Simula Summer School

In conjunction with the University of San Diego, Simula Research Laboratory is pleased to announce the 3rd edition of our annual Summer School in Computational Physiology

Total number of participants: 21
Total number of guests outside of CBC: 17
Number of different nationalities represented: 7
Total number of speakers: 12
Total number of talks: 17



Simula Research Laboratory, Oslo, Norway


All lectures June 13-21 will take place in “Klasserommet” auditorium at Simula.

All project work June 22-24 will take place in assigned workspaces at Simula (detailed below).


General Schedule:

Unless otherwise noted, the schedule for June 13-17, 20-21 will follow:

0900-1200: theoretical lectures

1200-1300: lunch break

1300-1700: theory, programming lab work, guest lectures

There will be two evening tutorial sessions (Tuesday June 14, and Wednesday June 15). These sessions will being at 1800 and finish no later than 2100. There is no set schedule for project work June 22-24, though it is recommended that teams take full advantage of this time. At least one project advisor will be available from 0900-1600 during that interval, and always via email.


Required Materials:

Laptop computer: If you do not plan on bringing your own laptop or do not have access to a laptop for the duration of the summer school, please notify us as soon as possible and we’ll find a solution.


Monday June 13

Morning session

Course introduction and overview (Dr. Andy Edwards)

  •  Welcome to Simula
  •  Scope and objectives of the summer school

L1: Physiological background

  •  Essential electrophysiology of excitable tissues
  •  Basic physiology of muscle contraction
  • Mathematics as the multiscale microscope

L2: Fundamental physical chemistry and enzyme behavior (Dr. Glenn Lines)

  • Mass action
  • Gibbs energy
  • Enzyme kinetics and cooperativity

Afternoon session

L3: Electrochemistry of biological cells (Dr. Glenn Lines)

  • Diffusion and Fick’s law
  • Planck’s equation and Nernst equilibrium
  • Cell membrane
  • Membrane potential
  • Carrier mediated transport

Afternoon introductory session (Dr. Molly Maleckar)

  • Norway for Foreigners: an introduction


Tuesday June 14

Morning session

L4: Ion channels (Dr. Glenn Lines)

  • Two-state channels
  • Channels with multiple subunits
  • Rate constants as probabilities
  • Waiting time and channel dynamics

L5: Constructing models of ionic currents from experimental data (Dr. Andy Edwards)

  • Basics of experimental recordings
    • Voltage clamp/current clamp  
    • Single channel/whole-cell recordings
    • Isolating measured currents
    • Case study: Hodgkin-Huxley model
    • Markov models Afternoon session

L6: Cardiac-specific cell models (Dr. Molly Maleckar)

  • Sino atrial node models
  • Atrial myocyte models
  • Ventricular myocyte models
  • Species-specific ventricular models

L7: Quantitative aspects of calcium handling in excitable tissues (Jonas van den Brink)

  • Calcium handling in cardiac muscle
  • Calcium handling in skeletal muscle
  • Calcium handling in smooth muscle
  • Calcium in synaptic transmission and neuroplasticity

Evening Session 1: Stochastic methods & ODE numerics (Dr. Glenn Lines)

Evening Session 2: Constructing models from V-clamp data (Dr. Andy Edwards)


Wednesday June 15

Morning session

L8: Electrical conduction in biology (Prof. Joakim Sundnes)

  • Derivation of the cable equation
  • Passive flow in neurons
  • Active flow in excitable cell
  • Gap junction and cell-cell coupling
    • Effective diffusion coefficient via homogenization
    • Travelling waves

L9: Models of electrical conduction in the heart (Dr. Hermenegild Arevalo)

  • Cardiac tissue models
    • Bidomain model
    • Monodomain reduction
  • Inverse problems in electrocardiography
    • Classical formulations and data sources
    • Vector cardiogram representations

Afternoon session

L10: Continuum methods for biological systems (Dr. Simon Funke)

  • Introduction to the finite element method
  • FEnICS and other FEM tools
  • Evening session 3: FEnICS tutorials

Thursday June 16

Prof. Gaute Einevoll (University of Oslo/NMBU)

Dr. Torbjørn Ness (NMBU)

Morning session

L11: Fundamentals of computational neuroscience (Prof. Gaute Einevoll)

  • The problems of computational neuroscience
  • Challenges in multiscale modeling of the brain

L12: Biophysical modeling of neurons (Dr. Torbjørn Ness)

  • Multicompartmental neuron modeling
  • Introduction to NEURON Afternoon session

L13: Linking neuron models to brain signals (Prof. Gaute Einevoll)

  • Biophysics of electrical brain recordings
  • Local field potentials from neurons and neural networks Neuronify demonstration and exercises (PhD-students from CINPLA)


Friday June 17

Morning session

L14: Fundamental cardiac mechanics (Prof. Joakim Sundnes)

  • The heart as a pump

    • The PV loop and phases of the cardiac cycle
    • Time-varying elastance models of heart mechanics
  • Introduction to sliding filament theory
    • Micro-structure of force development o Cross-bridge cycling
    • Regulation of force development
  • Models of myofilament mechanics
    • Models of cellular mechanics in the heart

Afternoon session

L15: Modeling the mechanical properties of cardiac muscle (Prof. Joakim Sundnes)

  • The mechanics of myocardial tissue
    • Macroscopic mechanical properties of cardiac muscle
    • Brief introduction to continuum mechanics
    • Strain-energy functions and their use in cardiac systems modeling
    • Combining active and passive heart tissue mechanics

Evening: Simula Summer Party Friday 17th June, 16:00 onwards


Monday June 20

Morning session

Guest Lectures: Prof. Colleen Clancy (University of California, Davis) 

  • Computational pharmacology

Guest Lectures: Prof. David Christini (Weil Cornell Medical College)

  • The unique benefits and challenges of combining experiments and simulations

Afternoon session

Research seminar: Prof. Colleen Clancy, UC Davis Department of Pharmacology

Title: ‘Modern pipelines for multiscale computational screening of candidate antiarrhythmic agents’

Research seminar: Prof. David Christini, Weill Cornell Medical College

Title: ‘Dynamic clamp: defining new protocols and approaches to improve model building in cell electrophysiology’


Tuesday June 21

Morning session

L16: Model robustness and error metrics (Dr. Valeriya Naumova)

  • Derivative-free optimization methods
  • Derivative-based optimization methods
  • Sensitivity analysis – importance and approaches
  • Concepts in uncertainty analysis

Afternoon session

Student presentation: Viviane Timmerman

‘Computational approaches to understanding the mechanisms of arrhythmia in mitral valve prolapse’


Wednesday June 22

Morning session

  • Expectations for project work
  • Research presentations (project advisors)


Wednesday June 22 afternoon - Friday June 24

Supervised project work in teams June 23-24 will take place in assigned workspaces, according to the project assignments provided below. The school will finish at 2 pm on Friday June 24th to simplify return travel for all involved. Please contact us if you will need to leave earlier, and keep in mind the final dinner on June 23rd.


Evening Thursday 23rd June (20:00): Dinner at Ekebergrestauranten

13/ Jun 2016 09.0017.00 24/ Jun 2016 17.00