afmExpDecay function

Exponential decay fit

Fits a viscoelastic exponential decay in a Force-Relaxation or Creep experiments as described in Nanotechnology 2010 (see references).

afmExpDecay(afmdata, nexp = 2, tmax = NULL, type = c("CH","CF"), plt = TRUE,
  ...)

Arguments

• afmdata: An object of afmdata class with a pause segment and a Time column in the data dataframe.

• nexp: Number of expontials in the Prony series to be fitted. Currently only one or two exponentials are supported. Default is 2.

• tmax: Maximum time considered in the relaxation curve. It defaults to Inf, meaning that the whole pause segment is considered.

• type: Type of the experiment. Can be either "CH" (Constant Height) for a force-relaxation experiment or "CF" (Constant Force) for a creep experiment. Default is type = "CH".

• plt: Logical. If TRUE (default) then a plot of the pause segment with the overlay of the fit is shown.

• ...: Options passed to the nlsM() function from the minpack.lm

  package. At least should contain the starting values (start = list(...)) for the Levenberg-Mardquart nonlinear least square method.

Returns

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

expdecayModel: A nls object returned from nlsM() function.

expdecayFit: The values predicted by the fit, returned from the predict() function.

Examples

data <- afmReadJPK("force-save-JPK-3h.txt.gz", path = path.package("afmToolkit"))
width <- 20
mul1 <- 1
mul2 <- 10
data <- afmContactPoint(data, width = width, mul1 = mul1, mul2 = mul2)
data <- afmDetachPoint(data, width = width, mul1 = mul1, mul2 = mul2)
data <- afmBaselineCorrection(data)
data <- afmExpDecay(data, nexp = 2, type = "CH")

References

Susana Moreno-Flores, Rafael Benitez, Maria dM Vivanco and Jose Luis Toca-Herrera (2010). "Stress relaxation and creep on living cells with the atomic force microscope: a means to calculate elastic moduli and viscosities of cell components". Nanotechnology, 21 (44), pp. 445101.