SSCP2018 PROGRAM. University of California San Diego, the University of Oslo, and Simula Research Laboratory welcome you to the joint

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SSCP2018 PROGRAM University of California San Diego, the University of Oslo, and Simula Research Laboratory welcome you to the joint 2018 Summer School in Computational Cardiac Physiology Models,

1 SSCP2018 PROGRAM University of California San Diego, the University of Oslo, and Simula Research Laboratory welcome you to the joint 2018 Summer School in Computational Cardiac Physiology Models, Tools, and Techniques for Excitable Tissues Oslo, Norway June 2018 San Diego (La Jolla) CA, USA 8-17 August 2018 GENERAL INFORMATION Required Materials: Laptop computer and power adaptors - In class tutorials will be conducted via Jupyter notebook. You will be provided with the server information upon arriving at Simula, but to access the server and tutorial repository you will be required to sign in using your github account (please create your account at: Assessment: All students will be required to present their project work in symposium format at the end of the August portion of the SSCP2018 in San Diego. These presentations are scheduled to take place on 17 August. Doctoral students will additionally be required to submit a final report (maximum 4 pages) detailing their project work. This report should take the form of brief scientific paper (Background, Methods, Results, Discussion and Conclusions), and is to be submitted no later than midnight (CET) August 22, Upload your paper here: podio.com/webforms/ / Suggested References: 1. Keener, James, and James Sneyd. Mathematical Physiology: I: Cellular Physiology. Vol. 1. Springer, Keener, James, and James Sneyd. Mathematical Physiology: II: Systems Physiology. Vol. 1. Springer, Katz, Arnold M. Physiology of the Heart. Lippincott Williams & Wilkins, Zipes, Douglas P. and Jose Jalife, Eds. Cardiac Electrophysiology: from Cell to Bedside. Elsevier Health Sciences, 25 Oct 2013 Course website: Contact persons: Dr. Andy Edwards andy@simula.no Dr. Rachel Thomas rachel@simula.no SSCP2018 Course Program Page 1

2 Oslo, Norway June 2018 Simula Research Laboratory: Oslo, Norway General Schedule: Theory (June 18-26): 09:00-12:00 lectures 12:00-13:00 lunch break 13:00-17:00 lectures, programming lab work Project (June 27-29): There is no set schedule for project work. It is, however, expected that project teams take full advantage of this time. At least one advisor for each project will be available on site from 9:00-16:00 during this interval, and always via . Most SSCP2018 lectures will take place in Storstua auditorium at Simula Research Laboratory. Monday June 18 SSCP2018 Formal Opening (9:00 9:30) (9:45 12:00) Course introduction and overview (Andy Edwards) Welcome to Simula Preliminaries for software and overall course layout Expectations and assessment L1: Physiological background (Andrew McCulloch) Overview of modelling and applications in multiscale physiology L2: Physical chemistry and electrochemistry (Jonas van den Brink) Mass action Gibbs energy Enzyme kinetics and cooperativity Reaction rates and equilibria code-based exercise (13:00 17:00) L3: Mass transport and membrane biophysics (Jonas van den Brink) Diffusion and Fick s law Planck s equation and Nernst equilibrium Cell membrane Membrane potential The passive cell membrane code-based exercise SOCIAL EVENT Evening MONDAY, 18 June (17:00): SSCP2018 Opening Dinner Location: Sjøflyhavna Kro restaurant (near Simula Research Laboratory) RSVP by 7 June 2018: podio.com/webforms/ / SSCP2018 Course Schedule Oslo, Norway June Page 2

3 Tuesday June 19 L4: Ion channel gating (Glenn Lines) Two-state channels Channels with multiple subunits Rate constants as probabilities Waiting time and channel dynamics Modelling sodium channel gating properties code-based exercise Stochastic and deterministic ion channel behavior code-based exercise L5: Building modern ion channel models (Andy Edwards) Markov models of ion channel function Incorporating experimental recordings to build ion channel models Parameterizing ion channel models to experimental data code-based exercise Major ion current formulations in the heart L6: Combining ion transporter models to simulate the action potential (Andy Edwards) Tissue-specific cell models (model lineages) Building an AP model by combining channel models code-based exercise Wednesday June 20 L7: Electrical conduction in biology (Joakim Sundnes) Derivation of the cable equation Passive flow in neurons Active flow in excitable cells L8: Modelling electrical conduction in cardiac tissue (Joakim Sundnes) Simulating an excitable cable code-based exercise Simulating reentry code-based exercise Refractoriness and restitution L9: Quantitative aspects of calcium handling (Jonas van den Brink) Calcium in excitation-contraction coupling The sarco-endoplasmic reticulum calcium ATPase The sarcolemmal Na + -Ca 2+ exchanger Calcium flux balance code-based exercise Thursday June 21 L10: Quantitative aspects of calcium handling (Viviane Timmermann) Ryanodine receptor Spatial aspects of excitation-contraction coupling code-based exercise Calcium buffering code-based exercise SSCP2018 Course Schedule Oslo, Norway June Page 3

4 L11: Fundamental cardiac mechanics (Kim McCabe) Introduction to sliding filament theory o Troponin C binding dynamics code-based exercise o Micro-structure of force development o Cross-bridge cycling o Regulation of force development Friday June 22 L12: Myofilament dynamics (Kim McCabe and Joakim Sundnes) Models of myofilament mechanics o Models of cellular mechanics in the heart Models for coupling cardiac EP and myofilament mechanics A mechanical ring model of cardiac contraction code-based exercise L13: Model robustness and error metrics (Valeriya Naumova) Derivative-free optimization methods Derivative-based optimization methods Sensitivity analysis importance and approaches Concepts in uncertainty analysis L14: Week 1 summary (Andy Edwards) Monday June 25 L15: Continuum methods for biological systems (Karl Erik Holter) Introduction to the finite element method Introduction to FEnICS code-based exercise L16: Applications in FEnICS (Karl Erik Holter) Cable equation in FEnICS 2-dimensional dynamics (spiral waves) code-based exercise Tuesday June 26 L17: An introduction to integrated cardiac-vascular modelling (Joost Lumens) Introduction to the CircAdapt cardiovascular system model Cardiovascular mechanics and hemodynamics: whole-heart modelling Cardiovascular mechanics and hemodynamics: the vascular system Branched curriculum see below (continues Wednesday) SSCP2018 Course Schedule Oslo, Norway June Page 4

5 Tuesday afternoon and Wednesday (June 26-27) Cardiac tissue mechanics and fluid dynamics Tuesday afternoon session L18A: Applications of CircAdapt in disease and therapy modelling Virtual AV optimization tutorial L19A: Higher order modelling of cardiac vascular fluid mechanics The Navier-Stokes equations in FEniCS 1-, 2-, and 3-D modelling of coronary artery flow: when and how? Wednesday morning session L20A: Modeling the mechanical properties of cardiac muscle (Steve Niederer, Joakim Sundnes) Lecture Fundamentals of cardiac continuum mechanics Lecture A brief history of cardiac mechanics and its simulation Tutorial Unit cube, passive properties tutorial, passive + active tutorial Wednesday afternoon session L21A: Simple whole-heart cardiac mechanics (Joakim Sundnes) Tutorial Combining passive and active tissue mechanics Tutorial Passive inflation of an ellipsoid LV model Tutorial Ellipsoid LV model with active contraction Cardiac tissue electrophysiology Tuesday afternoon session L18B: Cardiac tissue models (Hermenegild Arevalo and Ed Vigmond) Lecture The bidomain model and monodomain reduction Lecture Spiral wave and scroll wave dynamics Lecture Mechanisms of defibrillation Wednesday morning session L19B: Cardiac and Torso geometry (Ed Vigmond and Hermenegild Arevalo) Lecture Forward problem and body surface potential Tutorial Monodomain vs. Bidomain (Virtual Electrode Polarization) Tutorial Anatomical vs. Functional Reentry Wednesday afternoon session L20B: Clinical applications in cardiac electrophysiology modelling (Hermenegild Arevalo) Lecture Patient-specific modelling Diagnosis and therapy planning Tutorial Image-based model creation for patient-specific simulations Tutorial Simulating arrhythmia induction and termination in Carpentry SSCP2018 Course Schedule Oslo, Norway June Page 5

6 Neural electrophysiology Tuesday afternoon session L18C: Differences between neuronal and cardiac cell electrophysiology (Tuomo Mäki- Marttunen) Lecture Multicompartment neuron modeling Lecture Introduction to NEURON Tutorial The NEURON simulator Wednesday morning session L19C: Modeling measurements of neural activity in the brain (Tuomo Mäki-Marttunen) Lecture Measurements from the brain (in vitro: electrophysiology, Ca 2+ and VSD imaging; in vivo: ECoG & EEG, fmri) Tutorial Modelling tissue and organ level function of the brain (LFP, EEG, and BOLD) Wednesday afternoon session L20C: Modelling intracellular cascades and plasticity in NEURON (Tuomo Mäki- Marttunen) Lecture Simplified models of Hebbian synaptic plasticity Tutorial Reaction-diffusion extensions in NEURON Lecture Simplified models of neuronal networks and the signals they generate - Rate-based models and their role in understanding fmri - Challenges in multi-scale modelling of the brain Thursday through Friday (June 28-29) Supervised project work in teams June will take place in assigned workspaces. Please note that there may be some guest lectures during this period. The school will finish at 2 pm on Friday June 29 h. SOCIAL EVENT Evening THURSDAY, 28 June (19:00): SSCP2018 Closing Dinner Location: Louise Restaurant and Bar (downtown Oslo) RSVP by 7 June 2018: SSCP2018 Course Schedule Oslo, Norway June Page 6

7 San Diego, USA 9-17 August 2018 University of California San Diego: La Jolla, USA General Schedule: Unless otherwise noted, the schedule for August 9-17 will generally run from 9:00 to 17:00. Breakfast and dinner are served at the Café Ventanas dining facility (near the Village Apartments) at the following times: Breakfast 8-8:45, Dinner 6-6:45pm. Interactive map available here: act.ucsd.edu/maps/ Thursday 9 August Location: B003 Classroom (basement of bioengineering building) Time: 9:00 16:30 Workshop: Transforming Technical Presentations - Christine Haas Friday 10 August Location: B003 Classroom (basement of bioengineering building) Time: 9:00 16:30 Lecture: Transforming Technical Presentations - Christine Haas This Friday, the project teams give initial presentation a status update for the project. This will be recorded for a subsequent coaching session min presentations each team min feedback and coaching Monday Thursday (13-16 August) In general these three days will be used for project work in assigned workspaces at UC-San Diego from 9-4. There will however be several guest lectures from local San Diego contributors. Details for these guest lectures will be provided at a later date. Friday 17 August Location: Fung auditorium, bioengineering building Time: 9:00 - finished Final exam in the form of conference-style presentations in plenum ~15 minutes per project team plus questions SOCIAL EVENT Afternoon FRIDAY, August 17 th (after presentations are finished): La Jolla Shores Beach day Swimming, surfing, food and drink (catered by Tacos & Gorditas (Taco Truck) Food will be served from 1pm-4pm RSVP by 7 August 2018: SSCP2018 Course Schedule San Diego, USA August 9-17 Page 7

Introduction to Muscles

Introduction to Muscles Warm Up- Monday 1. Think of one good thing that happened to you over break. 2. On the left hand side of your next open page, write a big Unit 4. 3. Write the essential question