# Fick's 1st and 2nd Laws¶

Our goal in this tutorial is to evaluate Fick’s 1st and 2nd Laws using simulations of discrete diffusing particles. To do so, we design the simulation geometry and input conditions so that we obtain a concentration gradient and net flux along one dimension only. We will compare the simulation results to our expectations based on the expressions for Fick’s Laws, in particular Fick’s 2nd Law:

$$\frac{dc}{dt}=D\frac{d^2c}{dx^2}=D\frac{d}{dx}(\frac{dc}{dx})$$

where D is the diffusion coefficient used for the particles in the simulation. We begin by designing the 3-D geometry as illustrated below:

Using a cylindrical geometry, we wish to introduce diffusing particles such that:

1. There will be a concentration gradient along the x-axis only.
2. After some elapsed time, the system will reach a steady state with an unchanging concentration gradient along the x-axis (e.g., a 10-fold difference along the length of the cylinder).

How can we do this with MCell and CellBlender? Hint: Consider the concentration clamp command introduced previously.

We will conduct this tutorial in 2 sections. The first section will build and run the entire simulation. It turns out this will be the easy part.

The second part of the tutorial will involve building the "instrumentation" required to measure the concentration along the cylinder. This will be much more tedious.

Before getting started, you might find it helpful to watch the following video. This video walks you through the entire process of building, instrumenting, and running the simulation. However, the video was made with an earlier version of CellBlender and is not completely accurate when used with the current CellBlender. However, it does provide a good overview of the entire process. Additionally most of the Blender geometry manipulation hasn't changed much, so you might be able to follow those sections directly.

Warning

This video was made with older versions of both Blender and CellBlender. Much of the mesh manipulation is the same but the interface may look different. Additionally, as noted above, the cylinder is built along the "x" axis in the current verion of this tutorial while it was built along the "y" axis in the video.

## Part 1: Building the Model and Running the Simulation¶

Begin by starting Blender with CellBlender enabled.

Delete everything in your scene by first selecting everything with the a ("all") key until all objects - Cube, lamp, camera - are highlighted (orange outline). Then hit the x key and click Delete to delete the default Cube, lamp, camera, and anything else in your scene.

### Create the Cylinder Geometry¶

Create a cylinder by hitting Shift-a, and selecting Mesh>Cylinder. Hit s, Shift-z, 0.2, and Enter to confirm. Hit r, y, 90, and Enter to rotate it 90 degrees around the y-axis (aligns cylinder along the x axis). This will be the main cylinder through which the molecules diffuse. You may want to rotate and zoom to get a better view. It should looks something like this:

Be sure that the red arrow (x axis) is facing generally to the right so our definitions of "left" and "right" will be consistent with your view.

In the CellBlender panel, open the "Model Objects" subpanel. With your new cylinder selected, click the "+" button to add the Cylinder to the list of objects in your CellBlender model.

The name "Cylinder" should appear in the box with a green check mark beside it. Below that box is another box titled "Cylinder Display Options". Click the small triangle which expands the features in that box. You should see a drop down control with the label "Maximum Draw Type" and it is likely showing "Solid" or "Textured". Click on the control and change it to "Wire" so you can see through the Cylinder.

Then click the triangle again to close the "Cylinder Display Options" box.

Create two surface regions (below the Cylinder Display Options box) by clicking the + button twice and name them left_end and right_end.

Then, enter Edit Mode by hitting Tab (with mouse cursor in 3D window).

In order to select all vertices on both sides of an object (what we want), you should disable the "Limit selection to visible" button by clicking it into the "lighter gray" state as shown here:

Hit a once or twice (or more) until everything is unselected (black).

Hit b to start the Border Select mode.

Select the left end of the cylinder by clicking with the left mouse button and dragging around it.

Go back to the Model Objects subpanel and select the "left_end" region that you created earlier. Then click the "Assign" button to tag those selected faces to the "left_end" surface region of your Cylinder.

Hit a to deselect everything in the mesh. Then repeat the process for the right end of your cylinder (assign the faces on the right end to the "right_end" region).

Deselect everything with the "a" key and switch back to Object Mode by hitting Tab.

For objective viewing, switch to the top view with either the "7" key on your keypad (not the top row number keys) or by choosing "View" and "Top" from the view menu below the 3D viewport. Similarly, select orthographic mode with keypad "5" or by choosing "View" and "View Persp/Ortho" so that the words "Top Ortho" appear in the upper left corner of the 3D viewport.

Finally, hit the "a" key one (or more) times until the object is unselected (black). This will make it easier to see our molecules as they're added. Your view should look about like this:

### Define Constants for the Simulation¶

Click the "Parameters" button to open the "Model Parameters" subpanel.

Click the "+" button to define a new parameter. By default it will be "P1" with a value of 0.

Change the name to "iters" and give it a value of 5000 as shown in the table below. Repeat this process of adding and editing to define all of the model parameters in this table (note that the Units and Description are optional and not needed for the simulation):

Model Parameters:
Parameter Name Expression Units Description
iters 5000   Number of iterations to run
dt 1e-6 seconds Time step for each iteration
Na 6.0221415e23   Avogardros Number
area 1.2441e-11 cm^2 Cross-sectional area of cylinder
dx 5e-7 cm Width of sampling volumes 20 plus 21
dc 5e-6 cm^2 / sec Diffusion Constant
cl 2e-5 Molar Concentration on left end

When you're done, your Parameters panel should look like this:

### Define a Molecule Species¶

Click on the "Molecules" panel button to show the Defined Molecules subpanel.

Click the "+" button to define a new molecule species.

Change the Name to "vm" (representing a "volume molecule").

Leave the Molecule Type as "VolumeMolecule".

Set the Diffusion Constant to "dc" (the diffusion constant we defined in the parameters panel eariler).

When you're finished, it should look like this:

### Define a Clamp Concentration Surface Class¶

Click on the "Surface Classes" panel button to show the Defined Surface Classes subpanel.

Click the "+" button to define a new surface class.

Change the Surface Class Name to "clamp".

Click the "+" button beside the "clamp Properties" box (below the Surface Class Name) to define a new property for the "clamp" surface class.

Set the Molecule Name to "vm".

Set the Orientation to "Bottom/Back".

Set the Type to "Clamp Concentration".

Set the Value to "cl" (the concentration we defined in the parameters panel eariler).

When you're finished, it should look like this:

### Assign the Clamp Concentration Surface Class to the Left end of the Cylinder¶

Click on the "Assign Surface Classes" panel button to show the Assigned Surface Classes subpanel.

Click the "+" button to define a new surface class (it will show an "Undefined surface class" error).

Change the Surface Class Name to "clamp".

Change the Object Name to "Cylinder".

Uncheck the All Faces checkbox.

Change the Region Name to "left_end".

When you're finished, it should look like this:

### Define an Absorptive Surface Class¶

Click on the "Surface Classes" panel button to show the Defined Surface Classes subpanel.

Click the "+" button to define a new surface class.

Change the Surface Class Name to "absorb".

Click the "+" button beside the "absorb Properties" box (below the Surface Class Name) to define a new property for the "absorb" surface class.

Set the Molecule Name to "vm".

Set the Orientation to "Ignore".

Set the Type to "Absorptive".

When you're finished, it should look like this:

### Assign the Absorptive Surface Class to the Right end of the Cylinder¶

Click on the "Assign Surface Classes" panel button to show the Assigned Surface Classes subpanel.

Click the "+" button to define a new surface class (it will show an "Undefined surface class" error).

Change the Surface Class Name to "absorb".

Change the Object Name to "Cylinder".

Uncheck the All Faces checkbox.

Change the Region Name to "right_end".

### First Simulation¶

Click on the "Run Simulation" panel button to show the Run Simulation subpanel.

Change the Iterations to "iters / 10" ("iters" was defined as 5000, but we don't need to run that long while we're testing).

Change the Time Step to "dt" (defined in the parameters panel earlier).

This is a good time to save with "File / Save" in the top menu bar.

Click the Export & Run button to start the simulation.

The simulation should run quickly (only 500 iterations), and you should see a green check mark beside the completed run (you may have to hover your cursor over it to get it to update):

Next click the "Reload Visualization Data" button to load all of the molecules.

You can click and drag in the time line window to watch the molecules diffusing from the left side (source) to the right side over time.

If this is not working properly, now is the time to go back and correct any problems.

### Specify Plotting Data¶

Now let's define some data for MCell to collect from the simulation for us to plot.

Click on the "Plot Output Settings" button to begin specifying what to collect. You should see an initially empty panel with the title of "Reaction Data Output". Click the small plus sign one time to add the first output specification. You may see a "Name error" warning letting you know that you haven't selected a molecule or reaction to count yet. Click on the "Molecule" selector and select the "vm" molecule that we have in this simulation. That should clear the error and show a green check mark next to the specification of "Count vm in World". That's exactly what we want. Your Plot Output Settings panel should look like this:

### Full Length Simulation¶

If everything has gone as expected, try running for the entire time length of 5000 iterations.

Open the "Run Simulation" panel again and change the Iterations from to "iters / 10" back to "iters" and run again.

That may take some time to run, but when it's done you can click the "Reload Visualization Data" button and then press Blender's play button.

You should see something like the following animation (although this one is sampled in non-linear time):

### Plotting the Results¶

CellBlender can work with a number of different plotting packages and these are automatically detected every time CellBlender is restarted. These packages include xmGrace and Python's MatPlotLib. The system requirements for each plotting package are also detected when CellBlender is restarted, and CellBlender will only display buttons for the packages that are supported by the software on your system. For that reason, you may have different buttons than the ones shown in the following pictures. For this tutorial, you may use whichever plotting packages are available, and you're encouraged to try them all to explore the different advantages and limitations of each.

Again click on the "Plot Output Settings" button to see the different plotting packages available on your system. Click one (or more) to see the time history of the number of vm molecules in your simulation.

The following pictures show the output produced by each of the buttons shown above.

Simple Plotter Output

MatPlotLib Plotter Output

XmGrace Plotter Output

Java Plotter Output

Note

Since plotting requirements vary (along with individual tastes), the CellBlender plotting system may be extended fairly easily to work with many other plotting packages. This is done by adding your own "interface" files to the CellBlender addon folder to communicate with your favorite plotting software. The "Simple" plotter, for example, only contains about 100 lines of Python code and is a good starting template for anyone wishing to write code for their own favorite software.

Regardless of which plotter you use, you'll notice that the total number of vm molecules starts at zero and grows rapidly during the early part of the simulation. But as time goes on, the total count of vm molecules appears to stabilize at an equilibrium. This might be verified and quantified with additional runs and averaging of the data over many runs and over longer periods of time.

## Part 2: Instrumentation and Measurements¶

The model built and run in the previous section is complete, and we will not be modifying it in this section. We will, however, add some "instrumentation" which will help us make measurements so we can quantify the results obtained from that simulation.

Our "instrumentation" will consist of a series of disks and very short cylinder volumes which divide the test cylinder along its length to facilitate counting of the molecules by MCell. In this tutorial we will divide the cylinder into 40 segments. That will require 40 small cylinders and 39 small circular disks between those 40 cylinders. This can be done manually (segment by segment) or it can be automated. We will show some aspects of each approach.

• To create the raw geometry, we will demonstrate Blender's built-in array capability.
• To add the MCell features we will generate some of it within CellBlender and then show how to use the CellBlender-generated MDL as a template for automating the process through a text editor or any number of programming languages.

As with plotting, it's often a matter of preference as to which approach is best. Clearly for very small models, it's easy to do everything manually within CellBlender. Larger models, on the other hand, benefit much more from automation of any kind. The model we're using here is somewhere in between. It's managable to do it all by hand, but it can also benefit from automation if you have the skills to do so.

Warning

Note that any MDL modified by hand cannot currently be imported back into CellBlender. This might influence your decision on which approach to use. Be sure to back up any MDL that you edit by hand since CellBlender will overwrite those files when exporting for a new run.

### Preparation¶

Before getting started, let's hide the molecules that we've been simulating so they don't get in the way of our mesh building operations. In the upper right corner of the standard Blender screen layout you will find a panel known as the "Outliner" (shown below). The outliner can be used to show and explore all of the objects in the Blender scene (and more). For our purposes here, we just want to be able to show and hide the molecules that have been created by the simulation. These are all contained under the "molecules" object, so click the small plus sign next to the name "molecules" and that will display one line for each type of molecule ("species") that's been created in our simulation.

In this case, we've only defined one molecule type that we've called "vm", so we only see the entry "mol_vm" in the list. If you click on the "eye" symbol on that line it will toggle the display of the molecules. Click it a few times to hide and show the molecules. You'll notice that you can do the same for the Cylinder (or any other object in the scene). For this next step, we want to show the Cylinder but hide the molecules. Be sure to leave the outliner in that state before proceding. The next step also assumes that your 3D cursor is at the origin. You can ensure this with "Shift-S" and then clicking on "Cursor to Center".

Note

Blender uses the right mouse button for most selection, but this runs counter to the common "left click" used by common software. In Blender, the left click moves the 3D cursor - which is where new objects are placed. For this reason, it's handy to remember that the 3D cursor can be reset back to the origin with the "Shift-S" / "Cursor to Center" sequence.

### Strategy and Blender's Layers¶

Because we're dealing with 80 objects, we don't want to have to do a lot of individual selecting. That's both tedious and error prone. It's even worse in this case because many of the objects will be occupying the same space. So we will use Blender's concept of "Layers" to isolate each group of objects as we create them. So far, our main Cylinder and all of our molecules are (by default) on Layer 1. We'll leave them there and we'll create the small measuring cylinders on Layer 2 and the small disks on Layer 3. For this to work, be sure that you select the proper layer before each of these steps.

Note

There are other mechanisms for dealing with large numbers of objects. For example, the CellBlender addon contains a built-in Object Selector which allows selection by regular expressions. This particular tutorial uses Blender's "Layers" feature, but there are other tools that could have been used as well.

### Building Sampling Cylinders¶

We begin our "instrumentation" by creating a series of short sampling cylinders inside the long one ... but on Layer 2. Switch to Layer 2 by clicking the second small box in the layer panel as shown here:

When you click that box, everything will "disappear" because you're now looking at a new and empty layer. Your cylinder and molecules are still on Layer 1, but now they won't interfere with building the smaller sampling cylinders and disks. You can switch back and forth between layers by just clicking the little buttons shown above (try it). You can also view multiple layers simultaneously by shift-clicking them. For now we just want to work on Layer 2, so be sure that's the one selected (showing an empty window).

To begin building the small sampling cylinders, hit Shift-a (Add) and once again select Mesh>Cylinder. We will make these sampling cylinders slightly smaller than the main cylinder to avoid coincident meshes: Hit s, Shift-z, 0.199, and Enter. Hit r, y, 90, and Enter. Next, hit s, x, 0.024875, and Enter. Hit g, x, and -0.975 followed by Enter to move it very close to the left end of the end of larger cylinder back on Layer 1 (they don't touch though).

Triangulate this small cylinder by entering Edit mode with Tab, then pressing Control-T, then exiting Edit mode with Tab.

Using the outliner, rename this smaller cylinder from Cylinder.001 to C by double clicking on the Cylinder.001 and typing C followed by the Enter key.

Now, we will use Blender's (very useful) Array modifier to replicate this sampling cylinder 40 times. To do so, hit the Object Modifiers button (small wrench), and from the Add Modifier drop-down box, select Array. Change Count to 40. Deselect Relative Offset and select Constant Offset. Then change the third field under Constant Offset (Z axis of the cylinder) to 2.01005.

Now we need to make each cylinder a unique object. To do this, first hit the Apply button under the Array modifier. Then enter Edit Mode (with Tab key), hit p, and select By loose parts in the Separate menu. This will split each discontinuous mesh into a unique object.

They will be named C, C.001, C.002, etc. The first cylinder in the list will be named C. Rename it to C.040. This will make things cleaner when we want to count molecules in MCell later. Hit Tab to enter Object Mode and hit a until nothing is selected (nothing outlined in orange).

At this point, you can switch between the two layers (1 and 2) to see the original cylinder (wire outline with molecules) and the new measuring cylinders (solid). They should appear to be in the same exact place. If not, then retrace the steps to fix it.

### Building Sampling Disks¶

Finally, we will create a series of circular sampling planes that lie between each of these cylinders. We will put them on Layer 3, so click on the third small "layer" box:

As before, you will see a blank screen because you're looking at a new layer. You may notice that the first two layer boxes have a small 'dot' in them. That's a quick way of letting you know that there are objects in those layers. All the other layers should be solid (without that dot).

With layer 3 selected, create a circle by hitting Shift-a, and selecting Mesh>Circle. Open the Tool Shelf if needed (hit t to toggle it), and look for the "Add Circle" panel. You may need to scroll down to find it below the CellBlender panels. Change the "Fill Type" to "Triangle Fan". Hit s, 0.199, and Enter. Hit r, y, 90, and Enter. Hit g, x, and -0.95 and Enter to move it to the left of our window but very close to the right side of our smaller cylinder (which is on the left side of our larger cylinder).

Triangulate this small circle by entering Edit mode with Tab, then pressing Control-T, then exiting Edit mode with Tab.

Next, we will replicate this plane by adding an Array modifier similar to what we did previously with the cylinders. Click the Add Modifier button and select Array. Set Count to 39, disable Relative Offset, enable Constant Offset and set the Z value of the Constant Offset to be 0.251255.

Then click Apply to apply the modifier.

As before, separate the disks by entering edit mode (Tab) and use the "p" key to separate the object By loose parts in the same way you did with the small cylinders.

Exit edit mode with the Tab key, and then rename the final plane from Circle to Circle.039.

We need every objects' origin to be centered at the global origin. Even though our objects are on 3 different layers, we can easily view them all by shift clicking on the additional layers until they are all dark (selected). Do that now so that the first 3 layer boxes are selected (dark gray). Then select every mesh object by pressing the a key until everything is highlighted orange. Then hit Ctrl-a and select Location. Then hit Ctrl-a again and select Rotation.

At this point we have a total of 80 non-molecule objects in our model:

• 1 long cylinder named Cylinder
• 40 short cylinders named C.001 to C.040
• 39 circular disks named Circle.001 to Circle.039

You should be in "Object" mode, and you should be able to click on each object's name in the Outliner panel and see the object be selected in the 3D view. When you're done verifying this, deselect everything by pressing the a key until everything is unselected (black).

### Add Cylinders and Circles as Model Objects¶

In order for MCell to use the small cylinders and circles they need to be added to our CellBlender model. A CellBlender scene can contain all kinds of objects (cameras, lights, text, backplanes, etc). Many of these are helpful in creating a visual image or movie, but they're not really part of the simulation itself. We let CellBlender know which objects are actually part of the simulation by selecting them and adding them to the model objects list. In our case, we've made things easy by deleting the camera, lights and everything else. So everything in our simulation is intended to be part of our model objects list, and we can just add it all.

Click on the "Model Objects" button to show the Model Objects panel. Then use the "a" key to select "all". Toggle it until everything turns orange. Then click the small "+" button to the right of the model objects list to add all of those objects to our CellBlender model. You should see a long list of objects named C.xxx and Circle.xxx in the model objects window.

We could run the simulation now, but we'd find a problem. We'd find that there were very few molecules this time because all of our cylinders and disks are acting as "plugs" along the longer cylinder. With nowhere to go, the molecule density near the clamp will be very high since the molecules can't diffuse away.

### Making Sampling Cylinders Transparent to vm Molecules¶

In order for molecules to "flow" through all of these smaller cylinders and circles, we will need to make them transparent to any molecules that we want to flow through them. In our case, the only molecule we have is "vm" so we'll need to create a transparent surface class to apply to all of those objects.

Click on the "Surface Classes" button to show the Surface Classes panel. You should see the two classes ("clamp" and "absorb") that we defined earlier. Click the "+" button beside those two classes to add a third and name it "transp". Then click the "+" beside the "transp Properties" box one time to specify which molecule can pass through the "transparent" surface. Select the "vm" molecule for the "Molecule Name" field, set the Orientation to "Ignore", and set the "Type" to "Transparent".

The previous step has created a new "class" or "type" of surface which is transparent to vm molecules in both directions. But we haven't assigned that class to any of our surfaces yet. In order for our molecules to flow through all of those 40 cylinders and 39 disks, we need to assign our new "transp" class to each one of them. We will start by assigning the new "transp" class to the first 3 small cylinders and the first 3 small disks. After doing that for 6 of our 79 objects, you can decide if you'd like to continue doing that one by one for the remaining 73 objects or if you'd prefer to use a more automated method. There are tradeoffs in both cases.

'd rathWe will start by assigning it to the firsta

In order for molecules to "flow" through all of these smaller cylinders

## More work to be done ...¶

### Exporting the Project¶

We will now export these mdls. Under CellBlender Project Settings, set the Project Base Name to ficks_law. Then hit Export CellBlender Project, select a directory to save your project to (e.g. /home/user/mcell_tutorial/ficks_law/), and hit Export MCell MDL.

Also, make sure to save your project as a .blend project file via File->Save As and giving it a meaningful name.

### Annotating the MDL¶

We will now edit several of the exported MDL files and also add new ones to set up our simulations. First at the top of ficks_law.main.mdl add the following MDL commands (you will have to change the existing ITERATION and TIME_STEP statements):

iterations = 1
dt = 1e-06
ITERATIONS = iterations
TIME_STEP = dt

area = <insert from Blender>  /* area of sampling volumes in dm^2 */
dx   = <insert from Blender>  /* length of sampling volumes in dm */
samplingVol = dx * area       /* volume of sampling volume in dm^3 = l*/
dc = 5e-6 /* diffusion coefficient [cm^2/sec] */
Na = 6.0221415e23  /* Avogardros Number */

PARTITION_X = [[-0.1 TO 2.1 STEP .05]]
PARTITION_Y = [[-0.3 TO 0.3 STEP .05]]
PARTITION_Z = [[-0.3 TO 0.3 STEP .05]]


You can get the value of area and dx by using the Measure Panel script. Make sure you understand what these variables and MDL commands mean. Can you guess why we introduce separate iterations and dt variables? Also, since we do not have any reactions in our model comment out the line which includes the reactions (ficks_law.reactions.mdl). Next, open the file ficks_law.molecules.mdl and change the diffusion coefficient of our vm molecule to dc:

DEFINE_MOLECULES {
vm {DIFFUSION_CONSTANT_3D = dc}
}


So far so good. Now we have to think about how we can establish a concentration gradient between the left and right end of the big cylinder. As already hinted above, we can use MCell's surface clamp to clamp the left end of the cylinder at a certain value and make sure molecules get absorbed at the right end (why?). To this end, create the file ficks_law.surface_classes.mdl and enter a DEFINE_SURFACE_CLASSES block. You will have to complete the template given below yourself:

DEFINE_SURFACE_CLASSES {
transp {TRANSPARENT = vm }

/* define a clamp which release molecule at a concentration
of 1E-5 toward the inside of the cylinder */

/* define a surface class absorptive to vm */
}


Now, we need to do some serious modifications to our existing geometry. Both the sampling cylinders and sampling planes need to be made transparent to vm (why?). Also, we need to install the surface clamp at the left end of the big cylinder and make sure molecules are absorbed at the right. Below is a template for a MODIFY_SURFACE_REGIONS block that you will have to complete yourself (possibly with a script or a macro). Create the file ficks_law.mod_surf_regions.mdl and start editing:

MODIFY_SURFACE_REGIONS {

a concentration clamps at the left end of the cylinder
and absorb molecules at the right. Remember the surface
regions you created for this purposes when setting up the
mesh in Blender */

C.001[ALL] {
SURFACE_CLASS = transp
}

C.002[ALL] {
SURFACE_CLASS = transp
}

/* add statements for the remaining cylinders */

Circle.001[ALL] {
SURFACE_CLASS = transp
}
Circle.002[ALL] {
SURFACE_CLASS = transp
}

/* add statements for the remaining planes */
}


Next, we will add a reaction data output block. Again, you will need to add additional statements to output the data needed to work on the problems below. Create a file ficks_law.rxn_output.mdl and enter:

sprintf(seed,"%03g", SEED)

REACTION_DATA_OUTPUT {
STEP = 1*dt
/* Hint: These are examples.  You will need to add more to determine dC/dt. */
{COUNT[vm,Scene.Cylinder]}=>"./react_data/"&seed&"_vm_Cylinder.dat"
{COUNT[vm,Scene.C.001]}=>"./react_data/"&seed&"_vm_C.001.dat"
{COUNT[vm,Scene.Circle.001,FRONT_CROSSINGS]}=>"./react_data/"&seed&"_vm_Circle.001_front.dat"
/* more statements needed for Exercises 1 - 4 */
}


Finally, we add a visualization data block so we can check our simulation visually in CellBlender. Luckily, nothing needs to be added here and you are good to go! Create the file ficks_law.viz_output.mdl and enter:

VIZ_OUTPUT {
MODE = CELLBLENDER
FILENAME = "viz_data/ficksSecondLaw"
MOLECULES {
NAME_LIST {ALL_MOLECULES}
ITERATION_NUMBERS {ALL_DATA @ ALL_ITERATIONS}
}
}


This concludes our initial setup. Now let's run the simulation and see if everything checks out (the run will be quick since we are only simulating for a single iteration during the setup phase):

mcell ficks_law.main.mdl


Congratulations, if everything went well. If you encountered errors try to understand MCell's complaints and fix your errors.

Next, we need to figure out how long to simulate. We would like to reach a steady state where the concentration gradient in the cylinder remains constant (How would you determine if you reached steady state?). Start with 1000 iterations initially and see if this is enough. At this point it is crucial (as always really) to load your model into blender and make sure everything looks fine. You can use gnuplot for plotting: On the command line type gnuplot and enter:

gnuplot> plot "react_data/001_vm_Cylinder.dat"


to view the total number of molecules in the large cylinder.

Once you're confident you have a model with a proper concentration gradient we can finally tackle our examination of Fick's law.

As the concentration gradient is evolving along x, we wish to determine the rate of change in concentration ($$dC/dt$$) at each time point for the central sampling volume composed of the two subvolumes numbered 20 and 21. To see this clearly, you will probably want to run a series of simulations using different random number seeds, so you can average your results.

If you have done the Running Multiple Seed Values section, then you can use the script created there by copying the file run_seeds.py into your current directory:

cp /home/user/mcell_tutorial/seed/run_seeds.py /home/user/mcell_tutorial/ficks_law/


Otherwise, create the run_seeds.py now.

Along with the data you’ll need for Exercises 1 – 3 below, make sure that you output counts for molecules in subvolumes 1 and 40 (Exercise 4). Using MCell’s reaction data output, determination of the time course of dC/dt can be done in three ways which will explore now.

Note: Once you have verified your simulation it may be useful to turn visualization output off to speed up your simulations.

### Exercise 1¶

The most direct method is simply to count the number of molecules in subvolumes 20 and 21 at each timestep, convert the sum to concentration, export the concentration values for each timestep, and then differentiate to obtain the time course of $$\Delta C/ \Delta t \approx dC/dt$$.

Use MCell’s COUNT statements to output the concentration in subvolume 20 and 21 directly. Then use the below sample python script to do the averaging, smoothing and differentiation. Examine the output and make sure you understand what is going on. You may need to increase the number of seeds you average over if the data is too noisy. The script allows you to plot different quantities by commenting/uncommenting certain lines - take a look:

#!/usr/bin/env python

import numpy as np
import matplotlib.pyplot as plt

# name of files to average, smooth and differentiate
name = "vm_conc_20_21"
#name = "vm_conc_crossings"
#name = "vm_conc_ficks_law"

# number of seeds
numSeeds = 50

# this function does window smoothing
# from <http://www.scipy.org/Cookbook/SignalSmooth>
def smooth(x, window_len=11, window='hanning'):
if x.ndim != 1:
raise ValueError, "smooth only accepts 1 dimension arrays."
if x.size < window_len:
raise ValueError, "Input vector needs to be bigger than window size."
if window_len<3:
return x
if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']:
raise ValueError, ("Window is on of 'flat', 'hanning', 'hamming', \
'bartlett', 'blackman'")
s=np.r_[2*x[0]-x[window_len-1::-1],x,2*x[-1]-x[-1:-window_len:-1]]
if window == 'flat': #moving average
w=np.ones(window_len,'d')
else:
w=eval('np.'+window+'(window_len)')
y=np.convolve(w/w.sum(),s,mode='same')
return y[window_len:-window_len+1]

mol_conc = None
for seed in range(1,numSeeds):

data = np.genfromtxt("./react_data/%03d_%s.dat" %
(name, seed), dtype=float)
timePoints = data[:, 0]
rxn_data = data[:,1]

if mol_conc is None:
mol_conc = rxn_data
else:
# built up 2d array of molecule counts (one col/seed)
mol_conc = np.column_stack((mol_conc, rxn_data))

# compute the mean
mol_conc = mol_conc.mean(axis=1)

# smooth
smoothed_conc = smooth(mol_conc, window_len=200)

# differentiate data
diff_conc = np.diff(smoothed_conc)

# plot different results
plt.plot(timePoints, mol_conc, 'b')
#plt.plot(timePoints[0:len(timePoints)-1], diff_conc, 'b')

plt.title("dC/dt in subvolumes 19 and 20")
plt.show()


### Exercise 2¶

The next method is based on determination of the net fluxes into and out of the combined subvolumes 20 and 21. Again using MCell’s COUNT statements (Hint: specify FRONT_CROSSINGS and BACK_CROSSINGS), determine the net flux into the space across plane 19, as well as the net flux out of the space across plane 21. Use these results to compute the final net number of molecules in subvolumes 20 and 21 at each timestep, convert to concentration, and then output the result. Again use the above python script to differentiate and smooth, and compare your result to what you obtained for Exercise 1.

### Exercise 3¶

Now we wish to calculate $$dC/dt$$ based on Fick’s 2nd Law (make sure you understand how). For this we need to estimate the value of $$d^2C/dx^2$$ across the sampling volume, i.e., across subvolumes 20 and 21. Hence, you will need to determine $$dC/dx$$ at plane 19, as well as dC/dx at plane 21, and then find the difference to obtain $$d^2C/dx^2$$. To do this you will need to determine the concentration in subvolumes 19 and 22, as well as in subvolumes 20 and 21. Finally multiply by the diffusion coefficient D. Once you have calculated $$d^2C/dx^2$$ using COUNT statements, you can output the result, and again use the python script from above for averaging, smoothing and differentiating.

When considering the methods used to compute $$dC/dt$$ in Exercises 1, 2 and 3 which final result do you expect to show the most noise? Why? Do you results reflect this.

### Exercise 4¶

Finally, plot the ratio of variance to mean number of molecules for subvolumes 1, 20, 21, and 40. What do you observe and why?

You can use the following python script to do the analysis:

#!/usr/bin/env python

import numpy as np
import matplotlib.pyplot as plt
import os

startOfFileToAverage = "vm_C01"   # beginning of filenames to average
# over

mol_counts = None
files = os.listdir('react_data')   # build a list of reaction data file names
files.sort()                       # sort that list alphabetically

for f in files:                    # iterate over the list of file names
if f.startswith(startOfFileToAverage):
rxn_data = np.genfromtxt("./react_data/%s" % f, dtype=float)
rxn_data = rxn_data[:, 1]  # take the second column
if mol_counts is None:
mol_counts = rxn_data
else:
# built up 2d array of molecule counts (one col/seed)
mol_counts = np.column_stack((mol_counts, rxn_data))
else:
pass

mol_mean = mol_counts.mean(axis=1)  # take the mean of the rows
mol_var = mol_counts.var(axis=1)    # compute the variance of the rows
plt.plot(mol_mean/mol_var, 'g')     # plot ratio of mean and variance
plt.show()