Teaching#
Current teaching#
Mechanics of the Cell (graduate, PhD/MSc), PHY9805.
Western University Physics, winter 2024
Material: Mechanics of the Cell by David Boal, Cambridge Univ. Press.
Topics: The origin and determination of elastic properties and shape fluctuations of cells, and the properties of protein networks, in particular, actin filament networks that determine the mechanical properties of cells and soft materials; Brief introduction to cells; Emphasis is on theoretical treatment (using classical mechanics, statistical mechanics and thermodynamics, and the theory of elasticity) of cellular structures such as filament networks (cytoskeleton) and membranes, and how they give rise to mechanical versatility of cells; Cellular shapes, sizes, structures; Polymers: Filaments in cells, chain configuration and elasticity, elasticity of cellular filaments; Two dimensional networks: Actin filament Networks in 2d and their theoretical modelling; Three dimensional networks: Networks of biological polymers; Elastic moduli, entropic networks, rheological properties of the cytoskeleton; Membranes: biomembranes: self-assembly, elastic properties (compression, bending, Helfrich model); Membrane undulations: Curvature of membranes, scaling properties of membranes and polymers; Mechanical design: Tension and compression. Application to soft materials.
Scientific Computing, SC9502B (graduate, PhD/MSc).
Western University Collaborative Graduate Program in Scientific Computing, winter 2024
Last edition’s lecture notes: Scientific Computing.
Topics include: Common methods used in scientific computing, high performance computing methods, visualization of data, numerical solutions to various problems, error analysis, parallel programming paradigm, and introduction to machine learning. This is a hands-on course - it involves programming and using open source software; you must have access to a computer & ability to install and run software on it.
New lectures notes will be distributed in class. New topic to be discused this year: Introduction to machine learning.
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Continuously throughout the year
Compulsory for all MSc and PhD students in the Collaborative GraduateProgram in Scientific Computing.
2022-2023#
Molecular Dynamics Simulations, Chemistry 9664B (graduate, PhD/MSc)
Description: To aim of this course is to familiarize the student with modern computational methods and methodology in materials and biomaterials modeling. Emphasis is put on direct hands-on experience. The course provides a broad overview of the common methods in the framework of molecular dynamics and their applicability and, importantly, how to relate the data to experiments. Simulations of proteins, lipid bilayers and solvation of organic molecules will be performed. The course will be a balanced treatment of modeling, data analysis, visualization and relation to experimentally observable / measurable phenomena. Programming with Python. Gromacs will also be used.
Lecture notes: Molecular dynamics
Special topics in condensed matter physics, Physics 9815 (graduate, PhD).
Material: Principles of Condensed Matter Physics by Chaikin and Lubensky
Topics: Field theories, renormalization group, correlations and response, topolgical defects, generalized elasticity.
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2021-2022#
Scientific Computing, SC9502B (graduate, PhD/MSc).
Western University Applied Mathematics/ Scientific Computing Program
Lecture notes: Scientific Computing
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2020-2021#
Computer methods in Chemistry, Chemistry 3300G (undergraduate)
Topics: Linux, the Python programming language, overview of MD simulations - algorithms, thermostats, potentials, Gromacs and how it works, review of thermodynamics and statistical mechanics, data analysis - structure, correlations, visualization
Phase field modeling, Applied Mathematics 9635B (graduate, PhD/MSc).
Western University Applied Mathematics, Theoretical Physics Program
This course focused on phase field modeling and the numerical techniques used in solving finite difference equations.
Topics: Ginzburg-Landau theory, mathematical derivation of phase field models, asymptotic expansions, finite difference schemes in solving the phase field partial difference equations, conservation laws and constitutive relations; characteristics; transformations.
Material: Phase‐Field Methods in Materials Science and Engineering, N. Provatas and K. Elder, Wiley (2010)
Scientific Computing, SC9502B (graduate, PhD/MSc).
Western University Applied Mathematics/ Scientific Computing Program
Lecture notes: Scientific Computing
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2019-2020#
Special topics in multiscale modeling, Applied Mathematics 9628A (graduate, PhD/MSc).
Western University Applied Mathematics / Theoretical Physics
Content: Modern methods in multiscale simulations with emphasis on analytical techniques based on the Fokker-Planck equation and Mori-Zwanzig -based projection methods.
Partial differential equations, Applied Mathematics 9505B (graduate, PhD/MSc)
Western University Applied Mathematics
Content: PDEs including reaction-diffusion equations such Turing systems, Ginzburg-Landau type equations, derivations of PDEs using symmetry, instabilities: pattern formation and non-equilibrium patterns heat equation, numerical solutions, Green’s functions
Computer methods in Chemistry, Chemistry 3300G (undergraduate)
Material: Lecture notes
Topics: Linux, the Python programming language, overview of MD simulations - algorithms, thermostats, potentials, Gromacs and how it works, review of thermodynamics and statistical mechanics, data analysis - structure, correlations
International Winter School “Physics of the Cell”.
Dept. of Physics, University of Trento, Italy, Jan. 20-31, 2020.
Lecture series and computer labs on computational modeling of the mechanical properties of cells.
European Credit Transfer and Accumulation System (ECTS) credited course.
Other lecturers: Garegin Papoian (University of Maryland, College Park, United States of America), Sarah Harris (University of Leeds, UK), Patricia Faisca (University of Lisbon, Portugal), Giuseppe Milano (University of Salerno and Yamagata University, Japan), Ralf Everaers (ENS de Lyon, France), Angelo Rosa (SISSA, Trieste).
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2018-2019#
Materials and Biomaterials, Western Integrated Science 3001F/G (undergraduate).
Western University
Material: Marc Andre Meyers and Po-Yu Chen: Biological Materials Science, Cambridge University Press (2014).
Chapters 1-6 (Evolution of materials science and engineering: from natural to bioinspired materials, Self-assembly, hierarchy, and evolution, Basic building blocks: biopolymers, Cells, Biomineralization, Silicate- and calcium-carbonate-based composites)
Molecular Dynamics Simulations, Chemistry 9664B (graduate, PhD/MSc)
hands-on experience using production-quality molecular dynamics software. The course provides a broad overview of the common methods in the framework of molecular dynamics and their applicability and, importantly, how to relate the data to experiments. Simulations of proteins, lipid bilayers and solvation of organic molecules will be performed.
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2017-2018#
Partial differential equations, Applied Mathematics 9505B (graduate, PhD/MSc)
Western University Applied Mathematics
Content: PDEs including reaction-diffusion equations such Turing systems, Ginzburg-Landau type equations, derivations of PDEs using symmetry, instabilities: pattern formation and non-equilibrium patterns heat equation, numerical solutions, Green’s functions
2016-2017#
First year calculus, 2WBB00 (undergraduate)
Eindhoven University of Technology Mathematics & Computer Science.
Topics: arithmetic skills and functions, limits, differentiation, integration, (first order) differential equations, simple vector calculation of planes and space
Introduction to Molecular Modeling and Simulation, 2MMN40 (graduate, MSc)
Eindhoven University of Technology Mathematics & Computer Science, shared teaching.
Topics: Molecular simulations, hands-on computer exercises.
2015-2016#
First year calculus, 2WBB00 (undergraduate).
Eindhoven University of Technology Mathematics & Computer Science.
Topics: arithmetic skills and functions, limits, differentiation, integration, (first order) differential equations, simple vector calculation of planes and space
2014-2015#
Special Topics in Nanoscale Simulations, NE452 (undergraduate).
University of Waterloo Nanotechnology Engineering
Applications and extensions of the Monte Carlo method. Applications in modelling magnetic materials and phase transitions. Ising model, XY model, lattice gas, phase-field models.
Mechanics of the Cell (graduate, PhD/MSc).
University of Waterloo Physics
Material: Mechanics of the Cell by David Boal, Cambridge Univ. Press.
2013-2014#
Special Topics in Nanoscale Simulations, NE452 (undergraduate).
University of Waterloo Nanotechnology Engineering
Applications and extensions of the Monte Carlo method. Applications in modelling magnetic materials and phase transitions. Ising model, XY model, lattice gas, phase-field models.
NE451 Simulation Methods in Nanotechnology Engineering (undergraduate).
University of Waterloo Nanotechnology Engineering
Description: This course provides an introduction to and an overview of computational methods that are currently employed for the simulation of structural and bulk properties of matter, particularly as applied to physical and biological systems at the nanometer scale.
Topics: Energy functions and force fields, geometry optimization (molecular), normal mode analysis, and reaction–path techniques at the molecular level, and an introduction to the simulation of static and dynamic properties of substances via both Monte Carlo and molecular dynamics (MD) methodologies.
Mechanics of the Cell, (graduate, PhD/MSc).
University of Waterloo Physics
Material: Mechanics of the Cell by David Boal, Cambridge Univ. Press.
Transport in Nanoscales (graduate, PhD/MSc).
University of Waterloo Physics
Material: Quantum Transport Atom to Transistor, by Supriyo Datta, Cambridge University Press
2012-2013#
NE451 Simulation Methods in Nanotechnology Engineering (undergraduate).
University of Waterloo Nanotechnology Engineering
Description: This course provides an introduction to and an overview of computational methods that are currently employed for the simulation of structural and bulk properties of matter, particularly as applied to physical and biological systems at the nanometer scale.
Topics: Energy functions and force fields, geometry optimization (molecular), normal mode analysis, and reaction–path techniques at the molecular level, and an introduction to the simulation of static and dynamic properties of substances via both Monte Carlo and molecular dynamics (MD) methodologies.
Mathematical Methods for Chemistry, CHEM240 (undergraduate)
University of Waterloo Chemistry
Mathematical techniques useful for Chemistry students. Introduction to complex numbers; topics chosen from calculus; differential equations; vector spaces and vector algebra; matrices and determinants; basic group theory and symmetry. Applications to problems of chemical interest.
Material: D.A. McQuarrie, Mathematics for Physical Chemistry
2011-2012#
NE451 Simulation Methods in Nanotechnology Engineering (undergraduate).
University of Waterloo Nanotechnology Engineering
Description: This course provides an introduction to and an overview of computational methods that are currently employed for the simulation of structural and bulk properties of matter, particularly as applied to physical and biological systems at the nanometer scale.
Topics: Energy functions and force fields, geometry optimization (molecular), normal mode analysis, and reaction–path techniques at the molecular level, and an introduction to the simulation of static and dynamic properties of substances via both Monte Carlo and molecular dynamics (MD) methodologies.
Mathematical Methods for Chemistry, CHEM240 (undergraduate)
University of Waterloo Chemistry
Mathematical techniques useful for Chemistry students. Introduction to complex numbers; topics chosen from calculus; differential equations; vector spaces and vector algebra; matrices and determinants; basic group theory and symmetry. Applications to problems of chemical interest.
Advanced Methods of Applied Mathematics, Applied Mathematics 9607 (graduate, PhD/MSc).
Western University
Team taught course. My share (1/3): Introduction to pattern formation and reaction-diffusion equations.
2010-2011#
Scientific Computing, Applied Mathematics 9502 (graduate, PhD/MSc).
Western University
Topics: Random numbers, errors in scientific computing, interpolation, numerical differentiation and integration, parallel programming using MPI.
Statistical Physics, Applied Mathematics 9531 (graduate, PhD/MSc)
Western University, Theoretical Physics Program
Material: Mehran Kardar, Statistical Physics of Particles
Complex variables, Applied Mathematics 3811 (undergraduate).
Western University Applied Mathematics
Contents: The algebra of complex numbers, point representation, vectors and polar form, the complex exponential powers and roots, planar sets, functions of complex variables, limits and continuity, Cauchy-Riemann equations, harmonic functions, polynomials and rational functions, the exponential, trigonometric, and hyperbolic functions, logarithmic functions, complex powers and inverse trigonometric functions, contours & contour integrals, independence of paths, cauchy’s integral formula and its consequences, sequences and series, the residue theorem
Soft matter and biological physics, AM 9605 (graduate, PhD/MSc).
Western University, Theoretical Physics Program
Material: Lecture notes and “Physics in Molecular Biology” by Kim Sneppen and Giovanni Zocchi
Materials Modelling, Applied Mathematics 9567 (graduate, PhD/MSc)
Western University Applied Mathematics, Theoretical Physics Program
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2009-2010#
Statistical Physics II (graduate, PhD).
Western University
Material: Mehran Kardar, Statistical Physics of Fields
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2008-2009#
Theoretical Condensed Matter Physics, Applied Mathematics 9579 (graduate, PhD).
Western University, Theoretical Physics Program
Material: Lecture notes
Topics: Structure, thermodynamics and statistical mechanics, symmetries and conservation laws, topological defects.
Finite Element Method, Applied Mathematics 4613B / 9595 (undergraduate and graduate, MSc).
Western University
Material: Lecture notes
Topics: The basics of the Finite Element Method (FEM). FEM is a very powerful and general method, and we will focus on the general aspects and the background of the method. After gaining the necessary theoretical background (calculus of variations) during the first half of the course, in the second half we put the ideas and concepts into practice and study the methods from the computational point of view. This second half contains a good amount of programming, and it is essential that the students have a good background in C, C++, Java, Fortran or comparable. The course also contains a project work which is of computational nature.
Mathematical Modeling, Applied Mathematics 3911G / 9570 (undergraduate and graduate, MSc).
Contents: Random number generators, random walks (RW), oscillatory systems, normal modes and waves, bifurcation and bifurcation control, complex systems: Hopfield Model and neural networks, Monte Carlo simulation: Ising model, chaos control and chaos synchronization, fractal dimension, particle simulations This course involves programming. Prior knowledge of some programming language is essential (e.g. C/C++, Fortran, Java, Python, Pascal)
Jyväskylä International Summer School, Jyväskylä, Finland, Aug. 11-15, 2008.
Lecture series (\(5 \times 2\)hrs) on Electrostatic effects in Biological and Soft Matter.
The course is accepted in European Credit Transfer and Accumulation System (ECTS) for graduate students.
SC9501 / SC9601: Scientific Computing MSc/PhD Seminar
Compulsory for all MSc and PhD students in the Scientific Computing Collaborative Program.
2007-2008#
Statistical Physics, Applied Mathematics 531 / Physics 504b (graduate, PhD/MSc).
Western University, Theoretical Physics Program
Topics: Review of thermodynamics, thermodynamic potentials, basic concepts of probability, distribution functions, the Liouville’s theorem, ideal gases, real gases, virial expansion, cluster expansion. Liquids, BBGY hierarchy. Quantum liquids and solids. The Ising model. Phase transitions.
Theoretical Condensed Matter Physics, Applied Mathematics 579B (graduate, PhD).
Western University, Theoretical Physics Program
Material: Lecture notes
Topics: Structure, thermodynamics and statistical mechanics, symmetries and conservation laws, topological defects.
2006-2007#
Applied mathematics (mathematics for Engineers), Applied Mathematics 375a (undergraduate).
Western University
Material: Advanced Engineering Mathematics by Zill and Cullen, 2nd edition, Jones and Bartlett Publ.
Topics: Laplace transforms and their applications to ordinary differential equations, Fourier Series and their applications to partial differential equations, Fourier transforms and boundary value problems, the Sturm Liouville problem, heat equation.
Finite Element Method, Applied Mathematics 466b / 562b (undergraduate/graduate).
Western University
Material: Lecture notes
Topics: The basics of the Finite Element Method (FEM). FEM is a very powerful and general method, and we will focus on the general aspects and the background of the method. After gaining the necessary theoretical background (calculus of variations) during the first half of the course, in the second half we put the ideas and concepts into practice and study the methods from the computational point of view. This second half contains a good amount of programming, and it is essential that the students have a good background in C, C++, Java, Fortran or comparable. The course also contains a project work which is of computational nature.
2005-2006#
Applied mathematics (mathematics for Engineers), Applied Mathematics 375a (undergraduate).
Western University
Material: Advanced Engineering Mathematics by Zill and Cullen, 2nd edition, Jones and Bartlett Publ.
Topics: Laplace transforms and their applications to ordinary differential equations, Fourier Series and their applications to partial differential equations, Fourier transforms and boundary value problems, the Sturm Liouville problem, heat equation.
Statistical Physics, Applied Mathematics 531 / Physics 504b (graduate, PhD/MSc).
Western University, Theoretical Physics Program
Topics: Review of thermodynamics, thermodynamic potentials, basic concepts of probability, distribution functions, the Liouville’s theorem, ideal gases, real gases, virial expansion, cluster expansion. Liquids, BBGY hierarchy. Quantum liquids and solids. The Ising model. Phase transitions.
Summer School of the RQMP – Regroupement québécois sur les matériaux de pointe, Sherbrooke, Canada, Jul. 1-3, 2005.
Lecture series on Phase transitions and soft matter systems.
Introduction to soft matter physics, Tfy-3.363 (undergraduate)
Helsinki University of Technology.
For 2nd and 3rd year MSc students in physics.
Material: Lecture notes and I.W. Hamley: Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals, Wiley (2000).
Topics include: Basic statistical mechanics & thermodynamics, phase transition, properties of polymers, inter- and intramolecular interactions, colloids, electrostatics, amphiphilic systems, basics of liquid crystalline systems, and biomembranes.
2004-2005#
Advanced Topics in Biological and Soft-Matter Systems, Tfy-3.462 (graduate, PhD)
Helsinki University of Technology.
Material: Lecture notes.
Contents: introduction to colloidal systems, electrostatic interactions, Poisson-Boltzmann theory, DLVO theory, properties of surfactants, lipids and water.
Introduction to soft matter physics, Tfy-3.363 (undergraduate)
Helsinki University of Technology.
For 2nd and 3rd year MSc students in physics.
Material: Lecture notes and I.W. Hamley: Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals, Wiley (2000).
Topics include: Basic statistical mechanics & thermodynamics, phase transition, properties of polymers, inter- and intramolecular interactions, colloids, electrostatics, amphiphilic systems, basics of liquid crystalline systems, and biomembranes.
2003-2004#
Special topics in computational science, S114.250 (MSc)
Helsinki University of Technology.
Topics: Particle and continuum simulations: Molecular dynamics, free energy, dissipative particle dynamics. Introduction to phase field modeling and lattice-Boltzmann.
Finnish National Graduate School for Pharmaceutical Research, Helsinki, Finland, Dec. 13-17. 2004.
Audience: PhD students in biochemistry and pharmaceutical research.
Lecture series on biomolecular modeling and its relation biochemical and pharmaceutical research.
Material: Lecture notes
Introduction to soft matter physics, Tfy-3.363 (undergraduate)
Helsinki University of Technology.
For 2nd and 3rd year MSc students in physics.
Material: Lecture notes and I.W. Hamley: Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals, Wiley (2000).
Topics include: Basic statistical mechanics & thermodynamics, phase transition, properties of polymers, inter- and intramolecular interactions, colloids, electrostatics, amphiphilic systems, basics of liquid crystalline systems, and biomembranes.
2002-2003#
Special topics in computational science, S114.250 (MSc)
Helsinki University of Technology.
Topics: Particle and continuum simulations: Molecular dynamics, free energy, dissipative particle dynamics. Introduction to phase field modeling and lattice-Boltzmann.
Modeling Soft Materials and Biological Systems (graduate, PhD/MSc).
Dept. of Physics, University of Santiago, Chile, Sep. 2002. One week intensive course.
Audience: For PhD students in theoretical and computational physics.
Material: Lecture notes
Topics include: Biological systems, review of basic concepts in statistical mechanics, molecular dynamics, force fields, coarse-graining in time and space, and a brief review of recent developments. Applications to biologically motivated systems, e.g. biomembranes and polymeric systems.
Introduction to soft matter physics, Tfy-3.363 (undergraduate)
Helsinki University of Technology.
For 2nd and 3rd year MSc students in physics.
Material: Lecture notes and I.W. Hamley: Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals, Wiley (2000).
Topics include: Basic statistical mechanics & thermodynamics, phase transition, properties of polymers, inter- and intramolecular interactions, colloids, electrostatics, amphiphilic systems, basics of liquid crystalline systems, and biomembranes.
Mathematical Modeling and Methods in Natural Sciences & Engineering, S114.240 (MSc).
Helsinki University of Technology.
Compulsory for students majoring in computational science
Material: Computational Methods in Physics, Chemistry and Mathematical Biology, Paul Harrison, Wiley (2001).
Topics include: Numerical solutions of the Schrödinger’s equation, quantum wells, quantum dots; Evolutionary methods: Genetic algorithms and their applications; Stochastic simulations: Randomness, tests & limits; Percolation theory: Disease propagation, magnetic systems
S114.100: Computational Science, S114.100 (MSc)
Helsinki University of Technology.
For 2nd & 3rd year students in mathematics, engineering and physics.
Compulsory for students majoring in computational science.
Material: Lecture notes and Cheney and D. Kincaid: Numerical Mathematics and Computing, Brooks/Cole 1999.
Topics includes: Monte Carlo integration, basic optimization methods, simulated annealing, data analysis, random numbers, basic numerical integration methods, curve fitting.
2001-2002#
Special topics in computational science, S114.250 (MSc)
Helsinki University of Technology.
Topics: Particle and continuum simulations: Molecular dynamics, free energy, dissipative particle dynamics. Introduction to phase field modeling and lattice-Boltzmann.
Finnish National Graduate School in Materials Physics in Sjökulla, Finland, Aug. 27.-30., 2001. Lecture series on Coarse-Graining in Time and Space, Structural Properties, Effective Interactions and Dissipative Particle Dynamics of Fluid Systems.
Introduction to soft matter physics, Tfy-3.363 (undergraduate)
Helsinki University of Technology.
For 2nd and 3rd year MSc students in physics.
Material: Lecture notes and I.W. Hamley: Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals, Wiley (2000).
Topics include: Basic statistical mechanics & thermodynamics, phase transition, properties of polymers, inter- and intramolecular interactions, colloids, electrostatics, amphiphilic systems, basics of liquid crystalline systems, and biomembranes.
Mathematical Modeling and Methods in Natural Sciences & Engineering, S114.240 (MSc).
Helsinki University of Technology.
Compulsory for students majoring in computational science
Material: Computational Methods in Physics, Chemistry and Mathematical Biology, Paul Harrison, Wiley (2001).
Topics include: Numerical solutions of the Schrödinger’s equation, quantum wells, quantum dots; Evolutionary methods: Genetic algorithms and their applications; Stochastic simulations: Randomness, tests & limits; Percolation theory: Disease propagation, magnetic systems
S114.100: Computational Science, S114.100 (MSc)
Helsinki University of Technology.
For 2nd & 3rd year students in mathematics, engineering and physics.
Compulsory for students majoring in computational science.
Material: Lecture notes and Cheney and D. Kincaid: Numerical Mathematics and Computing, Brooks/Cole 1999.
Topics include: Monte Carlo integration, basic optimization methods, simulated annealing, data analysis, random numbers, basic numerical integration methods, curve fitting.
2000-2001#
S114.100: Computational Science, S114.100 (MSc)
Helsinki University of Technology.
For 2nd & 3rd year students in mathematics, engineering and physics.
Compulsory for students majoring in computational science.
Material: Lecture notes and Cheney and D. Kincaid: Numerical Mathematics and Computing, Brooks/Cole 1999.
Topics include: Monte Carlo integration, basic optimization methods, simulated annealing, data analysis, random numbers, basic numerical integration methods, curve fitting.