src/context.jl

MEDYAN.MembraneSpeciesParams

Membrane protein physical parameters.

  • diffusion_coeff::Float64: Membrane diffusion coefficients (nm^2/s).
  • area::Float64: Protein area projected onto the surface (nm^2).
  • kbend::Float64: Bending rigidity (pN nm).
  • eqcurv::Float64: The protein’s own spontaneous mean curvature (/nm). Can be used in bending energy computations with curvatures.

MEDYAN.Context

Context(sys_def::SysDef, grid::CubicGrid; kwargs...)

  • agent_names::MEDYAN.AgentNames

  • sys_def::MEDYAN.SysDef

  • compartments::Vector{MEDYAN.Compartment}

  • grid::Any

  • time::Ref{Float64}: time (s)

  • stats::MEDYAN.PerformanceStats

  • β::Float64: inverse kT (1/(nm*pN))

  • base_diffusion_coeffs::Vector{Float64}: Diffusion coefficients indexed by diffusing species id (nm²/s)

  • membrane_species_params::StaticArraysCore.SVector{NUM_MEMBRANEDIFFUSINGSPECIES, MEDYAN.MembraneSpeciesParams} where NUM_MEMBRANEDIFFUSINGSPECIES: Membrane species parameters indexed by membrane diffusing species id.

  • min_compartment_volume_ratio::Float64: Smallest volume a compartment can have before being deactivated as a ratio to a full compartment volume.

  • chemistryengine::MEDYAN.RDMESampler: The reaction diffusion master equation sampler, contains the diffusing and regular fixed species state

  • chem_cylinders::Vector{MEDYAN.ChemCylinders}: Data about filament cylinders, indexed by filament type id

  • membranes::Vector: All membrane meshes.

  • link_manager::MEDYAN.LinkManager

  • decimated_2mon_site_managers::Vector{MEDYAN.AbstractDecimated2MonSiteManager}: Site managers, indexed by site id

  • filamentsites::Tuple{Vararg{Tuple{Vararg{MEDYAN.SiteData}}}}: The filament site definitions, indexed by filament type id, filament site id to get a SiteData with fields of id, site, fxsid

  • filamentendsites::Tuple{Vararg{Tuple{Vararg{MEDYAN.SiteData}}}}: The filamentend site definitions, indexed by filament type id, filamentend site id to get a SiteData with fields of id, site, fxsid

  • maxfilsite_plusrange::Vector{Int64}: The maximum plus range in monomers that any filament site or end site can see. Indexed by filament type id

  • maxfilsite_minusrange::Vector{Int64}: The maximum minus range in monomers that any filament site or end site can see. Indexed by filament type id

  • membranesites::Tuple{Vararg{MEDYAN.SiteData}}: Maps membrane site id to a SiteData with fields of id, site, fxsid.

  • map_membranediffusingspeciesindex_membranesiteindices::Tuple{Vararg{Vector{Int64}}}: Maps membrane diffusing species index to a list of membrane sites using this species as reactant. This is initialized during context init and should not be changed.

  • decimated_2mon_sites::Vector{MEDYAN.SiteData}: Site definitions, indexed by site id to get a SiteData with fields of id, site, fxsid

  • possiblecadherinsite_managers::Tuple{Vararg{MEDYAN.AbstractPossibleCadherinSiteManager}}: Site managers, indexed by site id

  • check_sitecount_error::Bool: If true site counts are checked for errors on every chem update. This is extremely slow, but useful for testing chem update errors.

  • compartmentreactioncallbacks::Any

  • bulkreactioncallbacks::Any

  • memdiff_bulks_index::Int64: Mock bulk species index for membrane diffusion.

  • viscosity::Float64: viscosity (pNs/nm² or MPas) water is about 1E-9

  • g_tol::Float64: maximum force magnitude after minimization (pN)

  • nforce_fractbit::Int64: number of fractional bits used to scale force values into Int64

  • nenergy_fractbit::Int64: number of fractional bits used to scale energy values into Int64

  • shake_before_minimization::Bool: If true, add noise to coordinates before starting minimization.

  • iter_max_cg_minimization::Int64: Max number of steps in conjugate gradient minimization.

  • maxstep::Float64: max step to take during line search (nm)

  • max_cylinder_force::Float64: max cylinder force when two cylinders are at zero distance (pN)

  • check_neighborlist_error::Bool: If true neighborlists are checked for errors on every force calc. This is extremely slow, but useful for testing neighborlist errors.

  • nthreads::Int64: Experimental Set to more than 1 to enable multi threading. This is currently may result in non bitwise reproducable simulations. Results should be statistcally identical, but this is currently not well tested.

  • enable_cylinder_volume_exclusion::Ref{Bool}: Are cylinder volume exclusion forces calculated

  • enable_triangle_bead_volume_exclusion::Bool: Are triangle-bead volume exclusion forces calculated.

  • cylinder_skin_radius::Float64: Extra cell list cutoff radius in nm. The cell lists are reset after a bead moves over this amount

  • filamentmechparams::Vector{MEDYAN.FilamentMechParams}: The filament mechanical parameters, indexed by filament type id

  • membranemechparams::Vector{MEDYAN.MembraneMechParams}: Membrane mechanical parameters, indexed by membrane type id.

  • func_membranespeciespotentialenergy::Any: Membrane species potential energy function. See docs on default function for more info.

  • membranefilamentmechparams::MEDYAN.MembraneFilamentMechParams: Membrane-filament mechanical interaction parameters.

  • external_energy_forces!::Any: External energy/force expressions. This should be a mutating function taking a (fc::MEDYAN.ForceContext), which adds to fc.forces, fc.energies, and fc.energy. The energy and force must be consistent, and this is not checked. This can be used as ad-hoc solutions to experiment with uncommon forces, such as specifically designed attachments, etc. If this variable is used often, consider moving it into MEDYAN.

  • chemboundary::MEDYAN.Boundary: chemical boundary, updates compartment volumes and diffusion rates

  • meshindex_as_chemboundary::Ref{Int64}: The membrane index used as chemical boundary. If values other than 0 is used, the actual interior region of the chemical boundary is the intersection between

    • the interior of chemboundary, and
    • the interior of the membrane mesh at this index.

    Note: Since the membrane may change its shape often, set_chemboundary! might need to be called often accordingly to update volumes of compartments.

  • mechboundary::MEDYAN.Boundary: mechanical boundary

  • sharedtypedconfigs::MEDYAN.SharedTypedConfigs: Shared configurations stored in type parameters.

  • validflags::MEDYAN.ValidFlags: Interval system consistency validation flags.

MEDYAN.set_time!

set_time!(c::MEDYAN.Context, x::Float64) -> Float64

Time (s)

MEDYAN.set_enable_cylinder_volume_exclusion!

set_enable_cylinder_volume_exclusion!(
    c::MEDYAN.Context,
    x::Bool
) -> Bool

Are cylinder volume exclusion forces calculated.

MEDYAN.set_chemboundary!

set_chemboundary!(
    c::MEDYAN.Context;
    meshindex_as_chemboundary,
    kwargs...
) -> MEDYAN.Boundary

Set chemical boundary and update compartment volumes and diffusion rates. Note, the chemboundary should be outside the mechboundary so that it is rare for filaments to go outside the chemboundary.

Calling this will invalidate the chem cache.

See also Boundary

Keywords

  • planes::Vector{SVector{4,Float64}} = []

Planes that make up the chemical boundary of the simulation

inside = signbit(pos ⋅ planes[bi][1:3] - planes[bi][4])

For example, a plane [1,0,0,3] is inside if x < 3 nm.

2.0*[1,0,0,3] is also inside if x < 3 nm.

  • capsules::Vector{SVector{8,Float64}} = []

Capsules that make up the chemical boundary of the simulation.

capsules[bi][1:3] is the starting point of the spine line segment (nm). capsules[bi][4:6] is the axis of the spine line segment (nm). capsules[bi][7] is the radius (nm). capsules[bi][8] is ignored.

if capsules[bi][4:6] is zero then the capsule is a sphere. Capsule boundaries can be combined with plane boundaries to create cylinder boundaries.

  • meshindex_as_chemboundary::Int = 0: Index of membrane mesh that further restricts the chem boundary. 0 for none.

The system geometry information must be up-to-date. This mesh index is not stored in the boundary object, but is directly set in the context.

MEDYAN.set_mechboundary!

set_mechboundary!(
    c::MEDYAN.Context;
    kwargs...
) -> MEDYAN.Boundary

See also Boundary

MEDYAN.chem_adddiffusingcount!

chem_adddiffusingcount!(c::Context, sid, cid, inccount)

Add inccount to diffusing species id sid in compartment id cid

MEDYAN.add_diffusing_count!

add_diffusing_count!(c::Context; species, chem_voxel, inccount)

Add inccount to diffusing species id sid in chem_voxel

MEDYAN.chem_addfixedcount!

chem_addfixedcount!(c::Context, sid, cid, inccount)

Add inccount to fixed species id sid in compartment id cid

MEDYAN.adddiffusingcount_rand!

adddiffusingcount_rand!(c::Context, dsid, inccount)

Distribute the added diffusing species count randomly to compartments weighted by volume.

  • dsid: diffusing species id.
  • inccount: amount to add.

MEDYAN.addmembranediffusingcount_rand!

addmembranediffusingcount_rand!(
    c::MEDYAN.Context,
    membraneindex::Int64,
    speciesindex::Int64,
    addcount::Int64
)

Distribute the added membrane species count randomly to membrane cells, ignoring cell area difference. Does NOT update propensity.

MEDYAN.run_chemistry!

run_chemistry!(c::Context, Δt)

Run chemistry for Δt time.

Update c.time.

MEDYAN.defer_chem_caching!

defer_chem_caching!(c::Context)::Nothing

This should only be used for advanced optimizations.

During chemistry, the context mutating functions will typically try to avoid invalidating various cached data needed to quickly sample sites.

However, if you want to mutate the context outside of chemistry, for example right before or after minimization, you may not want to pay the cost of revalidating all the caches because minimization will already invalidate the caches. Caching will be enabled again and caches will be made valid the next time chemistry is run. Caching can also be manually refreshed and reenabled with: refresh_chem_cache!

MEDYAN.refresh_chem_cache!

refresh_chem_cache!(c::Context)::Nothing

Normally this isn’t needed as it will happen automatically.

MEDYAN.is_chem_cache_valid

is_chem_cache_valid(c::Context)::Bool

Return true if the chemistry cache is valid, false otherwise.

Base.empty!

empty!(c::Context)

Remove all filaments, membranes, links, diffusing species, fixed species, bulk species, chemboundary, and mechboundary.

MEDYAN.newmembrane!

newmembrane!(c::MEDYAN.Context; type, meshinit)

Add a new membrane to the system.

Keyword arguments

  • meshinit is structure containing mesh shape initialization information, such as a named tuple (vertlist, trilist) containing vertex coordinates and triangle list, MeshInitEllipsoid, MeshInitPlane or a general MeshInitSurfaceFunc.