A basic model of the short-term carbon cycle.

The Logistic Map is a polynomial mapping (equivalently, recurrence relation) of degree 2, often cited as an archetypal example of how complex, chaotic behaviour can arise from very simple non-linear dynamical equations. The map was popularized in a seminal 1976 paper by the biologist Robert May, in part as a discrete-time demographic model analogous to the logistic equation first created by Pierre François Verhulst. 

Mathematically, the logistic map is written

where:

 is a number between zero and one, and represents the ratio of existing population to the maximum possible population at year n, and hence x0 represents the initial ratio of population to max. population (at year 0)r is a positive number, and represents a combined rate for reproduction and starvation. To generate a bifurcation diagram, set 'r base' to 2 and 'r ramp' to 1
To demonstrate sensitivity to initial conditions, try two runs with 'r base' set to 3 and 'Initial X' of 0.5 and 0.501, then look at first ~20 time steps

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

A system dynamics model of a predator-prey lifecycle relationship

The purpose of this deer management model is to explore the capacity of wildlife management actions to help us adapt to the effects of climate change.

This model prototypes the working of an Smart Grid with Electric Vehicles

The objective is testing the theoretical advantages of batteries (also batteries in Electric Vehicles) in combination with renewable energies. The model considers two houses, that store energy both in Electric Vehicles (Vehicle to Grid), and in a communal battery.

Except when specified otherwise, the units of all variables are expressed in W/h.

Press "Story" in the lower bar for a guided tour over the model. Better seen at 50% zoom.

by Carlos Varela (cvarela@gmx.at)

An attempt to model some of the features in the national water market in Australia.

This model is a classic simulation of the production cycle in the ocean, including the effects of the thermocline in switching off advection of dissolved nutrients and detritus to the surface layer.

It illustrates a number of interesting features including the coupling of three state variables in a closed cycle, the use of time to control the duration of advection, and the modulus function for cycling annual temperature data over multiple years.

The model state variables are expressed in nitrogen units (mg N m-3), and the calibration is based on:

Baliño, B.M. 1996. Eutrophication of the North Sea, 1980-1990: An evaluation of anthropogenic nutrient inputs using a 2D phytoplankton production model. Dr. scient. thesis, University of Bergen.
 
Fransz, H.G. & Verhagen, J.H.G. 1985. Modelling Research on the Production Cycle of Phytoplankton in the Southern Bight of the Northn Sea in Relation to Riverborne Nutrient Loads. Netherlands Journal of Sea Research 19 (3/4): 241-250.

This model was first implemented in PowerSim some years ago by one of my M.Sc. students, who then went on to become a Buddhist monk. Although this is a very Zen model, as far as I'm aware, the two facts are unrelated.

This model implements the equations proposed by Ketchum in 1954. The rationale behind the concept is that only phytoplankton that grows above a certain rate will not be flushed out of an estuary.

For biological processes:

Pt  =  Po exp(kt)

Where Pt is the phytoplankton biomass at time t, Po is the initial biomass, and k is the growth rate.

For physical processes:

Pm  =  Po (1-r)^m

Where Pm is the phytoplankton biomass after m tidal cycles, and r is the exchange ratio (proportion of estuary water which does not return each tidal cycle).

By substitution, and replacing t by m in the first equation, we get:

Pm = Poexp(km).(1-r)^m

For phytoplankton to exist in an estuary, Pm = Po (at least), i.e. 1 / (1-r)^m = exp(km)
ln(1) - m.ln(1-r) = km
-m.ln(1-r) = km
k = -ln(1-r)

Ketchum (1954) Relation between circulation and planktonic populations in estuaries. Ecology 35: 191-200.

In 2005, Ferreira and co-workers showed that this balance has direct implications on biodiversity of estuarine phytoplankton, and discussed how this could be relevant for water management, in particular for the EU Water Framework Directive 60/2000/EC (Ecological Modelling, 187(4) 513-523).

Primitives for Watershed modeling project. Click Clone Insight at the top right to make a copy that you can edit.

How the 4-H club became a marketing thingy for DuPont

This diagram provides a stylised description of important feedbacks within a shallow-lake system.

Diagrams of theories of control of destiny at multiple scales as fundamental causes of social determinants of health from Whitehead 2016 article in Health and Place

Primitives for Watershed modeling project. Click Clone Insight at the top right to make a copy that you can edit.

The converter in this file contains precipitation for Tucson only. Tucson watersheds are Arroyo Chico, Canada Agua, and Lower Canada del Oro.

This model illustrates predator prey interactions using real-life data of wolf and moose populations on the Isle Royale.

We incorporate logistic growth into the moose dynamics, and we replace the death flow of the moose with a kill rate modeled from the kill rate data found on the Isle Royale website.

I start with these parameters:
Wolf Death Rate = 0.15
Wolf Birth Rate = 0.0187963
Moose Birth Rate = 0.4
Carrying Capacity = 2000
Initial Moose: 563
Initial Wolves: 20

I used RK-4 with step-size 0.1, from 1959 for 60 years.

The moose birth flow is logistic, MBR*M*(1-M/K)
Moose death flow is Kill Rate (in Moose/Year)
Wolf birth flow is WBR*Kill Rate (in Wolves/Year)
Wolf death flow is WDR*W

Simple model to illustrate oyster growth based on primary production of Phytoplankton as a state variable, forced by light and nutrients, running for a yearly period.

Phytoplankton growth based on on Steele's and Michaelis-Menten equations), where: 

Primary Production=(([Pmax]*[I]/[Iopt]*exp(1-[I]/[Iopt])*[S])/([Ks]+[S]))

Pmax: Maximum production (d-1)
I: Light energy at depth of interest (uE m-2 s-1)
Iopt: Light energy at which Pmax occurs (uE m-2 s-1)
S: Nutrient concentration (umol N L-1)
Ks: Half saturation constant for nutrient (umol N L-1).

Further developments:
- Nutrients as state variable in cycle with detritus from phytoplankton and oyster biomass.
- Light limited by the concentration of phytoplankton.
- Temperature effect on phytoplankton and Oyster growth.

This model is a classic simulation of the production cycle in the ocean, including the effects of the thermocline in switching off advection of dissolved nutrients and detritus to the surface layer.

It illustrates a number of interesting features including the coupling of three state variables in a closed cycle, the use of time to control the duration of advection, and the modulus function for cycling annual temperature data over multiple years.

The model state variables are expressed in nitrogen units (mg N m-3), and the calibration is based on:

Baliño, B.M. 1996. Eutrophication of the North Sea, 1980-1990: An evaluation of anthropogenic nutrient inputs using a 2D phytoplankton production model. Dr. scient. thesis, University of Bergen.
 
Fransz, H.G. & Verhagen, J.H.G. 1985. Modelling Research on the Production Cycle of Phytoplankton in the Southern Bight of the Northn Sea in Relation to Riverborne Nutrient Loads. Netherlands Journal of Sea Research 19 (3/4): 241-250.

This model was first implemented in PowerSim some years ago by one of my M.Sc. students, who then went on to become a Buddhist monk. Although this is a very Zen model, as far as I'm aware, the two facts are unrelated.

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

Teilmodell für die Umweltbelastung mit den Parametern Schadstoffeintrag, Erholungsrate und Schadschwelle.

Integrated Climate Model

Primitives for Watershed modeling project. Click Clone Insight at the top right to make a copy that you can edit.

The converter in this file contains precipitation for Tucson only. Tucson watersheds are Arroyo Chico, Canada Agua, and Lower Canada del Oro.

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.