Active propagation parameters

stepLengthX: It is defined as the direction taken by the molecule in the given unit time on X-axis.

stepLengthY: It is defined as the direction taken by the molecule in the given unit time on Y-axis.

stepLengthZ: It is defined as the direction taken by the molecule in the given unit time on Z-axis.

mediumDimensionX: It is defined as the length of X dimension.

mediumDimensionY: It is defined as the length of Y dimension.

mediumDimensionZ: It is defined as the length of Z dimension.

maxSimulationTime: It is given as the time taken or the time calculated for the simulation of the whole system per molecule. The time is measured in terms of nano seconds.

distSendReciever: This is the distance between the Sender and the Receiver.

*** Considering the distance between the sender and receiver to be 'd' and considering the origin or the center, the distance between the sender and
center is 'd/2' and distance between center and receiver is 'd/2'. The molecule propagated can be on the rail or it can be outside the rail in the given boundary of the medium where molecules are trying to communicate. Sender is considered to be a sphere , but a point in the present project. Both center and radius are taken into consideration for Receiver. For getting or assigning the position of the molecule which is derailed or which is not on the rail then the new position of the molecule coordinated should be within the following coordinates boundary.

x-coordinate [-mediumDimensionX/2 , mediumDimensionX/2] y-coordinate [-mediumDimensionY/2 , mediumDimensionY/2] z-coordinate [-mediumDimensionZ/2 , mediumDimensionZ/2]

The following are the constraints which satisfies the above boundaries senderPosition (10,10,10) recieverCenter (20,20,20) recieverRadius 2

The following give information about the molecules noOfMolecules 10: 10 molecules are been propagated stepLengthX 1: moves a unit length in x direction stepLengthY 1: moves a unit length in y direction stepLengthZ 1: moves a unit length in z direction

velRail: It is defined as the distance propagated by a molecule along the rail in a given unit time. probDrail: This is defined as the probability of derailing of a molecule from the rail.

The following parameters are considered to be important when considering microtubule plusEndCentre and minusEndCentre are to be considered as the microtubule shows polarity + and -. Depending on the type of molecule the molecule might transfer from plus to minus or minus to plus. This determines the direction of the molecule. plusEndCentre () minusEndCentre () radiusMicroTubule It exhibits a property of multiple microtubules. If the user enters one set of values for plusEndCentre () minusEndCentre () radiusMicroTubule , then it is considered as 1 microtubule in the medium. If the user enters second set of values then it is considered as 2 microtubules and so on.

-input [filename] - Specifies the name of the parameter file to use. -reachfile [filename] - Specifies the name of the output file containing the time values for molecules reaching the destination

Contributors:

Chinmay, Sourav,Ruhavi, Tyrone, Narayanan.