MesoRD

[…] 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 […]

[…] 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 […]

[…] [], and gridcel []), while voxel-based methods calculate changes in the number of molecules occurring in small well-stirred compartments in which the space modelled is partitioned (e.g., steps [], mesord [], and neurord [])., particle-based modelling is very computationally intensive, because it means to solve the equation of motion for each molecule of the system, which is appropriate […]

[…] values and , respectively, whereas the densities of membrane-bound proteins were initially set to zero., to simulate the stochastic reaction diffusion kinetics (1)–(7) in three dimensions, we used mesord , a tool to solve the stochastic master equation using a reaction diffusion master equation. it is based on the next subvolume method ., we thank r.d. mullins for introducing us to a22 […]

[…] and movement of species., to support diffusion and transport, sk adds ‘next-subvolume’ diffusion () to the kappa framework. this positions sk among other meso-scale modelling techniques, e.g. mesord () and smartcell (). several existing approaches handle spatially constrained models (), but none builds on a rule-based approach, with the notable exception of cbng which extends the bng […]