can be detected optically.

• "Introductory Quantum Optics", C.C. Gerry and P.L. Knight, Cambridge Univ. Press (2005) • Degen, C. L., Reinhard, F. & Cappellaro, P. Quantum sensing. Rev. Mod. Phys. 89, 035002 (2017). • Aslam, N. et al. Quantum sensors for biomedical applications. Nat. Rev. Phys. 5, 157–169 (2023).

This course is open to multidisciplinar background students.

1. DNAchip concept of successive photoexposures to develop high throughput chips
2. The electrical field within the cell

• Basics in electrophysiology,
• Huxley model of action potential propagation, Simulation of the Action potential (practicals), Resolution of the propagation of electrical signal (co-axial cable vs Axon)

3. Electrical monitoring of ion-channels

• Main systems for ion channel recording, patch clamp, planar patch clamp,
• Artificial lipid bilayers systems: Structure and fabrication of membrane protein chip, Liposomes, Giant liposomes, electroformation, droplet contacting method
• Architecture and clean room microfabrication of the microfluidic devices for ion-channel recording
• Paper reading exercice

4. Nanopore sensing technology

• Use of biological nanopores for the single molecule sensing
• Use of solid state nanopores for large molecules sensing
• Paper reading exercice Practicals – Laboratory Simulation of the action potential (4h),

The basics of electrical engineering for the biology will be provided to students during this course. This course proposes to review most recent research and industrial developments in micro and nanotechnology devoted to the electrical characterization of ion channels, for electrophysiology purposes, as well as the use of those ion channels as sensing devices for single molecules sensing (DNA, proteins..). Practical courses, where real experiments are conducted on biomicrosystems, are confronted to the theory and simulation are proposed in the framework of this course.

This course browses the main electrical engineering aspects for the living cell monitoring, from the basics of electrophysiology to the latest research and industrial developments in micro and nanotechnology devoted to biological applications. The impact of nano and microtechnologies on biology is quite huge, as demonstrated by the DNA chips that became nowadays a commonly used technology for many applications. The principle and fabrication of DNA chips will be presented. Then the course will focus on protein chips – soluble proteins or membrane proteins - and more particularly on devices used to characterize and monitor ion-channel proteins. Main architectures of microfluidic devices found in the literature devoted to this purpose will be described, based either on the reconstitution of planar lipid bilayers or on the droplet contacting principle.

Finally, the use of those ion-channels as natural nanopores can be used for electrically sense the properties of single molecules. The fabrication of devices for such a purpose will be described, and scientific papers on the subject will be analysed.

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

1. Introduction

• Scaling laws in Microsystems

2. Microfluidic technology

• Clean room, Photolithography and Microelectronics technology glass, silicon, polymer (molding-casting)

3. Physics of microfluidic

• Poiseuille flow
• hydrodynamic separation: wall effect, shear stress effect - Diffusion and mixing
• Capillarity: digital microfluidics – Droplet
• Case of study exercises

4. Microfluidics for the cell sorting and characterization

• Acoustophoresis of cells in microfluidic devices
• Magnetophoresis in cell chips
• Dielectrophoresis separation within microfluidic devices
• Amperometric sensing / convection-diffusion-consumption
• Case of study (research paper reading exercises) Practical training (8h)
• Fabrication and testing of a micromixer in PDMS
• Droplet generator and phase diagram characterization MODULE TP: Microfluidic sorting using hydrodynamic forces

Microfluidics lectures aim to introduce students to fluid mechanics at the microscale, in the framework of lab-on-a-chips and their technology associated. Fluid mechanics at the microscale has the particularity to be multiphysics. Lectures contain both theoretical backgrounds and microfabrication analysis. Examples of technical solutions illustrate the course. Practical work will give the possibilty for students to design, fabricate and characterise a microfluidic chip.

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

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

• PART ONE: Photonic crystals/nonlinear photonic crystals and applications  1D, 2D, and 3D photonic crystals: theory, simulation  Photonic crystal and photonic quasi-crystals  Photonic crystal with defect and applications  Nonlinear photonic crystals  Fabrication technologies and applications

• PART TWO: Plasmonic effect  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; 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: Metal nanoparticles under laser pulses: Light-heat nanometric conversion; Thermo-optical properties  Selected applications: Light-heat conversion: Nanoscale hyperthermia against cancer, drug or DNA delivery, laser damage and laser shaping, photothermal imaging, optical limitation

• PART THREE: Single molecules  Energy levels in molecular systems; Light-matter interaction (from two level system to molecules)  Single molecule spectroscopy: confocal spectroscopy, photon statistics…  Single Molecules for BioImaging

This course aims at giving knowledge from a basic background of photonic crystals and plasmonics and applications in different domains, including physics/bio/chemistry, and in particular at single molecule scale.

book « Photonic Crystals Moulding the Flow of Light (Second Edition) »

“Quantum Optics”, M. Fox; “Quantum Mechanics”, I et II C. Cohen-Tannoudji, B. Diu & F. Laloë