Synthesis through an analytic tunnel (cylinder model)

The cylinder runner is the analytic-tunnel variant of protein synthesis: it replaces the explicit coarse-grained ribosome of the coarse-grained ribosome model with a cylindrical bore drilled through an infinite wall (a “hole in an infinite wall”). There are no ribosome beads — the simulated system is the nascent chain only — so it is fast, never jams on ribosome excluded volume, and the analytic tunnel keeps the in-tunnel segment extended so the chain threads out the exit.

  • CLI: cosmo-cylinder -f cylinder.ini (or python -m cosmo.csp.cylinder -f cylinder.ini)

  • Worked example: tutorials/07_csp_cylinder/ (α-synuclein); a larger production configuration lives in sandbox/validate/cylinder.ini.

  • Module: cosmo.csp.cylinder — a parallel of the explicit-bead cosmo.csp.protocol. It reuses the shared engine cosmo.csp.core (length model, seed / restrain / output path) and the timing core cosmo.csp.kinetics, adding only the one analytic tunnel force (add_tunnel_cylinder) and a nascent-only synthesis loop.

Tip

Same codon kinetics as the coarse-grained-ribosome runner (cosmo-csp) — each residue’s MD length comes from its codon dwell time — but the cylinder runs one MD segment per residue rather than three sub-stages, because the analytic tunnel has no A→P translocation to model. For the full kinetics derivation (codon → seconds → integration steps) see the coarse-grained ribosome page; this page describes the tunnel model and the cylinder.ini options.

Note

Why the cylinder exists. The explicit-bead exit tunnel in the truncated CG ribosome is geometrically tight, and a disordered chain tends to jam or ball up at the PTC rather than thread it. The analytic bore is a clean idealization that reliably extrudes an IDP chain — purely steric, no electrostatics, no bead clashes.

Quick start

cd tutorials/07_csp_cylinder
cosmo-cylinder -f cylinder.ini         # -> synth_out_cyl/

cosmo-csp-movie -o synth_out_cyl --tunnel cylinder.ini   # stitch + draw the analytic tunnel
cd synth_out_cyl && vmd -e movie.tcl                     # movie.tcl loads its files by basename

cosmo-cylinder writes, per residue L, a standalone trajectory under <outdir>/L_<L>/, optional post-synthesis phases (stall/, ejection/), and a per-residue dwell-time log <outdir>/dwell_times.dat.

The model: analytic exit tunnel

The tunnel is a cylindrical bore of radius r along the X-axis, drilled through an infinite wall from the closed PTC end (x_lo) to the exit face (x_exit = x_lo + tunnel_length):

   d                              (cytosol: free, any d)
   ^   |##### solid ribosome S #####|
 r |···|············ bore ··········|··············>  allowed past exit
   +---|----------------------------|----------------> x
     x_lo (PTC)                  x_exit
       |##### solid ribosome S #####|
                              ^ infinite exit-face wall (d > r)

A single CustomExternalForce over every nascent bead penalises its penetration depth into the solid region S:

S   = { x < x_exit AND d > r } ∪ { x < x_lo },   d = |(y,z) − (y0,z0)|
U   = k·max(0, pen)²  +  k·min(0, x − x_lo)²
pen = (rounded) min( x_exit − x , d − r )        # 0 outside S; > 0 inside S

A bead escapes S via whichever face is nearer — the bore wall (d − r, a radial inward push that keeps the in-tunnel chain extended) or the exit face (x_exit − x, a +x push), so a cytosol bead can only re-enter through the bore, never off-axis. The 90° inner corner at the mouth is rounded by a fillet of radius rho = tunnel_mouth_round so the potential stays continuous and the MD stays stable.

The C-terminus is position-restrained on the tunnel axis at the PTC (x_lo, y0, z0) (stiffness restraint_k). Each new residue is seeded one equilibrium peptide bond deeper than that rest point — toward the closed PTC end — so the new L-1↔L bond starts at its equilibrium length instead of collapsed onto the previous C-terminus; the restraint and the closed-end wall then lift the new residue back onto the PTC while the older chain ratchets forward. (This is the analytic-tunnel analogue of the explicit protocol’s A/P-site offset, without the ribosome, and is what keeps a rigid AllBonds build stable here too.) There is no A/P tRNA tether and no translocation switch — the chain simply extrudes forward as it grows.

Note

How it differs from the coarse-grained ribosome model. (1) No ribosome PDB — the tunnel is analytic, its geometry set by the tunnel_* keys. (2) One MD segment per residue (no peptidyl-transfer / translocation / tRNA-binding sub-stages), so time_stage_1 / time_stage_2 are inherited but unused — the whole codon dwell is a single segment. (3) The post-synthesis phases are stall_steps (hold at the PTC with the C-terminus restraint still on — ribosome stalling) then ejection_steps (free run, dropping the C-terminus restraint) — same keywords as the explicit-ribosome runner. (4) The explicit-ribosome knobs (trna_tether, tunnel_wall) and the always-on PTC-geometry optimization do not apply. (5) Purely steric — no ribosome electrostatics.

Configuration

Read by cosmo.csp.cylinder.read_cylinder_config. Every control key is documented in one place: Synthesis control options — the shared keys (inputs, kinetics, integrator, post-synthesis, resume) plus the Cylinder-runner-only tunnel_* geometry keys (tunnel_radius, tunnel_length, tunnel_x_lo, tunnel_center, tunnel_k, tunnel_mouth_round) that define the analytic bore. A runnable cylinder.ini example is on that page and in tutorials/07_csp_cylinder/.

Two cylinder-specific points: there is no ribosome PDB (the tunnel is analytic), and time_stage_1 / time_stage_2 are accepted but have no effect — with a single MD segment per residue the whole codon dwell τ is one segment, not a three-way split.

Outputs

<outdir>/
├── L_<L>/                  # one folder per residue L (single MD segment)
│   ├── traj.dcd            # (nascent-only) trajectory for that length
│   ├── traj_final.pdb      # last conformation (seeds the next residue)
│   └── traj.log, traj.psf, ...
├── stall/                  # held at PTC, restraint on (if stall_steps > 0)
├── ejection/               # free run, restraint off (if ejection_steps > 0)
├── dwell_times.dat         # per-residue: codon, sampled dwell (s), ns, integration steps
└── progress.log            # append-only DONE/RUNNING resume status

Movie. cosmo-csp-movie -o <outdir> --tunnel cylinder.ini stitches the per-length trajectories (it auto-detects the flat L_<L>/ layout used here vs. the 3-stage layout of cosmo-csp) and draws the analytic tunnel — bore tube, closed PTC cap, and the infinite exit-face wall — reading the geometry from the same cylinder.ini. Omit --tunnel for a plain movie. For the interactive vs. cd <outdir> recipe, see Visualizing the synthesis process.

Resume. Like cosmo-csp, an interrupted cylinder run continues from the last completed residue when re-invoked (resume = auto, on by default) — the schedule is re-read from dwell_times.dat and the seed reloaded from the last L_<L>/traj_final.pdb, tracked by progress.log. See Resuming long synthesis runs.

See also