afmExpDecay {afmToolkit}

Exponential decay fit

Description

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

Usage

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.

Value

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.

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.

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")