affectors
Class CleavageA_ICDipAff

java.lang.Object
  affectors.Affector
      affectors.CleavageA_ICDipAff

All Implemented Interfaces:

java.lang.Cloneable

public class CleavageA_ICDipAff

extends Affector

Diploid version of CleaveageA_ICAff. Reduces to same result if the two alleles are identical. Assumptions for diploidizing: (1) Two alleles catalyze reactions instantly so there's no chance that one allele is able to bind and not cleave (thus inhibiting the other). (2) There is no synergy or cooperativity between the two (i.e. the two alleles don't see each other or interact) and the total activity is simply the sum of the individual activities. It would be interesting to compare this where the nonlinearity depends on some function of the sum of the concentrations

This is one half of an affector that cleaves a single node into two other nodes. The rate of cleavage is regulated by a separate activator node (an enzyme). Use this affector in the uncleaved species. Use the B version in each of the product species.
dNODEX/dt = -0.5*SUBSTRATE(CMax1 * ( (ACTIVATOR1 ^ nu1) / ( K1 ^ nu1 + ACTIVATOR1 ^ nu1) )+ CMax2 * ( (ACTIVATOR2 ^ nu2) / ( K2 ^ nu2 + ACTIVATOR2 ^ nu2) )

Parameters

Substrate [SUBSTRATE]	The uncleaved Node
Activator1 [ACTIVATOR1]	The regulator Node allele 1 which is activating cleavage
Activator1 [ACTIVATOR1]	The regulator Node allele 2 which is activating cleavage
Kappa1 [K_ACTIVATOR1_SUBSTRATE]	The level of the activator allele 1 at which it acts half-maximally.
Kappa2 [K_ACTIVATOR2_SUBSTRATE]	The level of the activator allele 2 at which it acts half-maximally.
nu1 [nu_ACTIVATOR1_SUBSTRATE]	Cooperativity of the activation allele 1.
nu2 [nu_ACTIVATOR2_SUBSTRATE]	Cooperativity of the activation allele 2.
CMax1 [CMax1_SUBSTRATE]	Maximal rate of cleavage for allele 1.
CMax2 [CMax2_SUBSTRATE]	Maximal rate of cleavage for allele 2.

Usage
&CLEAVED_NODE

&CleavageB_IC SUBSTRATE ACTIVATOR1 ACTIVATOR2 K_ACTIVATOR1_SUBSTRATE K_ACTIVATOR2_SUBSTRATE nu_ACTIVATOR1_SUBSTRATE nu_ACTIVATOR2_SUBSTRATE C1_SUBSTRATE C2_SUBSTRATE

&endCLEAVED_NODE

Field Summary

Fields inherited from class affectors.Affector

ADesc, affectorType, CC, CERTIFICATION, CONVERSION, copyNumber, DEGRADATION, FF, firstFreeParam, GG, GUI_CAPABLE, HH, KK, MATHTYPE, NDesc, PDesc, PRODUCTION, RETURNS_DERIV, RETURNS_PARTIALS, TERMTYPE, TT, Type, UNSPECIFIED

Constructor Summary

CleavageA_ICDipAff()

Method Summary

float	getNCValue(Node which_node)
float	getValue(Node which_node)
protected void	setLabelsAndTypes()
void	setParameterNumbers(int[] param_nums)

Methods inherited from class affectors.Affector

addDefaultParam, Chi, clearStatic, copy_, copy, doesContainTarget, findOrCreateParam, findParam, fixNodes, getNodes, getNumNodes, getNumParameters, getOtherSide, getParameter, getParameter, getParamName, getParamPos, getParamValue, getParamValue, getParamVariationMode, init, isLinearInTarget, Phi, Psi, setContainsTarget, setDescriptions, setParameter, setParamRange, setParamRange, setParamValue, setParamValue, setSide, setSided

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CleavageA_ICDipAff

public CleavageA_ICDipAff()

Method Detail

setLabelsAndTypes

protected void setLabelsAndTypes()

Specified by:

setLabelsAndTypes in class Affector

setParameterNumbers

public void setParameterNumbers(int[] param_nums)

Specified by:

setParameterNumbers in class Affector

getValue

public float getValue(Node which_node)

Overrides:

getValue in class Affector

getNCValue

public float getNCValue(Node which_node)

Overrides:

getNCValue in class Affector