#!/usr/bin/env python
# coding: utf-8

# ### `A` up-regulates `B` , by being *the limiting reagent* in the reaction:     
# ### `A + X <-> 2B` (mostly forward), where `X` is plentiful
# 1st-order kinetics.   
# If [A] is low, [B] remains low, too.  Then, if [A] goes high, then so does [B].  However, at that point, A can no longer bring B down to any substantial extent.
# 
# **Single-bin reaction**
# 
# Based on experiment `reactions_single_compartment/up_regulate_1`

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LAST_REVISED = "May 5, 2025"
LIFE123_VERSION = "1.0.0rc3"        # Library version this experiment is based on


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#import set_path                    # Using MyBinder?  Uncomment this before running the next cell!


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#import sys
#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path   

from experiments.get_notebook_info import get_notebook_basename

from life123 import check_version, ChemData, BioSim1D, GraphicLog


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# Initialize the HTML logging
log_file = get_notebook_basename() + ".log.htm"    # Use the notebook base filename for the log file

# Set up the use of some specified graphic (Vue) components
GraphicLog.config(filename=log_file,
                  components=["vue_cytoscape_2"],
                  extra_js="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js")


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# Initialize the system.  NOTE: Diffusion not applicable (just 1 bin)
chem_data = ChemData(names=["A", "X", "B"], plot_colors=['red', 'darkorange', 'green']) 

bio = BioSim1D(n_bins=1, chem_data=chem_data)

bio.set_uniform_concentration(chem_label="A", conc=5.)     # Scarce
bio.set_uniform_concentration(chem_label="X", conc=100.)   # Plentiful
# Initially, no "B" is present

bio.describe_state()


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reactions = bio.get_reactions()

# Reaction A + X <-> 2B , with 1st-order kinetics for all species
reactions.add_reaction(reactants=["A" , "X"], products=[(2, "B", 1)],
                       forward_rate=8., reverse_rate=2.)

reactions.describe_reactions()

# Send the plot of the reaction network to the HTML log file
reactions.plot_reaction_network("vue_cytoscape_2")


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# ### Enable History

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# Let's enable history for all the chemicals
bio.enable_history(take_snapshot=True)     # Taking a snapshot to include the current initial state in the history


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bio.get_bin_history(bin_address=0)


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# ## Take the initial system to equilibrium

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bio.react(time_step=0.0005, n_steps=30)
bio.describe_state()


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bio.get_bin_history(bin_address=0)


# A, as the scarse limiting reagent, stops the reaction.  
# When A is low, B is also low.

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# ### <a name="sec_equilibrium"></a>Equilibrium

# Consistent with the 4/1 ratio of forward/reverse rates (and the 1st order reactions),
# the systems settles in the following equilibrium:

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# Verify that the reaction has reached equilibrium
bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc=bio.bin_snapshot(bin_address = 0))


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# # Plots of changes of concentration with time

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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction A + X <-> 2B")


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# # Now, let's suddenly increase [A]

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bio.set_bin_conc(bin_address=0, chem_index=0, conc=50.)
bio.describe_state()


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bio.capture_snapshot(caption="[A] suddenly increased externally")


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bio.get_bin_history(bin_address=0)


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# ### Again, take the system to equilibrium

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bio.react(time_step=0.0005, n_steps=40)
bio.describe_state()


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bio.get_bin_history(bin_address=0)


# A, still the limiting reagent, is again stopping the reaction.  
# The (transiently) high value of [A] led to a high value of [B]

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# Verify the equilibrium
bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc=bio.bin_snapshot(bin_address = 0))


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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction A + X <-> 2B")


# `A`, still the limiting reagent, is again stopping the reaction.  
# The (transiently) high value of [A] led to a high value of [B]

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# # Let's again suddenly increase [A]

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bio.set_bin_conc(bin_address=0, chem_index=0, conc=30.)
bio.describe_state()


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bio.capture_snapshot(caption="[A] again suddenly increased externally")


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bio.get_bin_history(bin_address=0)


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# ### Yet again, take the system to equilibrium

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bio.react(time_step=0.0005, n_steps=70)
bio.describe_state()


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bio.get_bin_history(bin_address=0)


# A, again the scarse limiting reagent, stops the reaction yet again

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# Verify the equilibrium
bio.reaction_dynamics.is_in_equilibrium(conc=bio.bin_snapshot(bin_address = 0), 
                                        tolerance=2)


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bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction A + X <-> 2B")


# `A`, again the scarse limiting reagent, stops the reaction yet again.  
# And, again, the (transiently) high value of [A] up-regulated [B]  
# 
# Note: `A` can up-regulate `B`, but it cannot bring it down.  
# `X` will soon need to be replenished, if `A` is to continue being the limiting reagent.

# # For additional exploration, see the experiment `reactions_single_compartment/up_regulate_1`

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