public interface IKinetics
Modifier and Type  Field and Description 

static double 
K_UNSPECIFIED
Reaction rate (k) is unspecified; typically used by Transition.

static int 
KINETICS_BASIC_PTNET
default
Basic place/transition net kinetics as described in:
http://en.wikipedia.org/wiki/Petri_net
"a transition of a Petri net may fire whenever there are sufficient tokens at the start of all input arcs;
when it fires, it consumes these tokens, and places tokens at the end of all output arcs."

static int 
KINETICS_CUSTOM
The kinetics is defined in a Java subclass;
or in a separate child node possibly written in a scripting language.

static int 
KINETICS_DEFAULT
The default kinetics.

static int 
KINETICS_DIFFUSION
Diffuse or move tokens from one place to another place.

static int 
KINETICS_GRID
Using a Grid is also a type a kinetics.

static int 
KINETICS_LOGIC_AND
AND
A typical use is to represent an AND Gate in a digital circuit (2 inputs, 1 output).

static int 
KINETICS_LOGIC_NOT
NOT
NOT assumes a single input and typically one output.

static int 
KINETICS_LOGIC_OR
OR
If any input has at least one token,
[then consume that one token, NO]
and add one token to all outputs.

static int 
KINETICS_MASS_ACTION
Mass action kinetics as described in Baez (2011) Network Theory (Part 3),
and in Feinberg (1980) Lectures on Chemical Reaction Networks (Lectures 1 and 2).

static int 
KINETICS_MAX_VALID
Maximum valid kinetics type.

static int 
KINETICS_MAXIMAL_PARALLELISM
Membrane Computing, PSystems
This is a variant of KINETICS_BASIC_PTNET.

static int 
KINETICS_MICHAELIS_MENTEN
MichaelisMenten enzyme/catalyst kienetics.

static int 
KINETICS_MIN_VALID
Minimum valid kinetics type.

static int 
KINETICS_NULL
Take no action at run time.

static int 
KINETICS_UNSPECIFIED
The kinetics type is unspecified.

static double 
KM_UNSPECIFIED
MichaelisMenten km is unspecified; typically used by Transition.

static double 
LOGIC_FALSE
For use with KINETICS_LOGIC_ types.

static double 
LOGIC_TRUE
For use with KINETICS_LOGIC_ types.

static double 
P_UNSPECIFIED
Probability (p) is unspecified; typically used by Transition.

static double 
VMAX_UNSPECIFIED
MichaelisMenten vmax is unspecified; typically used by Transition.

Modifier and Type  Method and Description 

int 
getKineticsType()
Get kinetics type.

void 
setKineticsType(int kineticsType)
Set kinetics type.

static final int KINETICS_UNSPECIFIED
static final int KINETICS_NULL
static final int KINETICS_BASIC_PTNET
static final int KINETICS_MASS_ACTION
"the rate of an elementary reaction ... is proportional to the product of the concentrations of the participating molecules" (http://en.wikipedia.org/wiki/Law_of_mass_action)
also see: http://en.wikipedia.org/wiki/Rate_equation
static final int KINETICS_GRID
static final int KINETICS_MICHAELIS_MENTEN
static final int KINETICS_MAXIMAL_PARALLELISM
static final int KINETICS_CUSTOM
static final int KINETICS_DIFFUSION
According to Feinberg Lectures (p.227), "Species A and B diffuse from cell to cell at rates proportional to the difference in species concentration between the cells."
For this type of kinetics, k is a "diffusion constant".
It's probably not strictly necessary to have a separate diffusion kinetics. It's equivalent to using mass action. k(A2A1) = +kA2 kA1 Diffusion is just a recognition that A1 and A2 are the same species. It's a convenience concept.
static final int KINETICS_LOGIC_AND
static final int KINETICS_LOGIC_OR
static final int KINETICS_LOGIC_NOT
static final int KINETICS_DEFAULT
static final int KINETICS_MIN_VALID
static final int KINETICS_MAX_VALID
static final double K_UNSPECIFIED
static final double P_UNSPECIFIED
static final double KM_UNSPECIFIED
static final double VMAX_UNSPECIFIED
static final double LOGIC_TRUE
static final double LOGIC_FALSE