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Simulating a Multi-Scale and Multi-Physics Model of a Dendritic Spine – Towards a communication framework for multi-scale modeling.
KTH, School of Computer Science and Communication (CSC).
2011 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Maya Brandi

Simulating a multi-scale and multi-physics model

Towards a communication framework for multi-scale modeling

Absract

The nervous system encompasses structure and phe- nomena at different spatial and temporal scales. In addi- tion, different scales are described by different physical and mathematical formalisms. In neuroscience, there is an in- creasing need to study phenomena where multiple scales and physical formalisms are covered by a single model. Most models developed thus far are limited to one scale and one type of physical process, but in many cases it would be relatively easy to develop multi-scale and multi-physics models of the nervous system only by integrating existing models. However, the lack of interoperability between dif- ferent simulators has made it difficult to reuse models. This project aims to be a preparatory work towards a frame- work for multi-scale modeling which builds on the concept of multi-simulations. We have built and studied a proto- type model of the electrical activity and calcium dynamics in a dendritic spine using two different simulators, MOOSE and NeuroRD. The combined system and the numerical methods used by both simulators are studied analytically and experimentally in terms of stability and accuracy.

Abstract [sv]

Nervsystemet omfattar strukturer och fenomen som rymmer olika rums- och tidsmässiga skalor. Dessutom beskrivs olika skalor av olika fysikaliska och matematiska formalismer. Inom neurovetenskapen ökar behovet att undersöka fenomen där flera skalor eller fysikaliska processer täcks av en och samma modell. De flesta modeller som hittills utvecklats är begränsade till en skala och en typ av fysikalisk process men i många fall skulle man relativt enkelt kunna utveckla multiskal- och multifysikmodeller av nervsystemet endast genom att integrera redan befintliga modeller. Dock har bristen på interoperabilitet mellan olika simulatorer gjort det svårt att återanvända modeller. Detta projekt syftar till att vara ett förberedande arbete mot ett ramverk för multiskalmodellering som bygger på idéen om multi-simuleringar. Vi har byggt och studerat en prototypmodell av den elektriska aktiviteten och calciumdynamiken i en dendritiskt spine med hjälp av två olika simulatorer, MOOSE och NeuroRD. Det kombinerade systemet samt de numeriska metoder som används av de båda simulerarna studeras analytiskt och experimentiellt med avseende på stabilitet och noggrannhet.

Place, publisher, year, edition, pages
2011.
Series
Trita-CSC-E, ISSN 1653-5715 ; 2011:123
National Category
Computational Mathematics
Identifiers
URN: urn:nbn:se:kth:diva-130671OAI: oai:DiVA.org:kth-130671DiVA: diva2:654118
Educational program
Master of Science - Computational and Systems Biology
Uppsok
Physics, Chemistry, Mathematics
Supervisors
Examiners
Available from: 2013-10-07 Created: 2013-10-07

Open Access in DiVA

No full text

Other links

http://www.nada.kth.se/utbildning/grukth/exjobb/rapportlistor/2011/rapporter11/brandi_maya_11123.pdf
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Computational Mathematics

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