TEM Image formation and periodic assemblies

Question 1

Advantages and disadvantages of negative staining

Answer 1

Advantages of negative stain:
* Dry specimen
* Radiation resistance
* High contrast
Disadvantages of negative stain:
* Dry specimen (artefacts)
* No information on internal structure
* Resolution limited by grain size
Resolution limited to > 20 Å

Question 2

The main strategy in imaging for improving noise

Answer 2

averaging multiple images

Question 4

how does SNR scale with increasing number of images acquired

Answer 4

sqrt(N) = N(number of images) / sqrt(N) (variance)

Question 5

the two main processes that deform TEM image quality

Answer 5

noise and modulation

Question 6

What is contrast?

Answer 6

Contrast is the difference in intensity between the object and background

Question 7

what is the highest frequency represented on a fourier pattern, what is the frequency at the edge?

Answer 7

the nyquist freq

Question 8

difference between direct electron diffraction and optical diffraction

Question 9

what information does electron and optical diffraction patterns provide

Answer 9

electron diffraction patterns provide very high quality frquency information because the signal is not modulated by CTF as there are no lenses used. However, phase information is lost. Optical diffraction imaging on the ohter hand has poor quality frequency information but high quality phase information.

Question 10

What are the defining parameters of helical assemblies

Answer 10

You can describe them in two different ways:
- rise translation distance between two neighbouring monomers
- rotational transformation distance between two monomers

or

-pitch translational distance aka distance of one helical turn
-number of monomers in one helical turn

Question 11

The defining feature of helical assemblies diffraction pattern

Answer 11

Cross shape. This is because both the front and backside of the helix are being imaged resulting in an overlay of the two as if there are two mirroring 2D crystal structures. Because of the curvature of the structure there is also a significant smear of the higher frequencies along the x axis.

Question 12

how can you determine the pitch of a helical structure from diffraction pattern

Answer 12

the vertical distance between spots corresponds to the inverse of the pitch. This bigger distance would signify lower pitch.

Question 13

how can you determine the width of a helix from diffraction pattern

Answer 13

from the angle of the X. Lower angle signifies a higher width of the helix.

Question 14

2D Lattices and Helical Assemblies