Download User Manual MUscle SImulation COde

1. Introduction
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Introduction
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. For a detailed introduction of the molecular structure of muscle cells
refer to [3]. 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 (cf. [1]) to model
the fibers. To resemble the chemical reactions which happen in the crossbridges, the Monte Carlo simulation is used. Thus the numerical procedure can be seen as a staggering scheme. 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.
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Installation/Build
Currently the software can be installed in a Windows environment, using the
Cygwin environment, under Linux and on Apple’s OS-X.
2.1
Installation Windows XP/Cygwin
The code for simulating the muscle fibers itself should be rather unproblematic with respect to portability. Unfortunately, the deal.II library uses
many advanced language features which are not supported by the usual development environments that are available under Windows. Therefore, the
Cygwin library has to be used to provide Unix like API calls and the GNU
compiler collection.