MUSICO

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Contents

General Information

  • Application's name: MUscle SImulation COde
  • Application's acronym: MUSICO
  • Scientific domain: Bioengineering
  • Contact person: Djordje NEDIC, Faculty of Science, University of Kragujevac, Serbia
  • Main Developers: Oliver Kayser-Herold, Srboljum Mijailovich, Boban Stojanovic, Djordje Nedic
  • Co-developers: Milos Ivanovic
  • Allocation period: 01/08/2013-31/10/2013
  • Web site:

Objectives of the computing project

Parallelization of the existing application for muscle simulation in order to reduce computational time to the acceptable level for usage on daily basis. The existing sequential code consists of Monte Carlo and Finite element algorithms which can be parallelized using various strategies.Most of the parallelization strategies are already developed and can be fully tested and modified in the period of two months.A single simulation using existing code can last for hours or even days, depending on type of the simulation and loading conditions, which raises need for employment of HPC resources.Potential users of the applications are leading world researches in this field, ready to provide huge HPC resources for the application if it is proved that simulations take reasonable time.

Application's description

The program is based on a modular object oriented code, which implements a flexible framework for programming simulation codes which deal with biological systems, in particular muscle cells.

Currently, most of the code is focused on Monte Carlo simulations of muscle cells. Basically the muscle cells consist of thick (myosin) and thin (actin) fibers which are arranged in a comb like structure. Between these fibers, crossbridges are dynamically created by molecules which are attached to the myosin fibers and bind to the actin.

The Monte Carlo simulation uses a 1D finite element code to model the fibers. To resemble the chemical reactions which happen in the crossbridges, the Monte Carlo simulation is used. After computing the mechanics, the crossbridges may change their state which then influence the mechanics again.

Besides the Monte Carlo simulation, three other numerical procedures for simulating the mechanical response of muscle fibers are implemented.

Results expected in the allocation period

In the period of two months, we expect to improve muscle simulation code to reduce computational time at least one level of magnitude.

Activity report

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