Description Usage Arguments Value Examples
Simulates either a single pulse or a double pulse chronoamperometry experiment using either an E, EC, or CE mechanism, where E is a redox reaction and where C is a chemical reaction that either precedes or follows the redox reaction.
1 2 3 4 5 | simulateCA(e.start = 0, e.pulse = -0.5, e.form = -0.25,
mechanism = c("E", "EC", "CE"), ko = 1, kcf = 0, kcr = 0,
pulses = c("single", "double"), t.1 = 10, t.2 = 0, t.end = 30,
n = 1, alpha = 0.5, d = 1e-05, area = 0.01, temp = 298.15,
conc.bulk = 0.001, t.units = 2000, x.units = 180, sd.noise = 0)
|
e.start |
Initial potential (in volts). |
e.pulse |
Potential after applying the initial pulse (in volts). |
e.form |
Formal potential for the redox reaction (in volts). |
mechanism |
Mechanism for the electrochemical system; one of |
ko |
Standard heterogeneous electron transfer rate constant for the redox reaction (in cm/s). |
kcf |
Homogeneous first-order rate constant for the forward chemical reaction (in s^-1). |
kcr |
Homogeneous first-order rate constant for the reverse chemical reaction (in s^-1). |
pulses |
Either |
t.1 |
The time at which the first pulse is applied (in s). |
t.2 |
The time at which the second pulse is applied (in s). |
t.end |
The time at which the experiment ends (in s). |
n |
Number of electrons in the redox reaction. |
alpha |
Transfer coefficient. |
d |
Diffusion coefficient for Ox and Red (in cm^2 s^-1). |
area |
Surface area of the electrode (in cm^2). |
temp |
Temperature (in K). |
conc.bulk |
Initial bulk concentration of Ox or Red for an E or an EC mechanism, or the combined initial concentrations of Ox and Z, or of Red and Z for a CE mechanism (in mol/L). |
t.units |
The number of increments in time for the diffusion grids. |
x.units |
The number of increments in distance for the diffusion grids. |
sd.noise |
The standard deviation for noise as a percent of maximum current (in μA). |
Returns a list with the following components
expt |
type of experiment; defaults to CA for a chronoamperometry simulation |
mechanism |
type of mechanism used for the simulation |
file_type |
value that indicates whether the output includes all data (full) or a subset of data (reduced); defaults to full for |
current |
vector giving the current as a function of time |
potential |
vector giving the potential as a function of time |
time |
vector giving the times used for the diffusion grids |
distance |
vector giving the distances from electrode surface used for the diffusion grids |
oxdata |
diffusion grid, as a matrix, giving the concentration of Ox |
reddata |
diffusion grid, as a matrix, giving the concentrations of Red |
chemdata |
diffusion grid, as a matrix, giving the concentrations of Z |
formalE |
formal potential for the redox reaction |
initialE |
initial potential |
pulseE |
potential after apply the initial pulse |
electrons |
number of electrons, n, in the redox reaction |
ko |
standard heterogeneous electron transfer rate constant |
kcf |
homogeneous first-order rate constant for forward chemical reaction |
kcr |
homogeneous first-order rate constant for reverse chemical reaction |
alpha |
transfer coefficient |
diffcoef |
diffusion coefficient for Ox and Red |
area |
surface area for electrode |
temperature |
temperature |
conc.bulk |
initial concentration of Ox or Red for an E or EC mechanism, or the combined initial concentrations of Ox and Z, or of Red and Z for a CE mechanism |
tunits |
the number of increments in time for the diffusion grids |
xunits |
the number of increments in distance for the diffusion grids |
sdnoise |
standard deviation, as percent of maximum current, used to add noise to simulated data |
direction |
-1 for an initial reduction reaction of Ox to Red; +1 for an initial oxidation reaction of Red to Ox |
pulses |
number of pulses: either single or double |
time_pulse1 |
time when first pulse is applied |
time_pulse2 |
time when second pulse is applied |
time_end |
time when experiment ends |
k_f |
vector of forward electron transfer rate constant as a function of potential |
k_b |
vector of reverse electron transfer rate constant as a function of potential |
jox |
vector giving the flux of Ox to the electrode surface as a function of potential |
jred |
vector giving the flux of Red to the electrode surface as a function of potential |
1 2 3 | ex_ca = simulateCA(e.start = 0.25, e.pulse = -0.25, e.form = 0,
pulses = "double", t.2 = 20, x.units = 100, t.units = 1000)
str(ex_ca)
|
List of 34
$ expt : chr "CA"
$ mechanism : chr "E"
$ file_type : chr "full"
$ current : num [1:1001] 0 0.000552 0.000399 0.00033 0.000288 ...
$ potential : num [1:1001] 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 ...
$ time : num [1:1001] 0 0.03 0.06 0.09 0.12 0.15 0.18 0.21 0.24 0.27 ...
$ distance : num [1:101] 0 0.00104 0.00208 0.00312 0.00416 ...
$ oxdata : num [1:1001, 1:101] 1 1 1 1 1 ...
$ reddata : num [1:1001, 1:101] 0.00 5.94e-05 5.94e-05 5.94e-05 5.94e-05 ...
$ chemdata : num [1:1001, 1:101] 0 0 0 0 0 0 0 0 0 0 ...
$ formalE : num 0
$ initialE : num 0.25
$ pulseE : num -0.25
$ electrons : num 1
$ ko : num 1
$ kcf : num 0
$ kcr : num 0
$ alpha : num 0.5
$ diffcoef : num 1e-05
$ area : num 0.01
$ temperature: num 298
$ conc.bulk : num 0.001
$ tunits : num 1000
$ xunits : num 100
$ sdnoise : num 0
$ direction : num -1
$ pulses : chr "double"
$ time_pulse1: num 10
$ time_pulse2: num 20
$ time_end : num 30
$ k_f : num [1:1001] 0.00771 0.00771 0.00771 0.00771 0.00771 ...
$ k_b : num [1:1001] 130 130 130 130 130 ...
$ jox : num [1:1001] 0.00 -5.72e-13 -4.13e-13 -3.43e-13 -2.99e-13 ...
$ jred : num [1:1001] 0.00 5.72e-13 4.13e-13 3.43e-13 2.99e-13 ...
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