Add MMC isotherm by Nfor 2010

doc/interface/binding/mmc_nfor.rst

@@ -0,0 +1,131 @@
+.. _mmc_nfor_config:
+
+MMC Nfor 2010
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MMC_NFOR**
+
+For information on model equations, refer to :ref:`_mmc_nfor_model`.
+
+
+``IS_KINETIC``
+   Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =
+   quasi-stationary. If a single value is given, the mode is set for all
+   bound states. Otherwise, the adsorption mode is set for each bound
+   state separately.
+
+===================  =========================  =======================
+**Type:** int        **Range:** {0,1}           **Length:** 1/NTOTALBND
+===================  =========================  =======================
+
+``MMCNFOR_KA``
+   Adsorption rate constant
+
+**Unit:** :math:`m_{MP}^{3}~m_{SP}^{-3}~s^{-1}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+``MMCNFOR_KD``
+   Desorption rate constant
+
+**Unit:** :math:`s^{-1}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+``MMCNFOR_KP``
+   Protein-salt interaction factor (dependence of activity of solved protein from salt concentration)
+
+**Unit:** :math:`s^{-1}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+``MMCNFOR_KS``
+   Protein-protein interaction factor (dependence of activity of solved protein from protein concentration)
+
+**Unit:** :math:`s^{-1}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+``MMCNFOR_NU``
+   Characteristic charges of the protein; The number of sites
+   :math:`\nu` that the protein interacts with on the resin surface
+
+**Unit: [-]**
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+
+``MMCNFOR_N``
+   Number of hydrophobic ligands occupied during binding
+
+**Unit: [-]**
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+
+``MMCNFOR_SIGMA``
+   Steric factors for ionic binding of the protein; The number of sites :math:`\sigma` on
+   the surface that are shielded by the protein and prevented from
+   exchange with the salt counterions in solution
+
+**Unit: [-]**
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+``MMCNFOR_S``
+   Steric factor for hydrophobic binding of the protein;; The number of sites :math:`\sigma` on
+   the surface that are shielded by the protein and prevented from
+   exchange with the salt counterions in solution
+
+**Unit: [-]**
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** NCOMP
+===================  =========================  =========================================
+
+
+``SMA_LAMBDA``
+   Stationary phase capacity (monovalent salt counterions); The total
+   number of binding sites available on the resin surface
+
+**Unit:** :math:`mol~m_{SP}^{-3}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\ge 0`   **Length:** 1
+===================  =========================  =========================================
+
+``SMA_REFC0``
+   Reference liquid phase concentration (optional, defaults to
+   :math:`1.0`)
+
+
+**Unit:** :math:`mol~m_{MP}^{-3}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\gt 0`   **Length:** 1
+===================  =========================  =========================================
+
+``SMA_REFQ``
+   Reference solid phase concentration (optional, defaults to
+   :math:`1.0`)
+
+
+**Unit:** :math:`mol~m_{SP}^{-3}`
+
+===================  =========================  =========================================
+**Type:** double     **Range:** :math:`\gt 0`   **Length:** 1
+===================  =========================  =========================================

doc/modelling/binding/hic_water_on_hydrophobic_surfaces.rst

@@ -1,4 +1,4 @@
-.. _hic_water_on_hydrophobic_surfaces_model:
+.. _mmc_nfor_model:
 
 HIC Water on Hydrophobic Surfaces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

doc/modelling/binding/mmc_nfor.rst

@@ -0,0 +1,39 @@
+.. _hic_water_on_hydrophobic_surfaces_model:
+
+MMC Nfor 2010
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This model implements the mixed mode chromatography isotherm described by Nfor et al 2010 :cite:`Nfor2010`.
+
+.. math::
+
+		\begin{aligned}
+		 \frac{\mathrm{d}q_i}{\mathrm{d}t} &= k_{a,i} c_{p,i} \widetilde{\gamma_i} \left[ \Lambda - \sum_j\left( \nu_j + \sigma_j \right) q_j \right]^{\nu_i}\left[ \Lambda - \sum_j\left( n_j + s_j \right) q_j \right]^{n_i} - k_{d,i} q_i c_{s}^{\nu_i} \\
+		                               c_s &= c_{p,0}\\
+		              \widetilde{\gamma_i} &= e^{K_{p,i}c_{p,i} + K_{s,i}c_{s}}
+		\end{aligned}
+
+where :math:`c_{p,0}` and :math:`q_0` denote the salt concentrations in the liquid and solid phase of the beads, respectively.
+The number of free binding sites
+
+.. math::
+
+    \begin{aligned}
+        \bar{q}_0 = \Lambda - \sum_{j=1}^{N_{\text{comp}} - 1} \left( \nu_j + \sigma_j \right) q_j = q_0 - \sum_{j=1}^{N_{\text{comp}} - 1} \sigma_j q_j
+    \end{aligned}
+
+is calculated from the number of bound counter ions :math:`q_0` by taking steric shielding into account.
+In turn, the number of bound counter ions :math:`q_0` (electro-neutrality condition) is given by
+
+.. math::
+
+    \begin{aligned}
+        q_0 = \Lambda - \sum_{j=1}^{N_{\text{comp}} - 1} \nu_j q_j,
+    \end{aligned}
+
+which also compensates for the missing equation for :math:`\frac{\mathrm{d} q_0}{\mathrm{d}t}`.
+
+The concept of reference concentrations (:math:`c_{\text{ref}}` and :math:`q_{\text{ref}}`) is explained in the respective paragraph in Section�:ref:`reference_concentrations`.
+
+
+For more information on model parameters required to define in CADET file format, see :ref:`hic_water_on_hydrophobic_surfaces_config`.

src/libcadet/BindingModelFactory.cpp

@@ -44,6 +44,7 @@ namespace cadet
 			void registerBiLangmuirLDFModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
 			void registerHICWaterOnHydrophobicSurfacesModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
 			void registerHICConstantWaterActivityModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
+			void registerMMCNforModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
 		}
 	}
 
@@ -73,6 +74,7 @@ namespace cadet
 		model::binding::registerBiLangmuirLDFModel(_bindingModels);
 		model::binding::registerHICWaterOnHydrophobicSurfacesModel(_bindingModels);
 		model::binding::registerHICConstantWaterActivityModel(_bindingModels);
+		model::binding::registerMMCNforModel(_bindingModels);
 		registerModel<model::SimplifiedMultiStateStericMassActionBinding>();
 	}
 

src/libcadet/CMakeLists.txt

@@ -100,6 +100,7 @@ set(LIBCADET_BINDINGMODEL_SOURCES
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/BiLangmuirLDFBinding.cpp
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/HICWaterOnHydrophobicSurfacesBinding.cpp
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/HICConstantWaterActivityBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/MMCNfor.cpp
 )
 
 # LIBCADET_REACTIONMODEL_SOURCES holds all source files of reaction models