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#dynamics

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A new COPASI version 4.45 was released.

New features:
- tool to parse arbitrary ODEs into reaction-based model.
- menu entry allowing definition and running of external tools (scripts ,etc)

Many bug fixes, including:
- better scaling for MCA in the presence of small compartment volumes
- fixed intervals for time courses running backwards (negative time)
- improvement in steady state criteria in models with conserved moieties
- Improved parsing SED-ML & SBML

copasi.org/Download/
#SystemsBiology #Chemistry #Simulation #Dynamics

copasi.orgCOPASI: DownloadCOPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Continued thread

For the five cases here, the integrals can be calculated exactly, although they turn out to be piecewise functions.
The equivalent dynamic response curves now look somewhat complicated and are here.

It is difficult to explain the meaning of these curves to someone who is unfamiliar and it took me a while to figure out what they related to. Even then, explaining them to others is equally challenging.

Continued thread

The #DynamicResponse for periodic loading is quite widely known and looks like this, where beta is the ratio of the forcing to natural frequencies and xi is damping ratio.

When the two frequencies are close (beta is around 1) then you can get resonance occuring and this can be hazardous as the dynamic deflections are so much larger than their static equivalents. Fmax is termed the #DynamicMagnificationFactor.
(Continues...)

Vortex Trapping Of Suspended Sand Grains Over Ripples
--
doi.org/10.1029/2023JF007620 <-- shared paper
--
“KEY POINTS
• Observations of vortex-trapped grains suggest delayed settling of advected grains, as well as delayed advection of grains mobilized from the bed
• Quantitative comparisons of vortex-trapped sand grains compared well with theoretical formulations by Nielsen (1992, doi.org/10.1142/1269) for a forced vortex
• Improved understanding of vortex trapping effects on sediment dynamics may decrease uncertainty in large-scale coastal model predictions..."
#spatial #model #modeling #water #hydrology #hydrodynamics #vortex #sand #sediment #transport #sedimentation #sedimentology #morphodynamics #fluiddynamics #ripples #coast #coastal #research #velocimetry #suspension #experimentation #dynamics #geology #processes #geomorphology #geomorphometry #vortextrapping #sand #grains #flow #ripple #sandwaves #ripples