Models

DeerLab provides a wide selection of built-in models. These are instances of the deerlab.Model object class and can be manipulated and expanded as described in the Modeling guide.

These are models particularly oriented towards the modeling of dipolar EPR spectroscopy data.

Experiment models

These generator functions model different dipolar EPR experiments, and provide the means to refine the dipolar signal models by introducing experimental information.

ex_3pdeer	Generate a 3-pulse DEER dipolar experiment model.
ex_4pdeer	Generate a 4-pulse DEER dipolar experiment model.
ex_rev5pdeer	Generate a reverse 5-pulse DEER dipolar experiment model.
ex_fwd5pdeer	Generate a forward 5-pulse DEER dipolar experiment model.
ex_sifter	Generate a 4-pulse SIFTER dipolar experiment model.
ex_dqc	Generate a 6-pulse DQC dipolar experiment model.
ex_ridme	Generate a 5-pulse RIDME dipolar experiment model.

Distance distribution models

These models provide parametrizations of the interspin distance distributions.

Basis functions

This group of distribution models is based on functions that can serve as basis functions for modeling more general distributions.

dd_gauss	Gaussian distribution model
dd_gauss2	Sum of two Gaussian distributions model
dd_gauss3	Sum of three Gaussian distributions model
dd_rice	3D-Rice distribution model
dd_rice2	Sum of two 3D-Rice distributions model
dd_rice3	Sum of two 3D-Rice distributions model
dd_gengauss	Generalized Gaussian distribution model
dd_skewgauss	Skew Gaussian distribution model
dd_cos	Raised-cosine parametric model

Disordered physical models

This group of distribution models represents spin labels attached to disordered macromolecular structures.

dd_wormchain	Worm-like chain model near the rigid limit.
dd_wormgauss	Worm-like chain model near the rigid limit with Gaussian convolution.
dd_randcoil	Random-coil model for an unfolded peptide/protein

Sphere/shell models

This group of distribution models represents spin labels in simple partitions of 3D space.

dd_sphere	Particles uniformly distributed on a sphere.
dd_spheresurf	Particles uniformly distributed on a sphere's surface.
dd_spherepoint	One particle distanced from particles uniformly distributed on a sphere
dd_shell	Uniform distribution of particles on a spherical shell
dd_shellshell	Particles uniformly distributed on a spherical shell and on another concentric spherical shell.
dd_shellsphere	Particles uniformly distributed on a sphere and on an outer spherical shell.
dd_shellvoidshell	Particles uniformly distributed on a spherical shell and on another concentric spherical shell separated by a void.
dd_shellvoidsphere	Particles uniformly distributed on a sphere and on a concentric outer spherical shell separated by a void.

Toy models

This group contains distribution models that have absolutely no physical relevance. They are useful for testing numerical algorithms.

dd_circle	Semicircle distribution model
dd_triangle	Triangular distribution model.
dd_uniform	Uniform distribution model.

Background models

These models provide parametrizations of the signal contribution arising from intermolecular dipolar interactions.

Physical models

This category involves models that describe particular distributions of spin labels in space. These models depend on physical parameters such as spin concentration, exclusion distances, and dimensionality.

bg_hom3d	Background from a homogeneous distribution of spins in a 3D medium
bg_hom3dex	Background from a homogeneous distribution of spins with excluded volume
bg_homfractal	Background from homogeneous spin distribution in a space of fractal dimension

Additionally, the following models describe the time-dependent phase-shifts arising from these particular distributions of spin labels in space.

bg_hom3d_phase	Phase shift from a homogeneous distribution of spins in a 3D medium
bg_hom3dex_phase	Phase shift from a homogeneous distribution of spins with excluded volume
bg_homfractal_phase	Phase shift from a homogeneous distribution of spins in a fractal medium

Phenomenological models

This category comprises phenomenological models that represent various mathematical functions that are intended to mimic the background decay, without reference to a particular spatial distribution of spins. The parameters of these models do no have direct physical meaning.

bg_exp	Exponential background model
bg_strexp	Stretched exponential background model
bg_sumstrexp	Sum of two stretched exponentials background model
bg_prodstrexp	Product of two stretched exponentials background model
bg_poly1	Polynomial 1st-order background model
bg_poly2	Polynomial 2nd-order background model
bg_poly3	Polynomial 3rd-order background model