afmRelax: Stress relaxation/ Creep model fit

In rbensua/afmToolkit: Functions for Atomic Force Microscope Force-Distance Curves Analysis

Description

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

Usage

afmRelax(afmdata, model = c("power","exp"), 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.
model	Type of model to be fitted. Could be either "power" for a power law model or "exp" for an exponential decay model.
nexp	Number of expontials in the Prony series to be fitted if model is "exp". 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. For use only if model is "exp".

Value

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

model: The model used in the fit.

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

relaxFit: 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 <- afmRelax(data, model = "exp", nexp = 2, type = "CH")

rbensua/afmToolkit documentation built on Dec. 1, 2020, 2:14 a.m.