Virtual Human Brain Simulations with Abaqus in the Cloud

Virtual Human Brain Simulations
with Abaqus in the Cloud

Presenters
Karl D’Souza
Dassault Systemes
Director, Life Sciences Industry Solutions
Ægir Rafn Magnússon
Advania Data Centers
Business Development Director
Ebru Taylak
UberCloud
Marketing Manager

UberCloud
Over 200+ UberCloud Experiments,
4000+ community members
Sponsors Recognized with Prestigious Industry Awards
HPC for Everyone!
Neuromodulation
of Brain Project

UberCloud CAE Platform
UberCloud Cloud Compute Environment
Easy to use, instant access to Abaqus and CST
simulations in the cloud:
• latest, best in class hardware on demand
• software pre-installed, configured & tested
• ongoing support
UberCloud CAE Software
Container Technology
Abaqus
CST
SupportSoftwareHardware
Full Solution for Simulation in the Cloud

CONFIDENCE IN ANALYSIS
FASTER DEVELOPMENT CYCLE
COLLABORATE EFFECTIVELY
UNLOCK NEW CAPABILTIES
UberCloud brings many benefits
for scientists and engineers

Brain Neuromodulation Project
Winner of 2018 Hyperion Innovation Excellence Award!
UberCloud - Cloud CAE Platform
HPC CLOUD
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UberCloud Software
Container
Abaqus + Tools
seamless access
for the end user
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Centers

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what is it?
1 Server 100 Hours 100 Server 1 Hour
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JBOC offerings (Just a bunch of Cores)

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Why

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Reserved Extra Capacity
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Additional Capacity

Pure On Demand
2 2
5
1
10
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0%
10%
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30%
40%
50%
60%
70%
80%
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100%
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5
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• Setup & Architecture
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On Demand HPC
ADC provided Flexible HPC on Demand for efficient execution
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Setup and configuration of HPC cluster prior to the setup and operational start of the workload
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Our contribution

Benchmark Program
Apply at:
advaniadc.com/benchmark/

3DS.COM©DassaultSystèmes|ConfidentialInformation|3/4/19|ref.:3DSCorporatePresentation2016
2
Dassault Systemes
a Scientific
company
Combining Science,
Technology and Art for a
sustainable society
16,000
passionate people
• 130 nationalities / 179 sites
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• Operating margin: 32%*
* Figures as of FY 2017 / Non-IFRS

3DS.COM©DassaultSystèmes|ConfidentialInformation|3/4/19|ref.:3DSCorporatePresentation2016
3
Simulation in Life Sciences
Combination Products
- Pre-filled Syringes
- Metered-dose Inhalers
- Transdermal Patches
- Drug-Eluting Stents
Dental Implants
Hearing Aids
Brain Injury
Cardiovascular Implants
MRI Safety
Orthopedic Implants

4
3DS.COM©DassaultSystèmes|ConfidentialInformation|3/4/19|ref.:3DS_Document_2013
Background: Neuromodulation
q Neural activity ~ number of action potentials
fired per unit time
q Some mental disorders cause increased or
decreased neural activity in specific brain
regions
q Leads to abnormal cognitive function
associated with those regions
q Clinical interventions to restore/improve neural
activity
q Behavioral therapy (psychological)
q Chemical therapy (pharmacological)
q Electrical therapy (neuromodulation)

5
Background: Neuromodulation

6
Transcranial Electrical Stimulation (tES)
q Form of brain stimulation
q Noninvasive
q Non-convulsive
q tDCS, tACS, tRNS
q Delivers low doses of electrical current
q Patient is conscious
q Minimal discomfort
q Modulates spontaneous neuronal activity
q Neurons become more or less likely to fire
q Does not trigger action potentials (sub-threshold excitation)
q Longer application duration => longer lasting effect
Schematic of tES modalities [Yavari 2017]

7
tDCS: Clinical Applications
q Neurological disorders
q Stroke recovery
q Parkinson’s Disease
q Chronic pain
q Psychiatric disorders
q Depression
q Hunger Cravings
q Schizophrenia

8
tDCS: Motivation for Computational Modeling
q Conventional Method:
q Predefined criteria used to select electrode placement and dosage
q Not patient-specific
q No quantitative/rigorous metrics to evaluate outcome efficacy
q Difficult to correlate input parameters with treatment outcomes
q Computational Method:
q Predicts current distribution with high resolution
q Patient-specific and quantifiable
q Facilitates parameter sensitivity analyses and montage variations
q Clinician can devise the most effective treatment protocol for specific patient

9
tDCS: Personalized Modeling
*Image to Mesh using Simpleware ScanIP

10
International 10/10 Convention
showing Anode AF3 (red) and Cathode
CP5 (blue)
Subject-specific Models (Left: Responder; Right:
Non-responder)

11
FE Model Regions and Conductivities

12
EPG Magnitude on Exterior Surface of GM for Both Subjects

13
tACS with Temporal Interference (TI): Hypothesis
Temporal Interference in tACS [Grossman 2017]

14
tACS: Optimization for Patient-specific Treatment
Selected Results of Subject-specific TI-tACS Simulations

15
tACS: Optimization for Patient-specific Treatment
q Two-step Methodology to Optimize Subject-specific tACS Treatment
q Cloud computation: 25min per model on 128 CPUs on UberCloud
q 16 electrode locations per patient

16
Computational Workflow for Personalized Neuromodulation
*Image to Mesh using Simpleware ScanIP

17
Conclusion
q Summary of Current Effort
q Developed and demonstrated a clinical workflow for
personalized neuromodulation
q 2-step optimization of patient-specific treatment
q Future Work
q More research into tDCS/tACS protocols
q Extend computational framework to include model-
based and data-driven approaches
q Model-based: 3D patient-specific physics-based
simulation
q Data-driven: Augment models with ML to include
genetic, clinical, biometric, behavioral, and
environmental information

Contact Us!
help@theubercloud.com - https://www.theubercloud.com
Combining Abaqus simulation capability and Advania Data Centers powerful
HPC cloud hardware in UberCloud’s Cloud CAE Platform provided clinical
researchers:
• A seamless solution to run and manage the most complex problems and
workflows in the cloud
• The necessary boost in their simulation performance enabling innovation
and development of new clinical treatment methodology
HPC for Everyone!

Virtual Human Brain Simulations with Abaqus in the Cloud

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