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AcCoRD Examples

This page contains links to and descriptions of configuration and post-processing file examples to run in the AcCoRD simulator. To run these examples yourself, you will need to download and install AcCoRD. For more information on how to use these files, you can refer to the How to Use AcCoRD page.

The examples are sorted into two main categories. The configuration files of the latest release examples are included with every download of AcCoRD and are kept up to date to run on the latest release. The specific release examples are maintained for a specific version and are intended to recreate results from a specific publication or demonstrate a new feature associated with that release.

Note (2016-11-04): This page is new and a work-in-progress. More content will be added to show images and link to videos that use some of the example files.

Latest Release Examples

The following configuration files are kept up to date for the latest version of AcCoRD. To limit execution times, most of these simulations only run a single realization. To access these files, you can download the latest version of AcCoRD.

  • “accord_config_sample” – Places 2 molecules in a microscopic box and tracks their locations as they diffuse. No reactions. This is one of only two sample configuration files that track molecule locations.
  • “accord_config_sample_all_shapes_hybrid” – Places molecules uniformly in a large box that is divided into a mix of microscopic and mesoscopic regions. Demonstrates the nesting of regions. No reactions.
  • “accord_config_sample_all_shapes_meso” – Places molecules uniformly in a large box that is divided into a number of mesoscopic regions. Demonstrates the nesting of regions. No reactions.
  • “accord_config_sample_all_shapes_micro” – Places molecules uniformly in a large box that is divided into a number of microscopic regions. Demonstrates the nesting of regions. No reactions.
  • “accord_config_sample_communication” – Small spherical source releases finite-width pulses of molecules that are observed as they pass through a transparent spherical receiver. Environment is all microscopic. The transmitter modulates its signal according to a pre-defined sequence of bits. Each symbol has two bits. The symbols (0, 1, 2, 3) result in (0, 1000, 2000, 3000) molecules being released over a release interval of 1ms, which is 10% of the symbol interval. No reactions.
  • “accord_config_sample_communication_chemical” – Point source releases finite-width pulses of molecules that can bind to a spherical receiver. Environment is all microscopic. Transmitter modulates its signal according to a randomly-generated bit sequence. Each symbol has 2 bits (values are 0, 1, 2, 3). The value of the symbol is multiplied by a stochastic generation rate of 120000 molecules per second that is active for 1ms of the transmitter’s 10ms symbol interval. Molecules can reversibly bind to the surface of the receiver.
  • “accord_config_sample_crowding” – Places 10 molecules in a microscopic box that has a reflecting box nested inside. A bimolecular reaction with a finite unbinding radius maintains a minimum distance between pairs of molecules.
  • accord_config_sample_flow” – Point source releases an impulse of molecules that are counted inside a spherical observer. There is a net flow in the direction from the source to the observer, and the flow has a slower velocity within the observer. Environment is all microscopic.
  • accord_config_sample_flow_closed_hybrid” – Places molecules inside a pipe that is closed to form a square. Each side of the pipe has a different flow direction, such that the molecules undergo a net counterclockwise motion. Two of the sides are mesoscopic and two of the sides are microscopic. This is one of only two sample configuration files that track molecule locations.
  • “accord_config_sample_hybrid” – Places molecules in a box that is one half microscopic and one half mesoscopic. The mesoscopic region has 125 subvolumes.
  • “accord_config_sample_pipe_reaction_diffusion” – Places molecules at one end of a rectangular pipe. An absorbing region with a finite absorption rate is at the other end of the pipe. The pipe is mesoscopic.
  • “accord_config_sample_pipe_reaction_diffusion_microscopic” – Places molecules at one end of a rectangular pipe. An absorbing region with a finite absorption rate is at the other end of the pipe. The pipe is microscopic.
  • “accord_config_sample_point_diffusion” – Point source releases an impulse of molecules that are observed by various transparent receivers, including a sphere and a box. Environment is all microscopic. No reactions.
  • “accord_config_sample_reactor” – Creates and destroys molecules in a mesoscopic box. On average, one molecule is created every second and has an expected lifetime of 100 seconds.
  • “accord_config_sample_reactor_2nd_order” – Places molecules in a mesoscopic box. The molecules can degrade by participating in an enzyme kinetic reaction. The diffusion coefficients of all molecule are set to zero but there is only one subvolume so no diffusion is needed (molecules are always assumed to have a random location inside a mesoscopic subvolume).
  • “accord_config_sample_reactor_microscopic” – Creates and destroys molecules in a microscopic box. On average, one molecule is created every second and has an expected lifetime of 100 seconds.
  • “accord_config_sample_surface” – Places molecules of many types in a microscopic box. Some types of molecules can pass through one face of the box into an adjacent box, and some types of molecules can be absorbed by one face of the box (either reversible or irreversibly). This environment re-creates that used for Figure 6a in this paper by Steven S. Andrews, where he derived the surface reaction probabilities for Smoldyn (and which are also implemented in AcCoRD).

Specific Release Examples

The following configuration files were written for a specific version of AcCoRD. Old versions of AcCoRD can be found here.

Sample Videos in the AcCoRD Journal Paper

The AcCoRD journal paper, “Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion” (and which can be accessed here), refers to a series of 8 videos. The simulations were run using version 0.7 and 0.7.0.1, and the videos were generated using version 1.0, but they can all be re-created using just 1.0.

Here are configuration files that can be used to run the simulations: accord_config_journal_video.zip

Here are Video Maker wrappers that can be used to build the videos once the simulation output has been imported into MATLAB: accord_journal_video_build.zip

Last but not least, here are the videos themselves: