biocrnpyler.mechanisms.PositiveHillTranscription

class biocrnpyler.mechanisms.PositiveHillTranscription(name='positivehill_transcription', mechanism_type='transcription')[source]

Bases: Mechanism

Transcription regulated by positive Hill function (activation).

A ‘transcription’ mechanism that models transcriptional activation using a proportional positive Hill function. The transcription rate increases with regulator (activator) concentration according to Hill kinetics, capturing cooperative binding and activation.

The reaction follows the schema:

\[{\text{G}} \rightarrow {\text{G}} + {\text{T}} \]

with rate:

\[{\text{rate}} = k [\text{G}] \frac{[\text{R}]^n}{K + [\text{R}]^n}\]

where R is the regulator (activator), \(n\) is the Hill coefficient, and \(K\) is the activation constant. Optionally includes a basal leak reaction at rate ‘kleak’.

Parameters:

  • name (str, default 'positivehill_transcription') – Name identifier for this mechanism instance.

  • mechanism_type (str, default 'transcription') – Type classification of this mechanism.

Attributes:

  • name (str) – Name of the mechanism instance.

  • mechanism_type (str) – Type classification (‘transcription’).

See also

NegativeHillTranscription

Transcriptional repression with Hill function.

SimpleTranscription

Simple transcription without regulation.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models transcriptional activation by regulatory proteins such as transcription factors. The Hill function captures the sigmoidal response typical of cooperative binding, where multiple regulator molecules bind to the promoter to activate transcription.

Key features:

  • Sigmoidal activation response

  • Cooperative binding through Hill coefficient

  • Optional basal transcription (leak)

  • Saturation at high regulator concentrations

Common applications include:

  • Activatable promoters

  • Positive feedback loops

  • Transcriptional cascades

  • Genetic switches and toggles

Required parameters for this mechanism:

  • ‘k’ : Maximum transcription rate constant

  • ‘K’ : Activation constant (regulator concentration for half-maximal activation)

  • ‘n’ : Hill coefficient (cooperativity)

  • ‘kleak’ : Basal transcription rate (optional, for leak reaction)

Examples

Model transcriptional activation by an inducer:

>>> LacI = bcp.Protein('AraC')
>>> plac = bcp.ActivatablePromoter('pBAD', LacI)
>>> gene = bcp.DNAassembly(
...    name='activiated_GFP',
...    promoter=plac, rbs='RBS_medium', protein='GFP')
>>> tx_mechanism = bcp.PositiveHillTranscription()
>>> mixture = bcp.Mixture(
...     components=[LacI, gene],
...     mechanisms={
...         'transcription': tx_mechanism,
...         'translation': bcp.SimpleTranslation(),
...     },
...     parameters={'k': 1.0, 'K': 10.0, 'n': 2, 'kleak': 0.01},
...     parameter_file='mixtures/pure_parameters.tsv',
... )
>>> mixture.compile_crn()

Methods

update_reactions

Generate reactions for positive Hill transcription.

update_species

Generate species for positive Hill transcription.
update_reactions(dna, regulator, component, part_id, transcript=None, leak=False, protein=None, **kwargs)[source]

Generate reactions for positive Hill transcription.

Creates regulated transcription reaction(s) using a proportional positive Hill function, with optional basal leak reaction.

Parameters:

  • dna (Species) – The DNA species (promoter) being transcribed.

  • regulator (Species) – The activator species that regulates transcription.

  • component (Component) – Component containing parameter values. Required for parameter lookup.

  • part_id (str) – Identifier for parameter lookup in the component’s parameter database. Required for parameter lookup.

  • transcript (Species, optional) – The mRNA transcript species produced. If None and protein is provided, protein is produced directly.

  • leak (bool, default False) – If True, includes a basal leak reaction.

  • protein (Species, optional) – Protein species for expression mixtures.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing one or two reactions:

  • Regulated transcription with ProportionalHillPositive propensity

  • Optional leak reaction (if leak=True)

Return type:

list of Reaction

Raises:

AttributeError – If component or part_id is None (required for parameter lookup).

Notes

The regulated reaction uses ProportionalHillPositive propensity:

\[ {\text{DNA}} \rightarrow {\text{DNA}} + {\text{Product}} \quad ({\text{rate}} = k [\text{G}] [\text{R}]^n/(K + [\text{R}]^n)) \]
where Product is either transcript or protein depending on mixture type. If leak=True, adds:

\[{\text{DNA}} \rightarrow {\text{DNA}} + {\text{Product}} \quad ({\text{rate}} = {\text{kleak}}) \]

update_species(dna, regulator, transcript=None, leak=False, protein=None, **kwargs)[source]

Generate species for positive Hill transcription.

Returns all species involved in the regulated transcription reaction.

Parameters:

  • dna (Species) – The DNA species (promoter) being transcribed.

  • regulator (Species) – The activator species that regulates transcription.

  • transcript (Species, optional) – The mRNA transcript species produced. If None and protein is provided, protein is produced directly.

  • leak (bool, default False) – If True, includes a leak reaction for basal transcription.

  • protein (Species, optional) – Protein species for expression mixtures without explicit transcription.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing [dna, regulator] plus any non-None transcript/protein species.

Return type:

list of Species