dipolarbackground

Constructs the total multi-pathway background function

Syntax

B = dipolarbackground(t,pathinfo,Bmodel)
B = dipolarbackground(___,'Property',Value)
Parameters
  • t - Time axis vector (N-element array), in microseconds
  • pathinfo - Modulation depths, refocusing times, and harmonics (px2 or px3 array) for multiple dipolar pathways
  • Bmodel - Background model function handle
Returns
  • B - Multi-pathway background (N-element array)

Description

B = dipolarbackground(t,pathinfo,Bmodel)

Computes the multipathway background B for the time axis t (in microseconds) corresponding to the dipolar pathways specified in pathinfo. The total background is computed from the basis background function model specified in Bmodel. This model must be a function handle of the type Bmodel @(t,lambda) bg_model(t,params,lambda).

For a multi-pathway DEER signal (e.g, 4-pulse DEER with 2+1 contribution; 5-pulse DEER with 4-pulse DEER residual signal, and more complicated experiments), pathinfo is a 2D array that contains a list of modulation depths (amplitudes), refocusing times (in microseconds), and optional harmonics for all modulated pathway signals.

Each row of pathinfo contains two values: one modulation depth and one refocusing time. For a pathway with unmodulated signal, set the refocusing time to NaN.

Optionally, the harmonic (1 = fundamental, 2 = first overtone, etc.) can be given as a third value in each row. This can be useful for modeling RIDME signals. If not given, the harmonic is 1 for all pathways.

Example:
To calculate the background for the standard model for 4-pulse DEER with an unmodulated offset and a single dipolar pathway that refocuses at time 0, use
t = linspace(-5,20,501);
lambda = 0.4; % modulation depth main signal
conc = 200;   % spin concentration (uM)

pathinfo = [1-lambda NaN; lambda 0];

% alternative input
pathinfo(1,:) = [1-lambda NaN];    % unmodulated part, gives offset
pathinfo(2,:) = [lambda 0];        % main modulation, refocusing at time zero

Bmodel = @(t,lambda) bg_hom3d(t,conc,lambda)

B = dipolarbackground(t,pathinfo,Bmodel);
plot(t,B);

Additional Settings

Additional settings can be specified via name-value pairs. All property names are case insensitive and the property-value pairs can be passed in any order after the required input arguments have been passed.

B = dipolarbackground(___,'Property1',Value1,'Property2',Value2,___)
  • 'OvertoneCoeffs' - RIDME overtone coefficients

    1D array containing the overtone coefficients for RIDME experiments.

    Default: [empty]

    Example:

    B = dipolarbackground(___,'OvertoneCoeffs',[0.4 0.2 0.4])   % fundamental, 1st, and 2nd overtone
  • 'Renormalize' - Re-normalization of multi-pathway background

    The multi-pathway background does not necessarily satisfy V(0) == 1. This option enables(true) or disables(false) a re-normalization to ensure that equality is satisfied.

    Default: true

    Example:

    B = dipolarbackground(___,'Renormalize',false)