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.

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Quick start

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

cosmo-csp-movie -o synth_out_cyl       # stitch per-length trajectories into a movie
vmd -e synth_out_cyl/movie.tcl

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

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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 seeded and position-restrained on the tunnel axis at the PTC (x_lo, y0, z0) (stiffness restraint_k); each new residue is seeded there. 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 free runs are ejection_steps then dissociation_steps (same keywords as the explicit-ribosome runner, both drop the C-terminus restraint). (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.

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Configuration reference (cylinder.ini)

Read by cosmo.csp.cylinder.read_cylinder_config. Units are OpenMM defaults. The kinetics and MD keys share the semantics of the Synthesis control options page; the tunnel geometry and post-elongation phase are specific to this runner.

Example cylinder.ini:

[OPTIONS]
; --- inputs (no `ribosome` PDB: the tunnel is analytic) ---
pdb_file = asyn.pdb          ; full native PDB of the nascent chain
model    = hps_kr            ; nascent IDP force field

; --- length schedule ---
L0    = 5
L_max = 10                   ; blank -> full residue count

; --- kinetics (same O'Brien codon timing as cosmo-csp) ---
mrna         = mrna.txt      ; one codon per residue (required for per-codon timing);
                             ; or "fastest"/"slowest"/"median" to auto-build a synonymous-codon mRNA
codon_times  = ../../assets/csp/codon_dwell_times/ecoli/ecoli_codon_dwell_times_310K.txt  ; table path (required; or a number of s = uniform)
scale_factor = 4331293
random_seed  = 1
max_steps_per_stage = 60     ; TEST CLAMP (delete for production)
min_steps_per_stage = 30

; --- mechanics / integrator ---
restraint_k = 83680          ; C-terminus -> PTC restraint (kJ/mol/nm^2)
minimize    = yes
dt = 0.01 ; ref_t = 300 ; tau_t = 0.01 ; nstout = 20

; --- analytic exit tunnel ---
tunnel_radius      = 0.9     ; bore radius r (nm); ~3 CG beads wide
tunnel_length      = 10.0    ; bore length (nm); x_exit = x_lo + length
tunnel_x_lo        = 0.0     ; PTC / closed end (nm); C-terminus seeded on-axis here
tunnel_center      = 0.0, 0.0 ; tunnel axis (y0, z0) (nm)
tunnel_k           = 8368    ; wall stiffness (kJ/mol/nm^2 = 20 kcal/mol/A^2)
tunnel_mouth_round = 0.2     ; mouth-corner fillet radius rho (nm)

; --- post-synthesis free runs (both release the C-terminus restraint) ---
ejection_steps     = 40   ; release restraint -> chain diffuses out the exit; 0 -> skip
dissociation_steps = 40   ; second free run -> chain drifts fully clear; 0 -> skip

; --- hardware / output ---
device = CPU ; ppn = 1 ; outdir = synth_out_cyl

Analytic tunnel geometry

Key	Default	Meaning
tunnel_radius	0.9	Bore radius r (nm); ~3 CG beads wide.
tunnel_length	10.0	Bore length (nm). x_exit = tunnel_x_lo + tunnel_length (derived).
tunnel_x_lo	0.0	PTC / closed end (nm); the C-terminus is seeded on-axis here.
tunnel_center	0.0, 0.0	Tunnel axis (y0, z0) (nm). The axis runs along +x.
tunnel_k	8368	Wall stiffness (kJ/mol/nm² = 20 kcal/mol/Ų).
tunnel_mouth_round	0.2	Mouth-corner fillet radius rho (nm).

Post-elongation

Key	Default	Meaning
ejection_steps	0	Free run with the C-terminus restraint released so the finished chain diffuses out the exit (+x); 0 = skip. Use a long run so the chain can clear the tunnel.
dissociation_steps	0	Second free run (restraint still off) so the chain drifts fully clear of the exit; 0 = skip.

Shared kinetics & MD keys

These behave exactly as on the Synthesis control options page (inherited from the shared RunParams): model (default hps_kr; any IDP model works), scale_factor, codon_times, random_seed, ribosome_traffic / initiation_rate (traffic correction), max_steps_per_stage / min_steps_per_stage (testing-only), constraints (None flexible default, or AllBonds for rigid bonds), restraint_k, minimize, dt / ref_t / tau_t / nstout, device / ppn.

Warning

time_stage_1 / time_stage_2 are accepted (inherited) but have no effect in the cylinder runner: with a single MD segment per residue, each residue’s step count comes from its whole codon dwell, not a three-way split.

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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, ...
├── ejection/               # free run, restraint off (if ejection_steps > 0)
├── dissociation/           # second free run (if dissociation_steps > 0)
└── dwell_times.dat         # per-residue: codon, sampled dwell (s), ns, integration steps

Movie. cosmo-csp-movie -o <outdir> stitches the per-length trajectories (it auto-detects the flat L_<L>/ layout used here vs. the 3-stage layout of cosmo-csp).

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See also

• Synthesis on a coarse-grained ribosome — the explicit coarse-grained ribosome runner (cosmo-csp): the same codon kinetics with three MD sub-stages per residue and an explicit-bead tunnel.

• Synthesis control options — the shared kinetics / MD control options in full.

• cosmo.csp package — the API reference.