4 Electrophoresis

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4 Electrophoresis
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30 (Lecture 2 missing)
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Lecture 4 - electrophoresis. George Phillies lectures on polymer dynamics based on his book "Phenomenology of Polymer Solution Dynamics" (Cambridge University Press, 2011).
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Bird vocalization Coating Hot working Colorfulness Autumn Bahnelement Stock (firearms) Year Vise FACTS (newspaper) Kette <Zugmittel>
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Volatility (chemistry) Sunlight Short circuit Year Crystal structure Aircraft carrier Cosmic distance ladder Dyeing Mitsubishi A6M Zero Kette <Zugmittel> Separation process Roll forming Orbital period Leistungsanpassung Telephone Ballpoint pen Stock (firearms) Molekülmasse Single (music) Gas Concentrator Angle of attack Sizing Weight Autumn Literary fragment Theodolite Noise figure
Matrix (printing) Quality (business) Day Measurement Absorbance Ring strain Kette <Zugmittel> Separation process Clock Low-pressure area Orbital period Television set Video Leistungsanpassung Atmosphere of Earth Lifting hook Sensor Ground station Single (music) Train Paper Microscope FACTS (newspaper) Concentrator Finger protocol Direct current Autumn Laser Voltaic pile Friction Noise figure
Matrix (printing) Hot working Grey Effects unit Transmission line Day Coulomb's law Year Measurement Force Light Kette <Zugmittel> Sharpening Separation process Roll forming Volumetric flow rate Limiter Low-pressure area Orbital period New Year Spare part Electromigration Water vapor Linear motor Transmission tower Space probe Molekülmasse Ground station Power (physics) Gas FACTS (newspaper) Cogeneration Concentrator Black hole Sizing Direct current Cartridge (firearms) Remote control Fahrgeschwindigkeit Theodolite Pager RRS Discovery Noise figure Wire Acoustic membrane Holzfaserplatte Model building
Matrix (printing) Weapon Theory of relativity Prozessleittechnik Observational error Effects unit Unmanned aerial vehicle Geokorona Scouting Light Kette <Zugmittel> Particle Bird vocalization Separation process Continuum mechanics Fender (vehicle) Drill bit Magnetic moment Linear motor Water vapor Cantina Ferrari Progressive lens Mechanic Space probe Molekülmasse Display device Black Season Power (physics) Paper FACTS (newspaper) Quantum fluctuation Buckelschweißen Monday Direct current Series and parallel circuits Autumn Cartridge (firearms) Fahrgeschwindigkeit Mode of transport Measurement Book design Noise figure Ruler Alternator Hot working Diffusion Grey Transmission line Nuclear submarine Measurement Year Force Green politics Electric beacon Viscosity Cell (biology) Weather front Field-effect transistor Wasserwiderstand Bahnelement Ship class Wednesday Spare part Video Leistungsanpassung Wind farm Electric charge Material Star Typesetting Array data structure home office Stock (firearms) Digital electronics Field strength Buick Century Car seat Bending (metalworking) Weak interaction Bridge (nautical) Cogeneration Concentrator Black hole Sizing Hour Pager Theodolite Trade wind Model building Week Last
classes in polymer dynamic based on
George Phillies book phenomenology of polymer solution dynamics Cambridge University Press 2011
ends today this lecture E is
lecture for electrophoresis
I'm professor Phil is this is 597 the phenomenology of polymer solution that's what I'll be doing today is to discuss the the way for a reason but in the lecture yesterday we discussed a charged particle and solutions and the electrical forces that actually act on a list that is slightly longer than you might fall from a From a naive treatment of electors in particular at I think we have here is charged particle the obvious for you the direct costs on charges itself but that's only a moderate form of the total the particles charged that the solution has counter the ions of candidates from July and was going to be subject to electrical force in the opposite direction because they have opposite charge and because they're being dragged the opposite direction 2 things that 1st of all the founder of filed around this is distorted so that more negative charge here and there and that creates a direct electrical was on this charge Saturday these ions are all moving they create awakens solution a hydrodynamic forces and that also acts on the streets To make life even more interesting someplace out here the walls of the veins and the walls of container will be technically be charged positively or negatively not always and the walls the positive charges on they have charges because they have counter ions in solutions the counter ions right wall or subject to the same electrical forces these some off that way and if there is a lot of each Walter the floated between is obliged to along and that's the usual lotions hydrodynamic boundary conditions namely and wall you typically have called state boundary conditions and is the velocity of the flu Apple is the same as the velocity of the ball here however we can the things that functions as a wall the are movement with respect to the glass and the flow would seize the islands and floats along with the ions of the wall now you might ask how can we show but this effect and that affect the manufacturer and there you could do a series of different experiments which is very separately however warned of these effects it's for example if you're interested in the behavior of the ions in the wall if you didn't believe might find this electoral laws might affect exists the two-way exchange 1 is to take some molecule but stakes to the wall and changes the walls charge for example you could put down on the wall so molecule is negatively charged reversed the charge on the wall that means the camera homes and outgoing positive come around to hopeful that way and the direction of the electoral osmotic flow is is reversed furthermore if you said she was defined attached to the wall hold of parliament seeks to the wall part and stays out solution for so long distance also In that case the are surrounded by polymers and while they tried to move the momentum they don't the full of is granted off by polymers and his staff directly into the wall as far as someone here is concerned writing policies although most people there is no longer any driving flow to drive electoral laws most and therefore by
moderating by changing what you do wall coating you can change the electoral laws osmotic flow this turns out to be an extremely important issue in engineering technical engineering aspects of doing separation of DNA you can change this flow and therefore increase enormously in improving the efficiency of a column this is basically a plastic to very small then narrow asking who would receive this weakening enormously changed the efficiency of call by being the clever you can also change the charge radius of probe you can change the amount of salt you put into solution which has effects on this boundary layer local and there and therefore the of experiments you can do to confirm that this picture which I greatly oversimplified artist is basically correct so that is a picture both the forces acting in electrophoresis now on last lecture which video will go probably today there is a technical issue I have to do multiple video conversions and even with a very fast computer we're talking about hours of computer time to get video from a pretty camera up on you too are however we talked about models and we talked about how you calculate electrophoresis after said but many of the picture I gave shows 3 sources of physical models for how you describe the church object moving through Paul Merson the charge object could be a sphere where it would be a polymer itself and oneself conclusions based on and to limit treatments in the matter of the match the crisscrossed and warm movement changes interest charges somehow have to find holes in this transient mesh through which it would advance a 2nd set of models were hydrodynamic models there are several classes of hydrodynamic models but the major issues that make all the object of sphere of interest for the display and neighboring Poland changed life he is translated and from and therefore interior chain link through I'm being very imprecise and details of how they translate wrote I also noted last Friday called followers to obstruction models are actually very similar to these however Hoxton talk more about spheres movements years and polymer oils are also the artist model treats the instructions just sitting there permanently and this model makes the entanglement models models make allowance for the fact that he's crisscrossed always chains are also overs they also perform diffusion and there were misled lattice Paul McShane's is Francie it comes and goes and solves the Austin obstruction models made a fairly specific prediction for how the Paul matrix effects the electorate for editor of mobility namely there isn't effect the minus concentration of the matrix 1st power radius that's a little more complicated than sounds of the moving object that the 2nd power and molecular weight of matrix 0 why is radius more complicated than it sounds as well as over this picture which is already set up these polymers strings they are not they are objects of physical radius but there is long polymers we say that this fall Austria obstructs the motion of the year if the sphere Christ moved through the stretch the distance the Council is the song while the radius from the CIA itself and some sort of radius of a polymer strands as the center's Saturdays and includes both of the thickness and so this is a center center distance if the probe is decently large it's much bigger than the thickness of a polymer strands and this is approximately probe size square but has imprecise and if you make the the pros small you actually think about this here the end the 0 is the requirement of polymer strands are very long relative to the space the the size of the holes as the polymer strands are really very long it really doesn't matter how long they are because you never see area that is an argument
which the 1st time hear it sounds a little odd why shouldn't the molecular weight man the answer is sensitive here is polished he's very very long and sphere moments here sees this get in here I suppose I this polymer strand in change the molecular weight by factor also never will I history and here where it makes a difference almost always all counted out here yes I have made a small change in the average full-size because the hold 1 hole here has got twice as big but almost all the holes are the same size and work for all of that is they can issue which you sort of have to internalize you should realize that I have said which of these models is correct I just said If you go to literature you can find these models that France OK so we are now ready to advance in Chapter and Chapter 3 in large part discusses the use of polymer matrix solutions where the things to do in the sequence the on providing us with probe are what are called DNA restriction fragments it's were restrictions Fred I'm not going to go through all of the chemistry but I want to show you what's going on because it's actually a brilliant trial Human science here is a village along the or animal it's like all polymers is composed of monomers and no matter whether it's DNA or RNA therefore distinct monitors also biological information well until recently when he started talking about methylation Holding is to some extent contained in the sequence the aura and a huge biological project which came to fruition a decade ago was determining the sequence of DNA in the end the sequence of the DNA of fellow was running project all what I was your age and undergraduate work younger people in the pen "quotation mark sequence was transfer or in transfer or a really really tiny by comparison with the human DNA I was in enormous project involving a large number of people it wasn't really in the extreme were and ,comma was made as long as this is the method no one's ever going to do it again but people found some answers In the 1st dancers once called the restrictions what restrictions that about cover that the theater but it's a very clever you only inserts cots that exam points as opposed to something that just goes in and shops of like chain and cousin of real this only considered exam .period and so you can take the DNA to DNA and you can breaking into pieces and you can then use electrophoresis seemed to sort out and isolated pieces of each time and the amendment for making many many copies of pieces of each type that was is to say well known chemically 1 approach is to say chemically protect all and some of these and we will somehow go and we will digest shoot well the enzyme To using enzymes will choose what these chains from the order and so angry change has the same and here this is 1 of the unique pieces by afterward on digesting it the little short pieces that year long pieces of steel and here and now very cleverly attached to this said what is usually used his a died of fluorescent dyes I think and fluorescent dyes giants and label was red green blue and upheld the air quality has the teacher who we should die attaches depends on which of the 4 monomers is present at this so I produced all of these brands that's all can you exactly the same place they are all different lengths and I have a color coded the depending on what the latter is here I will not give its standards there thank you then so I have this word corresponds to this check it always ends at the same point however I had gone in with dies English shall that I slightly more dies before and I have confidence so and the 5th letter hours
age and the work letter out isn't he as the 3rd letter about his health and the 2nd letter about his health and his letter is also and I itinerary read off Hello is clever however there is 1 step which skip this is just a mixture of all the different ways chain all of which are color and what I have to do is somehow identified the fact that it is the 5 change that has energy to formalize chain that hasn't so
how and why do they the and electrophoresis column that filled with polymers high-profit the mixture of all these years I apply an electrical field that migrate to the other half but because they migrate in different lengths madam to which fastest in which slowest the this fall comes out 1st and then the stock with the element comes out next and L and the and finally H and I can do this fight tuning Rembrandt talked about surface coating such I couldn't move which were things come out on the important issue is the slot the smallest and largest ,comma out 1st arrived on the story In the condition why because I have this stuff in the call that selectively return words everything but is more effective in Regarding little ones and the big ones or vise versa I happened to write this so you can read the words so that slows down a little ones and the big ones most
and that's the experiment you're going to see there are those papers but I could have done in reverse order this way to reduce the love we start out with Stage III Elton L. call out of each other in a little wall and the applied field and there as they migrate these migrate faster boats carrying might ask this takes us into the a paper why do you need the Polaroid why don't you
just feel was with water and the answer is if I have DNA from different sides the different sizes so they have different charges on them it was their charges with more force on yes but there was also experienced more hydrodynamic during and that aresult is that all these restrictions fragments migrate through pure water at about the same speed and therefore it you this column experiments and you just have to call on filled with water there's been no separation and put them all in together and they all come out together at the same time because the other different electrical forces on them the different drank forces on them and guess what those 2 effects us sigh if you just knew about electrophoresis and water you say you couldn't separate DNA and all this approach would work fortunately is inspected the site fumigation election lectured to it was discovered 50 years ago that if you want polymer and solutions to do something fumigation sedimentation Apollo selectively retards so materials relative to others and you can do separations and policy solutions that you could not do do invite solved so far as I can tell that the fact was actually forgotten 15 years and what actually happened is people want to do electrophoresis but if you do a bulk electrophoresis this big across you're passing electrical current through water you get the feeling you get convection and because you have convection things are makes you don't get separation and 1 fine day because their 45 years maybe not quite as part of someone said let's do this separation and instead of doing and water will do shelves and jails always sort of solid no settlement there is no connection gels you separations you could not get In find solutions however chugging ahead toward present if you trying to load jail into little plastic to how you do that it's solid well generally Austria's you make the shell in place the story you have something which is a liquid want temperature and a solid were solid like highly viscous and mother and there are things you can do with this with block copolymers successful and there real cross-linked gels which you can try to make it to the attention they may make them they tend to be non-uniform they tend to give you gas bubbles that's very bad they give you all sorts of problems and someone along way said it's not his trio lets users polled solutions instead because ,comma solution to just look at what's they floaters like water with enough followed by his easily they flopped so using polymer solution the as the answer to the problem of show we now show that has to figure 3 . born and figure 3 . 1 is on page 4 and 6 of them what we see in the year 3 . 1 well it is a lot of little ability how fast things move per unit applied field against Paul concentrated and in the office ,comma concentration is
0 you're looking at a a lot lots of zeros not actually in figures polymer concentration of 0 everything migrated the same rate dance experimental but as you increase the Paul concentrate you discover that mobility dropped further more the mobility of small object drops last volatility of the larger over here and the figure actually shows this for a bunch of different size objects and if you look at that and discovered by the time you have a restriction fragment with 23 thousand 500 . 3 1 third base pairs based carrier gasses is DNA it's the story of this fall flounder around each other and it has to recover from the year is correct so for example if you hadn't here the scene there and I'm being kibbutz all reminded him the year and yet she's there and therefore the length of determined by the number of shares this is actually fairly fat molecules because this is a very complicated structure but it hasn't won away in his usually labeled base pairs you can take half things that are quite sure that are still so lover base-pairs data there doesn't show what people will think this that shortest and base areas they still want separated OK so there's there's the experiment and then the anomaly cross perhaps among crops if you do the correct description of polymer dynamics as the entanglement picture there is a feature known our molecular property and so the molecular weight between entanglements that is if you just throw ball Austrians solution for that they don't want around each other like 2 words forms instead they go around every so often I just every so often they do something that creates handled the nature of the
something is not specified most of these theories and the people will say Well it's not really a softening discrete places it's a mean field affair that we can describe this way yeah but and the biological named melts not solvent at all for polystyrene this distance might be 10 thousand dolphins of polymer 10 thousand a year which means it's something like a hundred monomer you if you don't moved the ball the distance between it and woman's is set to go something like 1 over the concentration of amusing 5 the symbol for volume fraction so if 10 per cent wage follower instead of being fed thousands from all over 10 thousand dolphins between .period you might be a 100 thousand please do not take these nominees literally the sort of approximations of the important issue is the distance between entanglements quite large it you diagnosed all the distance gets bigger and bigger because that strands instead of them being spread this fall over long years majoring polymers that failed to Bangalore everywhere this fall reducing sold them all well I should keep value in whole over eventually something happens and what happens is we diluted these polymers and he eventually the distance nominal distance between entanglement points is larger than the length of a single change and sunlight each chain is only entangled maybe once or not at all so this this change is in the hands of the year the distance along this change where you would expect the next president .period that tears are placed at the end the this chain is only entangled wants and there is no more knowledgeable and there is no no longer a match and so should die lose followers solution not you go from an angle to well and and there is a transition concentrations called C stock which is the concentration for intentional obvious feature of C-Star which I will let you think about suppose I have polymers of several different weights molecular weights several different way is C-Star the same for all what's all think about their I seeing head-shaking well OK well let's try picture here I have died including polymer until the mean distance between here and playing with points is that so here is a lot calls over the Internet and here is a sure Hall is barely in here is a short ball user long enough to stretch between 2 of the angle .period Aussie entangled .period random so I'm just saying the averages and therefore see the transition concentration the hands on your phone molecular weight belong ,comma is for more information downloaded still say the former is entangled where these
experiments Figure 3 . 1 or all done with the same poll and therefore were at ,comma there is some concentration meanwhile which followers do not entangle because they're not alone well if this measure feature entanglements picture of what you were getting separation is correct namely polymers our long enough they should form match those holders filtration that if you're down here and I will solution there is no match and there should be be no separation having not been there myself I infer from the review articles that there was a period when people knew that this was the fact that not try experiments down here Air One fine day and sparing is the author of the paper they actually did the experiments out of here and discovered very important result you still got separation down here don't solution excellent super question which camera will not pick up y well we will get there later in the lecture if I talk fast enough but the short answer is but for a here DNA and there is a single polymers area all by itself on very dilute solution and the DNA is the this way under the influence of the electric field and the other day and snared around ball and while it is clock on polymer strain the of the DNA goes up however the sharing DNA is the less likely it is to hook up with polymer for Grand
Polymer and there were a lot of all along the Anais spent lots of time like this the shortest EU nations spent blast and as a result but what DNA is far more to slow down with this quality and price might ask Is there any way of confirming this test the it's at least areas for really big apology really be allowed use the enemy is extremely long haul it looks if I were to take the DNA out of 1 of yourselves and your not talking about something 10 areas along we're talking about something that would be long and loss about life to see with the naked eye well the difficulties therefore if you follow my across to the video might cross the other DNA undergoing electrophoresis disappears later share you can actually see the DNA molecules blobs if you will contain video pictures you can watch a lot of migrating along the streams and if you toss in the polymer suddenly you see kind of DNA confirmation the looks like that she loved metrics followers are invisible you can see the kind of thing that question happens to be in a mall laughter also only a few inches wide the answer is that we have hardened we have died molecules of interrelated 2 little otherwise following and I molecules have properties that of you hit them with a laser beam and floor last will on the dark and because they're alone .period the DNA since there in gives off light you can actually see the DNA because the resolution of the optical microscope is quite limited relative to the training with the actual molecule but you can see the glow roughly where the DNA chain television the company distinguished different the other the DNA is very low salt concentration and so if you look in the field of the microscope for only a few of these and therefore you can see how the city and the matrix fall over something from the quite different was not mine died all and is invisible suspicion this I will not let you distinguish different molecules just wants to see you know what happens if you wash his confirmation is and if you what should be discovered 2 things 1st of all Everything moves and saddened to long and DNA also the shorten the DNA around and as it is described to me what happens is that the DNA founded on the scene obstacles here dreads the obstacles along but also pulls off of some the obstacles drops back to back the pending on the concentration of Paul you see confirmation as that described like that you see confirmations that the described as being more like that why don't you see something more like this all the concentration of matrix is higher than their more obstacles all of which can vary widely in their mention my fingers were to Baltimore they can slide over each other and there is essentially no friction and therefore as the DNA this when the obstacles addressed in the other direction pile up so together if you were currently had also received confirmations will like there were 2 obstacles on the same shade you crank up the polymer concentration of matrix concentration and you run on the electric field of something dramatic what is called the of if you run off the electric field goal of the DNA no longer looks like this a life that is centered stretches out its little regular and just proceed headfirst through the solution and when proceeds headfirst through solution the mobility is now formal less not quite all after indeed handed the length of the DNA and you can't do separations and so if your matrix concentration changes you from this linear regime where you get that linear their that separations to a different regime where you don't but there is no direct evidence that you could actually the man this would come back to why and I said Why is that strands grabbed each other this is Lisa analysts parents interpretation and her interpretation this can be found in or experimentally was used for very long amazed you could actually see the story bring jobs yes the questions the assumption that the restrictions noted that it's in interest of the matrix fall is neutral it's so that that they can be effective in the 2nd half of it will have some cannot consistent with the view that movie yesterday and I was trying to move with respect to the home matrix fall which is neutral I now you have
to be a little careful matrix polymers neutral but the electoral laws like the fact that I described causes the entire solution Mendoza neutral major exporters to chug along in 1 direction and therefore they actually do the experiment you have heard capillary you're observing you need reservoirs the chance because there will be some net loyalties neutral solution from 1 resident to the other vets how electoral loss Moses was originally discovered the Russian discovers applied electric fields to neutral water and discovered that if they were still claim membrane away suddenly you got flow even you know there should be no electric force of the water so we have discussed 3 . 1 this various discovery that was extremely surprising if you believed in him if you believe in the higher dynamic pictures that I've described the result that I just described is not at all surprising it's exactly what I would have expected however you will discover yourselves in your professional life when you were doing experiments it is often the case that your mental model of what should be happening tells you which experiments are worth doing and which are obviously totally pointless if you have good mental model of those expectations that to save a lot of work but every so often your mental model wasn't quite as good as you hope and if you do what looked like a pointless experiment you make a remarkable discovery which is exactly what happened here OK Fear 3 . 2 Johnson said that figures 3 . 1 and 3 . to have all these data points and we have a lot of applying limitations there is exactly the same except for 1 detail in Figure 3 . 1 I plot holes ability versus concentration the lined his probe of different sides In the years straight .period I take the same measurements and blocking for mobility against the problem size 4 probes at given concentration yeah concentration was concentration too but in the year 3 . 2 we see something quite remarkable namely the movers the chugs along at increased probes size and that there's a problem size of which almost nothing and there is a transition probes lines now how often these 2 figures both be the center of the same age as well 8 fixed concentration in here a line like this corresponds to all of these measures 8 figs froze ties here corresponds to veterans with a view to probe if you did a three-dimensional plots would say these 2 figures a two-dimensional slices if I have lot concentration probes eyes mobility coming out of the board for exhumed some data and the holographic blackboards and be able to do this yes you realize this is that this is the year it which would take slices white bread on the New Birth those something spaced out here but I'm taking slices as Ivory concentration 4 different probes has often on at this the year I'm taking slices and 6 concentrations and the mobility is doing some things I change the probe size so I'm showing you two-dimensional slices in 2 different directions treatment but there are a few slightly tricky features of 3 . 2 particularly if you look out here there things look more like a straight line now that the year has something here in New year along the there and that should tell you something about what the shape of those lines are except those lines that would demonstrate income are not actually it's a and straight and these lines are and they have mobility for all the promo size to some power Absalon where epsilon is very small it's not 0 if Epsilon was 0 those lines with be horizontal not horizontal but after all this time moreover so he was ask she wants that transition my 1st answer is that transition is extremely annoying if you're trying to do experiments because out here the mobility changes very little with probe size and problems of different sizes all have the same mobility you can't separated period there are experiments "quotation mark 1 of the authors of this thing and the experiments tends to indicate what the transition it's and what happens is that humanitarian mobility versus applied electric field but we found him the
velocity of migration velocity his mobility let you even if he is small was just a constant but if you increase the feel and increase the field at some point it's quite something mobility starts to depend on me you have a transition between mobility that goes in 0 power in any way you want fortunate to eat To the sum is some fairly small this is a transition from a linear transport property to a nonlinear trends were proper nonlinear meaning you change the driving force whatever areas and the response changes but not linearly and changes made the driving force the transition observed by many but here isn't properties correspond to this transition I have not found any I suspect someplace in literature in the human chemistry where Solomon has confirmed that they transition in this transition on the same however the proper behavior that Mitnick found as to where this transition occurred as you change the matrix concentration as you change the matrix molecular weight you change the probe size this transition and that transition seemed to be the same thing also they both appear to be being somewhat weak on making this claim of Puritan B the same as the transition from CGA confirmations with large wrote articles to see light of day and it is reasonable that is straightforward to see what this transition would give you not only a sharp change and nonlinear behavior because the way this object moves through solutions and the way this object moves solutions are fundamentally different I actually make side which is a general statistical physics from although there is a lot of statistical physics and physics behavior .period on systems where are you hear linear behavior for example almost which will also offer way back in high school physics you remember that far back and almost lost as the current is linear and the applied field but if you crank up the electric field and you get your behavior there are lots of transitions from in here along with your behavior and a lot of them are part of a study because you really have to wear the system pretty hard to get into your behavior here you have a system in which you have a linear nonlinear transition in a complicated system and you are really pushing very hard on the system at all in fact this a very gentle you get changed all right and therefore In essence physics problems it may be interesting to study because will lenient and nonlinear transition under conditions where you are worried about the wire melting away all sorts of other on sex and birth lineage of nonlinear other case also if you were clever and push the lyrics of nonlinear transition that way he curves in them for a while before got transition and if you could push the transition out that way you can saturate a larger range of DNA is with a single experiment lost 1 obvious way to do that you you believe this interpretation you just turn the electric field that and if you turn the electric field that the transition does not occur because it's not the chains are being driven part those experiments have not that I seen I say there's a huge biochemistry with literature and the smart money says there really have been seen some have found OK so that is all the behavior of DNA as a function of probe size as a function of concentration and there was already a big surprise namely if you said DNA was being separated because form an entanglement with students behave like this they should behave sort of life where low concentrations nothing opinion about and some someplace near the start of the began a transition in the polymer mesh starts all about being chains little let me emphasize I said there's this transition from no entanglements to and then there are almost no calculations that examined the question of how sharp that transition and so you could say the transition is fairly sharp where the transition is somewhat diffuse and therefore will I through this a wine they the failure of someone served with his gas from here and there you the effect said simply doesn't just turn on lights moreso than this however if you're significantly below here the prediction is there should be no separation and that's not OK I have talked about electrophoresis question and on top of the page in 1 for tower which triggered even place on 3 . 2 there are at the top of 3 . to the open circles yeah the yes OK what do what are we looking at it's 3 . 2 will 1st of all circles are DNA pure water and if you have DNA of different-sized pure water remote abilities are all the same and therefore at very low concentrations
we're here at very low concentrations there's no separation at all if we increase the polymer concentration a little bit you get for example black circles and in fact the black circles to fall often very weakly because it's very very very low concentrations you still get some separation and then we get to rather high concentrations and 1st we see this it's actually a stretched exponential fall of concentration With probes Eisenstein and honestly making probes bigger and where high concentration we 1st get a stretched exponential dropped and then we get this very slowly power Waldrop OK Charlotte had appeared page 53 Figure 3 . 7 at this time and 327 suddenly looks at mobility as a function of matrix collectively remember tourist Terrace where we have a neutral Paul and Indiana and because we have both the neutral polymer beginning the neutral matrix faltering and so molecular weight as of yesterday the Crowley has some molecular weight he the and these 2 are different from each other and what we do and that figure is to look at the question of how the probe was slowed down by followers of different molecular weights and how slowed down by different polymers the important thing you can carry away from that figure is most obvious in the year 3 . 7 seats which shows quite large probes and several different molecular weights of 1 Paul and what you find there is that hasn't changed the molecular weight of the matrix you change the mobility of the problem so we can say matrix called the matrix affects the mobility of the probe the probability that the function of the traditional and as we make the matrix bigger and bigger it is more effective at slowing down probe Of course given concentration it also gives us solutions that are more and more more viscous and therefore harder and harder moment Capitola there are a series of challenges experimental challenges here which are not completely trivial and choosing a matrix polymer that has won so attractive properties may give you problems at a different point you then have tried optimal How can we seen this discussed the war yes vote that my discussion later I think the point was to make his followers left home for a few lengths and I on the loose lawmakers matrix polymers that are much smaller than 1 of these hypothesized walls once the matrix polymers really big that it shouldn't matter how big it yeah as the holes are small major chains along if for example you randomly shot major chains often change their mind you always almost never create change the size of this whole and therefore there was a there is a model expectations some models that mobility should be more more or less independent than what matrix molecular weight until the matrix gets really really sure you make a manufacturer of the terms of this model is putting his Gomez plus suddenly you don't have holes and hats anymore you just KFC chain well this prediction for expectation natural predictions of strong words this expectation is not sustained by by experimental mobility is not independent matrix molecular weight as you can see in the let's push ahead 3 . 9 and 3 . 9 Charlotte you a clever thing you can do with modern biotechnology well it's a clever thing do it was a very smart people and they work very hard and I know exactly what is doing here is a typical Indian name of however you can make synthetic DNA and if you were very clever making synthetic DNA which forms across like there is a reasonable would do that is each of those 4 elements has different DNA has a different GAC TAC plans on and you arrange the GAC TAC .period this is leaders verified farm so this is the only way they can cross match and reason you have these arms out here these arms corresponds virus DNA world which has the interesting pieces that have which is only single-stranded suddenly you take the virus DNA and make what is basically an X-shaped where the arms of the expert very very long this is terrible as 190 thousand rounds of base pairs but the Stockholm has the interesting feature but all of the arms are exactly the same way and all the stars are the same size there is stop always extremely model was 1st it's here you comparative ability of stock along with the mobility of linear polymer is very very nearly the same molecular weight that's an important feature of biological macromolecules reviewing followers and DNA can be made so they're extremely large and they're extremely close to the same molecular weight if you use synthetic polymers like the makers Baldwin's we've been talking about you have a complication synthetic processes if they workers Apollo almost all within a few percentage each other subjects were 10 per cent Indiana well in Figure 3 . 1 3 . 2 a reference to use any of the 3 thousand 130 base-pairs that's 23 thousand 130 not 23 thousand 131 you really is 23 thousand 130 may get broken up a bit so there will be a contamination of shorter bits but the pieces that is this logic is really exactly this large and work introduced macromolecules whose molecular weight you know too well what part 10 4 for all sorts of physics studies where the effect the properties may change with molecular weight this is incredibly useful and now we look at the year 3 . 9 and 3 . 9 shows the electrophoresis of 2 linear and start DNA of the same molecular weight In 2 different matrix fall the formalized in comparing the compares with wider here told melody versus Paul makers concentration and each character lines are pretty much on top of each other you would be extremely enthusiastic and your confidence in your measurements if you said those revived measurements and moved the 2
wines in Feira actually of job within experimental error in each makers former the 2 DNA is a DNA and costly in the same molecular weight moved at the same speed well that raises some interesting questions because there models ,comma dynamics I would say linear chains move 1 way start the and stock always cannot use that mechanism of motion than most other mechanisms mode therefore star molecules should encounter much more resistance as they moved through followers relative linear chains now there's some technical issues which I make it into the next election as to whether that observation relevant to that figure is what you're seeing is that the mobility of linear chains and stars for electrophoresis for really big polymers are practically identical very important results Wednesday I am going to skip section for almost skipped Section 3 . 5 electrophoresis of denatured prompting I will tell you why it's significant amendments and the issue is supposed to want to revive separate proteins by molecular weight using electrophoresis there is a problem namely you're funny shapes and have service charges and there is a solution Maryland fall from a cross-linked Salford reviews typically so it's even a lot together for what you do is you take protein I reduce these bridges and SH rules and put the protein carefully chosen detergent and molecule of In the detergent it's so makes myself with this myself and myself protein-surface somehow and because there myself stock to the proteins service this is sort of uniform object will statistical work myself and a charge green light is constant an alliance is determined by just the molecular weight of the protein and if you do electrophoresis of this unit shall or polymer solution you can saturate them because he's straightened out so to to speak from the that was a big biochemical advanced once upon a time and it's still very important Monday and now we advance and we're going to talk about a slightly different set of Britain so far I have been talking about electrophoresis of DNA is the sort of long floppy molecules really short DNA is a very rigid rock but you could imagine putting something else into the solution if you know enough as free the following season so there is always the serious of polystyrene Blake you can also use the nomination from King's you can use viruses they're all sorts of things people have used bottom half biological cells very large objects you could drop this year to make some Nunavut former matrix and electrophoresis and asked how fast these things through as you change the properties of the matrix it it's the same experiment as before but now microbe object is a sphere and the measurements were talking about going back to experiments in the eye not going to sort out literature the manner they actually did these experiments now the experiments are actually worked for another reason to 1 of the papers cited 1 of my favorites and because I use the Web scientists search that I told the use for your major homework assignment ,comma I found the citation and I moved to the article suddenly I realized that here is an alternative method of study polymers solutions I knew about sedimentation experiments that I wrote about for a long time but I think that our courage maybe you can use electrophoresis the same way physical studies of the lawmakers always it never occurred to anyone else that was the case I'm here if you look at the review articles I've told you look there were few look up books on all polymer physics the polymer solution dynamics you'll find a bunch of physical experiments method mentioned different methods but 1 method you will not find discussed this 1 because there was no recognition well below book coming out that this was a technique for studying the matrix as opposed to a method for studying broke well it is that for starting the matrix and hear people studying the matrix the figure 3 . 14 which is on page 65 doesn't comparison which I do not have to be in but so we have a lot display concentration of matrix Paul and 1 thing they did was measure the viscosity and the viscosity she is the resistance the larger the polymer concentration more viscous solution be so they measure the viscosity this is actually more of a leader of the increase is not quite simple exponential best and then the authors also measured the Electra Ferrari mobility of several different problems now complication is that if you use problems of different size the charges are different social forces on different the charges are about the same year is there In the final slot mobility in pure water as a normalizing factor so I plot mobility of labor mobility in pure water we would expect the mobility fall as Paul concentration increases Alzheimer's "quotation mark the I'm the water over the mobility which is something I expect to be proportional to the solution viscosity because it's proportional to the resistance of the particle experiences move and I will normalize that high mobility and groundwater out the charges spheres and I discovered different spheres are turning different amounts of policy solutions but there is a trick and there's a trick which I found some surprising I checked the papers several times and it's definitely true the 2 small approaches to these larger drones and it is dramatically cases problems get larger and larger the polymer solution is less effective at slowing down OK no why might this be surprising well you can find in literature it's related to the table models people will say that if you make crossed really big really big relative follow along there's Baltimore knows what they could actually be quite concentrated drawing so you see the problem would see the polymer solution just as it continues because the probe is being the center tiny and there are almost as tiny as solvent molecules relative to grow and therefore really big problems with the always solution is a continuum and because they're seen as a continuum all the motion should be determined by the macroscopic viscosity and the expectation that the opposite of the experimental data as it really large the present mobility would just be determined by the viscosity well that is not at all what you observed experiments OK questions at this point OK now are going to 1 of full of at end relies on some statistical Indiana probably have not seen complete details so I will sketch the results and the result is called by you fluctuation dissipation or is called me here In response from Americans very complicated but the net result is supposed to be fairly simple 1 here citizens solution and I applied to a very weak force if I applied to a very weak forested moves admittedly slowly and the velocity is proportional song problems I'm sorry that I had the velocity is proportional to the cost divided by some constant after tyrannical fish and if I apply a very weak for there's a drag coefficient here which is just a number a version now suppose I instead the same horrible doing Brownian motion Brownian motion is what gives you the future is in fact decision even if you're talking about In now about metallic alloy in Ireland's moving from last location less locations very general phenomenon materials the object moves the driving force the worst thing that is firm alleging Katie and there is resistance to this grinding effort through there is array animal linear response tells us is that this coefficient and that coefficient should be the same so that the drag coefficient the court determines how fast diffusion proceeds and the direct coefficient determines house they ask really weekly driven motion received those 2 should be the same this is known as the stocks Einstein's diffusion grace very classical result not licensed interesting in this case well you really interested in this case is that more these 2 direct coefficients speed said that sort of time supplying him with their the method all object users who what is being dragged through solution and what it's doing random diffusion through solution must also be the same they may have used what the object what mechanism of motion was being drafted by this war and another 1 of those diffusing 30 no reason for me to ask to be equal except by accident so I suppose we take a DNA and we'll put what we think is a very weak field ,comma so we are in the linear reaching and that face the mechanism that we see that the NRA users who must be the same as the mechanism that the DNA users to move when it's diffuser Of course there isn't even if there is a very important to as I said you have to use a weak field and it is often the case for sometimes the case that if you on a nonlinear reading it's not really living here you get a pseudo linear behavior and the velocity is locally linear in the field strength driving force but you're not really in a very weak field regime urine sample of regime where you will also see what appears to be new behavior also the numbers don't change very much often put it straight line through data even if it really is straight conscience should be telling you the data nonetheless let us suppose people have actually observed DNA moving in the week linear field regime well there are people who who don the yellow line crossing the references are in there and I observed the answer is moving through matrix what so far as I can tell from the papers appeared be the last TUC for linear DNA it's in a linear regimes the confirmation is like this today and you can also get a transition from the a field the transition to this is the life of the nation and in that very clearly moved into a nonlinear reaching what Nelson is out stock this is start of the NRA just floating and if it's there's not much lonely tends to be an actor we pretty much when applied field you can it is leniently stretches out and what you see is starting today moving through solution does that farmers 1st body behind wife with because the chains majors chains track years and slow down the middle Wells now leads the field gets weaker and weaker this fresh effect gets less and less than a year in many areas being the 1st little bit of the old will still give you the arms at the time of day and the world widened by Lance behind how can we describe this motion was going to give a word for it the word is he didn't unless you be actually were studied Latin which under modern conditions of likely will not immediately threatened provides the 2 things that are where is this or apoptosis animal lives under water there are also sold Kalam area you go through Italian restaurants and calamari look like this and they typically swim like this for many of those women like that sometimes went like this but I'm talking about once chased the predator like this arms 1st and you get little squared the little fish you really large square going after Wales or at least try to and there was 1 unfortunate case 1 has to go after the American nuclear submarine force would damage has this nice shot beacon front end of the clear something's plastics on article doctrine let's not think about taxpayer opposition but in any motions to the meeting Our for instance arms 1st century molecule trading volume this picture is totally different from the entanglement reputation picture I talked about last except this is direct observation you can however still believe reputational and they have to say these pictures show sumo linear Regine if you were actually in the linear regime you see something different however I see I am of time classes dismissed OK and if you were wondering why sort of stand there at the front of the enemy I knew that we have entered the video and it is really convenient the front and and I have this nice section where I just standing there smiling about wing of my mouth shut so looks OK on the video OK word on the modern-day version May next time next Monday you need to have made significant progress on their homework assignment at least to discover how all those little references I gave you leery


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