biocrnpyler.mechanisms.NegativeHillTranscription

class biocrnpyler.mechanisms.NegativeHillTranscription(name='negativehill_transcription', mechanism_type='transcription', parameter_file='mechanisms/txtl_parameters.tsv')[source]

Bases: Mechanism

Transcription regulated by negative Hill function (repression).

A ‘transcription’ mechanism that models transcriptional repression using a proportional negative Hill function. The transcription rate decreases with regulator (repressor) concentration according to Hill kinetics, capturing cooperative binding and repression.

The reaction follows the schema:

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

with rate

\[{\text{rate}} = k * [\text{G}] * \frac{1}{K + [\text{R}]^n} \]

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

Parameters:

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

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

  • parameter_file (str, default 'mechanisms/txtl_parameters.tsv',) – Path to file containing default parameter values for this mechanism.

Attributes:

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

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

See also

PositiveHillTranscription

Transcriptional activation with Hill function.

SimpleTranscription

Simple transcription without regulation.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models transcriptional repression by regulatory proteins such as repressor proteins. The Hill function captures the response where increasing repressor concentration decreases transcription rate, with cooperativity determined by the Hill coefficient.

Key features:

  • Decreasing transcription with increasing repressor

  • Cooperative repressor binding through Hill coefficient

  • Optional basal transcription (leak)

  • Saturation at high repressor concentrations

Common applications include:

  • Repressible promoters

  • Negative feedback loops

  • Transcriptional repression cascades

  • Genetic switches and oscillators

Required parameters for this mechanism:

  • ‘k’ : Maximum transcription rate constant (when repressor is absent)

  • ‘K’ : Repression constant (repressor concentration for half-maximal repression)

  • ‘n’ : Hill coefficient (cooperativity)

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

Examples

Model transcriptional repression:

>>> LacI = bcp.Protein('LacI')
>>> plac = bcp.RepressiblePromoter('plac', LacI)
>>> gene = bcp.DNAassembly(
...    name='repressed_GFP',
...    promoter=plac, rbs='RBS_medium', protein='GFP')
>>> tx_mechanism = bcp.NegativeHillTranscription()
>>> 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

get_parameter

Retrieve a parameter from the mixture's parameter database.

update_reactions

Generate reactions for negative Hill transcription.

update_species

Generate species for negative Hill transcription.
get_parameter(mechanism, part_id, param_name)[source]

Retrieve a parameter from the mixture’s parameter database.

Parameters:

  • mechanism (str) – Mechanism identifier for the parameter lookup key.

  • part_id (str) – Part identifier for the parameter lookup key.

  • param_name (str) – Name of the parameter to retrieve.

Returns:

The parameter object, or None if not found.

Return type:

Parameter or None

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

Generate reactions for negative Hill transcription.

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

Parameters:

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

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

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

  • part_id (str) – Identifier for parameter lookup. Required.

  • transcript (Species, optional) – The mRNA transcript species produced.

  • 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 ProportionalHillNegative propensity, and optional leak reaction.

Return type:

list of Reaction

Notes

The regulated reaction uses ProportionalHillNegative propensity:

\[ {\text{DNA}} \rightarrow {\text{DNA}} + {\text{Product}} \quad ({\text{rate}} = k [\text{G}] / (K + [\text{R}]^n)) \]
If leak=True, adds:
\[ {\text{DNA}} \rightarrow {\text{DNA}} + {\text{Product}} \quad (rate = {\text{kleak}}) \]

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

Generate species for negative Hill transcription.

Returns all species involved in the regulated transcription reaction.

Parameters:

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

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

  • transcript (Species, optional) – The mRNA transcript species produced.

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

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

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

Returns:

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

Return type:

list of Species