Master 1
FIRST YEAR OF THE BME PARIS MASTER’S PROGRAM – M1
The first year of the BME-Paris Master’s (M1) is intended to strengthen and broaden students’ capacities in specific engineering and biomedical subjects. Students have one full year to learn fundamental and practical concepts that are required to obtain an interdisciplinary core before following a specific track of the M2.
The first semester starts with an integration week composed of:
- A general kickoff meeting that gives a condensed overview of the Master program
- An individual meeting with your academic tutor who is one of the M1 chairs
- 3 orientation days (team building, student organization, outdoor walking rally, Skills workshop, Pitch workshop, Mock interviews)
The courses will then take place on weekly basis. The students undertake a scientific thinking module and courses to the value of 30 ECTS credits (European Credit Transfer Scale). Student choices need to be approved by their academic tutor.
The Scientific thinking module is a compulsory common core (6 ECTS):
- Scientific communication
- Medicine and Science
- Open Your Mind seminars (every Friday, for M1 and M2 students)
- Culture and language (course of English and/or French as a foreign language)
Considering the wide variety of academic origins and backgrounds of the students, all the M1 courses are proposed at two levels, basic or advanced, to fill-in gaps in individual students’ capacities in a wide spectrum of fundamental science subjects. Students can design their own individualized curriculum by chosen at least six 4-credit (ECTS) courses from among the 15 offered.
NB. No schedule or syllabus will be provided before the kick-off meeting. You must know that it is a full-time program though.
Semester 1
Course Title: Anatomy & Physiology for engineers
Description: This course gives a general view of organs and tissues organization and physiological functions in the human body. It is divided in 2 parts: 1/ lectures on anatomy of human body with special focus on: the cardiovascular system, urogenital system, digestive system and neuroanatomy. The course material is covered in traditional lecture format as well as videos on the 3D anatomy. 2/ lectures on major physiological functions of human body with special focus on bone, cardiovascular and respiratory physiology illustrated with research articles.
Main objectives are:
– to understand anatomical structures and functional anatomy with their related pathologies
– to train the abilities to adapt the biotechnology to anatomical structures
– to become familiar with the applications of numeric tools for anatomy
– to understand fonctional links between organs/tissues sustaining physiological functions.
Key words: Anatomy, Physiology, functions, pathologies
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: No prerequisite
Teaching methods and activities: lab sessions (TP) lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Vincent DELMAS, Professor Dominique PRIE
Course Title: Molecular & cellular biology for engineers
Description: This course is designed for engineers and non-biologists to provide the essentials of cell and molecular biology and to get into more cellular complex networks important in biomedical research. The course material will be covered in traditional lecture format as well as practical sessions illustrating main techniques used in cellular biology research. Based on this course, the student will (i) acquire knowledge allowing to understand functional organization of eukaryotic cells: from macromolecules composing cells to organization and function of cell components ; (ii) be sensitized to “hot topics” of biomedical field such as epigenetics, bioenergetics, or in more integrated systems as the role of microbiota in organ integrity.
Main objectives are:
• To acquire knowledge in cellular and molecular biology
• To have all basic notions of technics used to study cellular components and functions
• To develop data analysis skills of cellular and molecular biology studies
• To be able to interact with researchers in the biomedical research field
Key words: Eukaryotic cell organization, Macromolecules, Cellular functions
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Teaching methods and activities: lab sessions (TP) lectures (CM)
Course supervisor: Associate Professor Anne-Sophie ARMAND
Course Title: Supramolecular chemistry
Description: This course is fundamental and interdisciplinary: the aim is for the student to be able to acquire a general vision of the concepts non-covalent interactions in order to understand molecular processes (self-assembly, structures of complex chemical systems, molecular recognition) and to be able to create new assemblies (synthesis, recognition and detection).
Course outline:
– Historical background – first examples, emergence of the field: crown ether (Lehn, Pedersen, and Cram).
– Definitions: weak interactions, chemistry at the thermodynamic equilibrium.
– Overview of the spectroscopic and analytical methods
– Towards complex structures: a) different classes (helix, macrocycle, cage, foldamer, grid, etc…). b) topological chemistry (catenanes, rotaxanes, knots, etc…).
– Synthetic methods and template effect.
– Structure-function relationship.
– Molecular devices (molecular machines, sensors for anions or cations).
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University.
Key words: Molecular processes, complex structures, structure-function relationship, molecular devices
Total number of hours: 30 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic knowledge and concepts in chemistry: thermodynamics, kinetics, coordination chemistry, atomistic (molecular orbital theory)
Teaching methods and activities:
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Benoit COLASSON
Course Title: Chemical engineering of nanoparticles for therapy and diagnostic
Description: This course deals with innovation approaches on nanomedecine in the fields of therapy, diagnosis and theranostic. Nanomedicine is at the forefront of modern healthcare. Nanoparticles offer a new platform for drug delivery that can extend the “patent life” of drugs, but also greatly increase the targeting and effectiveness of therapy. They can enhance most of the medical imaging modalities, and in some cases offer a combined diagnostic and therapy, now called “theranostics”. This course aims to provide students with the necessary training to be able to understand the principles of nanotechnology and its application in medical research and clinical practice. The practical course aims to broaden the knowledge and skills of the students in the areas of nanoparticle synthesis, characterization and processing in biomedical applications.
Course outline:
1/ Drug release and Diagnostic
– Nanomedecine – introduction (biodistribution, targeting, clearance)
– Drug release
– Diagnostic
2/ Therapy – thermotherapy
– Interaction between nanoparticles and cells
– Hyperthermia
Practical sessions:
– Synthesis of nanoparticles and characterization ;
– Biomedical applications: fonctionnalization by biomolecules and thermotherapy
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University
Key words: nanomedecine, drug delivery, thermotherapy, diagnostics
Total number of hours: 24 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of molecular and material chemistry and biology
Teaching methods and activities: lab sessions (TP) lectures (CM)
Exact location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Claire MANGENEY
Course Title: Mechanics I : Basics in non-deformable Solid Mechanics
Description: Non-deformable Solid Mechanics describes the motion of macroscopic objects, from projectiles to parts of machinery. If the present state of an object is known, it is possible to predict by the laws of classical mechanics how it will move in the future (determinism) and how it has moved in the past (reversibility). The earliest development of classical mechanics is often referred to as Newtonian mechanics. It consists of the physical concepts employed by and the mathematical methods invented by Isaac Newton and Gottfried Wilhelm Leibniz and others in the 17th century to describe the motion of bodies under the influence of a system of forces. The objective of this course is to train the students of the Life Sciences (Biologists sub-track) to the tools of the mechanics of the non-deformable solids. This course will be based on examples from the biomedical field and more particularly from biomechanical applications: articular biomechanics, muscular force evaluation, … etc. The course is divided into 16 hours of lectures and 16 hours of guided exercises, part of which will be performed on computer (Matlab).
Course outline:
1. Cinematics of point and solid.
2. Mechanical joints & kinematic diagram.
3. Modeling of mechanical actions.
4. Kinetics and Dynamics of solids.
5. Fundamental Principles of mechanics.
6. Energy theorems.
Key words: Solid mechanics, none-deformable solids, biomechanics
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of mathematics: Linear algebra (vector and matrices), Multivariate functions (derivatives and integrals), Vector and affine mathematical spaces.
Teaching methods and activities: lectures (CM) practical sessions (TD)
Exact location: Arts et Métiers ParisTech
Course supervisor: Professor Sebastien LAPORTE
Course Title: Physics for bIoImaging I – Magnetic resonance : towards biomedical applications
Description: Students will learn the basics of the spin physics that is underlying magnetic resonance, and discover the most recent spectroscopic and imaging applications based on this phenomenon.
The course is divided in 4 parts:
Introduction to Magnetic Resonance: physical basis, principle of pulsed NMR spectroscopy, principle of MRI.
Metabolomics: Introduction to « omics » sciences, and the contribution of metabolomics. Analytical techniques in metabolomics: Nuclear Magnetic Resonance and Mass Spectrometry, experiments, comparison of strengths and weaknesses. Basics of statistical analysis for metabolomics. Examples.
Magnetic Resonance Imaging: physical basis, gradient spatial encoding, concept of k space, contrast, spatial / spectral resolution issues. Introduction of contrast agents, comparison to other imaging techniques. Examples.
NMR in Biomedical Research and Development: Structural and dynamics analyses in biology, drug design (« SAR by NMR »).
Students will acquire basics of quantum mechanics for the description of the spin dynamics occurring during magnetic resonance experiments. They will be able to identify the potential of magnetic resonance techniques for providing an insight into a variety of systems in chemical, biological or medical studies, and to select the most adapted MR-based tools to address specific issues.
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University.
Key words: Nuclear Magnetic Resonance, Magnetic Resonance Imaging, Metabolomics
Total number of hours: 28 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions in organic structural chemistry, physical chemistry and biochemistry
Teaching methods and activities: lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Nicolas GIRAUD
Course Title: Physics for BioImaging II
Description: This course covers the physical principles of major bio-imaging modalities: from optical microscopy to ultrasound, positron emission tomography and magnetic resonance imaging. We will show how existing physical principles transcend into bio-imaging and establish an important link into life sciences, illustrating the contributions physics can make to life sciences. For each specific imaging instrumentation, biomedical applications will be shown to illustrate the respective imaging modality, its use, advantages and limitations. It is a project-based learning course where students work in groups on a specific imaging instrumentation. Based on this course, the student will be able to judge which imaging modality is adequate for specific life science needs and to understand the limits and advantages of each technique.
We will meet the objectives through a combination of the following activities in this course:
– Develop collective working (groups of 3 students) and project management
– Collect and select information and knowledge (inverted classroom)
– Plan and build a project-based learning
– Lab visit and demonstration
– Write a technical application note
Key words: Bioimaging, physics, instrumentation, project-based learning
Total number of hours: 18 Number of ECTS: 4 Semester 1
No prerequisite
Teaching methods and activities: lectures (CM), other: project-based learning, inverted classroom.
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Sophie BERNARD
Course Title: A mathematical introduction to data analysis
Description: The course is an introduction or a review of some fundamental topics in mathematics that are used in most domains where models have to be achieved. The main tool introduced is matrix and secondary tool deals with multivariate functions. The course material will be covered in traditional lecture format as well as practical sessions. In the end, students will have to compare their analytical results with those obtained with the aid of a mathematical software (Matlab).
Course objectives:
• Be familiar with operations and characteristics computed from matrices.
• Be able to introduce matrices to solve some problems.
• Understand how a matrix can model a linear transform.
• Understand how a matrix can model a quadratic form and define some distance notions.
• Be able to study the extreme points of multivariate functions.
• Be able to solve optimization problems under equality constraints.
• Be familiar with the least square method.
Key words: Matrices, multivariate functions, models
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: No prerequisite
Teaching methods and activities: lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Nicole VINCENT
Course Title: Applied Mathematics for biological systems
Description: This course will develop intermediate level mathematics with an emphasis on their utility for modeling in biology, physics or imaging. The course will have four main parts: 1/ Differential equations (systems, existence and unicity, maximal and global solutions, stability, numerical integrators: Euler, Runge-Kutta), 2/ Optimization (unconstrained and constrained, convexity, projection, algorithms: gradient and projected gradient descents), 3/ Probability (limit theorems, Markov chains, stochastic algorithms), 4/ Fourier Transforms (continuous and discrete, series, convolution, Fast Fourier Transforms). Sessions will alternate between standard lectures, analytical exercises and programming sessions (with Matlab and XPPAUT) to illustrate the topics and develop the practice of programming.
Key words: Differential equations, Optimization, Fourier Transform, Algorithms, Matlab
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: linear algebra (vectors and matrices), real analysis (continuity, limits, derivatives, integrals), numerical and geometrical sequences and series, Taylor series, multivariate calculus (limits, continuity, partial derivatives, multiple integrals)
Teaching methods and activities: lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Alexis GLAUNES
Course Title: Computer Programming
Description: The objective of this course is to give the student who has no skill in computer programming, the basic principles of object oriented programming. The studied object oriented languages will be Python and JAVA. As Python is an interpreted language and has basic syntax that is common to JAVA, it will help the student in their learning process in how to design simple programs (operators, flow control statements, functions). Then the focus will be put with the use of JAVA on the design of classes, the instanciation and the manipulation of objects. Finally, the relations between the objects (aggregation, inheritance) will be addressed.
Key words: Computer programming, Python, JAVA
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Teaching methods and activities: lab sessions (TP), lectures (CM)
Course supervisor: Associate Professor Florence CLOPPET,
Course assistant : Associate Professor Camille KURTZ
Course Title: BioMedical Modeling
Description: This course is an introduction to Biomedical Modeling, using Matlab software. With biomechanics and biomedical relevant examples, students will see: 1) How this tool can be used as an objective mean for automated data analysis, 2) How current biomedical knowledge can be implemented into models and simulations, 3) How it helps designing and analyzing new experiments.
Course objectives:
– Understand the need for physics and informatics in biomedical systems
– Learn the basics of Matlab programming and of programming thinking in general
– Learn how to simplify problems in order to extract the important parameters
– Learn how to generate understandable graphics for data interpretation
– Learn how to perform simple automated signal, image or video analysis
You will meet the objectives listed above through a combination of the following activities in this course:
– Putting together all the knowledge acquired in the Biology, Physics, Computer programming and Mathematics courses
– Being able to structure an algorithm and understand quickly where the code bugs
– Develop biologically relevant algorithms for data analysis and simulation
This course consists of lectures (Matlab basics 10h), 3 short project sessions (3x4h) and a final project.
Key words: Modeling, simulations, data analysis, Matlab
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Teaching methods and activities: lab sessions (TP), lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Sophie BERNARD
Course assistant: Researcher Ramon GUEVARA
Course Title: Biological modeling and dynamical systems
Description: This course aims at giving the sound bases for modeling biological systems. The emphasis will be put on modeling in neuroscience at different scales, from the molecular level to the collective dynamics of neuronal populations in the brain, but the concepts and methods taught in the course have a much broader relevance in biology. The interdisciplinary approach used in this course will rely on basic notions of biology, physics, chemistry, mathematics and computer programming. Lectures will be intertwined with practical sessions of modeling, analytical studies and numerical simulations that will heavily relied on the easy to use freeware XPPAUT. Students will learn: 1) the basic operating principles of neurons (and cells), 2) their biophysical and biochemical underpinning (receptors, signaling pathways), 3) how to model them with systems of ordinary differential equations, 4) how to analyze these mathematical models, 5) and how to simulate them numerically. This course will be particularly useful for students with a particular interest in neuroscience, while give a solid background in biology to all. It will constitute an introduction to dynamical systems theory (attractors, bifurcations), which is used in numerous scientific fields, and will demonstrate the usefulness of mathematical and physical concepts for understanding the operation of biological systems.
Key words:Biophysics of neurons, action potential, signaling pathways, receptors, dynamical systems
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of mathematics: matrices and linear differential equations. Basic notion of chemistry: reaction rates and kinetic equations. Familiarity with a programming language.
Teaching methods and activities: lab sessions (TP), lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints-Pères
Course supervisor: Researcher Claude MEUNIER
Course Title: Biology Advanced level: From molecular to cellular and tissue biology
Description: This course will cover several aspects of molecular, cellular and tissue biology focusing on the key actors of cellular /tissue homeostasis and their deregulation at the root of pathologies.
This course will provide a framework for students with basic (Bachelor) level in biochemistry and cell biology to acquire a comprehensive knowledge on topics in close contact with active research.
It is composed of 12 classes organized in 5 parts:
– Development & teratogenic effect of drugs
– Steroid hormones: signaling, physiological functions & deregulation
– Stem cells & tumoregenesis
– Brain homeostasis: from development to neurodegneration
– Imunology & deregulation during infection
and 4 training session on article analysis.
Course objectives are:
– to understand biological phenomena and their related pathology at the molecular level through the knowledge of signal transduction
– to train the abilities to collect, understand, summarize and present published data via article analyses.
– to become familiar with modern molecular and cellular biology techniques.
Key words: Cellular and tissue homeostasis, signaling, pathologic deregulations
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basis in Biochemistry and cellular biology
Teaching methods and activities: lectures (CM), other: research papers analysis
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Mathéa PIETRI
Course Title: Medicine & Science
Description: This course provides to students the opportunity to discover hot topics of Biomedical research and to encounter international researchers conducing these topics. The course is divided in 2 parts:
– Preparation and participation to scientific conferences in a subject closed to Biomedical engineering field. The preparation of conferences is conducted by groups of 2 to 4 students that have to present (i) a bibliography of a speaker, and (ii) a scientific topic corresponding to one conference session. During the conference, student pairs play the role of chairman and have to (i) introduce the speaker; (ii) ask questions after the talk and (iii) make an interview of the speaker.
– Analysis of scientific articles on Biomedical or Engineer topics. This part includes (i) the presentation of a topic by a researcher introducing articles to be analyzed, (ii) analysis and oral presentation of articles by pairs of students.
Key words: Scientific conference, article analysis, team work
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Teaching methods and activities: lectures (CM), practical sessions (TD), other: conferences
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Mathéa PIETRI
Course Title: Scientific thinking and Communication
Description: The goal of this course is to enhance students’ communication skills and give practical methods to effectively present and discuss scientific results. The course is designed to provide students with a range of resources and skills to write a thesis, prepare a presentation and develop constructive critical scientific thinking. Topics covered in this course include: – searching the scientific literature, – structure of a scientific paper, – references management and ethics in writing, – writing a literature review, – writing an internship report, – creating an effective presentation, – delivering an attractive talk, – designing a poster, The course consists of lectures, discussions, group work and practical exercises.
Total number of hours: 16 Number of ECTS: 2 Semester 1
Key words:Communication, methodology, scientific thinking
No prerequisite
Teaching methods and activities: lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints-Pères
Course supervisor: ProfessorSophie BERNARD
Under construction
Under construction
Course Title: Mechanics II : Continuous media mechanics
Description: This lecture is an introduction to Solids Mechanics. In this course, we will study the relationships between the external loads applied to a deformable body and the intensity of internal forces denoted stresses acting within the body. Illustrated on linear elastic material, we will define the relationship between stress and strain (constitutive relation) in order to provide tools allowing the sizing of structures. We will propose a systematic approach to solve these analytic problems and we will generalize these formulations using energetic theorems that will become the basis of the finite-elements theory.
Total number of hours: 32 Number of ECTS: 4 Semester 1
Key words: Strain tensor, stress tensor, constitutive relation, potential energy, strain energy
Prerequisite/skills needed: Basics in non-deformable Solid Mechanics
Teaching methods and activities: Lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Arts et Métiers ParisTech
Course supervisor: Philippe ROUCH (professor)
Full time Two-year program Entirely in English
M1 entry requirements: any Bachelor’s degree in Science
Two-subtracks were designed to fit with most common students' backgrounds:
Proposed M1 track for Engineers
Compulsory courses
Course Title: Anatomy & Physiology for engineers
Description: This course gives a general view of organs and tissues organization and physiological functions in the human body. It is divided in 2 parts: 1/ lectures on anatomy of human body with special focus on: the cardiovascular system, urogenital system, digestive system and neuroanatomy. The course material is covered in traditional lecture format as well as videos on the 3D anatomy. 2/ lectures on major physiological functions of human body with special focus on bone, cardiovascular and respiratory physiology illustrated with research articles.
Main objectives are:
– to understand anatomical structures and functional anatomy with their related pathologies
– to train the abilities to adapt the biotechnology to anatomical structures
– to become familiar with the applications of numeric tools for anatomy
– to understand fonctional links between organs/tissues sustaining physiological functions.
Key words: Anatomy, Physiology, functions, pathologies
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: No prerequisite
Teaching methods and activities: lab sessions (TP) lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Vincent DELMAS, Professor Dominique PRIE
Course Title: Molecular & cellular biology for engineers
Description: This course is designed for engineers and non-biologists to provide the essentials of cell and molecular biology and to get into more cellular complex networks important in biomedical research. The course material will be covered in traditional lecture format as well as practical sessions illustrating main techniques used in cellular biology research. Based on this course, the student will (i) acquire knowledge allowing to understand functional organization of eukaryotic cells: from macromolecules composing cells to organization and function of cell components ; (ii) be sensitized to “hot topics” of biomedical field such as epigenetics, bioenergetics, or in more integrated systems as the role of microbiota in organ integrity.
Main objectives are:
• To acquire knowledge in cellular and molecular biology
• To have all basic notions of technics used to study cellular components and functions
• To develop data analysis skills of cellular and molecular biology studies
• To be able to interact with researchers in the biomedical research field
Key words: Eukaryotic cell organization, Macromolecules, Cellular functions
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Teaching methods and activities: lab sessions (TP) lectures (CM)
Course supervisor: Associate Professor Anne-Sophie ARMAND
Course Title: Applied Mathematics for biological systems
Description: This course will develop intermediate level mathematics with an emphasis on their utility for modeling in biology, physics or imaging. The course will have four main parts: 1/ Differential equations (systems, existence and unicity, maximal and global solutions, stability, numerical integrators: Euler, Runge-Kutta), 2/ Optimization (unconstrained and constrained, convexity, projection, algorithms: gradient and projected gradient descents), 3/ Probability (limit theorems, Markov chains, stochastic algorithms), 4/ Fourier Transforms (continuous and discrete, series, convolution, Fast Fourier Transforms). Sessions will alternate between standard lectures, analytical exercises and programming sessions (with Matlab and XPPAUT) to illustrate the topics and develop the practice of programming.
Key words: Differential equations, Optimization, Fourier Transform, Algorithms, Matlab
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: linear algebra (vectors and matrices), real analysis (continuity, limits, derivatives, integrals), numerical and geometrical sequences and series, Taylor series, multivariate calculus (limits, continuity, partial derivatives, multiple integrals)
Teaching methods and activities: lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Alexis GLAUNES
Course Title: Biological modeling and dynamical systems
Description: This course aims at giving the sound bases for modeling biological systems. The emphasis will be put on modeling in neuroscience at different scales, from the molecular level to the collective dynamics of neuronal populations in the brain, but the concepts and methods taught in the course have a much broader relevance in biology. The interdisciplinary approach used in this course will rely on basic notions of biology, physics, chemistry, mathematics and computer programming. Lectures will be intertwined with practical sessions of modeling, analytical studies and numerical simulations that will heavily relied on the easy to use freeware XPPAUT. Students will learn: 1) the basic operating principles of neurons (and cells), 2) their biophysical and biochemical underpinning (receptors, signaling pathways), 3) how to model them with systems of ordinary differential equations, 4) how to analyze these mathematical models, 5) and how to simulate them numerically. This course will be particularly useful for students with a particular interest in neuroscience, while give a solid background in biology to all. It will constitute an introduction to dynamical systems theory (attractors, bifurcations), which is used in numerous scientific fields, and will demonstrate the usefulness of mathematical and physical concepts for understanding the operation of biological systems.
Key words:Biophysics of neurons, action potential, signaling pathways, receptors, dynamical systems
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of mathematics: matrices and linear differential equations. Basic notion of chemistry: reaction rates and kinetic equations. Familiarity with a programming language.
Teaching methods and activities: lab sessions (TP), lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints-Pères
Course supervisor: Researcher Claude MEUNIER
Two elective courses among
Course Title: Physics for BioImaging II
Description: This course covers the physical principles of major bio-imaging modalities: from optical microscopy to ultrasound, positron emission tomography and magnetic resonance imaging. We will show how existing physical principles transcend into bio-imaging and establish an important link into life sciences, illustrating the contributions physics can make to life sciences. For each specific imaging instrumentation, biomedical applications will be shown to illustrate the respective imaging modality, its use, advantages and limitations. It is a project-based learning course where students work in groups on a specific imaging instrumentation. Based on this course, the student will be able to judge which imaging modality is adequate for specific life science needs and to understand the limits and advantages of each technique.
We will meet the objectives through a combination of the following activities in this course:
– Develop collective working (groups of 3 students) and project management
– Collect and select information and knowledge (inverted classroom)
– Plan and build a project-based learning
– Lab visit and demonstration
– Write a technical application note
Key words: Bioimaging, physics, instrumentation, project-based learning
Total number of hours: 18 Number of ECTS: 4 Semester 1
No prerequisite
Teaching methods and activities: lectures (CM), other: project-based learning, inverted classroom.
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Sophie BERNARD
Course Title: Computer Programming
Description: The objective of this course is to give the student who has no skill in computer programming, the basic principles of object oriented programming. The studied object oriented languages will be Python and JAVA. As Python is an interpreted language and has basic syntax that is common to JAVA, it will help the student in their learning process in how to design simple programs (operators, flow control statements, functions). Then the focus will be put with the use of JAVA on the design of classes, the instanciation and the manipulation of objects. Finally, the relations between the objects (aggregation, inheritance) will be addressed.
Key words: Computer programming, Python, JAVA
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Teaching methods and activities: lab sessions (TP), lectures (CM)
Course supervisor: Associate Professor Florence CLOPPET,
Course assistant : Associate Professor Camille KURTZ
Under construction
Course Title: Mechanics II : Continuous media mechanics
Description: This lecture is an introduction to Solids Mechanics. In this course, we will study the relationships between the external loads applied to a deformable body and the intensity of internal forces denoted stresses acting within the body. Illustrated on linear elastic material, we will define the relationship between stress and strain (constitutive relation) in order to provide tools allowing the sizing of structures. We will propose a systematic approach to solve these analytic problems and we will generalize these formulations using energetic theorems that will become the basis of the finite-elements theory.
Total number of hours: 32 Number of ECTS: 4 Semester 1
Key words: Strain tensor, stress tensor, constitutive relation, potential energy, strain energy
Prerequisite/skills needed: Basics in non-deformable Solid Mechanics
Teaching methods and activities: Lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Arts et Métiers ParisTech
Course supervisor: Philippe ROUCH (professor)
Proposed M1 track for Biologists
Compulsory courses
Course Title: Scientific thinking and Communication
Description: The goal of this course is to enhance students’ communication skills and give practical methods to effectively present and discuss scientific results. The course is designed to provide students with a range of resources and skills to write a thesis, prepare a presentation and develop constructive critical scientific thinking. Topics covered in this course include: – searching the scientific literature, – structure of a scientific paper, – references management and ethics in writing, – writing a literature review, – writing an internship report, – creating an effective presentation, – delivering an attractive talk, – designing a poster, The course consists of lectures, discussions, group work and practical exercises.
Total number of hours: 16 Number of ECTS: 2 Semester 1
Key words:Communication, methodology, scientific thinking
No prerequisite
Teaching methods and activities: lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: ProfessorSophie BERNARD
Course Title: A mathematical introduction to data analysis
Description: The course is an introduction or a review of some fundamental topics in mathematics that are used in most domains where models have to be achieved. The main tool introduced is matrix and secondary tool deals with multivariate functions. The course material will be covered in traditional lecture format as well as practical sessions. In the end, students will have to compare their analytical results with those obtained with the aid of a mathematical software (Matlab).
Course objectives:
• Be familiar with operations and characteristics computed from matrices.
• Be able to introduce matrices to solve some problems.
• Understand how a matrix can model a linear transform.
• Understand how a matrix can model a quadratic form and define some distance notions.
• Be able to study the extreme points of multivariate functions.
• Be able to solve optimization problems under equality constraints.
• Be familiar with the least square method.
Key words: Matrices, multivariate functions, models
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: No prerequisite
Teaching methods and activities: lab sessions (TP), lectures (CM), practical sessions (TD)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Nicole VINCENT
Course Title: Computer Programming
Description: The objective of this course is to give the student who has no skill in computer programming, the basic principles of object oriented programming. The studied object oriented languages will be Python and JAVA. As Python is an interpreted language and has basic syntax that is common to JAVA, it will help the student in their learning process in how to design simple programs (operators, flow control statements, functions). Then the focus will be put with the use of JAVA on the design of classes, the instanciation and the manipulation of objects. Finally, the relations between the objects (aggregation, inheritance) will be addressed.
Key words: Computer programming, Python, JAVA
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Teaching methods and activities: lab sessions (TP), lectures (CM)
Course supervisor: Associate Professor Florence CLOPPET,
Course assistant : Associate Professor Camille KURTZ
Course Title: BioMedical Modeling
Description: This course is an introduction to Biomedical Modeling, using Matlab software. With biomechanics and biomedical relevant examples, students will see: 1) How this tool can be used as an objective mean for automated data analysis, 2) How current biomedical knowledge can be implemented into models and simulations, 3) How it helps designing and analyzing new experiments.
Course objectives:
– Understand the need for physics and informatics in biomedical systems
– Learn the basics of Matlab programming and of programming thinking in general
– Learn how to simplify problems in order to extract the important parameters
– Learn how to generate understandable graphics for data interpretation
– Learn how to perform simple automated signal, image or video analysis
You will meet the objectives listed above through a combination of the following activities in this course:
– Putting together all the knowledge acquired in the Biology, Physics, Computer programming and Mathematics courses
– Being able to structure an algorithm and understand quickly where the code bugs
– Develop biologically relevant algorithms for data analysis and simulation
This course consists of lectures (Matlab basics 10h), 3 short project sessions (3x4h) and a final project.
Key words: Modeling, simulations, data analysis, Matlab
Total number of hours: 32 Number of ECTS: 4 Semester 1
No prerequisite
Teaching methods and activities: lab sessions (TP), lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Sophie BERNARD
Course assistant: Researcher Ramon GUEVARA
Under construction
Two elective courses among
Course Title: Mechanics I : Basics in non-deformable Solid Mechanics
Description: Non-deformable Solid Mechanics describes the motion of macroscopic objects, from projectiles to parts of machinery. If the present state of an object is known, it is possible to predict by the laws of classical mechanics how it will move in the future (determinism) and how it has moved in the past (reversibility). The earliest development of classical mechanics is often referred to as Newtonian mechanics. It consists of the physical concepts employed by and the mathematical methods invented by Isaac Newton and Gottfried Wilhelm Leibniz and others in the 17th century to describe the motion of bodies under the influence of a system of forces. The objective of this course is to train the students of the Life Sciences (Biologists sub-track) to the tools of the mechanics of the non-deformable solids. This course will be based on examples from the biomedical field and more particularly from biomechanical applications: articular biomechanics, muscular force evaluation, … etc. The course is divided into 16 hours of lectures and 16 hours of guided exercises, part of which will be performed on computer (Matlab).
Course outline:
1. Cinematics of point and solid.
2. Mechanical joints & kinematic diagram.
3. Modeling of mechanical actions.
4. Kinetics and Dynamics of solids.
5. Fundamental Principles of mechanics.
6. Energy theorems.
Key words: Solid mechanics, none-deformable solids, biomechanics
Total number of hours: 32 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of mathematics: Linear algebra (vector and matrices), Multivariate functions (derivatives and integrals), Vector and affine mathematical spaces.
Teaching methods and activities: lectures (CM) practical sessions (TD)
Exact location: Arts et Métiers ParisTech
Course supervisor: Professor Sebastien LAPORTE
Course Title: Physics for bIoImaging I – Magnetic resonance : towards biomedical applications
Description: Students will learn the basics of the spin physics that is underlying magnetic resonance, and discover the most recent spectroscopic and imaging applications based on this phenomenon.
The course is divided in 4 parts:
Introduction to Magnetic Resonance: physical basis, principle of pulsed NMR spectroscopy, principle of MRI.
Metabolomics: Introduction to « omics » sciences, and the contribution of metabolomics. Analytical techniques in metabolomics: Nuclear Magnetic Resonance and Mass Spectrometry, experiments, comparison of strengths and weaknesses. Basics of statistical analysis for metabolomics. Examples.
Magnetic Resonance Imaging: physical basis, gradient spatial encoding, concept of k space, contrast, spatial / spectral resolution issues. Introduction of contrast agents, comparison to other imaging techniques. Examples.
NMR in Biomedical Research and Development: Structural and dynamics analyses in biology, drug design (« SAR by NMR »).
Students will acquire basics of quantum mechanics for the description of the spin dynamics occurring during magnetic resonance experiments. They will be able to identify the potential of magnetic resonance techniques for providing an insight into a variety of systems in chemical, biological or medical studies, and to select the most adapted MR-based tools to address specific issues.
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University.
Key words: Nuclear Magnetic Resonance, Magnetic Resonance Imaging, Metabolomics
Total number of hours: 28 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions in organic structural chemistry, physical chemistry and biochemistry
Teaching methods and activities: lectures (CM)
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Nicolas GIRAUD
Course Title: Supramolecular chemistry
Description: This course is fundamental and interdisciplinary: the aim is for the student to be able to acquire a general vision of the concepts non-covalent interactions in order to understand molecular processes (self-assembly, structures of complex chemical systems, molecular recognition) and to be able to create new assemblies (synthesis, recognition and detection).
Course outline:
– Historical background – first examples, emergence of the field: crown ether (Lehn, Pedersen, and Cram).
– Definitions: weak interactions, chemistry at the thermodynamic equilibrium.
– Overview of the spectroscopic and analytical methods
– Towards complex structures: a) different classes (helix, macrocycle, cage, foldamer, grid, etc…). b) topological chemistry (catenanes, rotaxanes, knots, etc…).
– Synthetic methods and template effect.
– Structure-function relationship.
– Molecular devices (molecular machines, sensors for anions or cations).
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University.
Key words: Molecular processes, complex structures, structure-function relationship, molecular devices
Total number of hours: 30 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic knowledge and concepts in chemistry: thermodynamics, kinetics, coordination chemistry, atomistic (molecular orbital theory)
Teaching methods and activities:
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Benoit COLASSON
Course Title: Chemical engineering of nanoparticles for therapy and diagnostic
Description: This course deals with innovation approaches on nanomedecine in the fields of therapy, diagnosis and theranostic. Nanomedicine is at the forefront of modern healthcare. Nanoparticles offer a new platform for drug delivery that can extend the “patent life” of drugs, but also greatly increase the targeting and effectiveness of therapy. They can enhance most of the medical imaging modalities, and in some cases offer a combined diagnostic and therapy, now called “theranostics”. This course aims to provide students with the necessary training to be able to understand the principles of nanotechnology and its application in medical research and clinical practice. The practical course aims to broaden the knowledge and skills of the students in the areas of nanoparticle synthesis, characterization and processing in biomedical applications.
Course outline:
1/ Drug release and Diagnostic
– Nanomedecine – introduction (biodistribution, targeting, clearance)
– Drug release
– Diagnostic
2/ Therapy – thermotherapy
– Interaction between nanoparticles and cells
– Hyperthermia
Practical sessions:
– Synthesis of nanoparticles and characterization ;
– Biomedical applications: fonctionnalization by biomolecules and thermotherapy
This course is proposed by the Master “Frontiers in Chemistry” of Paris Descartes University
Key words: nanomedecine, drug delivery, thermotherapy, diagnostics
Total number of hours: 24 Number of ECTS: 4 Semester 1
Prerequisites/skills needed: Basic notions of molecular and material chemistry and biology
Teaching methods and activities: lab sessions (TP) lectures (CM)
Exact location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Professor Claire MANGENEY
Semester 2
The second semester (M2) is mainly devoted to complementary and experimental skills (30 ECTS):
Under construction
Under construction
Course Title: Scientific Writing
Description: This personal student work consists in writing a review paper on a subject matter central to your internship or project. By organizing, integrating and summarizing previously published data, this work will benefit to improve your scientific communication and will give you a solid understanding of how your research project fits in to what the scientific community has already done.
Main objectives are:
– to understand a topic
– to strengthen the critical thinking
– to become more familiar with software used for illustration, bibliography…
Total number of hours: Number of ECTS: 3 Semester 2
Key words:scientific communication, critical thinking, literature review
No prerequisite
Teaching methods and activities: report
Location: Université Paris Descartes, Centre Universitaire des Saints Pères
Course supervisor: Associate Professor Mathéa PIETRI
Course Title: BioTech FabLab projects
Description: The aim of these interdisciplinary projects is to promote active learning by real case studies to face. We will challenge a group of 4 students with a real scientific question and they will have to explore and find a solution by designing and developing their own experiment and collect data. Finally, they will have to propose a model which behavior matches the data they recorded. These collaborative projects will be carried out throughout the second semester of the M1 to allow students to apply theoretical knowledge and skills learned during the first semester. Students will be leaded by a researcher and they will have access to a BioTech FabLab to build, engineer, design and make a prototype for their projects. If they need they will have also access to the technological platforms (FACS, imaging, biochemistry…) of the Biomedical department but also to labs. These projects will consolidate their understanding of an interdisciplinary subject and develop transversal skills such as team spirit, leadership and also the capacity to take initiative, to test, to overcome problems and to innovate.
Key words: FabLab, project-based learning, team working, interdisciplinarity
Total number of hours: Personal work Number of ECTS: 12 Semester 2
No prerequisite
Teaching methods and activities: lab sessions (TP)other: Project management and team working
Location: Université Paris Descartes, Centre Universitaire des Saints-Pères
Course supervisor: ResearcherVincent FLEURY, Professor Sophie BERNARD
Please note that you must have successfully completed the M1 year (60 ECTS) at Université Paris Cité in order to progress to M2. You will be enrolled as a Université Paris Cité student for the two years.
