afmAdhesionEnergy function

Adhesion Energy

Finds the adhesion and the full detach energies from the retract segment of the AFM F-d curve.

afmAdhesionEnergy(afmdata, width = 1, lagdiff = width, mul, mdj = NULL)

Arguments

• afmdata: An afmdata or afmexperiment class variables. Baseline correction should have been done already.
• width: Width of the window for the local regression (in vector position units)
• lagdiff: Lag for estimating the differences in Delta (or slopes) signal. By default it takes the same value as the window with.
• mul: Multiplier for the calculating the threshold inthe estimation of jumps and peaks in the Delta signal
• mdj: Minimum distance between jumps. If none is given then it will be set equal to width

Returns

An afmdata class variable which will consist on the original input afmdata variable plus a new list named AdhEner with the following fields:

Points Array containing the indices of the retract segment where the adhesion begins, the unbinding event takes place and the adhesion ends.

Energies Data frame with three columns: E1adh, E2adh and Etotal, being the first one the energy from the begining of the adhesion until the unbinding event, then second one the energy from the unbinding event until the full detachment of the tip, and the third one, the sum of them.

Examples

path <- path.package("afmToolkit")
data <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path)
data <- afmContactPoint(data, width = 20, mul1 = 1, mul2 = 10)
data <- afmDetachPoint(data, width = 20, mul1 = 2, mul2 = 30)
data <- afmBaselineCorrection(data)
data <- afmAdhesionEnergy(data, width = 20, mul = 10)
str(data$AdhEner)