This is a simple simulation of basic
polymers
; i.e., molecular networks. In this mini-project, we simulate linear chains
of soft spheres. The interaction between spheres, both bonded and non-bonded
interactions are modeled with simplistic math and brownian dynamics is used
to update the sphere positions using random movement, directed by the interaction
terms.
See these related projects for more details on methodology.
You can adjust the parameters of the simulation by changing the JavaScript code
below. Just hit the "Start" button to begin simulation. Note, the full simulation
runs within your web browser; nothing is done server side. At the bottom of this page,
we plot the progression of internal energy to track the relaxation/equilibration of
the simulated system.
Steps: 0
var r = 0.05;
Polymers.run({
polymerLength: 8,
NPolymers: 50,
particleRadius: r,
// minimum energy length of bonds
rBondZero: 3 * r,
// multiplicative factor of bond strength
bondFactor: 0.1,
// LJ interaction strength
epsilon: 0.00002,
// LJ length scale
sigma: 2 * r,
// BD update length scale
randomScale: 0.5 * r,
// How frequently to update the neighbor lists in simulation
cycleDuration: 50,
// How frequently to sample the internal engery
analysisRate: 10,
// How frequently the visulaization is updated
visualizationRate: 10
});