3 ms·

So at what point do we hit the Uncertainty Principle of disturbing atoms so strongly that we're no longer sure of their velocity or position?

jdmichal 6y ago
Do you mean the uncertainty principle or the observer effect? From Wikipedia: https://en.wikipedia.org/wiki/Uncertainty_principle https://en.wikipedia.org/wiki/Uncertainty_principle > In quantum mechanics, the uncertainty principle (also known as Heisenberg's uncertainty principle) is any of a variety of mathematical inequalities asserting a fundamental limit to the precision with which the values for certain pairs of physical quantities of a particle ... can be predicted from initial conditions. > Historically, the uncertainty principle has been confused with a related effect in physics, called the observer effect, which notes that measurements of certain systems cannot be made without affecting the system, that is, without changing something in a system. The former just means that the more precisely we know the location, the less precisely we can predict the momentum given the initial information of the system. It has nothing to do with "disturbing the atoms"; as Wikipedia explains it's a property of wave-like systems. https://en.wikipedia.org/wiki/Observer_effect_(physics) https://en.wikipedia.org/wiki/Observer_effect_(physics) On the other hand, the observer effect simply says that measurements involve active processes and those can effect the system. But it has nothing to do with velocity or position per se, just the fact that measurements can have effects.
tgbugs 6y ago
UP doesn't really apply here. The data the underlies the reconstructions requires massive averaging of individual objects as part of the tomography (see Radon transform for the core approach). In addition those objects/particles need to have the requisite symmetry/similarity/regularity in structure (not universally applicable), or the population of them needs to be completely homogeneous (hard to achieve). I suspect that there are now better techniques for detecting outliers so homogeneity might not be as important.
bodhiandpysics1 6y ago
So in some sense that's what this is all about. The resolution of an electron microsocope is dependant on the energy of the electron, but higher energy electrons rip your sample apart. The trick that cryo-em does is to stiffen the structure of the protein by embedding it in a glass matrix (the glass is actually just really cold water that is prevented from freezing). Since the protein is stiff, you can use higher energy electrons, and thus get a higher resolution.
- cinquemb 6y ago
  Are things besides water used? Like a vacuum or something else? Would the stiffness be dependent on the energy density gradient between what it is embedded in? The technique reminds of those i've seen in sparse eigen decomposition of a matrix, where some non square matrix X is embedded in a larger sparse matrix of zeros of the form: ⎡ zeros(X.n_rows, X.n_rows) X ⎤ ⎣ X.t() zeros(X.n_cols, X.n_cols) ⎦ Except for in this case the larger matrix of zeros would be replaced by a repeated structure. Though I can't help but think that using non zeros would get some weird energy feedbacks (due to the interaction of the protein with the embedding matrix molecules) that would require some renormalizations.

jdmichal 6y ago

Do you mean the uncertainty principle or the observer effect? From Wikipedia: https://en.wikipedia.org/wiki/Uncertainty_principle https://en.wikipedia.org/wiki/Uncertainty_principle > In quantum mechanics, the uncertainty principle (also known as Heisenberg's uncertainty principle) is any of a variety of mathematical inequalities asserting a fundamental limit to the precision with which the values for certain pairs of physical quantities of a particle ... can be predicted from initial conditions. > Historically, the uncertainty principle has been confused with a related effect in physics, called the observer effect, which notes that measurements of certain systems cannot be made without affecting the system, that is, without changing something in a system. The former just means that the more precisely we know the location, the less precisely we can predict the momentum given the initial information of the system. It has nothing to do with "disturbing the atoms"; as Wikipedia explains it's a property of wave-like systems. https://en.wikipedia.org/wiki/Observer_effect_(physics) https://en.wikipedia.org/wiki/Observer_effect_(physics) On the other hand, the observer effect simply says that measurements involve active processes and those can effect the system. But it has nothing to do with velocity or position per se, just the fact that measurements can have effects.

tgbugs 6y ago

UP doesn't really apply here. The data the underlies the reconstructions requires massive averaging of individual objects as part of the tomography (see Radon transform for the core approach). In addition those objects/particles need to have the requisite symmetry/similarity/regularity in structure (not universally applicable), or the population of them needs to be completely homogeneous (hard to achieve). I suspect that there are now better techniques for detecting outliers so homogeneity might not be as important.

bodhiandpysics1 6y ago

So in some sense that's what this is all about. The resolution of an electron microsocope is dependant on the energy of the electron, but higher energy electrons rip your sample apart. The trick that cryo-em does is to stiffen the structure of the protein by embedding it in a glass matrix (the glass is actually just really cold water that is prevented from freezing). Since the protein is stiff, you can use higher energy electrons, and thus get a higher resolution.

cinquemb 6y ago
Are things besides water used? Like a vacuum or something else? Would the stiffness be dependent on the energy density gradient between what it is embedded in? The technique reminds of those i've seen in sparse eigen decomposition of a matrix, where some non square matrix X is embedded in a larger sparse matrix of zeros of the form: ⎡ zeros(X.n_rows, X.n_rows) X ⎤ ⎣ X.t() zeros(X.n_cols, X.n_cols) ⎦ Except for in this case the larger matrix of zeros would be replaced by a repeated structure. Though I can't help but think that using non zeros would get some weird energy feedbacks (due to the interaction of the protein with the embedding matrix molecules) that would require some renormalizations.