MichaelisMentenReactionRate.H
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23 
24 Class
25  Foam::MichaelisMentenReactionRate
26 
27 Description
28  Michaelis-Menten reaction rate for enzymatic reactions.
29 
30  Reference:
31  \verbatim
32  Michaelis, L., & Menten, M. L. (1913).
33  Die Kinetik der InwertinWirkung.
34  Biochem., (49), 333-369.
35  \endverbatim
36 
37 SourceFiles
38  MichaelisMentenReactionRateI.H
39 
40 \*---------------------------------------------------------------------------*/
41 
42 #ifndef MichaelisMentenReactionRate_H
43 #define MichaelisMentenReactionRate_H
44 
45 #include "Reaction.H"
46 
47 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
48 
49 namespace Foam
50 {
51 
52 // Forward declaration of friend functions and operators
53 
54 class MichaelisMentenReactionRate;
55 
56 Ostream& operator<<(Ostream&, const MichaelisMentenReactionRate&);
57 
58 
59 /*---------------------------------------------------------------------------*\
60  Class MichaelisMentenReactionRate Declaration
61 \*---------------------------------------------------------------------------*/
62 
64 {
65  // Private Data
66 
67  //- List of species present in reaction system
68  const speciesTable& species_;
69 
70  //- The maximum reaction rate at saturating substrate concentration
71  scalar Vmax_;
72 
73  //- The Michaelis constant
74  // the substrate concentration at which the reaction rate is half Vmax_
75  scalar Km_;
76 
77  //- The substrate specie index
78  label s_;
79 
81 
82 
83 public:
84 
85  // Constructors
86 
87  //- Construct from dictionary
89  (
90  const speciesTable& species,
91  const dictionary& dict
92  );
93 
94 
95  // Member Functions
96 
97  //- Return the type name
98  static word type()
99  {
100  return "MichaelisMenten";
101  }
102 
103  inline scalar operator()
104  (
105  const scalar p,
106  const scalar T,
107  const scalarField& c,
108  const label li
109  ) const;
110 
111  inline scalar ddT
112  (
113  const scalar p,
114  const scalar T,
115  const scalarField& c,
116  const label li
117  ) const;
118 
119  //- Third-body efficiencies (beta = 1-alpha)
120  // non-empty only for third-body reactions
121  // with enhanced molecularity (alpha != 1)
122  inline const List<Tuple2<label, scalar>>& beta() const;
123 
124  //- Species concentration derivative of the pressure dependent term
125  inline void dcidc
126  (
127  const scalar p,
128  const scalar T,
129  const scalarField& c,
130  const label li,
132  ) const;
133 
134  //- Temperature derivative of the pressure dependent term
135  inline scalar dcidT
136  (
137  const scalar p,
138  const scalar T,
139  const scalarField& c,
140  const label li
141  ) const;
142 
143  //- Write to stream
144  inline void write(Ostream& os) const;
145 
146 
147  // Ostream Operator
148 
149  inline friend Ostream& operator<<
150  (
151  Ostream&,
153  );
154 };
155 
156 
157 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
158 
159 } // End namespace Foam
160 
161 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
162 
164 
165 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
166 
167 #endif
168 
169 // ************************************************************************* //
dictionary dict
intWM_LABEL_SIZE_t label
A label is an int32_t or int64_t as specified by the pre-processor macro WM_LABEL_SIZE.
Definition: label.H:59
A list of keyword definitions, which are a keyword followed by any number of values (e...
Definition: dictionary.H:158
A 1D array of objects of type <T>, where the size of the vector is known and used for subscript bound...
Definition: HashTable.H:59
scalar dcidT(const scalar p, const scalar T, const scalarField &c, const label li) const
Temperature derivative of the pressure dependent term.
Michaelis-Menten reaction rate for enzymatic reactions.
static word type()
Return the type name.
const dimensionedScalar & c
Speed of light in a vacuum.
A class for handling words, derived from string.
Definition: word.H:59
void dcidc(const scalar p, const scalar T, const scalarField &c, const label li, scalarField &dcidc) const
Species concentration derivative of the pressure dependent term.
const List< Tuple2< label, scalar > > & beta() const
Third-body efficiencies (beta = 1-alpha)
An Ostream is an abstract base class for all output systems (streams, files, token lists...
Definition: Ostream.H:54
void T(FieldField< Field, Type > &f1, const FieldField< Field, Type > &f2)
void write(Ostream &os) const
Write to stream.
scalar ddT(const scalar p, const scalar T, const scalarField &c, const label li) const
A wordList with hashed indices for faster lookup by name.
Ostream & operator<<(Ostream &, const ensightPart &)
MichaelisMentenReactionRate(const speciesTable &species, const dictionary &dict)
Construct from dictionary.
volScalarField & p
Namespace for OpenFOAM.