This applet is a demonstration of the axis system defined by a linear dichroism (LD) experiment with Couette flow orientation of absorbing molecules, which are reconstituted in the lipid bilayer of shear deformed vesicles.
The axis system is comprised of the following components, as described in reference [1]:
[math]X[/math]: Lipid bilayer normal
[math]Y[/math]: Axis orthogonal to [math]X[/math] and [math]Z[/math]
[math]Z[/math]: Orientation axis / Direction of Couette flow
[math]µ_i[/math]: Transition dipole moment
[math]v[/math]: Projection of [math]µ_i[/math] onto the [math]YZ[/math]-plane
[math]α[/math]: Angle between [math]µ_i[/math] and [math]X[/math]
[math]β[/math]: Angle between [math]v[/math] and [math]Z[/math]
[math]γ[/math]: Angle between the propagation direction of the incident light and [math]X[/math]
The three angles can be changed individually with sliders: [math]α[/math] between 0° and 90°, [math]β[/math] and [math]γ[/math] between 0° and 360°.
The sines (dotted) and cosines (dashed) of these angles are also depicted.
In addition, the macroscopic orientation parameter, [math]S[/math], can be changed between 0 and 1 with a slider, which is represented as an ellipsoidal deformation of the vesicle ranging from a spherical to an almost cylindrical appearance.
The isotropic absorbance, [math]A_{iso}[/math], can be changed with a slider between 0 and 1 to influence the length of the transition dipole moment according to [math]A_{iso} = \frac{µ_i^2}{3}[/math].
The incident and transmitted light with its alternating linear polarisation can be animated for improved visual perceivability; the amplitude of the transmitted light changes according to the magnitude of the orthogonal and parallel components of the transition dipole moment. These components are calculated and displayed at the bottom, in addition to the LD and reduced LD, [math]LD^r[/math].
[1] A. Rodger, J. Rajendra, R. Marrington, M. Ardhammar, B. Nordén, J. D. Hirst and A. T. B. Gilbert, [b]2002[/b], "Flow oriented linear dichroism to probe protein orientation in membrane environments," [i]Physical Chemistry Chemical Physics[/i], [b]4[/b] (16), 4051-4057.
