MesoRD

[…] on the surface of the cell, which is assumed to be a sphere of the radius 100 μm. Since Gillespie’s algorithm cannot take into account spatial effects, we solve the reaction-diffusion equations using MesoRD (Mesoscopic Reaction-Diffusion Simulator), a numerical solver for stochastic reaction diffusion equations using the next subvolume method.In reality, it is highly probable that there would be s […]

[…] All reactions–binding/unbinding of TFs, transcriptional initiation and termination–are solved using the MesoRD package (http://mesord.sourceforge.net/, []). Deterministic solution of the model (as a system of ODEs, ordinary differential equations; 4th order Runge-Kutta) is used to constrain the rate con […]

[…] -diffusion simulators. These simulators can be separated into two major categories, voxel-based and particle-based. Voxel-based simulators, such as STEPS (Hepburn et al., ), URDME (Drawert et al., ), MesoRD (Hattne et al., ), and NeuroRD (Oliveira et al., ), divide the geometry into small voxels where different spatial variants of the Gillespie Stochastic Simulation Algorithm (Gillespie SSA) (Gill […]

[…] eaddy [] feature microscale, particle-tracking algorithms for spatial stochastic simulation. STEPS [] and MesoRD [] support mesoscopic spatial stochastic simulations; STEPS on unstructured meshes and MesoRD on structured meshes. In contrast to the above software packages, StochSS features capabilities at the deterministic well-mixed level, the stochastic well-mixed level, and the mesoscopic spatia […]

[…] ion of the hb gene by the Bcd protein gradient in the anterior part was studied by modelling the noise observed in hb regulation using a chemical master equation approach. For solving this model, the MesoRD software package has been used which mainly follows a stochastic approach and the results indicate that Hb output noise is mostly dependent on the transcription and translation dynamics of its […]

[…] Stochastic and deterministic solutions of the model were computed with the MesoRD software package ([]; http://mesord.sourceforge.net). 1D computations were solved in a one-dimensional series of 60 subvolumes (each a cube 5μm on a side), corresponding to energids (nucleus pl […]