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Dipl.-Inf. Arne Bittig

Dipl.-Inf. Arne Bittig
Albert-Einstein-Str. 21
Office 106

Rostock , Germany 18059
Office Phone: +49 381 498 - 7445

PhD student in the (discontinued) DFG research training group "dIEM oSiRiS".

Research

Biological cells are not well-stirred environments, however, modelling and simulation methods based on this assumption are mostly better established theoretically and easier to apply than those that do not. In this project, we will establish concepts for the discrete, stochastic modelling of those processes taking the spatial dimensions of the system and actors into account. An important aspect will be the investigation of expressiveness.

We will explore existing approaches to discrete, stochastic modelling and evaluate their suitability for describing continuous coordinates as well as lattice-based discretisations of space, and integrating various forms of particle movement from Brownian motion to directed transport. This work led to the development of...

ML-Space

A simulator for particle-based and reaction-diffusion simulation of cell biological models, described in their own ML-Space modeling language. Example of a simple ML-Space model, consisting of constants, species definition (i.e. classes of model entities), rules (i.e. patterns to match for reactions) and initial state (i.e. actual instances of model entities):

1 rho = 0.1; // slowdown factor

2

3 Membrane(shape: rectangle, size: 500*736, aspectratio: (1,1.472) );

4 Raft(shape:circle, size:pi*25^2,diffusion:0.66);

5 Prot( /* shape:circle, size:4,*/ diffusion:2.);

6

7 Prot + Raft -> Raft[Prot(diffusion*=rho)] @ 1

8 Raft[Prot] -> Prot(diffusion/=rho) + Raft @ 1

9

10 1 Membrane(position:(0,0))[ 187 Raft + 2500 Prot ];


Availability: alpha version with command line at at link above, source code and possibly graphical user interface in preparation