pbg-medyan — MEDYAN-Driven Biophysics Demos

Three configurations driven by the actual MEDYAN C++ binary at /path/to/medyan through MedyanCxxProcess. All filament beads, motor and linker endpoints, and membrane mesh vertices shown below come straight from MEDYAN’s snapshot.traj and traj.h5 outputs — this is the upstream simulator, not a Python reimplementation.

Motor-Density Parameter SweepVesicle FilopodiaPBG Composability — External Actin Pulse
1

Motor-Density Parameter Sweep

Actomyosin contractile collapse vs MD copy number (Popov et al. 2016)

Four runs of the same actomyosin network at varying myosin-II minifilament densities (MD diffusing-species copy = 0 / 5 / 20 / 50). With more available motors, more bind to filaments per MEDYAN's low-duty-cycle catch-bond reactions and pull on neighbouring cylinders along the filament axis, contracting the network. The reported network span (bead bounding-box diagonal) is a classical MEDYAN metric for the contractile transition.

3D Network Snapshots — One Per Motor Density

MD copy = 0
n_motors=0 · n_linkers=0 · span=2887 nm · wall=1.1s
MD copy = 10
n_motors=5 · n_linkers=0 · span=2969 nm · wall=1.2s
MD copy = 40
n_motors=16 · n_linkers=0 · span=3088 nm · wall=1.6s
MD copy = 120
n_motors=8 · n_linkers=0 · span=2793 nm · wall=1.3s

Quantitative Sweep

Bigraph Architecture

Sub-run Metrics

2

Vesicle Filopodia

Polymerizing actin pushes a deformable lipid vesicle outward

A closed lipid vesicle (icosphere mesh, 1000+ vertices, Helfrich bending + constant tension + volume conservation) wraps a small actin network. Brownian-ratchet polymerization extends filament plus-ends; tip contact with the membrane is mediated by MEDYAN's triangle–bead repulsion force-field. The membrane geometry shown comes straight from snapshots/<i>/membranes/0/{vertexDataFloat64,triangleDataInt64} in MEDYAN's HDF5 trajectory. This is the flagship MEDYAN-vesicle subsystem in action.

Mem Vertices1076
Mem Triangles2148
Mean Radius495nm
Filaments6
Total L1474nm
Wall-clock21.1s

3D Vesicle & Cytoskeleton Viewer

Vesicle (translucent purple) wraps the filaments (cyan)
Drag to rotate · Scroll to zoom · Coords in nm
Components
Actin filament
Lipid vesicle
t = 0

Membrane & Filament Dynamics

Bigraph Architecture

Final-Frame Metrics

3

PBG Composability — External Actin Pulse

A separate PBG process drives MEDYAN's G-actin concentration

The wrapper exposes an actin_copy input port. On each update(state, interval), a sibling PBG process can push a new G-actin (AD) diffusing-species copy number; the wrapper rewrites the chemistry input and re-runs MEDYAN with the new value. Here the schedule is a square wave 800 → 100 → 800, simulating a regulatory pulse. Above the critical actin concentration the network grows; below it, koff dominates and filaments shrink. This kind of cross-process coupling is exactly what bare MEDYAN can't do — the wrapper turns it into a one-line input wiring in any larger Composite.

Intervals6
Schedule1500 → 1500 → 30 → 30 → 1500 → 1500
Final L1469nm
Wall-clock1.6s

Cytoskeleton Response

Filaments grow when AD copy is high, shrink when low
Drag to rotate · Scroll to zoom
i = 0 (AD=1500)

Input vs Response

Bigraph Architecture

Final-Frame Metrics

Generated by pbg-medyan · MEDYAN v5.4.0 via MedyanCxxProcess · HDF5 traj.h5 for membrane geometry · checkpoint-restart through FILAMENTFILE + PROJECTIONTYPE: PREDEFINED