diff --git a/master/.buildinfo b/master/.buildinfo
index 5f27e72c0..6e63aa432 100644
--- a/master/.buildinfo
+++ b/master/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 88abde309a18ff5ef5fc044ce4eada0b
+config: 69b458512336cd6bd91cce9a184069ef
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/master/.doctrees/README.doctree b/master/.doctrees/README.doctree
index 90f49251b..18ec521bd 100644
Binary files a/master/.doctrees/README.doctree and b/master/.doctrees/README.doctree differ
diff --git a/master/.doctrees/developer_guide/build_options.doctree b/master/.doctrees/developer_guide/build_options.doctree
index 31d97738e..cef62b454 100644
Binary files a/master/.doctrees/developer_guide/build_options.doctree and b/master/.doctrees/developer_guide/build_options.doctree differ
diff --git a/master/.doctrees/developer_guide/cadet_core_architecture.doctree b/master/.doctrees/developer_guide/cadet_core_architecture.doctree
index 8f128c662..c28f8bbc9 100644
Binary files a/master/.doctrees/developer_guide/cadet_core_architecture.doctree and b/master/.doctrees/developer_guide/cadet_core_architecture.doctree differ
diff --git a/master/.doctrees/developer_guide/debugging.doctree b/master/.doctrees/developer_guide/debugging.doctree
index 034ad1322..dbfb49bd2 100644
Binary files a/master/.doctrees/developer_guide/debugging.doctree and b/master/.doctrees/developer_guide/debugging.doctree differ
diff --git a/master/.doctrees/developer_guide/index.doctree b/master/.doctrees/developer_guide/index.doctree
index d1b1ad52d..c66bb90ce 100644
Binary files a/master/.doctrees/developer_guide/index.doctree and b/master/.doctrees/developer_guide/index.doctree differ
diff --git a/master/.doctrees/developer_guide/model_expansion.doctree b/master/.doctrees/developer_guide/model_expansion.doctree
index affda8f36..852a5fd09 100644
Binary files a/master/.doctrees/developer_guide/model_expansion.doctree and b/master/.doctrees/developer_guide/model_expansion.doctree differ
diff --git a/master/.doctrees/developer_guide/testing.doctree b/master/.doctrees/developer_guide/testing.doctree
index 8835bfe0c..2a64a2e36 100644
Binary files a/master/.doctrees/developer_guide/testing.doctree and b/master/.doctrees/developer_guide/testing.doctree differ
diff --git a/master/.doctrees/environment.pickle b/master/.doctrees/environment.pickle
index f1cd99f18..241df1f9d 100644
Binary files a/master/.doctrees/environment.pickle and b/master/.doctrees/environment.pickle differ
diff --git a/master/.doctrees/examples/batch_chromatography.doctree b/master/.doctrees/examples/batch_chromatography.doctree
index 416c1a8ae..964e69402 100644
Binary files a/master/.doctrees/examples/batch_chromatography.doctree and b/master/.doctrees/examples/batch_chromatography.doctree differ
diff --git a/master/.doctrees/examples/index.doctree b/master/.doctrees/examples/index.doctree
index 48f503620..2806a4793 100644
Binary files a/master/.doctrees/examples/index.doctree and b/master/.doctrees/examples/index.doctree differ
diff --git a/master/.doctrees/examples/load_wash_elute.doctree b/master/.doctrees/examples/load_wash_elute.doctree
index 2b7e796e1..83c89a18f 100644
Binary files a/master/.doctrees/examples/load_wash_elute.doctree and b/master/.doctrees/examples/load_wash_elute.doctree differ
diff --git a/master/.doctrees/examples/reaction_cstr.doctree b/master/.doctrees/examples/reaction_cstr.doctree
index a6687b7a6..7490a9569 100644
Binary files a/master/.doctrees/examples/reaction_cstr.doctree and b/master/.doctrees/examples/reaction_cstr.doctree differ
diff --git a/master/.doctrees/examples/rtd.doctree b/master/.doctrees/examples/rtd.doctree
index 2c11205bd..ad95cded4 100644
Binary files a/master/.doctrees/examples/rtd.doctree and b/master/.doctrees/examples/rtd.doctree differ
diff --git a/master/.doctrees/getting_started/build_linux.doctree b/master/.doctrees/getting_started/build_linux.doctree
index 5344b6391..01da80cb0 100644
Binary files a/master/.doctrees/getting_started/build_linux.doctree and b/master/.doctrees/getting_started/build_linux.doctree differ
diff --git a/master/.doctrees/getting_started/build_osx.doctree b/master/.doctrees/getting_started/build_osx.doctree
index 510a32517..102935c52 100644
Binary files a/master/.doctrees/getting_started/build_osx.doctree and b/master/.doctrees/getting_started/build_osx.doctree differ
diff --git a/master/.doctrees/getting_started/build_windows.doctree b/master/.doctrees/getting_started/build_windows.doctree
index 6365602ef..34ca1cefe 100644
Binary files a/master/.doctrees/getting_started/build_windows.doctree and b/master/.doctrees/getting_started/build_windows.doctree differ
diff --git a/master/.doctrees/getting_started/index.doctree b/master/.doctrees/getting_started/index.doctree
index 346c916f0..0dddba847 100644
Binary files a/master/.doctrees/getting_started/index.doctree and b/master/.doctrees/getting_started/index.doctree differ
diff --git a/master/.doctrees/getting_started/installation.doctree b/master/.doctrees/getting_started/installation.doctree
index d500bd4ab..729b18f47 100644
Binary files a/master/.doctrees/getting_started/installation.doctree and b/master/.doctrees/getting_started/installation.doctree differ
diff --git a/master/.doctrees/getting_started/overview.doctree b/master/.doctrees/getting_started/overview.doctree
index 60fa07213..0da0be210 100644
Binary files a/master/.doctrees/getting_started/overview.doctree and b/master/.doctrees/getting_started/overview.doctree differ
diff --git a/master/.doctrees/getting_started/tutorials/breakthrough.doctree b/master/.doctrees/getting_started/tutorials/breakthrough.doctree
index 337b128d4..df600fbd1 100644
Binary files a/master/.doctrees/getting_started/tutorials/breakthrough.doctree and b/master/.doctrees/getting_started/tutorials/breakthrough.doctree differ
diff --git a/master/.doctrees/index.doctree b/master/.doctrees/index.doctree
index 45f225fb6..a800ec590 100644
Binary files a/master/.doctrees/index.doctree and b/master/.doctrees/index.doctree differ
diff --git a/master/.doctrees/interface/binding/bi_steric_mass_action.doctree b/master/.doctrees/interface/binding/bi_steric_mass_action.doctree
index ef7195ebd..48b4bb180 100644
Binary files a/master/.doctrees/interface/binding/bi_steric_mass_action.doctree and b/master/.doctrees/interface/binding/bi_steric_mass_action.doctree differ
diff --git a/master/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree b/master/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree
index e4c7811ef..8248c1b47 100644
Binary files a/master/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree and b/master/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree differ
diff --git a/master/.doctrees/interface/binding/freundlich_ldf.doctree b/master/.doctrees/interface/binding/freundlich_ldf.doctree
index 7ddc7ad10..bf4831062 100644
Binary files a/master/.doctrees/interface/binding/freundlich_ldf.doctree and b/master/.doctrees/interface/binding/freundlich_ldf.doctree differ
diff --git a/master/.doctrees/interface/binding/generalized_ion_exchange.doctree b/master/.doctrees/interface/binding/generalized_ion_exchange.doctree
index 60c416187..400aaca8f 100644
Binary files a/master/.doctrees/interface/binding/generalized_ion_exchange.doctree and b/master/.doctrees/interface/binding/generalized_ion_exchange.doctree differ
diff --git a/master/.doctrees/interface/binding/hic_constant_water_activity.doctree b/master/.doctrees/interface/binding/hic_constant_water_activity.doctree
index c972d2f02..99a7933ae 100644
Binary files a/master/.doctrees/interface/binding/hic_constant_water_activity.doctree and b/master/.doctrees/interface/binding/hic_constant_water_activity.doctree differ
diff --git a/master/.doctrees/interface/binding/hic_water_on_hydrophobic_surfaces.doctree b/master/.doctrees/interface/binding/hic_water_on_hydrophobic_surfaces.doctree
index 9f0eba090..8ec00e0e5 100644
Binary files a/master/.doctrees/interface/binding/hic_water_on_hydrophobic_surfaces.doctree and b/master/.doctrees/interface/binding/hic_water_on_hydrophobic_surfaces.doctree differ
diff --git a/master/.doctrees/interface/binding/index.doctree b/master/.doctrees/interface/binding/index.doctree
index 95a611867..c1d04a005 100644
Binary files a/master/.doctrees/interface/binding/index.doctree and b/master/.doctrees/interface/binding/index.doctree differ
diff --git a/master/.doctrees/interface/binding/linear.doctree b/master/.doctrees/interface/binding/linear.doctree
index 3854d46f6..bd4297274 100644
Binary files a/master/.doctrees/interface/binding/linear.doctree and b/master/.doctrees/interface/binding/linear.doctree differ
diff --git a/master/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree b/master/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree
index 1a1a12529..7c48e2bb9 100644
Binary files a/master/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree and b/master/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_anti_langmuir.doctree b/master/.doctrees/interface/binding/multi_component_anti_langmuir.doctree
index 425bfa026..9551e0ed6 100644
Binary files a/master/.doctrees/interface/binding/multi_component_anti_langmuir.doctree and b/master/.doctrees/interface/binding/multi_component_anti_langmuir.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_bi_langmuir.doctree b/master/.doctrees/interface/binding/multi_component_bi_langmuir.doctree
index dc7123684..48681307e 100644
Binary files a/master/.doctrees/interface/binding/multi_component_bi_langmuir.doctree and b/master/.doctrees/interface/binding/multi_component_bi_langmuir.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_bi_langmuir_ldf.doctree b/master/.doctrees/interface/binding/multi_component_bi_langmuir_ldf.doctree
index 14490b99e..89d671c25 100644
Binary files a/master/.doctrees/interface/binding/multi_component_bi_langmuir_ldf.doctree and b/master/.doctrees/interface/binding/multi_component_bi_langmuir_ldf.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_colloidal.doctree b/master/.doctrees/interface/binding/multi_component_colloidal.doctree
index fe787a12f..f84497c47 100644
Binary files a/master/.doctrees/interface/binding/multi_component_colloidal.doctree and b/master/.doctrees/interface/binding/multi_component_colloidal.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_langmuir.doctree b/master/.doctrees/interface/binding/multi_component_langmuir.doctree
index 9e47d47f6..ec38357f1 100644
Binary files a/master/.doctrees/interface/binding/multi_component_langmuir.doctree and b/master/.doctrees/interface/binding/multi_component_langmuir.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_langmuir_ldf.doctree b/master/.doctrees/interface/binding/multi_component_langmuir_ldf.doctree
index dc0a368b2..074ae7324 100644
Binary files a/master/.doctrees/interface/binding/multi_component_langmuir_ldf.doctree and b/master/.doctrees/interface/binding/multi_component_langmuir_ldf.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_langmuir_ldf_liquid_phase.doctree b/master/.doctrees/interface/binding/multi_component_langmuir_ldf_liquid_phase.doctree
index 9a955ded7..cff57a2a2 100644
Binary files a/master/.doctrees/interface/binding/multi_component_langmuir_ldf_liquid_phase.doctree and b/master/.doctrees/interface/binding/multi_component_langmuir_ldf_liquid_phase.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_component_spreading.doctree b/master/.doctrees/interface/binding/multi_component_spreading.doctree
index 1a68c51aa..54904defb 100644
Binary files a/master/.doctrees/interface/binding/multi_component_spreading.doctree and b/master/.doctrees/interface/binding/multi_component_spreading.doctree differ
diff --git a/master/.doctrees/interface/binding/multi_state_steric_mass_action.doctree b/master/.doctrees/interface/binding/multi_state_steric_mass_action.doctree
index 2c1dc8dde..511e45995 100644
Binary files a/master/.doctrees/interface/binding/multi_state_steric_mass_action.doctree and b/master/.doctrees/interface/binding/multi_state_steric_mass_action.doctree differ
diff --git a/master/.doctrees/interface/binding/saska.doctree b/master/.doctrees/interface/binding/saska.doctree
index c4b2b092b..5c943d0ba 100644
Binary files a/master/.doctrees/interface/binding/saska.doctree and b/master/.doctrees/interface/binding/saska.doctree differ
diff --git a/master/.doctrees/interface/binding/self_association.doctree b/master/.doctrees/interface/binding/self_association.doctree
index 0d3debe64..847be563d 100644
Binary files a/master/.doctrees/interface/binding/self_association.doctree and b/master/.doctrees/interface/binding/self_association.doctree differ
diff --git a/master/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree b/master/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree
index a33de62b2..c996841eb 100644
Binary files a/master/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree and b/master/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree differ
diff --git a/master/.doctrees/interface/binding/steric_mass_action.doctree b/master/.doctrees/interface/binding/steric_mass_action.doctree
index a50461355..e7519a603 100644
Binary files a/master/.doctrees/interface/binding/steric_mass_action.doctree and b/master/.doctrees/interface/binding/steric_mass_action.doctree differ
diff --git a/master/.doctrees/interface/consistent_initialization.doctree b/master/.doctrees/interface/consistent_initialization.doctree
index 4280b3fad..e531f3650 100644
Binary files a/master/.doctrees/interface/consistent_initialization.doctree and b/master/.doctrees/interface/consistent_initialization.doctree differ
diff --git a/master/.doctrees/interface/flux_reconstruction.doctree b/master/.doctrees/interface/flux_reconstruction.doctree
index c1f06a079..a038aeb21 100644
Binary files a/master/.doctrees/interface/flux_reconstruction.doctree and b/master/.doctrees/interface/flux_reconstruction.doctree differ
diff --git a/master/.doctrees/interface/index.doctree b/master/.doctrees/interface/index.doctree
index f00092fcf..6c74f86e6 100644
Binary files a/master/.doctrees/interface/index.doctree and b/master/.doctrees/interface/index.doctree differ
diff --git a/master/.doctrees/interface/input_group.doctree b/master/.doctrees/interface/input_group.doctree
index dc252f091..73d62af5a 100644
Binary files a/master/.doctrees/interface/input_group.doctree and b/master/.doctrees/interface/input_group.doctree differ
diff --git a/master/.doctrees/interface/introduction.doctree b/master/.doctrees/interface/introduction.doctree
index 62484fe8d..70e2841f3 100644
Binary files a/master/.doctrees/interface/introduction.doctree and b/master/.doctrees/interface/introduction.doctree differ
diff --git a/master/.doctrees/interface/meta_group.doctree b/master/.doctrees/interface/meta_group.doctree
index 4ee5d09d0..9b931bb76 100644
Binary files a/master/.doctrees/interface/meta_group.doctree and b/master/.doctrees/interface/meta_group.doctree differ
diff --git a/master/.doctrees/interface/output_group.doctree b/master/.doctrees/interface/output_group.doctree
index def8be2d9..33cf41f02 100644
Binary files a/master/.doctrees/interface/output_group.doctree and b/master/.doctrees/interface/output_group.doctree differ
diff --git a/master/.doctrees/interface/parameter_dependencies.doctree b/master/.doctrees/interface/parameter_dependencies.doctree
index 62e53b34c..5fd2d84ac 100644
Binary files a/master/.doctrees/interface/parameter_dependencies.doctree and b/master/.doctrees/interface/parameter_dependencies.doctree differ
diff --git a/master/.doctrees/interface/reaction/index.doctree b/master/.doctrees/interface/reaction/index.doctree
new file mode 100644
index 000000000..fe1b1dae3
Binary files /dev/null and b/master/.doctrees/interface/reaction/index.doctree differ
diff --git a/master/.doctrees/interface/reaction/mass_action_law.doctree b/master/.doctrees/interface/reaction/mass_action_law.doctree
new file mode 100644
index 000000000..26e3239c6
Binary files /dev/null and b/master/.doctrees/interface/reaction/mass_action_law.doctree differ
diff --git a/master/.doctrees/interface/reaction/michaelis_menten_kinetics.doctree b/master/.doctrees/interface/reaction/michaelis_menten_kinetics.doctree
new file mode 100644
index 000000000..5bcd36b2f
Binary files /dev/null and b/master/.doctrees/interface/reaction/michaelis_menten_kinetics.doctree differ
diff --git a/master/.doctrees/interface/reactions.doctree b/master/.doctrees/interface/reactions.doctree
deleted file mode 100644
index 7b3955a7d..000000000
Binary files a/master/.doctrees/interface/reactions.doctree and /dev/null differ
diff --git a/master/.doctrees/interface/return_data.doctree b/master/.doctrees/interface/return_data.doctree
index 6ee752f83..491035323 100644
Binary files a/master/.doctrees/interface/return_data.doctree and b/master/.doctrees/interface/return_data.doctree differ
diff --git a/master/.doctrees/interface/sensitivities.doctree b/master/.doctrees/interface/sensitivities.doctree
index 1d2db3031..3d2f8fbf6 100644
Binary files a/master/.doctrees/interface/sensitivities.doctree and b/master/.doctrees/interface/sensitivities.doctree differ
diff --git a/master/.doctrees/interface/solver.doctree b/master/.doctrees/interface/solver.doctree
index 04464f6ce..0d37d4af9 100644
Binary files a/master/.doctrees/interface/solver.doctree and b/master/.doctrees/interface/solver.doctree differ
diff --git a/master/.doctrees/interface/spatial_discretization_methods.doctree b/master/.doctrees/interface/spatial_discretization_methods.doctree
index eae63d090..92014fa89 100644
Binary files a/master/.doctrees/interface/spatial_discretization_methods.doctree and b/master/.doctrees/interface/spatial_discretization_methods.doctree differ
diff --git a/master/.doctrees/interface/system.doctree b/master/.doctrees/interface/system.doctree
index 9a5b10245..3dc0fa944 100644
Binary files a/master/.doctrees/interface/system.doctree and b/master/.doctrees/interface/system.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/2d_general_rate_model.doctree b/master/.doctrees/interface/unit_operations/2d_general_rate_model.doctree
index 6418d4d96..04ebde829 100644
Binary files a/master/.doctrees/interface/unit_operations/2d_general_rate_model.doctree and b/master/.doctrees/interface/unit_operations/2d_general_rate_model.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/cstr.doctree b/master/.doctrees/interface/unit_operations/cstr.doctree
index 44e85a7bc..7ec0e97f7 100644
Binary files a/master/.doctrees/interface/unit_operations/cstr.doctree and b/master/.doctrees/interface/unit_operations/cstr.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/general_rate_model.doctree b/master/.doctrees/interface/unit_operations/general_rate_model.doctree
index de4b32489..cea64705a 100644
Binary files a/master/.doctrees/interface/unit_operations/general_rate_model.doctree and b/master/.doctrees/interface/unit_operations/general_rate_model.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/index.doctree b/master/.doctrees/interface/unit_operations/index.doctree
index af99f3ca9..52d57f5fc 100644
Binary files a/master/.doctrees/interface/unit_operations/index.doctree and b/master/.doctrees/interface/unit_operations/index.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/inlet.doctree b/master/.doctrees/interface/unit_operations/inlet.doctree
index ffc4af481..caf3b2d05 100644
Binary files a/master/.doctrees/interface/unit_operations/inlet.doctree and b/master/.doctrees/interface/unit_operations/inlet.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree b/master/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree
index a3dfabfa1..eadd44ad8 100644
Binary files a/master/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree and b/master/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree b/master/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree
index 92b769acf..4149fb460 100644
Binary files a/master/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree and b/master/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/multi_channel_transport_model.doctree b/master/.doctrees/interface/unit_operations/multi_channel_transport_model.doctree
index 682dc7067..589a26abf 100644
Binary files a/master/.doctrees/interface/unit_operations/multi_channel_transport_model.doctree and b/master/.doctrees/interface/unit_operations/multi_channel_transport_model.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/outlet.doctree b/master/.doctrees/interface/unit_operations/outlet.doctree
index 0ecd85bce..2a397321f 100644
Binary files a/master/.doctrees/interface/unit_operations/outlet.doctree and b/master/.doctrees/interface/unit_operations/outlet.doctree differ
diff --git a/master/.doctrees/interface/unit_operations/radial_flow_models.doctree b/master/.doctrees/interface/unit_operations/radial_flow_models.doctree
index 74cb559d5..3ede742a4 100644
Binary files a/master/.doctrees/interface/unit_operations/radial_flow_models.doctree and b/master/.doctrees/interface/unit_operations/radial_flow_models.doctree differ
diff --git a/master/.doctrees/license.doctree b/master/.doctrees/license.doctree
index b75302cea..399557f37 100644
Binary files a/master/.doctrees/license.doctree and b/master/.doctrees/license.doctree differ
diff --git a/master/.doctrees/modelling/binding/bi_steric_mass_action.doctree b/master/.doctrees/modelling/binding/bi_steric_mass_action.doctree
index d6b1c3218..cff610026 100644
Binary files a/master/.doctrees/modelling/binding/bi_steric_mass_action.doctree and b/master/.doctrees/modelling/binding/bi_steric_mass_action.doctree differ
diff --git a/master/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree b/master/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree
index 75471df9b..8a437e2f0 100644
Binary files a/master/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree and b/master/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree differ
diff --git a/master/.doctrees/modelling/binding/freundlich_ldf.doctree b/master/.doctrees/modelling/binding/freundlich_ldf.doctree
index 2570d2d39..d35af2cf9 100644
Binary files a/master/.doctrees/modelling/binding/freundlich_ldf.doctree and b/master/.doctrees/modelling/binding/freundlich_ldf.doctree differ
diff --git a/master/.doctrees/modelling/binding/generalized_ion_exchange.doctree b/master/.doctrees/modelling/binding/generalized_ion_exchange.doctree
index 3ab8e9db3..52dc48771 100644
Binary files a/master/.doctrees/modelling/binding/generalized_ion_exchange.doctree and b/master/.doctrees/modelling/binding/generalized_ion_exchange.doctree differ
diff --git a/master/.doctrees/modelling/binding/hic_constant_water_activity.doctree b/master/.doctrees/modelling/binding/hic_constant_water_activity.doctree
index b625370bc..123053184 100644
Binary files a/master/.doctrees/modelling/binding/hic_constant_water_activity.doctree and b/master/.doctrees/modelling/binding/hic_constant_water_activity.doctree differ
diff --git a/master/.doctrees/modelling/binding/hic_water_on_hydrophobic_surfaces.doctree b/master/.doctrees/modelling/binding/hic_water_on_hydrophobic_surfaces.doctree
index 829e67291..f02c45987 100644
Binary files a/master/.doctrees/modelling/binding/hic_water_on_hydrophobic_surfaces.doctree and b/master/.doctrees/modelling/binding/hic_water_on_hydrophobic_surfaces.doctree differ
diff --git a/master/.doctrees/modelling/binding/index.doctree b/master/.doctrees/modelling/binding/index.doctree
index fdd2a62b6..f0101855e 100644
Binary files a/master/.doctrees/modelling/binding/index.doctree and b/master/.doctrees/modelling/binding/index.doctree differ
diff --git a/master/.doctrees/modelling/binding/linear.doctree b/master/.doctrees/modelling/binding/linear.doctree
index 1b63a7872..95d757715 100644
Binary files a/master/.doctrees/modelling/binding/linear.doctree and b/master/.doctrees/modelling/binding/linear.doctree differ
diff --git a/master/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree b/master/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree
index 81f900a45..4d99e7bc7 100644
Binary files a/master/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree and b/master/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree b/master/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree
index 52f1b29bd..d9369de27 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree and b/master/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree b/master/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree
index ce5e99a7f..821d52e80 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree and b/master/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_bi_langmuir_ldf.doctree b/master/.doctrees/modelling/binding/multi_component_bi_langmuir_ldf.doctree
index f437ca65f..d7ead2111 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_bi_langmuir_ldf.doctree and b/master/.doctrees/modelling/binding/multi_component_bi_langmuir_ldf.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_colloidal.doctree b/master/.doctrees/modelling/binding/multi_component_colloidal.doctree
index ad0f155d6..dcff24e6d 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_colloidal.doctree and b/master/.doctrees/modelling/binding/multi_component_colloidal.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_langmuir.doctree b/master/.doctrees/modelling/binding/multi_component_langmuir.doctree
index 8131d9283..b7c747f47 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_langmuir.doctree and b/master/.doctrees/modelling/binding/multi_component_langmuir.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_langmuir_ldf.doctree b/master/.doctrees/modelling/binding/multi_component_langmuir_ldf.doctree
index 4a7bf81ba..c5771ca6d 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_langmuir_ldf.doctree and b/master/.doctrees/modelling/binding/multi_component_langmuir_ldf.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_langmuir_ldf_liquid_phase.doctree b/master/.doctrees/modelling/binding/multi_component_langmuir_ldf_liquid_phase.doctree
index 2e9ecf8c0..c14ded127 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_langmuir_ldf_liquid_phase.doctree and b/master/.doctrees/modelling/binding/multi_component_langmuir_ldf_liquid_phase.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_component_spreading.doctree b/master/.doctrees/modelling/binding/multi_component_spreading.doctree
index 4c35c7b46..54946373a 100644
Binary files a/master/.doctrees/modelling/binding/multi_component_spreading.doctree and b/master/.doctrees/modelling/binding/multi_component_spreading.doctree differ
diff --git a/master/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree b/master/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree
index d78c66a05..f13a41a1e 100644
Binary files a/master/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree and b/master/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree differ
diff --git a/master/.doctrees/modelling/binding/saska.doctree b/master/.doctrees/modelling/binding/saska.doctree
index c1a0b856b..fc0885698 100644
Binary files a/master/.doctrees/modelling/binding/saska.doctree and b/master/.doctrees/modelling/binding/saska.doctree differ
diff --git a/master/.doctrees/modelling/binding/self_association.doctree b/master/.doctrees/modelling/binding/self_association.doctree
index faa942578..f4f733aae 100644
Binary files a/master/.doctrees/modelling/binding/self_association.doctree and b/master/.doctrees/modelling/binding/self_association.doctree differ
diff --git a/master/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree b/master/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree
index 084c8f16e..6e0f227b3 100644
Binary files a/master/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree and b/master/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree differ
diff --git a/master/.doctrees/modelling/binding/steric_mass_action.doctree b/master/.doctrees/modelling/binding/steric_mass_action.doctree
index d17911341..b63cc0110 100644
Binary files a/master/.doctrees/modelling/binding/steric_mass_action.doctree and b/master/.doctrees/modelling/binding/steric_mass_action.doctree differ
diff --git a/master/.doctrees/modelling/index.doctree b/master/.doctrees/modelling/index.doctree
index 78d77284d..f719f6936 100644
Binary files a/master/.doctrees/modelling/index.doctree and b/master/.doctrees/modelling/index.doctree differ
diff --git a/master/.doctrees/modelling/networks.doctree b/master/.doctrees/modelling/networks.doctree
index 1f7adc4d5..64c4b4124 100644
Binary files a/master/.doctrees/modelling/networks.doctree and b/master/.doctrees/modelling/networks.doctree differ
diff --git a/master/.doctrees/modelling/reaction/index.doctree b/master/.doctrees/modelling/reaction/index.doctree
new file mode 100644
index 000000000..bccea454a
Binary files /dev/null and b/master/.doctrees/modelling/reaction/index.doctree differ
diff --git a/master/.doctrees/modelling/reaction/mass_action_law.doctree b/master/.doctrees/modelling/reaction/mass_action_law.doctree
new file mode 100644
index 000000000..0f3279ab3
Binary files /dev/null and b/master/.doctrees/modelling/reaction/mass_action_law.doctree differ
diff --git a/master/.doctrees/modelling/reaction/michaelis_menten_kinetics.doctree b/master/.doctrees/modelling/reaction/michaelis_menten_kinetics.doctree
new file mode 100644
index 000000000..08b5aca98
Binary files /dev/null and b/master/.doctrees/modelling/reaction/michaelis_menten_kinetics.doctree differ
diff --git a/master/.doctrees/modelling/reactions.doctree b/master/.doctrees/modelling/reactions.doctree
deleted file mode 100644
index 410b5c289..000000000
Binary files a/master/.doctrees/modelling/reactions.doctree and /dev/null differ
diff --git a/master/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree b/master/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree
index 00749d878..81b6f1320 100644
Binary files a/master/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree and b/master/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/cstr.doctree b/master/.doctrees/modelling/unit_operations/cstr.doctree
index d6e2ac451..477f694fb 100644
Binary files a/master/.doctrees/modelling/unit_operations/cstr.doctree and b/master/.doctrees/modelling/unit_operations/cstr.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/general_rate_model.doctree b/master/.doctrees/modelling/unit_operations/general_rate_model.doctree
index a0a02cf2a..3dadc9702 100644
Binary files a/master/.doctrees/modelling/unit_operations/general_rate_model.doctree and b/master/.doctrees/modelling/unit_operations/general_rate_model.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/index.doctree b/master/.doctrees/modelling/unit_operations/index.doctree
index 5ceb62e92..48ceda2f1 100644
Binary files a/master/.doctrees/modelling/unit_operations/index.doctree and b/master/.doctrees/modelling/unit_operations/index.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/inlet.doctree b/master/.doctrees/modelling/unit_operations/inlet.doctree
index e8660dfc2..13607aada 100644
Binary files a/master/.doctrees/modelling/unit_operations/inlet.doctree and b/master/.doctrees/modelling/unit_operations/inlet.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree b/master/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree
index bad0d24c1..862c31d25 100644
Binary files a/master/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree and b/master/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree b/master/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree
index e0f37e642..59333cbc4 100644
Binary files a/master/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree and b/master/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/multi_channel_transport_model.doctree b/master/.doctrees/modelling/unit_operations/multi_channel_transport_model.doctree
index d6e1d5856..5e862b3bd 100644
Binary files a/master/.doctrees/modelling/unit_operations/multi_channel_transport_model.doctree and b/master/.doctrees/modelling/unit_operations/multi_channel_transport_model.doctree differ
diff --git a/master/.doctrees/modelling/unit_operations/outlet.doctree b/master/.doctrees/modelling/unit_operations/outlet.doctree
index ccab92838..8a7ad5dae 100644
Binary files a/master/.doctrees/modelling/unit_operations/outlet.doctree and b/master/.doctrees/modelling/unit_operations/outlet.doctree differ
diff --git a/master/.doctrees/requirements.doctree b/master/.doctrees/requirements.doctree
index 08698f2e4..de59f2b5e 100644
Binary files a/master/.doctrees/requirements.doctree and b/master/.doctrees/requirements.doctree differ
diff --git a/master/.doctrees/simulation/index.doctree b/master/.doctrees/simulation/index.doctree
index 4cf6fb059..64a548925 100644
Binary files a/master/.doctrees/simulation/index.doctree and b/master/.doctrees/simulation/index.doctree differ
diff --git a/master/.doctrees/zbibliography.doctree b/master/.doctrees/zbibliography.doctree
index bcf6e7ed0..297b2bfca 100644
Binary files a/master/.doctrees/zbibliography.doctree and b/master/.doctrees/zbibliography.doctree differ
diff --git a/master/_sources/interface/input_group.rst.txt b/master/_sources/interface/input_group.rst.txt
index 5940e0964..9859c0a0d 100644
--- a/master/_sources/interface/input_group.rst.txt
+++ b/master/_sources/interface/input_group.rst.txt
@@ -9,7 +9,7 @@ Input Group
system
unit_operations/index
binding/index
- reactions
+ reaction/index
spatial_discretization_methods
flux_reconstruction
consistent_initialization
diff --git a/master/_sources/interface/reaction/index.rst.txt b/master/_sources/interface/reaction/index.rst.txt
new file mode 100644
index 000000000..5e00dd6d7
--- /dev/null
+++ b/master/_sources/interface/reaction/index.rst.txt
@@ -0,0 +1,46 @@
+.. _FFReaction:
+
+Reaction models
+===============
+
+.. toctree::
+ :maxdepth: 2
+
+ mass_action_law
+ michaelis_menten_kinetics
+
+Externally dependent reaction models
+------------------------------------
+
+Some reaction models have a variant that can use external sources as specified :ref:`/input/model/external/` (also see Section :ref:`dependence-on-external-function_react`).
+For the sake of brevity, only the standard variant of those reaction models is specified below.
+In order to obtain the format for the externally dependent variant, first replace the reaction model name ``XXX`` by ``EXT_XXX``.
+Each parameter :math:`p` (except for stoichiometric and exponent matrices) depends on a (possibly distinct) external source in a polynomial way:
+
+.. math::
+
+ \begin{aligned}
+ p(T) &= p_{\texttt{TTT}} T^3 + p_{\texttt{TT}} T^2 + p_{\texttt{T}} T + p.
+ \end{aligned}
+
+Thus, a parameter ``XXX_YYY`` of the standard reaction model variant is replaced by the four parameters ``EXT_XXX_YYY``, ``EXT_XXX_YYY_T``, ``EXT_XXX_YYY_TT``, and ``EXT_XXX_YYY_TTT``.
+Since each parameter can depend on a different external source, the dataset ``EXTFUN`` (not listed in the standard variants below) should contain a vector of 0-based integer indices of the external source of each parameter.
+The ordering of the parameters in ``EXTFUN`` is given by the ordering in the standard variant.
+However, if only one index is passed in ``EXTFUN``, this external source is used for all parameters.
+
+Note that parameter sensitivities with respect to column radius, column length, particle core radius, and particle radius may be wrong when using externally dependent reaction models.
+This is caused by not taking into account the derivative of the external profile with respect to column position.
+
+
+.. _multiple-particle-types_reactions:
+
+Multiple particle types
+-----------------------
+
+The group that contains the parameters of a reaction model in unit operation with index ``XXX`` reads ``/input/model/unit_XXX/reaction_particle``.
+This is valid for models with a single particle type.
+If a model has multiple particle types, it may have a different reaction model in each type.
+The parameters are then placed in the group ``/input/model/unit_XXX/reaction_particle_YYY`` instead, where ``YYY`` denotes the index of the particle type.
+
+Note that, in any case, ``/input/model/unit_XXX/reaction_particle_000`` contains the parameters of the first (and possibly sole) particle type.
+This group also takes precedence over a possibly existing ``/input/model/unit_XXX/adsorption_particle`` group.
diff --git a/master/_sources/interface/reactions.rst.txt b/master/_sources/interface/reaction/mass_action_law.rst.txt
similarity index 75%
rename from master/_sources/interface/reactions.rst.txt
rename to master/_sources/interface/reaction/mass_action_law.rst.txt
index f874dce2c..26c20b89f 100644
--- a/master/_sources/interface/reactions.rst.txt
+++ b/master/_sources/interface/reaction/mass_action_law.rst.txt
@@ -1,48 +1,9 @@
-.. _FFReaction:
+.. _mass_action_law_config:
-Reaction models
-===============
+Mass Action Law
+~~~~~~~~~~~~~~~
-Externally dependent reaction models
-------------------------------------
-
-Some reaction models have a variant that can use external sources as specified :ref:`/input/model/external/` (also see Section :ref:`dependence-on-external-function_react`).
-For the sake of brevity, only the standard variant of those reaction models is specified below.
-In order to obtain the format for the externally dependent variant, first replace the reaction model name ``XXX`` by ``EXT_XXX``.
-Each parameter :math:`p` (except for stoichiometric and exponent matrices) depends on a (possibly distinct) external source in a polynomial way:
-
-.. math::
-
- \begin{aligned}
- p(T) &= p_{\texttt{TTT}} T^3 + p_{\texttt{TT}} T^2 + p_{\texttt{T}} T + p.
- \end{aligned}
-
-Thus, a parameter ``XXX_YYY`` of the standard reaction model variant is replaced by the four parameters ``EXT_XXX_YYY``, ``EXT_XXX_YYY_T``, ``EXT_XXX_YYY_TT``, and ``EXT_XXX_YYY_TTT``.
-Since each parameter can depend on a different external source, the dataset ``EXTFUN`` (not listed in the standard variants below) should contain a vector of 0-based integer indices of the external source of each parameter.
-The ordering of the parameters in ``EXTFUN`` is given by the ordering in the standard variant.
-However, if only one index is passed in ``EXTFUN``, this external source is used for all parameters.
-
-Note that parameter sensitivities with respect to column radius, column length, particle core radius, and particle radius may be wrong when using externally dependent reaction models.
-This is caused by not taking into account the derivative of the external profile with respect to column position.
-
-
-.. _multiple-particle-types_reactions:
-
-Multiple particle types
------------------------
-
-The group that contains the parameters of a reaction model in unit operation with index ``XXX`` reads ``/input/model/unit_XXX/reaction_particle``.
-This is valid for models with a single particle type.
-If a model has multiple particle types, it may have a different reaction model in each type.
-The parameters are then placed in the group ``/input/model/unit_XXX/reaction_particle_YYY`` instead, where ``YYY`` denotes the index of the particle type.
-
-Note that, in any case, ``/input/model/unit_XXX/reaction_particle_000`` contains the parameters of the first (and possibly sole) particle type.
-This group also takes precedence over a possibly existing ``/input/model/unit_XXX/adsorption_particle`` group.
-
-.. _FFReactionMassActionLaw:
-
-Group /input/model/unit_XXX/reaction - REACTION_MODEL = MASS_ACTION_LAW
------------------------------------------------------------------------
+**Group /input/model/unit_XXX/reaction - REACTION_MODEL = MASS_ACTION_LAW**
``MAL_KFWD_BULK``
diff --git a/master/_sources/interface/reaction/michaelis_menten_kinetics.rst.txt b/master/_sources/interface/reaction/michaelis_menten_kinetics.rst.txt
new file mode 100644
index 000000000..76884ea2e
--- /dev/null
+++ b/master/_sources/interface/reaction/michaelis_menten_kinetics.rst.txt
@@ -0,0 +1,41 @@
+.. _michaelis_menten_kinetics_config:
+
+Michaelis Menten kinetics
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**Group /input/model/unit_XXX/reaction - REACTION_MODEL = MICHAELIS_MENTEN**
+
+``MM_STOICHIOMETRY_BULK``
+
+ Stochiometric matrix :math:`S`.
+ The substrate component :math:`c_S` is identified by the index of the first negative entry in the stoichiometry of the corresponding reaction.
+ Input as reaction index major.
+
+ ================ ============================= ========================================================
+ **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NCOMP}`
+ ================ ============================= ========================================================
+
+``MM_VMAX``
+
+ Limiting rate :math:`\mu_{\mathrm{max},j}` at saturation.
+
+ ================ ============================= ===================================
+ **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT}`
+ ================ ============================= ===================================
+
+``MM_KMM``
+
+ Michaelis constant :math:`k_{\mathrm{MM},j}`.
+
+ ================ ============================= ===================================
+ **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT}`
+ ================ ============================= ===================================
+
+``MM_KI``
+
+ Inhibition constant :math:`k_{\mathrm{I},j,i}` w.r.t component :math:`i` and reaction :math:`j`. If :math:`k_{\mathrm{I},j,i} <= 0`, the component does not inhibit the reaction.
+ Input as reaction index major.
+
+ ================ ============================= ========================================================
+ **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NCOMP}`
+ ================ ============================= ========================================================
\ No newline at end of file
diff --git a/master/_sources/modelling/index.rst.txt b/master/_sources/modelling/index.rst.txt
index 5741194d2..283c9f3a9 100644
--- a/master/_sources/modelling/index.rst.txt
+++ b/master/_sources/modelling/index.rst.txt
@@ -8,5 +8,5 @@ This section gives complete information about the supported unit operations, bin
.. toctree::
unit_operations/index
binding/index
- reactions
+ reaction/index
networks
diff --git a/master/_sources/modelling/reaction/index.rst.txt b/master/_sources/modelling/reaction/index.rst.txt
new file mode 100644
index 000000000..172908182
--- /dev/null
+++ b/master/_sources/modelling/reaction/index.rst.txt
@@ -0,0 +1,41 @@
+.. _reaction_models:
+
+Reaction models
+===============
+
+
+Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}` of a
+reaction mechanism.
+CADET features one reaction type:
+
+ - :ref:`mass_action_law_model` (most commonly used)
+ - :ref:`michaelis_menten_kinetics_model`
+
+
+.. _dependence-on-external-function_react:
+
+Dependence on external function
+-------------------------------
+
+A reaction model may depend on an external function or profile :math:`T\colon \left[ 0, T_{\mathrm{end}}\right] \times [0, L] \to \mathbb{R}`, where :math:`L` denotes the physical length of the unit operation, or :math:`T\colon \left[0, T_{\mathrm{end}}\right] \to \mathbb{R}` if the unit operation model has no axial length.
+By using an external profile, it is possible to account for effects that are not directly modeled in CADET (e.g., temperature).
+The dependence of each parameter is modeled by a polynomial of third degree.
+For example, the forward rate constant :math:`k_{\mathrm{fwd}}` is really given by
+
+.. math::
+
+ \begin{aligned}
+ k_{\mathrm{fwd}}(T) &= k_{\mathrm{fwd},3} T^3 + k_{\mathrm{fwd},2} T^2 + k_{\mathrm{fwd},1} T + k_{\mathrm{fwd},0}.
+ \end{aligned}
+
+While :math:`k_{\mathrm{fwd},0}` is set by the original parameter ``XXX_KFWD`` of the file format (``XXX`` being a placeholder for the reaction model), the parameters :math:`k_{\mathrm{fwd},3}`, :math:`k_{\mathrm{fwd},2}`, and :math:`k_{\mathrm{fwd},1}` are given by ``XXX_KFWD_TTT``, ``XXX_KFWD_TT``, and ``XXX_KFWD_T``, respectively.
+The identifier of the externally dependent reaction model is constructed from the original identifier by prepending ``EXT_`` (e.g., ``MASS_ACTION_LAW`` is changed into ``EXT_MASS_ACTION_LAW``).
+This pattern applies to all parameters and supporting reaction models.
+Note that the parameter units have to be adapted to the unit of the external profile by dividing with an appropriate power.
+
+Each parameter of the externally dependent reaction model can depend on a different external source.
+The 0-based indices of the external source for each parameter is given in the dataset ``EXTFUN``.
+By assigning only one index to ``EXTFUN``, all parameters use the same source.
+The ordering of the parameters in ``EXTFUN`` is given by the ordering in the file format specification.
+
+For the configuration of external function dependence and more information on model parameters required to define in CADET file format, see section :ref:`FFReaction`.
\ No newline at end of file
diff --git a/master/_sources/modelling/reactions.rst.txt b/master/_sources/modelling/reaction/mass_action_law.rst.txt
similarity index 70%
rename from master/_sources/modelling/reactions.rst.txt
rename to master/_sources/modelling/reaction/mass_action_law.rst.txt
index 578801021..79b25a400 100644
--- a/master/_sources/modelling/reactions.rst.txt
+++ b/master/_sources/modelling/reaction/mass_action_law.rst.txt
@@ -1,13 +1,4 @@
-.. _reaction_models:
-
-Reaction models
-===============
-
-
-Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}` of a
-reaction mechanism. The most common mechanism is the mass action law.
-
-.. _MRMassActionLaw:
+.. _mass_action_law_model:
Mass action law
---------------
@@ -59,7 +50,7 @@ where
The forward and backward rates of the liquid phase particle reactions can be modified by a power of every bound state in the solid phase of the particle.
The exponents of these powers are given by the matrices :math:`E^{ps}_{\mathrm{fwd}} = (e^{ps}_{\mathrm{fwd},m,j})` and :math:`E^{ps}_{\mathrm{bwd}} = (e^{ps}_{\mathrm{bwd},m,j})`, which are both of size :math:`(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}`.
-Whereas the exponent matrices :math:`E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{ps}_{\mathrm{fwd}}, E^{ps}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`.
+Whereas the exponent matrices :math:`E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{ps}_{\mathrm{fwd}}, E^{ps}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`.
Vice versa, the rates of solid phase reactions can be modified by liquid phase concentrations.
The corresponding exponent matrices :math:`E^{sp}_{\mathrm{fwd}} = (e^{sp}_{\mathrm{fwd},\ell,j})` and :math:`E^{sp}_{\mathrm{bwd}} = (e^{sp}_{\mathrm{bwd},\ell,j})` are both of size :math:`N_{\mathrm{comp}} \times N_{\mathrm{react}}`.
@@ -79,7 +70,7 @@ where
- k^p_{\mathrm{bwd},j} &\left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{s}_{\mathrm{bwd},m,j}}\right] \left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^p_{\ell}\right)^{e^{sp}_{\mathrm{bwd},\ell,j}}\right].
\end{split}
-Whereas the exponent matrices :math:`E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`.
+Whereas the exponent matrices :math:`E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`.
Correlation of forward- and backward rate constants
@@ -115,33 +106,3 @@ This can be achieved by a (nonlinear) parameter transform
F\left( k_{\mathrm{eq},i}, k_{\mathrm{bwd},i} \right) &= \begin{pmatrix} k_{\mathrm{eq},i} k_{\mathrm{bwd},i} \\ k_{\mathrm{bwd},i} \end{pmatrix} \\
\text{ with Jacobian } J_F\left( k_{\mathrm{eq},i}, k_{\mathrm{bwd},i} \right) &= \begin{pmatrix} k_{\mathrm{bwd},i} & k_{\mathrm{eq},i} \\ 0 & 1 \end{pmatrix}.
\end{aligned}
-
-
-.. _dependence-on-external-function_react:
-
-Dependence on external function
--------------------------------
-
-A reaction model may depend on an external function or profile :math:`T\colon \left[ 0, T_{\mathrm{end}}\right] \times [0, L] \to \mathbb{R}`, where :math:`L` denotes the physical length of the unit operation, or :math:`T\colon \left[0, T_{\mathrm{end}}\right] \to \mathbb{R}` if the unit operation model has no axial length.
-By using an external profile, it is possible to account for effects that are not directly modeled in CADET (e.g., temperature).
-The dependence of each parameter is modeled by a polynomial of third degree.
-For example, the forward rate constant :math:`k_{\mathrm{fwd}}` is really given by
-
-.. math::
-
- \begin{aligned}
- k_{\mathrm{fwd}}(T) &= k_{\mathrm{fwd},3} T^3 + k_{\mathrm{fwd},2} T^2 + k_{\mathrm{fwd},1} T + k_{\mathrm{fwd},0}.
- \end{aligned}
-
-While :math:`k_{\mathrm{fwd},0}` is set by the original parameter ``XXX_KFWD`` of the file format (``XXX`` being a placeholder for the reaction model), the parameters :math:`k_{\mathrm{fwd},3}`, :math:`k_{\mathrm{fwd},2}`, and :math:`k_{\mathrm{fwd},1}` are given by ``XXX_KFWD_TTT``, ``XXX_KFWD_TT``, and ``XXX_KFWD_T``, respectively.
-The identifier of the externally dependent reaction model is constructed from the original identifier by prepending ``EXT_`` (e.g., ``MASS_ACTION_LAW`` is changed into ``EXT_MASS_ACTION_LAW``).
-This pattern applies to all parameters and supporting reaction models.
-Note that the parameter units have to be adapted to the unit of the external profile by dividing with an appropriate power.
-
-Each parameter of the externally dependent reaction model can depend on a different external source.
-The 0-based indices of the external source for each parameter is given in the dataset ``EXTFUN``.
-By assigning only one index to ``EXTFUN``, all parameters use the same source.
-The ordering of the parameters in ``EXTFUN`` is given by the ordering in the file format specification in Section :ref:`FFReaction`.
-
-The layout of the matrices in the file format is presented in Table :ref:`FFReactionMassActionLaw`.
-
diff --git a/master/_sources/modelling/reaction/michaelis_menten_kinetics.rst.txt b/master/_sources/modelling/reaction/michaelis_menten_kinetics.rst.txt
new file mode 100644
index 000000000..2efe7cc40
--- /dev/null
+++ b/master/_sources/modelling/reaction/michaelis_menten_kinetics.rst.txt
@@ -0,0 +1,40 @@
+.. _michaelis_menten_kinetics_model:
+
+Michaelis Menten kinetics
+-------------------------
+
+Implements liquid phase Michaelis-Menten reaction kinetics of the form
+
+.. math::
+
+ \begin{aligned}
+ f_\text{react} = S \mathbf{\nu},
+ \end{aligned}
+
+where :math:`S` is the stoichiometric matrix and the fluxes are given by
+
+.. math::
+
+ \begin{aligned}
+ \nu_j = \frac{\mu_{\mathrm{max},j} \, c_S}{k_{\mathrm{MM},j} + c_S},
+ \end{aligned}
+
+where
+
+- :math:`j` is the reaction index,
+- :math:`c_S` is the substrate component,
+- :math:`\mu_{\mathrm{max},j}`, is the limiting rate approached by the system at saturation,
+- :math:`k_{\mathrm{MM},j}` is the Michaelis constant, which is defined as the concentration of substrate at which the reaction rate is half ov :math:`\mu_{\mathrm{max},j}`.
+
+
+In addition, the reaction might be inhibited by other components.
+In this case, the flux has the form
+
+.. math::
+
+ \begin{aligned}
+ \nu_j = \frac{\mu_{\mathrm{max},j} \, c_S}{k_{\mathrm{MM},j} + c_S} \prod_i \frac{k_{\mathrm{I},j,i}}{k_{\mathrm{I},j,i} + c_{\mathrm{I},i}}.
+ \end{aligned}
+
+Here, :math:`k_{\mathrm{I},j,i}` is the inhibition constant w.r.t component :math:`i` and reaction :math:`j`.
+If :math:`k_{\mathrm{I},j,i} <= 0`, component :math:`i` does not inhibit the reaction.
diff --git a/master/developer_guide/cadet_core_architecture.html b/master/developer_guide/cadet_core_architecture.html
index 58676a06e..49d78b4de 100644
--- a/master/developer_guide/cadet_core_architecture.html
+++ b/master/developer_guide/cadet_core_architecture.html
@@ -176,8 +176,8 @@
IDynamicReactionModel
-Defines functions for evaluating the reaction rates \(f_\text{react,i}\left( c \right)\) (as used in, e.g., the General rate model (GRM)), according to some Reaction models.
-If supported, reaction model parameters may have a Dependence on external function.
Some reaction models have a variant that can use external sources as specified /input/model/external/ (also see Section?:ref:dependence-on-external-function_react).
+For the sake of brevity, only the standard variant of those reaction models is specified below.
+In order to obtain the format for the externally dependent variant, first replace the reaction model name XXX by EXT_XXX.
+Each parameter \(p\) (except for stoichiometric and exponent matrices) depends on a (possibly distinct) external source in a polynomial way:
+
+\[\begin{aligned}
+ p(T) &= p_{\texttt{TTT}} T^3 + p_{\texttt{TT}} T^2 + p_{\texttt{T}} T + p.
+\end{aligned}\]
+
Thus, a parameter XXX_YYY of the standard reaction model variant is replaced by the four parameters EXT_XXX_YYY, EXT_XXX_YYY_T, EXT_XXX_YYY_TT, and EXT_XXX_YYY_TTT.
+Since each parameter can depend on a different external source, the dataset EXTFUN (not listed in the standard variants below) should contain a vector of 0-based integer indices of the external source of each parameter.
+The ordering of the parameters in EXTFUN is given by the ordering in the standard variant.
+However, if only one index is passed in EXTFUN, this external source is used for all parameters.
+
Note that parameter sensitivities with respect to column radius, column length, particle core radius, and particle radius may be wrong when using externally dependent reaction models.
+This is caused by not taking into account the derivative of the external profile with respect to column position.
The group that contains the parameters of a reaction model in unit operation with index XXX reads /input/model/unit_XXX/reaction_particle.
+This is valid for models with a single particle type.
+If a model has multiple particle types, it may have a different reaction model in each type.
+The parameters are then placed in the group /input/model/unit_XXX/reaction_particle_YYY instead, where YYY denotes the index of the particle type.
+
Note that, in any case, /input/model/unit_XXX/reaction_particle_000 contains the parameters of the first (and possibly sole) particle type.
+This group also takes precedence over a possibly existing /input/model/unit_XXX/adsorption_particle group.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/master/interface/reactions.html b/master/interface/reaction/mass_action_law.html
similarity index 63%
rename from master/interface/reactions.html
rename to master/interface/reaction/mass_action_law.html
index 6017bab5f..2522ad5b7 100644
--- a/master/interface/reactions.html
+++ b/master/interface/reaction/mass_action_law.html
@@ -1,25 +1,25 @@
-
+
- Reaction models — CADET
-
-
-
-
-
+ Mass Action Law — CADET
+
+
+
+
+
-
-
-
-
-
-
+
+
+
+
+
+
-
+
@@ -30,7 +30,7 @@
You're reading the documentation for a development version.
- For the latest released version, please have a look at v4.4.0.
+ For the latest released version, please have a look at v4.4.0.
-
-
Some reaction models have a variant that can use external sources as specified /input/model/external/ (also see Section Dependence on external function).
-For the sake of brevity, only the standard variant of those reaction models is specified below.
-In order to obtain the format for the externally dependent variant, first replace the reaction model name XXX by EXT_XXX.
-Each parameter \(p\) (except for stoichiometric and exponent matrices) depends on a (possibly distinct) external source in a polynomial way:
-
-\[\begin{aligned}
- p(T) &= p_{\texttt{TTT}} T^3 + p_{\texttt{TT}} T^2 + p_{\texttt{T}} T + p.
-\end{aligned}\]
-
Thus, a parameter XXX_YYY of the standard reaction model variant is replaced by the four parameters EXT_XXX_YYY, EXT_XXX_YYY_T, EXT_XXX_YYY_TT, and EXT_XXX_YYY_TTT.
-Since each parameter can depend on a different external source, the dataset EXTFUN (not listed in the standard variants below) should contain a vector of 0-based integer indices of the external source of each parameter.
-The ordering of the parameters in EXTFUN is given by the ordering in the standard variant.
-However, if only one index is passed in EXTFUN, this external source is used for all parameters.
-
Note that parameter sensitivities with respect to column radius, column length, particle core radius, and particle radius may be wrong when using externally dependent reaction models.
-This is caused by not taking into account the derivative of the external profile with respect to column position.
The group that contains the parameters of a reaction model in unit operation with index XXX reads /input/model/unit_XXX/reaction_particle.
-This is valid for models with a single particle type.
-If a model has multiple particle types, it may have a different reaction model in each type.
-The parameters are then placed in the group /input/model/unit_XXX/reaction_particle_YYY instead, where YYY denotes the index of the particle type.
-
Note that, in any case, /input/model/unit_XXX/reaction_particle_000 contains the parameters of the first (and possibly sole) particle type.
-This group also takes precedence over a possibly existing /input/model/unit_XXX/adsorption_particle group.
-
-
-
Group /input/model/unit_XXX/reaction - REACTION_MODEL = MASS_ACTION_LAW¶
Group /input/model/unit_XXX/reaction - REACTION_MODEL = MICHAELIS_MENTEN
+
MM_STOICHIOMETRY_BULK
+
+
Stochiometric matrix \(S\).
+The substrate component \(c_S\) is identified by the index of the first negative entry in the stoichiometry of the corresponding reaction.
+Input as reaction index major.
+
+
+
Type: double
+
Range:\(\mathbb{R}\)
+
Length:\(\texttt{NREACT} \cdot \texttt{NCOMP}\)
+
+
+
+
+
MM_VMAX
+
+
+
Limiting rate \(\mu_{\mathrm{max},j}\) at saturation.
+
+
+
+
Type: double
+
Range:\(\mathbb{R}\)
+
Length:\(\texttt{NREACT}\)
+
+
+
+
+
MM_KMM
+
+
+
Michaelis constant \(k_{\mathrm{MM},j}\).
+
+
+
+
Type: double
+
Range:\(\mathbb{R}\)
+
Length:\(\texttt{NREACT}\)
+
+
+
+
+
MM_KI
+
+
+
Inhibition constant \(k_{\mathrm{I},j,i}\) w.r.t component \(i\) and reaction \(j\). If \(k_{\mathrm{I},j,i} <= 0\), the component does not inhibit the reaction.
+Input as reaction index major.
+
+
+
+
Type: double
+
Range:\(\mathbb{R}\)
+
Length:\(\texttt{NREACT} \cdot \texttt{NCOMP}\)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/master/interface/return_data.html b/master/interface/return_data.html
index acc1d414c..a79a77da3 100644
--- a/master/interface/return_data.html
+++ b/master/interface/return_data.html
@@ -52,7 +52,7 @@
with \(\varepsilon_{k}\) and \(n_{k}\) denoting some error norm and the degrees of freedom of the kth approximation.
diff --git a/master/interface/system.html b/master/interface/system.html
index 898296ec2..ea73394a2 100644
--- a/master/interface/system.html
+++ b/master/interface/system.html
@@ -52,7 +52,7 @@
The network of unit operations uses “connectionâ€-variables \(c_{\text{con}}\) to connect the different unit operation ports with each other.
The inlet port variables \(c_{\text{in},n,k}\) of unit operation \(n\) are attached to \(c_{\text{con},n}\) via
-(23)¶\[\begin{aligned}
+(22)¶\[\begin{aligned}
c_{\text{in},n,k,i} &= c_{\text{con},n,k,i}, \qquad k = 1, \dots, N_{\text{port},\text{in},n},\quad i = 1, \dots, N_{\text{comp},n}.
\end{aligned}\]
While \(N_{\text{port},\text{in},n}\) denotes the number of inlet ports of unit operation \(n\), the number of outlet ports is given by \(N_{\text{port},\text{out},n}\).
The connection variables \(c_{\text{con},n,k,i}\) collect all inflows of component \(i\) into port \(k\) of unit operation \(n\):
where \(F_{m,\ell}\) denotes the volumetric flow rate from outlet port \(\ell\) of unit operation \(m\), \(S_{(n,k,i),(m,\ell,j)} \in \{0, 1\}\) is a connection matrix indicating whether component \(i\) at outlet port \(k\) of unit operation \(n\) is connected to component \(j\) at inlet port \(\ell\) of unit operation \(m\), and \(\hat{S}_{(n,k),(m,\ell)} \in \{0, 1\}\) is another connection matrix indicating whether outlet port \(k\) of unit operation \(n\) is connected to inlet port \(\ell\) of unit operation \(m\), that is
where \(t_s\) is the beginning of the time section that triggers the valve switch.
-
Note that the denominator in Eq. 24 must always be positive.
+
Note that the denominator in Eq. 23 must always be positive.
That is, the flow rate coefficients have to be chosen such that the flow into every connected inlet port is strictly positive at all times.
Each time step in the simulation requires the solution of a nonlinear system Eq. 25 (see Sec. Time stepping).
-The nonlinear problem is solved by a Newton iteration, which, in turn, requires the solution of a linear system that essentially consists of the Jacobians of the unit operations and some coupling matrices from Eqs. 23 and 24.
+
Each time step in the simulation requires the solution of a nonlinear system Eq. 24 (see Sec. Time stepping).
+The nonlinear problem is solved by a Newton iteration, which, in turn, requires the solution of a linear system that essentially consists of the Jacobians of the unit operations and some coupling matrices from Eqs. 22 and 23.
These linear systems are either solved in parallel or sequentially. The parallel method first solves each unit operation (in parallel) to compute the solution at its outlet.
Using these values, the inlets are adjusted and the unit operations are solved again.
This is iterated until the system is fully solved.
A reaction model may depend on an external function or profile \(T\colon \left[ 0, T_{\mathrm{end}}\right] \times [0, L] \to \mathbb{R}\), where \(L\) denotes the physical length of the unit operation, or \(T\colon \left[0, T_{\mathrm{end}}\right] \to \mathbb{R}\) if the unit operation model has no axial length.
+By using an external profile, it is possible to account for effects that are not directly modeled in CADET (e.g., temperature).
+The dependence of each parameter is modeled by a polynomial of third degree.
+For example, the forward rate constant \(k_{\mathrm{fwd}}\) is really given by
While \(k_{\mathrm{fwd},0}\) is set by the original parameter XXX_KFWD of the file format (XXX being a placeholder for the reaction model), the parameters \(k_{\mathrm{fwd},3}\), \(k_{\mathrm{fwd},2}\), and \(k_{\mathrm{fwd},1}\) are given by XXX_KFWD_TTT, XXX_KFWD_TT, and XXX_KFWD_T, respectively.
+The identifier of the externally dependent reaction model is constructed from the original identifier by prepending EXT_ (e.g., MASS_ACTION_LAW is changed into EXT_MASS_ACTION_LAW).
+This pattern applies to all parameters and supporting reaction models.
+Note that the parameter units have to be adapted to the unit of the external profile by dividing with an appropriate power.
+
Each parameter of the externally dependent reaction model can depend on a different external source.
+The 0-based indices of the external source for each parameter is given in the dataset EXTFUN.
+By assigning only one index to EXTFUN, all parameters use the same source.
+The ordering of the parameters in EXTFUN is given by the ordering in the file format specification.
+
For the configuration of external function dependence and more information on model parameters required to define in CADET file format, see section Reaction models.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/master/modelling/reactions.html b/master/modelling/reaction/mass_action_law.html
similarity index 54%
rename from master/modelling/reactions.html
rename to master/modelling/reaction/mass_action_law.html
index 7fef63d88..58a3641d7 100644
--- a/master/modelling/reactions.html
+++ b/master/modelling/reaction/mass_action_law.html
@@ -1,25 +1,23 @@
-
+
- Reaction models — CADET
-
-
-
-
-
+ Mass action law — CADET
+
+
+
+
+
-
-
-
-
-
-
+
+
+
+
-
+
@@ -30,7 +28,7 @@
You're reading the documentation for a development version.
- For the latest released version, please have a look at v4.4.0.
+ For the latest released version, please have a look at v4.4.0.
-
-
The mass action law reaction model is suitable for most reactions.
Note that the concentrations are directly used for calculating the fluxes.
Hence, the model only holds for dilute solutions under the assumption of a well-stirred reaction vessel.
@@ -126,7 +109,7 @@
Branches
where \(S^l = (s^l_{i,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\) is the stoichiometric matrix, \(\varphi^l_j(c)\) is the net flux of reaction \(j\), and \(k^l_{\mathrm{fwd},j}\) and \(k^l_{\mathrm{bwd},j}\) are the rate constants.
The matrices \(E^l_{\mathrm{fwd}} = (e^l_{\mathrm{fwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\) and \(E^l_{\mathrm{bwd}} = (e^l_{\mathrm{bwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\) are usually derived by the order of the reaction, that is,
The forward and backward rates of the liquid phase particle reactions can be modified by a power of every bound state in the solid phase of the particle.
The exponents of these powers are given by the matrices \(E^{ps}_{\mathrm{fwd}} = (e^{ps}_{\mathrm{fwd},m,j})\) and \(E^{ps}_{\mathrm{bwd}} = (e^{ps}_{\mathrm{bwd},m,j})\), which are both of size \((\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}\).
-Whereas the exponent matrices \(E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\) are initialized based on the stoichiometric matrix \(S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\), see Eq. 22, the exponent matrices \(E^{ps}_{\mathrm{fwd}}, E^{ps}_{\mathrm{bwd}}\) of the modifier terms default to \(0\).
+Whereas the exponent matrices \(E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\) are initialized based on the stoichiometric matrix \(S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}\), see Eq.?:eq:MRMassActionLawExpMatDefault, the exponent matrices \(E^{ps}_{\mathrm{fwd}}, E^{ps}_{\mathrm{bwd}}\) of the modifier terms default to \(0\).
Vice versa, the rates of solid phase reactions can be modified by liquid phase concentrations.
The corresponding exponent matrices \(E^{sp}_{\mathrm{fwd}} = (e^{sp}_{\mathrm{fwd},\ell,j})\) and \(E^{sp}_{\mathrm{bwd}} = (e^{sp}_{\mathrm{bwd},\ell,j})\) are both of size \(N_{\mathrm{comp}} \times N_{\mathrm{react}}\).
Whereas the exponent matrices \(E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}\) are initialized based on the stoichiometric matrix \(S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}\), see Eq. 22, the exponent matrices \(E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}\) of the modifier terms default to \(0\).
+
Whereas the exponent matrices \(E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}\) are initialized based on the stoichiometric matrix \(S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}\), see Eq.?:eq:MRMassActionLawExpMatDefault, the exponent matrices \(E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}\) of the modifier terms default to \(0\).
-
Correlation of forward- and backward rate constants¶
+
Correlation of forward- and backward rate constants¶
Note that forward rate constant \(k_{\mathrm{fwd},i}\) and backward
rate constant \(k_{\mathrm{bwd},i}\) of reaction \(i\) are
linearly correlated due to the form of the equilibrium constant
@@ -184,27 +167,6 @@
Correlation of forward- and backward rate constants
A reaction model may depend on an external function or profile \(T\colon \left[ 0, T_{\mathrm{end}}\right] \times [0, L] \to \mathbb{R}\), where \(L\) denotes the physical length of the unit operation, or \(T\colon \left[0, T_{\mathrm{end}}\right] \to \mathbb{R}\) if the unit operation model has no axial length.
-By using an external profile, it is possible to account for effects that are not directly modeled in CADET (e.g., temperature).
-The dependence of each parameter is modeled by a polynomial of third degree.
-For example, the forward rate constant \(k_{\mathrm{fwd}}\) is really given by
While \(k_{\mathrm{fwd},0}\) is set by the original parameter XXX_KFWD of the file format (XXX being a placeholder for the reaction model), the parameters \(k_{\mathrm{fwd},3}\), \(k_{\mathrm{fwd},2}\), and \(k_{\mathrm{fwd},1}\) are given by XXX_KFWD_TTT, XXX_KFWD_TT, and XXX_KFWD_T, respectively.
-The identifier of the externally dependent reaction model is constructed from the original identifier by prepending EXT_ (e.g., MASS_ACTION_LAW is changed into EXT_MASS_ACTION_LAW).
-This pattern applies to all parameters and supporting reaction models.
-Note that the parameter units have to be adapted to the unit of the external profile by dividing with an appropriate power.
-
Each parameter of the externally dependent reaction model can depend on a different external source.
-The 0-based indices of the external source for each parameter is given in the dataset EXTFUN.
-By assigning only one index to EXTFUN, all parameters use the same source.
-The ordering of the parameters in EXTFUN is given by the ordering in the file format specification in Section Reaction models.
\(\mu_{\mathrm{max},j}\), is the limiting rate approached by the system at saturation,
+
\(k_{\mathrm{MM},j}\) is the Michaelis constant, which is defined as the concentration of substrate at which the reaction rate is half ov \(\mu_{\mathrm{max},j}\).
+
+
In addition, the reaction might be inhibited by other components.
+In this case, the flux has the form
Here, \(k_{\mathrm{I},j,i}\) is the inhibition constant w.r.t component \(i\) and reaction \(j\).
+If \(k_{\mathrm{I},j,i} <= 0\), component \(i\) does not inhibit the reaction.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/master/modelling/unit_operations/2d_general_rate_model.html b/master/modelling/unit_operations/2d_general_rate_model.html
index e41f33445..c0b998e57 100644
--- a/master/modelling/unit_operations/2d_general_rate_model.html
+++ b/master/modelling/unit_operations/2d_general_rate_model.html
@@ -57,7 +57,7 @@
The IDAS time integrator adaptively changes the step size \({\Delta t_\tau = t_\tau-t_{\tau-1}}\) and order \(1 \le q_{\tau} \le 5\) in each time step and automatically determines the corresponding coefficients \(\alpha_{\tau,i}\).
This ansatz is inserted into the DAE and the resulting nonlinear algebraic equation system is solved for \(y_{\tau} = y\left( t_\tau \right)\) using a Newton method.
The BDF order \(q_{\tau}\) and size of the time step \(t_\tau\) are chosen such that the error bounds are satisfied with minimal work.
-Equation 25 is solved with a Newton iteration using very few iterations (MAX_NEWTON_ITER from Table Group /solver/time_integrator) since the starting point is assumed to be close to the solution as the time steps are small.
+Equation 24 is solved with a Newton iteration using very few iterations (MAX_NEWTON_ITER from Table Group /solver/time_integrator) since the starting point is assumed to be close to the solution as the time steps are small.
If the solution of the Newton iteration does not pass the convergence test, the step size \(t_\tau\) is reduced and the Newton iteration is tried again.
This may happen at most MAX_CONVTEST_FAIL times, otherwise time integration is aborted with failure.
Having a solution of the Newton iteration at hand, a local truncation error test is performed which controls the error of the BDF method.
-If this test fails, step size \(t_\tau\) and order \(q_{\tau}\) are adapted and the process restarts with solving the nonlinear system Eq. 25.
+If this test fails, step size \(t_\tau\) and order \(q_{\tau}\) are adapted and the process restarts with solving the nonlinear system Eq. 24.
The error test may be failed at most MAX_ERRTEST_FAIL times before time integration is aborted with failure.
Error bounds for the local truncation error test are specified by an absolute tolerance (ABSTOL) and a relative tolerance (RELTOL).
Note that the relative tolerance only works for non-zero values, whereas zero values are accounted for by the absolute tolerance.
@@ -255,7 +255,7 @@
Branches
\end{aligned}\end{split}\]
These linear DAEs depend on the solution \(y\), \(\dot{y}\) of the original DAE system.
Consequently, the sensitivity systems are solved together with the original DAE system in a staggered approach [25].
-
After the nonlinear Eq. 25 has been successfully solved using Newton iteration (i.e., it has passed the convergence test), each sensitivity is solved using the same Newton iteration.
+
After the nonlinear Eq. 24 has been successfully solved using Newton iteration (i.e., it has passed the convergence test), each sensitivity is solved using the same Newton iteration.
If direct linear solvers were used, this iteration would convergence with a single iteration as there is no nonlinearity.
The Newton method for the sensitivities performs at most MAX_NEWTON_ITER_SENS (see Table Group /solver/time_integrator) iterations.
Assuming the convergence test has passed for each sensitivity, the local truncation error test is performed for the full set of variables (i.e., original system and sensitivities).
diff --git a/master/sitemap.xml b/master/sitemap.xml
index 2e1c193a7..4557f8030 100644
--- a/master/sitemap.xml
+++ b/master/sitemap.xml
@@ -1,2 +1,2 @@
-https://cadet.github.io/master/en/README.htmlhttps://cadet.github.io/master/en/developer_guide/build_options.htmlhttps://cadet.github.io/master/en/developer_guide/cadet_core_architecture.htmlhttps://cadet.github.io/master/en/developer_guide/debugging.htmlhttps://cadet.github.io/master/en/developer_guide/index.htmlhttps://cadet.github.io/master/en/developer_guide/model_expansion.htmlhttps://cadet.github.io/master/en/developer_guide/testing.htmlhttps://cadet.github.io/master/en/examples/batch_chromatography.htmlhttps://cadet.github.io/master/en/examples/index.htmlhttps://cadet.github.io/master/en/examples/load_wash_elute.htmlhttps://cadet.github.io/master/en/examples/reaction_cstr.htmlhttps://cadet.github.io/master/en/examples/rtd.htmlhttps://cadet.github.io/master/en/getting_started/build_linux.htmlhttps://cadet.github.io/master/en/getting_started/build_osx.htmlhttps://cadet.github.io/master/en/getting_started/build_windows.htmlhttps://cadet.github.io/master/en/getting_started/index.htmlhttps://cadet.github.io/master/en/getting_started/installation.htmlhttps://cadet.github.io/master/en/getting_started/overview.htmlhttps://cadet.github.io/master/en/getting_started/tutorials/breakthrough.htmlhttps://cadet.github.io/master/en/index.htmlhttps://cadet.github.io/master/en/interface/binding/bi_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/extended_mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/freundlich_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/generalized_ion_exchange.htmlhttps://cadet.github.io/master/en/interface/binding/hic_constant_water_activity.htmlhttps://cadet.github.io/master/en/interface/binding/hic_water_on_hydrophobic_surfaces.htmlhttps://cadet.github.io/master/en/interface/binding/index.htmlhttps://cadet.github.io/master/en/interface/binding/linear.htmlhttps://cadet.github.io/master/en/interface/binding/mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_anti_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_bi_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_bi_langmuir_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_colloidal.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir_ldf_liquid_phase.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_spreading.htmlhttps://cadet.github.io/master/en/interface/binding/multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/saska.htmlhttps://cadet.github.io/master/en/interface/binding/self_association.htmlhttps://cadet.github.io/master/en/interface/binding/simplified_multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/consistent_initialization.htmlhttps://cadet.github.io/master/en/interface/flux_reconstruction.htmlhttps://cadet.github.io/master/en/interface/index.htmlhttps://cadet.github.io/master/en/interface/input_group.htmlhttps://cadet.github.io/master/en/interface/introduction.htmlhttps://cadet.github.io/master/en/interface/meta_group.htmlhttps://cadet.github.io/master/en/interface/output_group.htmlhttps://cadet.github.io/master/en/interface/parameter_dependencies.htmlhttps://cadet.github.io/master/en/interface/reactions.htmlhttps://cadet.github.io/master/en/interface/return_data.htmlhttps://cadet.github.io/master/en/interface/sensitivities.htmlhttps://cadet.github.io/master/en/interface/solver.htmlhttps://cadet.github.io/master/en/interface/spatial_discretization_methods.htmlhttps://cadet.github.io/master/en/interface/system.htmlhttps://cadet.github.io/master/en/interface/unit_operations/2d_general_rate_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/cstr.htmlhttps://cadet.github.io/master/en/interface/unit_operations/general_rate_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/index.htmlhttps://cadet.github.io/master/en/interface/unit_operations/inlet.htmlhttps://cadet.github.io/master/en/interface/unit_operations/lumped_rate_model_with_pores.htmlhttps://cadet.github.io/master/en/interface/unit_operations/lumped_rate_model_without_pores.htmlhttps://cadet.github.io/master/en/interface/unit_operations/multi_channel_transport_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/outlet.htmlhttps://cadet.github.io/master/en/interface/unit_operations/radial_flow_models.htmlhttps://cadet.github.io/master/en/license.htmlhttps://cadet.github.io/master/en/modelling/binding/bi_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/extended_mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/freundlich_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/generalized_ion_exchange.htmlhttps://cadet.github.io/master/en/modelling/binding/hic_constant_water_activity.htmlhttps://cadet.github.io/master/en/modelling/binding/hic_water_on_hydrophobic_surfaces.htmlhttps://cadet.github.io/master/en/modelling/binding/index.htmlhttps://cadet.github.io/master/en/modelling/binding/linear.htmlhttps://cadet.github.io/master/en/modelling/binding/mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_anti_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_bi_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_bi_langmuir_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_colloidal.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir_ldf_liquid_phase.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_spreading.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/saska.htmlhttps://cadet.github.io/master/en/modelling/binding/self_association.htmlhttps://cadet.github.io/master/en/modelling/binding/simplified_multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/index.htmlhttps://cadet.github.io/master/en/modelling/networks.htmlhttps://cadet.github.io/master/en/modelling/reactions.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/2d_general_rate_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/cstr.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/general_rate_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/index.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/inlet.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/lumped_rate_model_with_pores.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/lumped_rate_model_without_pores.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/multi_channel_transport_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/outlet.htmlhttps://cadet.github.io/master/en/requirements.htmlhttps://cadet.github.io/master/en/simulation/index.htmlhttps://cadet.github.io/master/en/zbibliography.htmlhttps://cadet.github.io/master/en/genindex.htmlhttps://cadet.github.io/master/en/search.html
\ No newline at end of file
+https://cadet.github.io/master/en/README.htmlhttps://cadet.github.io/master/en/developer_guide/build_options.htmlhttps://cadet.github.io/master/en/developer_guide/cadet_core_architecture.htmlhttps://cadet.github.io/master/en/developer_guide/debugging.htmlhttps://cadet.github.io/master/en/developer_guide/index.htmlhttps://cadet.github.io/master/en/developer_guide/model_expansion.htmlhttps://cadet.github.io/master/en/developer_guide/testing.htmlhttps://cadet.github.io/master/en/examples/batch_chromatography.htmlhttps://cadet.github.io/master/en/examples/index.htmlhttps://cadet.github.io/master/en/examples/load_wash_elute.htmlhttps://cadet.github.io/master/en/examples/reaction_cstr.htmlhttps://cadet.github.io/master/en/examples/rtd.htmlhttps://cadet.github.io/master/en/getting_started/build_linux.htmlhttps://cadet.github.io/master/en/getting_started/build_osx.htmlhttps://cadet.github.io/master/en/getting_started/build_windows.htmlhttps://cadet.github.io/master/en/getting_started/index.htmlhttps://cadet.github.io/master/en/getting_started/installation.htmlhttps://cadet.github.io/master/en/getting_started/overview.htmlhttps://cadet.github.io/master/en/getting_started/tutorials/breakthrough.htmlhttps://cadet.github.io/master/en/index.htmlhttps://cadet.github.io/master/en/interface/binding/bi_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/extended_mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/freundlich_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/generalized_ion_exchange.htmlhttps://cadet.github.io/master/en/interface/binding/hic_constant_water_activity.htmlhttps://cadet.github.io/master/en/interface/binding/hic_water_on_hydrophobic_surfaces.htmlhttps://cadet.github.io/master/en/interface/binding/index.htmlhttps://cadet.github.io/master/en/interface/binding/linear.htmlhttps://cadet.github.io/master/en/interface/binding/mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_anti_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_bi_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_bi_langmuir_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_colloidal.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir_ldf.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_langmuir_ldf_liquid_phase.htmlhttps://cadet.github.io/master/en/interface/binding/multi_component_spreading.htmlhttps://cadet.github.io/master/en/interface/binding/multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/saska.htmlhttps://cadet.github.io/master/en/interface/binding/self_association.htmlhttps://cadet.github.io/master/en/interface/binding/simplified_multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/binding/steric_mass_action.htmlhttps://cadet.github.io/master/en/interface/consistent_initialization.htmlhttps://cadet.github.io/master/en/interface/flux_reconstruction.htmlhttps://cadet.github.io/master/en/interface/index.htmlhttps://cadet.github.io/master/en/interface/input_group.htmlhttps://cadet.github.io/master/en/interface/introduction.htmlhttps://cadet.github.io/master/en/interface/meta_group.htmlhttps://cadet.github.io/master/en/interface/output_group.htmlhttps://cadet.github.io/master/en/interface/parameter_dependencies.htmlhttps://cadet.github.io/master/en/interface/reaction/index.htmlhttps://cadet.github.io/master/en/interface/reaction/mass_action_law.htmlhttps://cadet.github.io/master/en/interface/reaction/michaelis_menten_kinetics.htmlhttps://cadet.github.io/master/en/interface/return_data.htmlhttps://cadet.github.io/master/en/interface/sensitivities.htmlhttps://cadet.github.io/master/en/interface/solver.htmlhttps://cadet.github.io/master/en/interface/spatial_discretization_methods.htmlhttps://cadet.github.io/master/en/interface/system.htmlhttps://cadet.github.io/master/en/interface/unit_operations/2d_general_rate_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/cstr.htmlhttps://cadet.github.io/master/en/interface/unit_operations/general_rate_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/index.htmlhttps://cadet.github.io/master/en/interface/unit_operations/inlet.htmlhttps://cadet.github.io/master/en/interface/unit_operations/lumped_rate_model_with_pores.htmlhttps://cadet.github.io/master/en/interface/unit_operations/lumped_rate_model_without_pores.htmlhttps://cadet.github.io/master/en/interface/unit_operations/multi_channel_transport_model.htmlhttps://cadet.github.io/master/en/interface/unit_operations/outlet.htmlhttps://cadet.github.io/master/en/interface/unit_operations/radial_flow_models.htmlhttps://cadet.github.io/master/en/license.htmlhttps://cadet.github.io/master/en/modelling/binding/bi_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/extended_mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/freundlich_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/generalized_ion_exchange.htmlhttps://cadet.github.io/master/en/modelling/binding/hic_constant_water_activity.htmlhttps://cadet.github.io/master/en/modelling/binding/hic_water_on_hydrophobic_surfaces.htmlhttps://cadet.github.io/master/en/modelling/binding/index.htmlhttps://cadet.github.io/master/en/modelling/binding/linear.htmlhttps://cadet.github.io/master/en/modelling/binding/mobile_phase_modulator_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_anti_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_bi_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_bi_langmuir_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_colloidal.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir_ldf.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_langmuir_ldf_liquid_phase.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_component_spreading.htmlhttps://cadet.github.io/master/en/modelling/binding/multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/saska.htmlhttps://cadet.github.io/master/en/modelling/binding/self_association.htmlhttps://cadet.github.io/master/en/modelling/binding/simplified_multi_state_steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/binding/steric_mass_action.htmlhttps://cadet.github.io/master/en/modelling/index.htmlhttps://cadet.github.io/master/en/modelling/networks.htmlhttps://cadet.github.io/master/en/modelling/reaction/index.htmlhttps://cadet.github.io/master/en/modelling/reaction/mass_action_law.htmlhttps://cadet.github.io/master/en/modelling/reaction/michaelis_menten_kinetics.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/2d_general_rate_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/cstr.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/general_rate_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/index.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/inlet.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/lumped_rate_model_with_pores.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/lumped_rate_model_without_pores.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/multi_channel_transport_model.htmlhttps://cadet.github.io/master/en/modelling/unit_operations/outlet.htmlhttps://cadet.github.io/master/en/requirements.htmlhttps://cadet.github.io/master/en/simulation/index.htmlhttps://cadet.github.io/master/en/zbibliography.htmlhttps://cadet.github.io/master/en/genindex.htmlhttps://cadet.github.io/master/en/search.html
\ No newline at end of file
diff --git a/v4.3.0/.buildinfo b/v4.3.0/.buildinfo
index 7778f89c1..3558629d4 100644
--- a/v4.3.0/.buildinfo
+++ b/v4.3.0/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e636078aafd5b44b490cbfbae6dd2f52
+config: 60791852e9df0597463e49c4c5cdad99
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/v4.3.0/.doctrees/README.doctree b/v4.3.0/.doctrees/README.doctree
index 2411b05f3..598d1d1ff 100644
Binary files a/v4.3.0/.doctrees/README.doctree and b/v4.3.0/.doctrees/README.doctree differ
diff --git a/v4.3.0/.doctrees/environment.pickle b/v4.3.0/.doctrees/environment.pickle
index aee7b6afd..7fd536c42 100644
Binary files a/v4.3.0/.doctrees/environment.pickle and b/v4.3.0/.doctrees/environment.pickle differ
diff --git a/v4.3.0/.doctrees/examples/batch_chromatography.doctree b/v4.3.0/.doctrees/examples/batch_chromatography.doctree
index d83cce4d4..afd1778a8 100644
Binary files a/v4.3.0/.doctrees/examples/batch_chromatography.doctree and b/v4.3.0/.doctrees/examples/batch_chromatography.doctree differ
diff --git a/v4.3.0/.doctrees/examples/index.doctree b/v4.3.0/.doctrees/examples/index.doctree
index f907de136..7c49305c6 100644
Binary files a/v4.3.0/.doctrees/examples/index.doctree and b/v4.3.0/.doctrees/examples/index.doctree differ
diff --git a/v4.3.0/.doctrees/examples/load_wash_elute.doctree b/v4.3.0/.doctrees/examples/load_wash_elute.doctree
index 40f14c68f..53c028ecb 100644
Binary files a/v4.3.0/.doctrees/examples/load_wash_elute.doctree and b/v4.3.0/.doctrees/examples/load_wash_elute.doctree differ
diff --git a/v4.3.0/.doctrees/examples/reaction_cstr.doctree b/v4.3.0/.doctrees/examples/reaction_cstr.doctree
index c3e03b1ab..7085f9fb4 100644
Binary files a/v4.3.0/.doctrees/examples/reaction_cstr.doctree and b/v4.3.0/.doctrees/examples/reaction_cstr.doctree differ
diff --git a/v4.3.0/.doctrees/examples/rtd.doctree b/v4.3.0/.doctrees/examples/rtd.doctree
index d23b244ea..0b83f0b6d 100644
Binary files a/v4.3.0/.doctrees/examples/rtd.doctree and b/v4.3.0/.doctrees/examples/rtd.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/build_linux.doctree b/v4.3.0/.doctrees/getting_started/build_linux.doctree
index e4d3af18b..d9c7bbfdc 100644
Binary files a/v4.3.0/.doctrees/getting_started/build_linux.doctree and b/v4.3.0/.doctrees/getting_started/build_linux.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/build_osx.doctree b/v4.3.0/.doctrees/getting_started/build_osx.doctree
index 4e64fb2e5..f221d4f9b 100644
Binary files a/v4.3.0/.doctrees/getting_started/build_osx.doctree and b/v4.3.0/.doctrees/getting_started/build_osx.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/build_windows.doctree b/v4.3.0/.doctrees/getting_started/build_windows.doctree
index 013ca1178..40b49734d 100644
Binary files a/v4.3.0/.doctrees/getting_started/build_windows.doctree and b/v4.3.0/.doctrees/getting_started/build_windows.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/index.doctree b/v4.3.0/.doctrees/getting_started/index.doctree
index 1f696e559..4e83d0f2c 100644
Binary files a/v4.3.0/.doctrees/getting_started/index.doctree and b/v4.3.0/.doctrees/getting_started/index.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/installation.doctree b/v4.3.0/.doctrees/getting_started/installation.doctree
index 961b5c395..5c4428cfa 100644
Binary files a/v4.3.0/.doctrees/getting_started/installation.doctree and b/v4.3.0/.doctrees/getting_started/installation.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/overview.doctree b/v4.3.0/.doctrees/getting_started/overview.doctree
index cead3557f..38462dd46 100644
Binary files a/v4.3.0/.doctrees/getting_started/overview.doctree and b/v4.3.0/.doctrees/getting_started/overview.doctree differ
diff --git a/v4.3.0/.doctrees/getting_started/tutorials/breakthrough.doctree b/v4.3.0/.doctrees/getting_started/tutorials/breakthrough.doctree
index 094c83a49..0d4715cf7 100644
Binary files a/v4.3.0/.doctrees/getting_started/tutorials/breakthrough.doctree and b/v4.3.0/.doctrees/getting_started/tutorials/breakthrough.doctree differ
diff --git a/v4.3.0/.doctrees/index.doctree b/v4.3.0/.doctrees/index.doctree
index 8a3feb737..26b0757ec 100644
Binary files a/v4.3.0/.doctrees/index.doctree and b/v4.3.0/.doctrees/index.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/bi_steric_mass_action.doctree b/v4.3.0/.doctrees/interface/binding/bi_steric_mass_action.doctree
index 62e23f9e4..f60cc2114 100644
Binary files a/v4.3.0/.doctrees/interface/binding/bi_steric_mass_action.doctree and b/v4.3.0/.doctrees/interface/binding/bi_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree
index 1441b71ea..02fdb06ad 100644
Binary files a/v4.3.0/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/extended_mobile_phase_modulator_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/generalized_ion_exchange.doctree b/v4.3.0/.doctrees/interface/binding/generalized_ion_exchange.doctree
index 146753413..8d9a20a4d 100644
Binary files a/v4.3.0/.doctrees/interface/binding/generalized_ion_exchange.doctree and b/v4.3.0/.doctrees/interface/binding/generalized_ion_exchange.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/index.doctree b/v4.3.0/.doctrees/interface/binding/index.doctree
index 486005456..e7cd45f82 100644
Binary files a/v4.3.0/.doctrees/interface/binding/index.doctree and b/v4.3.0/.doctrees/interface/binding/index.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/kumar_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/kumar_langmuir.doctree
index 8b3567863..ca30cbf90 100644
Binary files a/v4.3.0/.doctrees/interface/binding/kumar_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/kumar_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/linear.doctree b/v4.3.0/.doctrees/interface/binding/linear.doctree
index 1bac67da3..4515c2b1f 100644
Binary files a/v4.3.0/.doctrees/interface/binding/linear.doctree and b/v4.3.0/.doctrees/interface/binding/linear.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree
index e5e035c5a..5b7f0f4c0 100644
Binary files a/v4.3.0/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/mobile_phase_modulator_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/multi_component_anti_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/multi_component_anti_langmuir.doctree
index 391f337e6..df2c62af2 100644
Binary files a/v4.3.0/.doctrees/interface/binding/multi_component_anti_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/multi_component_anti_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/multi_component_bi_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/multi_component_bi_langmuir.doctree
index eca4bfa7e..ef54fbb9b 100644
Binary files a/v4.3.0/.doctrees/interface/binding/multi_component_bi_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/multi_component_bi_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/multi_component_langmuir.doctree b/v4.3.0/.doctrees/interface/binding/multi_component_langmuir.doctree
index 5fa3716ac..163f9314f 100644
Binary files a/v4.3.0/.doctrees/interface/binding/multi_component_langmuir.doctree and b/v4.3.0/.doctrees/interface/binding/multi_component_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/multi_component_spreading.doctree b/v4.3.0/.doctrees/interface/binding/multi_component_spreading.doctree
index 65b2f1fdd..ec493b495 100644
Binary files a/v4.3.0/.doctrees/interface/binding/multi_component_spreading.doctree and b/v4.3.0/.doctrees/interface/binding/multi_component_spreading.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/multi_state_steric_mass_action.doctree b/v4.3.0/.doctrees/interface/binding/multi_state_steric_mass_action.doctree
index cf015bcaa..cc70b7ecd 100644
Binary files a/v4.3.0/.doctrees/interface/binding/multi_state_steric_mass_action.doctree and b/v4.3.0/.doctrees/interface/binding/multi_state_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/saska.doctree b/v4.3.0/.doctrees/interface/binding/saska.doctree
index fe58a1aa0..d08214fe3 100644
Binary files a/v4.3.0/.doctrees/interface/binding/saska.doctree and b/v4.3.0/.doctrees/interface/binding/saska.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/self_association.doctree b/v4.3.0/.doctrees/interface/binding/self_association.doctree
index 0f73b2f51..ca2017242 100644
Binary files a/v4.3.0/.doctrees/interface/binding/self_association.doctree and b/v4.3.0/.doctrees/interface/binding/self_association.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree b/v4.3.0/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree
index cdc6d20fe..43e5be3ab 100644
Binary files a/v4.3.0/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree and b/v4.3.0/.doctrees/interface/binding/simplified_multi_state_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/interface/binding/steric_mass_action.doctree b/v4.3.0/.doctrees/interface/binding/steric_mass_action.doctree
index a1ea99982..2bca089f4 100644
Binary files a/v4.3.0/.doctrees/interface/binding/steric_mass_action.doctree and b/v4.3.0/.doctrees/interface/binding/steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/interface/consistent_initialization.doctree b/v4.3.0/.doctrees/interface/consistent_initialization.doctree
index 10c3740fc..475341377 100644
Binary files a/v4.3.0/.doctrees/interface/consistent_initialization.doctree and b/v4.3.0/.doctrees/interface/consistent_initialization.doctree differ
diff --git a/v4.3.0/.doctrees/interface/flux_reconstruction.doctree b/v4.3.0/.doctrees/interface/flux_reconstruction.doctree
index 287be49f1..b0a1f25f4 100644
Binary files a/v4.3.0/.doctrees/interface/flux_reconstruction.doctree and b/v4.3.0/.doctrees/interface/flux_reconstruction.doctree differ
diff --git a/v4.3.0/.doctrees/interface/index.doctree b/v4.3.0/.doctrees/interface/index.doctree
index b30ac35ce..5836b354e 100644
Binary files a/v4.3.0/.doctrees/interface/index.doctree and b/v4.3.0/.doctrees/interface/index.doctree differ
diff --git a/v4.3.0/.doctrees/interface/input_group.doctree b/v4.3.0/.doctrees/interface/input_group.doctree
index 509e18f7a..91aae6542 100644
Binary files a/v4.3.0/.doctrees/interface/input_group.doctree and b/v4.3.0/.doctrees/interface/input_group.doctree differ
diff --git a/v4.3.0/.doctrees/interface/introduction.doctree b/v4.3.0/.doctrees/interface/introduction.doctree
index 3cbb6092c..2fe5e62d9 100644
Binary files a/v4.3.0/.doctrees/interface/introduction.doctree and b/v4.3.0/.doctrees/interface/introduction.doctree differ
diff --git a/v4.3.0/.doctrees/interface/meta_group.doctree b/v4.3.0/.doctrees/interface/meta_group.doctree
index 41e4933ad..c8b7c266b 100644
Binary files a/v4.3.0/.doctrees/interface/meta_group.doctree and b/v4.3.0/.doctrees/interface/meta_group.doctree differ
diff --git a/v4.3.0/.doctrees/interface/output_group.doctree b/v4.3.0/.doctrees/interface/output_group.doctree
index 803f05de1..b15a1ca3a 100644
Binary files a/v4.3.0/.doctrees/interface/output_group.doctree and b/v4.3.0/.doctrees/interface/output_group.doctree differ
diff --git a/v4.3.0/.doctrees/interface/reactions.doctree b/v4.3.0/.doctrees/interface/reactions.doctree
index dc6e46894..c7f6b3f1d 100644
Binary files a/v4.3.0/.doctrees/interface/reactions.doctree and b/v4.3.0/.doctrees/interface/reactions.doctree differ
diff --git a/v4.3.0/.doctrees/interface/return_data.doctree b/v4.3.0/.doctrees/interface/return_data.doctree
index f140bf459..76b452393 100644
Binary files a/v4.3.0/.doctrees/interface/return_data.doctree and b/v4.3.0/.doctrees/interface/return_data.doctree differ
diff --git a/v4.3.0/.doctrees/interface/sensitivities.doctree b/v4.3.0/.doctrees/interface/sensitivities.doctree
index 83e108a93..20634cf20 100644
Binary files a/v4.3.0/.doctrees/interface/sensitivities.doctree and b/v4.3.0/.doctrees/interface/sensitivities.doctree differ
diff --git a/v4.3.0/.doctrees/interface/solver.doctree b/v4.3.0/.doctrees/interface/solver.doctree
index 513e67fb1..38dd8d6b3 100644
Binary files a/v4.3.0/.doctrees/interface/solver.doctree and b/v4.3.0/.doctrees/interface/solver.doctree differ
diff --git a/v4.3.0/.doctrees/interface/system.doctree b/v4.3.0/.doctrees/interface/system.doctree
index 19cee7631..5972c4d4d 100644
Binary files a/v4.3.0/.doctrees/interface/system.doctree and b/v4.3.0/.doctrees/interface/system.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/2d_general_rate_model.doctree b/v4.3.0/.doctrees/interface/unit_operations/2d_general_rate_model.doctree
index 02383dc02..d59e2d69d 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/2d_general_rate_model.doctree and b/v4.3.0/.doctrees/interface/unit_operations/2d_general_rate_model.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/cstr.doctree b/v4.3.0/.doctrees/interface/unit_operations/cstr.doctree
index 27d4225a4..0c55c7825 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/cstr.doctree and b/v4.3.0/.doctrees/interface/unit_operations/cstr.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/general_rate_model.doctree b/v4.3.0/.doctrees/interface/unit_operations/general_rate_model.doctree
index 4ae15dcc4..db12b2dab 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/general_rate_model.doctree and b/v4.3.0/.doctrees/interface/unit_operations/general_rate_model.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/index.doctree b/v4.3.0/.doctrees/interface/unit_operations/index.doctree
index 29f0e743d..44381779d 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/index.doctree and b/v4.3.0/.doctrees/interface/unit_operations/index.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/inlet.doctree b/v4.3.0/.doctrees/interface/unit_operations/inlet.doctree
index 3b3e82b87..57d95c1bc 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/inlet.doctree and b/v4.3.0/.doctrees/interface/unit_operations/inlet.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree b/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree
index 9f7521e1c..b4553cbdb 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree and b/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_with_pores.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree b/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree
index a5fa019dc..7f1aa21c7 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree and b/v4.3.0/.doctrees/interface/unit_operations/lumped_rate_model_without_pores.doctree differ
diff --git a/v4.3.0/.doctrees/interface/unit_operations/outlet.doctree b/v4.3.0/.doctrees/interface/unit_operations/outlet.doctree
index a945bed39..94f8da2b9 100644
Binary files a/v4.3.0/.doctrees/interface/unit_operations/outlet.doctree and b/v4.3.0/.doctrees/interface/unit_operations/outlet.doctree differ
diff --git a/v4.3.0/.doctrees/license.doctree b/v4.3.0/.doctrees/license.doctree
index 2ffb5613d..cc848df19 100644
Binary files a/v4.3.0/.doctrees/license.doctree and b/v4.3.0/.doctrees/license.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/bi_steric_mass_action.doctree b/v4.3.0/.doctrees/modelling/binding/bi_steric_mass_action.doctree
index d202fd956..a0f96e618 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/bi_steric_mass_action.doctree and b/v4.3.0/.doctrees/modelling/binding/bi_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree
index 57721589f..3b7f470db 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/extended_mobile_phase_modulator_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/generalized_ion_exchange.doctree b/v4.3.0/.doctrees/modelling/binding/generalized_ion_exchange.doctree
index 4044fdb73..8b9ca8d07 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/generalized_ion_exchange.doctree and b/v4.3.0/.doctrees/modelling/binding/generalized_ion_exchange.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/index.doctree b/v4.3.0/.doctrees/modelling/binding/index.doctree
index 2d0d6f43e..8b024a5cd 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/index.doctree and b/v4.3.0/.doctrees/modelling/binding/index.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/kumar_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/kumar_langmuir.doctree
index cb5e37f29..c391de903 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/kumar_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/kumar_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/linear.doctree b/v4.3.0/.doctrees/modelling/binding/linear.doctree
index 38017fcdf..9dc5877c8 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/linear.doctree and b/v4.3.0/.doctrees/modelling/binding/linear.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree
index 6059a9365..9b3220a72 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/mobile_phase_modulator_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree
index 1ba4659c4..e59c65525 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/multi_component_anti_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree
index adf6aa8db..ae20f91ef 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/multi_component_bi_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/multi_component_langmuir.doctree b/v4.3.0/.doctrees/modelling/binding/multi_component_langmuir.doctree
index 339ef380a..940c1978a 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/multi_component_langmuir.doctree and b/v4.3.0/.doctrees/modelling/binding/multi_component_langmuir.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/multi_component_spreading.doctree b/v4.3.0/.doctrees/modelling/binding/multi_component_spreading.doctree
index c266bb534..18bec46bc 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/multi_component_spreading.doctree and b/v4.3.0/.doctrees/modelling/binding/multi_component_spreading.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree b/v4.3.0/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree
index 3bd56f52b..301aa28e1 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree and b/v4.3.0/.doctrees/modelling/binding/multi_state_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/saska.doctree b/v4.3.0/.doctrees/modelling/binding/saska.doctree
index 0cb51a288..315052631 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/saska.doctree and b/v4.3.0/.doctrees/modelling/binding/saska.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/self_association.doctree b/v4.3.0/.doctrees/modelling/binding/self_association.doctree
index 77aaee8b6..29eb84bb2 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/self_association.doctree and b/v4.3.0/.doctrees/modelling/binding/self_association.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree b/v4.3.0/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree
index 27e1198dc..f50c53a1e 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree and b/v4.3.0/.doctrees/modelling/binding/simplified_multi_state_steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/binding/steric_mass_action.doctree b/v4.3.0/.doctrees/modelling/binding/steric_mass_action.doctree
index 704763a05..4195c8375 100644
Binary files a/v4.3.0/.doctrees/modelling/binding/steric_mass_action.doctree and b/v4.3.0/.doctrees/modelling/binding/steric_mass_action.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/index.doctree b/v4.3.0/.doctrees/modelling/index.doctree
index 83219820d..1c2a26e23 100644
Binary files a/v4.3.0/.doctrees/modelling/index.doctree and b/v4.3.0/.doctrees/modelling/index.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/networks.doctree b/v4.3.0/.doctrees/modelling/networks.doctree
index 7b6aa0275..6f3338146 100644
Binary files a/v4.3.0/.doctrees/modelling/networks.doctree and b/v4.3.0/.doctrees/modelling/networks.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/reactions.doctree b/v4.3.0/.doctrees/modelling/reactions.doctree
index b05558061..e3bece8a3 100644
Binary files a/v4.3.0/.doctrees/modelling/reactions.doctree and b/v4.3.0/.doctrees/modelling/reactions.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree b/v4.3.0/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree
index 9a45c31e9..af54e735f 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/2d_general_rate_model.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/cstr.doctree b/v4.3.0/.doctrees/modelling/unit_operations/cstr.doctree
index 1ad794805..643974fda 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/cstr.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/cstr.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/general_rate_model.doctree b/v4.3.0/.doctrees/modelling/unit_operations/general_rate_model.doctree
index 2da127675..319808707 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/general_rate_model.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/general_rate_model.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/index.doctree b/v4.3.0/.doctrees/modelling/unit_operations/index.doctree
index a148a2106..7efea5186 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/index.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/index.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/inlet.doctree b/v4.3.0/.doctrees/modelling/unit_operations/inlet.doctree
index cc38da3e1..00d65d501 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/inlet.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/inlet.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree b/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree
index d07c1bbc0..248edb112 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_with_pores.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree b/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree
index a91b213b8..e766fa634 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/lumped_rate_model_without_pores.doctree differ
diff --git a/v4.3.0/.doctrees/modelling/unit_operations/outlet.doctree b/v4.3.0/.doctrees/modelling/unit_operations/outlet.doctree
index fbafaaf73..adb9524a6 100644
Binary files a/v4.3.0/.doctrees/modelling/unit_operations/outlet.doctree and b/v4.3.0/.doctrees/modelling/unit_operations/outlet.doctree differ
diff --git a/v4.3.0/.doctrees/requirements.doctree b/v4.3.0/.doctrees/requirements.doctree
index 91856bd01..892820ca4 100644
Binary files a/v4.3.0/.doctrees/requirements.doctree and b/v4.3.0/.doctrees/requirements.doctree differ
diff --git a/v4.3.0/.doctrees/simulation/index.doctree b/v4.3.0/.doctrees/simulation/index.doctree
index a6f630d0d..48e69c9d4 100644
Binary files a/v4.3.0/.doctrees/simulation/index.doctree and b/v4.3.0/.doctrees/simulation/index.doctree differ
diff --git a/v4.3.0/.doctrees/zbibliography.doctree b/v4.3.0/.doctrees/zbibliography.doctree
index 8e0b4f637..8ab2a2ad5 100644
Binary files a/v4.3.0/.doctrees/zbibliography.doctree and b/v4.3.0/.doctrees/zbibliography.doctree differ
diff --git a/v4.3.0/interface/reactions.html b/v4.3.0/interface/reactions.html
index 57c0ecac9..0c64d8ea0 100644
--- a/v4.3.0/interface/reactions.html
+++ b/v4.3.0/interface/reactions.html
@@ -88,7 +88,7 @@