Photons at the microbe scale... Curious Questions and Comments

I've studied light extensively, in college physics some but more on my own as a hobby. The more I've studied, the more questions arise. I have a cousin who majored in physics; I asked one of these questions to, and he couldn't answer it (although cleverly dodged it). Some may be considered noobish, but hey, I'm a bio major, I've altered the genetics of bacteria to make them glow and many other crazy stuff lol.

That was: is there a way to measure the amplitude as distance? I gave up on trying to find an answer years back, the more I learned about the strange quantum behavior and how it is not a wave nor particle; it is both with some additional mysteries (yep makes sense huh). I had wondered, since there is a distance in between the waves, what about the distances of "up/down" of the electric and the "side-to-side" of the magnetic portions.

I have a more practical question lately, related to an upcoming project. The blunt question is, Can a virus be destroyed by high energy light in which the wavelength is ~10 times larger than it? My answer would be, perhaps by the surrounding media heating rapidly, but...

I'm confused about how wavelength relates to absorption; the resolution of (reflected light in) a microscope is around the wavelength of the light (something makes me want to say half but can't remember specifics). I Does that mean an object the size of a virus is immune to being struck by light we see?

I'm inclined to say, No, it doesn't matter how small the object is; afterall, absorption is the whole photon 'disappearing' into a single electron and giving it higher energy; single molecules have absorbance values,( making a photospectrometer a very useful tool for enzyme- and more specifically- concentration measurements). But then considering this fact, I wonder why there is a limit of resolution. Absorbance must be significantly different than reflection, although it appears to be just a reversible process (absorbance of photon going in looks like reflection in rewind) In an attempt to answer my own question, I'd state that a virus absorbs and reflects some light, but since the wavelength is larger than it, resolution *somehow* is limited.

A random question, do protons absorb photons, or in some condition can they emit them?, Protons do interact electromagnetically but moreso with the stong nuclear force. Protons are constantly operating on (emitting and receiving) countless virtual photons. Maybe not photon emitting, because they have no energy level to jump to, so they ignore "real" photons, unless an incoming photon has a high enough wavelength to precisely strike it and bounce back (as with Rutherford's gold foil resulting in discovery of nucleus). Perhaps they are too engulfed in gluon (SNForce) interactions for photons to be produced. Maybe protons by themselves, through some kind of magnetic deceleration would produce light. (I could go into questions/musings about protons and relation to electricity but that is another topic completely.)

I guess the electron cloud as a whole is the photon target; would it make sense for the photons to be striking a practically size-less electron by itself with its comparatively huge "size"... well I was taught they do in fact strike them directly... I have to realize they are particles too, (related: Einstein's Nobel-prize winning Photoelectric Effect discovery

Maybe I'm thinking too classically (wavey), and as large particles they just run into electrons. Well I'm going to stop before I wear- myself and loyal readers who made it this far,- out.

As you can probably tell, I don't have friends to talk to about this; although one is interested in physics stuff he behaves as if what I'm talking about is over his head, perhaps due to lack of background. I do try to dumb it down, and even did here some for simplicity (and as a side effect, be more noob-friendly mainly for those who came here via google search; i.e. how I found this site.)

I hope I made some sense and raised legit questions. Perhaps later when less sleep deprived I'll clean it up.

I'm confident modern physicists have proper answers to these questions already; hopefully not just in long equations... As Einstein said, If you can't explain it to your grandpa, you don't truly understand it

I am NOT a physicist or a professional scientist, although I am a somewhat avid amateur scientist. I tend to approach questions like this with thought experiments and analogies.

(When I was abut 8 years old, I discovered the theory of relativity (I realized many years later) on my own, with a thought experiment involving an immortal, never-sleeping alien traveling at the speed of light towards Earth from millions of light-years away, looking at earth through an infinitely powerful telescope without interruption).

Anyway, here's a thought experiment and an analogy, for whatever pitiful value they might have.

Imagine that you have a macroscopic surface that is 100% coated with viruses. Not only is it 100% coated in two dimensions, but the coating is billions of viruses deep (a few inches, let's say).

If you shine a high power laser on to that surface, then either the virus layer is perfectly transparent; or it is perfectly reflective; or, some viruses in the layer will absorb the energy of some photons.

A related analogy is solar cells. I believe that the conversion of light to electricity happens on the molecular level. I would bet that those molecules are smaller than viruses. But they absorb photons and produce electricity when the reaction has run it's course.

I remember one of the Feynman lectures available online includes a (somewhat) related description of reflection, perhaps what you are suggesting, Shadowspawn. Dr. Feynman (my favorite physicist) says something to the affect of: this is how it works, and I invented the theory, but don't ask me how it works. I have no idea

It involved layering, and that some layers could reflect better if at a certain thickness, which could be calculated using a strange circular mathematical diagram. Yeah, light is quite strange. Dr. Feynman was a founder of QED; but I wonder if they have moved on to actually understanding IT beyond just mathematics/calculation tools. Whatever light really is, and how it "chooses" to reflect is very strange and mysterious enough... then throw in some entanglement and it gets even more fun

Time relative to the light is always 0; i.e. if one were to ride on a light beam, the edge of the universe would be reached instantaneously (and likely beyond into infinity). Instant infinity... how's that for a mindtrip. I'm enjoying it. This is Einstein's idea, and involves time dilation (confirmed). Although a person could never move at light speed, as their mass would be infinite and they'd be length contracted into some 2-D line. But 99.99 or beyond could be possible... who knows. At a constant 1G acceleration, like a spacecraft mimicking earth's gravity, one could make it to the edge of the universe (I think 46 billion L-years) in a lifetime, thanks to the mysterious time dilation.

I hope I haven't knocked my own topic off topic... I still want answers!!!

Alhough, after some thought and a 30sec skim of the wikipedia article on the optical microscope, I think that we can assume, for microbe destroying, that photons are very small particles and the reason we can't see down to more than half the wavelength is due to diffraction and the 'waves' "spreading out" basically. And yes, this is probably such a basic explaination that it could be scrutinized to be false on a true scientific scale, although since I'm more interested in killing microbes and not as much in the microscope, I'll accept this explaination.

The photons only transfer a minimal amount of momentum (strange, the classic equation requires mass and a zero mass in the equation would set it to Zero by default since it is multiplying by zero. But that is why classical physics is the wrong way to go in the fascinating atomic world. Classical physics are fine to get a ship into space but don't consider it proper for light, heh. I don't really consider Einstein's relativity as classical btw. My professors called Newton, and even Faraday/Maxwell classic, but not Einstein, so I keep that terminology. Maxwell's equations are quite brilliant and elegant though, and work fine if light is only a wave (which it can be considered as at wavelengths longer than light, usually).

So back to the microbes, the momentum doesn't do the damage, it is the absorbance which produces heat, and in the case of Near-UV, destructive ionization, i.e. stripping electrons off and causing chemical reactions to the molecules, most likely its outer shell/cell wall/cell membrane depending on the creature. I hope 405 and 445 can show some ionization, but kind of doubt it. Maybe one of the common laser wavelengths is very good at absorption on certain organisms and they can easily be fried

***Just did some searching on E. coli absorbance values (which are used to count # of bacteria usually), looks like 600nm is the magic number for what light they absorb, and in my case, what they get their asses kicked by. Hopefully, 635nm isn't too far from the peak.

I also found a pubmed abstract which used a CO2 laser @ 5W & 20 seconds, i assume in the far infrared,, which blasted 5 micron in size salivary samples and bacteria preps, which did not succeed when dry, but did when wet. They are indeed tough, but perhaps they were like mirrors to the wavelengths; or glass... the heated water is likely what killed them.

Here is a patent for a medical laser which operates at 480nm pulsed+Q-switched, argon and also has a UV between 210-360nm. I only skimmed but got the impression it hasn't been built yet.

I'll start by responding to your first post.

I'm only a third year physics major, so I'll do my best to explain what I know.

You present excellent questions, which I too have asked before.

Amplitude of can be described in a few ways, in terms of the classical light wave.

I'm sure you're aware that a light wave, has two components, the electric field and the magnetic field. They induce each other according to faraday's law. They are mutually existent upon each other. One cannot exist without the other if they are to propagate through some medium. Each component carries the same amount of energy as the other, but that doesn't always matter because of this next paragraph.

Now, as for amplitude. Most measurements of light are based on instruments that are sensitive to the electric component of the wave. This is because most materials are more respondent to a changing electric field, rather than a changing magnetic field.
Only recently, have materials been found that respond as strongly to the magnetic component.

If I have a 100W light bulb, I can stand some distance away from it and determine the intensity of the light reaching my eyes. The measurement would be in W/m^2. I will have to run and grab my physics book to find the equation but you CAN relate Intensity (W/m^2) to the magnitude of the electric field at that same distance. Units of the electric field are in Newtons of Force/ Coulomb of charge. But this is irrelevant as the units can also be described as Volts/Meter.

EDIT: Found that equation

I = (1/cu0)*E-rms-^2

Where u0 = Mu sub not and E-rms = E peak * .707

So if you picture the electric field as a changing vector, like a

------------>.

You can figure that such a field can apply a force to a charge (N/C), only because of the voltage that exists from the tail of the vector, to the head of the vector. The potential lines are always perpendicular to the electric field, so really there is a "voltage" that exists in midair along an electric field line, for every unit of length along that vector.

That is your amplitude. Volts per meter. So as an example, an electric field from a light wave which is some distance away, might reach my eye with 3.573E-4 N/C or 3.573E-4 Volts per meter. Now there really aren't many situations where you can pull out your ruler and say that the potential of the electric field line starts here and ends there resulting in an amplitude of X.

You simply know that overall, this light wave has an amplitude of the electric field A, because of the the beam's intensity I, at some distance d^2 from the point source of light of radiating power P.

Now, that's the electric field. I mentioned how the electric field is usually easier to interact with and measure. Just because of this, we can also determine amplitude of the magnetic field. The magnitude of the electric and magnetic field are related by a ratio of c, the speed of light.

c = E/M

If you simplify the units, you actually get

meters/second = (volts/meter) / (Tesla)

So while the the magnetic field is smaller than the electric field by an order of c, you cannot forget that the magnetic field stores just as much energy as the electric field. It's many time harder to interact with as it's magnitude is smaller, but its indeed there and just as important as the electric field.

As far as radiation absorption goes. It is very dependent on of course molecular structure and molecular components and bonds and other chemistry things I'm not so familiar with.

I'm not at all familiar with microscopy, but I do know two things. Ever heard of radio frequency burn? If you choose to stand next to an AM broadcast antennae, you can come out with some serious burns, even though the waves are much larger than you.

I also know that just about any wavelength is always both absorbed and reflected to some extent. Nothing is completely absorbed without also a very small amount of energy being reflected. So just don't forget that if you have enough power, even a visible light beam can punch through a mirror!

As for protons absorbing EM waves. Just remember this:

EVERY electromagnetic wave is the result of the acceleration (change in speed) of a charge.

Remember the units of the electric field? The force on a charge is equal to the magnitude of the charge times the magnitude of the electric field.

F=qE

This force (naturally) causes an acceleration on the charge. So just the same, if you accelerate a charge quickly enough, you will create an electric field with some wavelength, and magnitude of E.

So, find some way to hold and wiggle a proton, it will emit an EM wave. It just depends on the magnitude of the acceleration you give it, and the distance it goes through.

I hope I have answered some of your questions anyways. Next time, ask only a few at a time!

@ meatball, great post, I'm sure this offers some great information :beer:

@hoon:
I can't say I'm an expert in the field, but I am a physics major, I will be starting my second year this fall, though I have some 65 ish credit hours from summer classes/AP ect, and I've taken some intro quantum mechanics courses. Maybe I can offer a bit more advice, or at least steer you in the right direction, it seems like you have a lot of good questions, and you would just like to understand more about the nature of light.

Light is a strange, thing, and I think you got that part, describing it is a very difficult thing for creatures like us that live in the macroscopic world. A massless particle that is tiny, but also carries momentum and travels faster than anything else in the universe with an infinite lorentz factor is just astounding. I'm not sure what you know and what you don't know, so I'll preface any and all of my explanations with I'm sorry for repeating things you may have heard already.

The scaling factor you refered to when talking about time dialation and spacial contraction is called a lorentz factor, it is denoted with a gamma and calculated with gamma=1/(1-v^2/c^2)^1/2 where v is the observed velocity of an object and c is the speed of light. In the case of light, v is c and thus the factor approaches infinity, so in lights reference frame, it does exist at all points in space along it's path of travel, at the same time, crazy stuff. That's the relativistic side of things, but I think your questions seem to deal with the quantum nature of light, so I'll elaborate a bit more on that, from my own limited knowledge.

The quantum world is also very strange, Einstien famously described it as spooky, I believe in direct reference to the double slit experiment, when photons were shot through the slits one at a time, and they still created an interference pattern. Anyway, I don't know a terrible amount about amplitudes of light, but I remember only briefly talking about them in quantum mechanics class. Essentially the amplitude is a facet of the wave behavior of light that is simply not terribly useful in the quantum world. For our purposes, the most important things we can talk about are the momentum and the energy. These two quantities are concisely described for all particles in what is called the quantum wave function. A commonly used form of the quantum wave function for a free particle is the complex exponential, exp(ikx-wt) where i=(-1)^1/2 k=wave number=2pi/wavelength and w=omega=angular frequency= 2pi*f. This function gives us the two most important peices of information, the momentum (in the wave number term) and the energy (in the omega term). Also note that there is an i, which is an imaginary number, this is a peculiar quirk of mathematics, it turns out we can express typical wave functions (sines and cosines) with a complex exponential (e^ikx).

Needless to say, I don't think the amplitude has a lot to do with your question of absorbing a photon. Typically when a photon is absorbed, it is the electron that does the absorbing, not the proton (there could be cases when that happens though, but I am unfamiliar with them) The photon will be absorbed by a sample if and only if the energy of the photon corresponds to the difference in energy between a rest state and an excited state of an electron. These energy levels are finite, and are steplike in nature, that is, there are discrete allowable energy levels for electrons orbiting a nucleus. This does seem odd, but what it boils down to is the uncertainty principle. Electrons have both position and momentum when orbiting the nucleus. The uncertainty in measuring either of these two quantities on the quantum scale is (uncertainty in momentum)*(uncertainty in position) = hbar/2 where hbar is planck's constant/2pi Therefore, if we know little about the momentum of the electron, we know it's position with a fair degree of accuracy. Going beyond this gets messy, as we get into what is known as spherical harmonics. We must use spherical harmonics to predict the locations of electrons in a material, because like all other quantum particles, electrons are also waves. When you sing in a confined reflective room, there are certain pitches that resonate more strongly, go try singing different pitches in the shower, it works. This is because the reflected sound have overlaps perfectly with the incident wave, and the note sounds louder to you. The same thing happens with electron waves, except, we are now doing the math in three dimensional space, not two. The end result of this: electrons are only allowed to orbit at discrete radial distances, and thus have discrete energy levels, and thus only absorb certain wavelengths of light.

As for why or how the absorbing happens, we will go back to the wave interpretation. Absorbsion occurs when a wave (like light) is incident on a new medium. To create a simple real world analogy, lets use waves you create on a string by shaking one end, and watching the resulting bulge ride down the string. For a change in medium, let us imagine that the string is not uniform in thickness, but suddenly changes. Lets say we have one thin string and one thick, and we glue them together. When we shook the thin string alone, the wave traveled all the way down the string, but now we have attached a thicker string, therefore, the wave must travel into a thicker medium. When the wave reaches the thicker string, one of two things will happen, either 1) the wave will continue to move through the medium, but it's speed will be lower, by altering it's wavelength or frequency (v=wavelength* frequency, but v is independent of lambda or f, it is dependent only on the medium the wave travels through) or 2) the wave will be reflected if the thick rope is too thick, and the incident wave isn't strong enough to move the big rope. The quantum analogue to this is quite similar, when light (a wave) is incident on a surface, it must do one of two things: 1) be absorbed or 2) be reflected. There is also barrier penetration to talk about, but for purpose of focus, we will not get into that. Whether light is absorbed or reflected has to do with what the difference in potential energies between the mediums are. The real world analogue to this is, what is the difference in rope thickness? if the second rope is too thick the potential energy well in that area is too great for the wave to change mediums, and it is thus reflected.

I hope this helps you somewhat, light is a tricky beast, and even those who spend their entire lives trying to understand it can be puzzled sometimes. To truly understand it requires quantum mechanics and relativity, and a bit of imagination too.

hoon said:

I have a more practical question lately, related to an upcoming project. The blunt question is, Can a virus be destroyed by high energy light in which the wavelength is ~10 times larger than it?

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I think the essence of that question would be 'can something much smaller than the wavelength absorb light?

One straight and simple answer to this question woud be 'yes!'. If you look at materials that absorb light, you can consider a solution of a dye. This obviously does absorb light, despite the wavelength of that light being a few orders of magnitude larger than the size of a singe dye molecule.

It's the electrons doing the work here, never the nucleus. Surely an atomic nucleus can absorb photons as well, but those would have to be several orders of magnitude more energetic than visible light (think gamma radiation).

My absorption question(s) and the answers to them seem a bit obvious now, especially after the great posts above, which were a nice mix of review/reminders for me as well as a few new points I never have read about, such as amplitude being a force, which makes more sense why it can't be measured as a distance ("the photon is 532nm in wavelength and 2nm high by 2nm wide by 5m length")--- which is what I was hoping for; and maybe someday it can be done, but light seems too complicated for spacial dimensions.

I can see how its all confusing. One of the things that make it difficult to discuss that 4 terms are used for the exact same thing: wavelength, frequency, energy and mass. If you know one of the these, you can calculate the other three, and that caculation is the same for ALL photons: from radio waves to visible light to gamma radiation.

The energy aspect of it can be especially confusing since this works totally different from sound: In sound, the waves actually become stronger in amplitude with increasing loudness. With light, the only thing that changes when you increase the amount of power is the -number- of photons (per second).

@hoon: the quotes are roughly int he right order.

Maxwell's equations are quite brilliant and elegant though, and work fine if light is only a wave (which it can be considered as at wavelengths longer than light, usually).

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It can also describe how light behaves around subwavelength structures, it fails when the quantummechanical effect are important, such as the quantized nature of light or describing the effect behind absorbtion (absorbtion itself can also be described classically, the energy level things cannot).

is there a way to measure the amplitude (of light) as distance?

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No. The volts/meter unit has been mentioned, but that's the potential, not teh amplitude. The amplitude of light is the field strength, has no spatial meaning. The fancy arrows or wave that seem to indicate it has a tranversal spatial extent are just to illustrate the amplitude or field strength is higher, not "larger". A higher intensity light beam has a higher amplitude but the same spatial extent.
The amplitude describes the peak value of the electric field. The E field has a direction (the polarisation in this case) and a magnitude. These can vary spatially, but are not spatial properties.
Looking at light as photons the amplitude is the amount of photons present in a certain space. Photons are bosons, so they can stack perfectly. A higher amplitude means more photons, but the photons won't get bigger. The photon explanation is only usefull when the intensity is very low and the number of photons is important, or if quantummechanical processes are important and the particle nature of light is needed. Things like absorbtion can be explained both classically and quantummechanically. If you don't need the effect unique to quantummechanics the classical explanation is much simpeler.

Can a virus be destroyed by high energy light in which the wavelength is ~10 times larger than it?

I Does that mean an object the size of a virus is immune to being struck by light we see?

No, it doesn't matter how small the object is; afterall, absorption is the whole photon 'disappearing' into a single electron and giving it higher energy

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A virus is like other materials, it will absorb a certain spectrum. If the wavelength is 10x larger the absorbtion won't be very effective. It's like a giant wave on the ocean trying to push a swimmer in it, it won't be very efficient. A virus 10x smaller then the wavelength of the light won't be pushed very hard by the electric field, it's cross-section is so small it will only absorb a small part of the incident E field.
The same way you could most photons will miss the virus, but some will hit the virus and be absorbed. This can be by raising an electron to a higher energy level or the coupling to a vibration/rotation of the molecule, depending on the wavelength.

But then considering this fact, I wonder why there is a limit of resolution.

that photons are very small particles and the reason we can't see down to more than half the wavelength is due to diffraction and the 'waves' "spreading out" basically.

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This is the spatial extent of light. The spatial size is limited by diffraction, a wave effect that limits the spatial shapes light can make because of the large wavelength. How can you squeeze light into shapes if the waves don't even fit in there?
Photons have a finite size, this is gives by the uncertainty relation. The shorter it's spatial extent (a better defined position), the larger it's spectrum (the energy uncertainty). CW light and ultrashort pulses are the extremes in this situation.

Absorbance must be significantly different than reflection, although it appears to be just a reversible process (absorbance of photon going in looks like reflection in rewind)

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Absortion reversed it spontaneous emission, reflection reversed is reflection.
In the first case a photon comes in or flies out and that's it, case of reflection there's both a photon coming in and getting out.

do protons absorb photons, or in some condition can they emit them?

Maybe protons by themselves, through some kind of magnetic deceleration would produce light.

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Protons can absorb photons, but you'd have to have short wavelengths/high energies before the proton absorbs it, otherwise it will just scatter (reflect). Electrons in a circular accelerator emit photons, this happens in a synchrotron or cyclotron because they move through a magnetic field. Proton also do it, but very very litte. That why the LHC uses protons, they don't lose much energy by emitting photons.

I guess the electron cloud as a whole is the photon target;

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It often is, at lower energies it may be the vibration of a molecule, at higher energies it may be the proton.

ould it make sense for the photons to be striking a practically size-less electron by itself with its comparatively huge "size"...

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Clasically it's a E field which interacts with a pointlike particle, quantummechanically the electron is just a wavefunction, having a spatial extent just as the photon has.

I wonder if they have moved on to actually understanding it

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The way I see it science just describes nature, it's "explaining" is just describing an observed causal relation. Why things happen a certain way is a question for God. We scientist just try to get used to the math describing a causal relation. Newton described gravity because he saw an apple falling, but why that stupid apple should fall is a completey different question.

it is the absorbance which produces heat, and in the case of Near-UV, destructive ionization, i.e. stripping electrons off and causing chemical reactions to the molecules, most likely its outer shell/cell wall/cell membrane depending on the creature.

I hope 405 and 445 can show some ionization, but kind of doubt it.

Maybe one of the common laser wavelengths is very good at absorption on certain organisms and they can easily be fried

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Absorbtion doesn't necessarily mean the light is converted to heat, for example flourescence. 405nm and 445nm probably won't ionise, try a nitrogen laser for that or a tripled yag. Excimer lasers probably work better, those are used in eye surgery to vaporise tissue. they laser deeper in the UV.

I also found a pubmed abstract which used a CO2 laser @ 5W & 20 seconds, i assume in the far infrared,, which blasted 5 micron in size salivary samples and bacteria preps, which did not succeed when dry, but did when wet. They are indeed tough, but perhaps they were like mirrors to the wavelengths; or glass... the heated water is likely what killed them.

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It indeed looks like the water absorbed the light from the CO2 laser and "cooked" the bacteria.

hoon said:

***Just did some searching on E. coli absorbance values (which are used to count # of bacteria usually), looks like 600nm is the magic number for what light they absorb, and in my case, what they get their asses kicked by. Hopefully, 635nm isn't too far from the peak.

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Why not get a concentrated E.coli sample and run a UV-Vis spectrum on them?

I wonder if that wouldn't scatter the light rather than absorb it. To a spectrometer only light that goes straight trough is measured, so it wouldnt matter much if you tried to measure, for example, a cuvet full of ink or milk.

That said, i'm sure 635 or 660 willl opticute bacteria if the power is sufficient. Even 1064 nm does if the intensity is too high (often its an undesired effect when holding a cell in optical tweezers).

Excellent post Bluefan; you definitely cleared the subject up for me quite a bit.

Very interesting subject; I'll post more when I can think clearer.