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Basic EM Theory 

Electric and magnetic fields are two aspects of a single phenomena (EM field). An accelerated 

charge produces an E-field that varies over time. A time-varying E-field creates a time-varying B-

field which in turn sustains the time-varying E-field. As you can see, this phenomena produces awave that is capable of sustaining itself forever.

Polarization

The electric field defines the polarization orientation of the EM field. 

The plane of polarization of the wave is defined as the electric field vector and the direction

of wave propagation. 

Every single atom or molecule that emits light is emitting plane-polarized light instantaneously.

However, any sample of light we might examine is made up from the contributions of billions of atoms, all of which are changing the polarization of their emitted waves quite rapidly. Therefore,

unless we had some way of making the atoms behave cooperatively with each other (such as a

laser), we would expect to find all possible wave orientations or polarization in equal amounts.

A polarizer is a material that allows only light with a specific

orientation to pass through.

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If two polarizers are set up in series so that their optical axes are parallel, light passes

through both. However, if the polarization axes are orthogonal, the polarized lightfrom the first is extinguished by the second (also called an analyzer). As the angle

rotates from 0 to 90 degrees, the amount of light that is transmitted decreases. The

relationship between polarization angles and transmitted light intensity is given by

Malus' Law. 

I(q) = I(0) cos2(q)  Where I = intensity (W/m

2) 

Some substances have two different light bending powers (indexes of refraction) that depend on the

 polarization of the light entering the substance. These substances, usually crystals, are called  BIREFRINGENT .

It was noted that an incident ray of light perpendicular to the principal plane can be thought of as

two rays, one for vertical polarization and one for horizontal polarization. Within the birefringent

material, the atoms are arranged in a regular way and held in place by strong forces. These materials

are said to be non-isotropic, i.e. there is directionality to their properties. Since any light passingthrough the birefringent material is passed from atom to atom, it is not too surprising that the

material behaves differently in response to electric field vibrations in one direction than it does inresponse to those which are perpendicular to the first direction. The two perpendicular polarizations

of light have, in general, different indices of refraction within the material.

The next effect of this phenomenon is that birefringent materials are characterized by their ability torotate the angle of polarization of the light that goes through them. Biological examples of 

 birefringent materials are tissues that have fibril structures such as collagen (a triple helix) and the

actin-myosin structure of muscle fibers. 

Thermally-induced partial and complete loss of native birefringence in muscle and collage are

objective histologic markers of thermal damage. The birefringence of muscle is due to the regular,crystalline-like array of actin and myosin molecules within the sarcomere of striated muscle and thelongitudinal fascicles of the same contractile proteins in the cytoplasm of smooth muscle cells. Loss

of birefringence in striated muscle is due to the destruction of the regular relationship of the

contractile proteins of the sarcomere by thermal denaturization of the contractile proteins. The birefringence in collagen is related to the regular arrangement of molecules forming the collagen

fibrils. Thermally damaged collagen reveal unraveling of collagen fibrils with loss of the unique

striations of collagen and an increase in fibrillar diameters.