archive-edu.com » EDU » C » COLORADO.EDU

Total: 304

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".
  • Crowd-Folding | JILA-PFC
    former research associate Nick Dupuis graduate student Erik Holmstrom and Fellow David Nesbitt The researchers found that under crowded conditions that begin to mimic those found in cells single RNA molecules folded 35 times faster than in the dilute solutions typically used in test tube experiments Crowding also led to a modest decrease in the unfolding rate The results strongly support the idea that compact structures such as folded RNA molecules and proteins may be much more stable in living cells than they are in test tubes where there s lots of room to stretch out and flop around The idea that crowding favors compact structures in cells makes intuitive sense Imagine trying to make headway through a crowd at a popular concert or sports event Keeping your arms and possessions close to your body works much better for making headway through a throng of people than waving your arms and packages as far away from your body as possible The same principles apply to biological activity inside cells Not surprisingly the biologicaly active forms of RNA proteins and other important large molecules found in cells are nearly always compact folded structures Dupuis and his colleagues work on RNA folding under crowded conditions was reported online May 21 2014 in the Proceedings of the National Academy of Sciences The Nesbitt group s research was the first to use using single molecule fluorescence techniques to precisely measure the effects of crowding on the rates of folding and unfolding of individual RNA molecules With this technique an RNA molecule fluoresces green when it s unfolded and red when it s folded Under crowded conditions the molecule spent a lot less time green because it folded so much more quickly The researchers chose long chains of antifreeze molecules polyethylene glycol or PEG as

    Original URL path: http://jila-pfc.colorado.edu/highlights/crowd-folding (2016-04-29)
    Open archived version from archive


  • The Measure of Small Things | JILA-PFC
    over time Unfortunately with commercial AFM cantilevers the delicate diving board like structures to which the measurement tip is attached researchers could only get one or two of these things to happen at the same time but never all three That s why the Perkins group has just spent more than five years improving AFM cantilevers and tips which are actually attached to the protein under study Most recently the researchers modified a short AFM cantilever to be much less noisy and much more stable These two changes allowed them to resolve the motion of single proteins This long sought capability was made possible by the merger of nanofabrication and biophysics It was reported online in ACS Nano in March of 2014 CU undergraduate Matt Bull now a graduate student at Stanford University led the research effort The goal was to make flexible but short cantilevers However like a shorter diving board shorter cantilevers are inherently stiffer Bull used and improved upon a popular nanofabrication technique to come up with a soft and short cantilever capable of making precise force measurements And he did this without sacrificing long term stability or the ability to detect changes in real time The three key modifications of the short AFM cantilever were 1 the use of a focused ion beam to carefully cut out a large rectangular hole at the base of the cantilever increasing its sensitivity and responsiveness 2 the addition of a transparent protective patch over the cantilever s gold coating preserving the cantilever s high reflectivity and 3 the removal of the remaining unprotected gold coating from cantilever and the probe tip enhancing stability These improvements resulted in dramatically improved cantilever performance To show that the new cantilevers worked with real proteins Bull and his colleagues mechanically unfolded then studied

    Original URL path: http://jila-pfc.colorado.edu/highlights/measure-small-things (2016-04-29)
    Open archived version from archive

  • The Unfolding Story of Telomerase | JILA-PFC
    enzyme telomerase Telomerase employs both protein and RNA components to lengthen chromosomes which are shortened every time they are copied If one short piece of the RNA in telomerase is folded into an organized structure called a pseudoknot then the enzyme works properly The enzyme repeatedly adds short pieces of DNA to the chromosomes within the cells of people and many other organisms Because it counteracts the natural shortening of chromosomes telomerase is vital for keeping cells alive and healthy through multiple cell divisions If however the pseudoknot contains mutations that interfere with folding the result can be the serious genetic disorder dyskeratosis congentia which causes a variety of skin and blood diseases New work by Holmstrom has revealed why mutations in the pseudoknot are so harmful When the pseudoknot unfolds telomerase stops working In normal people telomerase works efficiently because the pseudoknot is folded about 99 9 of the time But in people who suffer from dyskeratosis congentia this enzyme does not work properly because it is only folded half the time Holmstrom discovered why In the laboratory a mutated pseudoknot folds 400 times more slowly than a normal pseudoknot and unfolds five times faster Holmstrom was able to determine the rates of folding and unfolding using a technique known as single molecule fluorescence resonance energy transfer smFRET He attached dyes that fluoresce green and red to a small piece of RNA consisting of just the pseudoknot Then Holmstrom shined laser light on the pseudoknots causing the green dye to to fluoresce green When the RNA folds the two dye molecules are brought close together which allows the green dye to transfer energy to the nearby red dye causing it to fluoresce red By carefully monitoring the patterns of red and green dots in a microscope Holstrom could watch

    Original URL path: http://jila-pfc.colorado.edu/highlights/unfolding-story-telomerase (2016-04-29)
    Open archived version from archive

  • Good Vibrations: The Experiment | JILA-PFC
    goal of one day building a quantum information network Large scale fiber optic networks capable of preserving fragile quantum states which encode information will be necessary to realize the benefits of superfast quantum computing Such networks will require new technology to reversibly convert low frequency microwave light i e electrical signals to high frequency infrared or visible light without losing any information The JILA collaboration has just made important progress toward developing a device that will be able to accomplish this conversion The two JILA groups partnered with researchers at NIST to build a converter that not only links the low frequency microwave and high frequency optical portions of the electromagnetic spectrum but also preserves classical information encoded in the light The converter works equally well in both directions and faithfully and efficiently transfers the information The researchers responsible for this accomplishment were graduate students Reed Andrews and Robert Peterson research associate Tom Purdy Fellows Cindy Regal and Konrad Lehnert and NIST scientists Katarina Cicak and Ray Simmonds The light conversion experiment was reported online this week in Nature Physics In the experiment researchers transferred classical signals between microwave and optical light with conversion efficiencies of 10 The experiment worked so well that the researchers have calculated that if the device were cooled from its current operating temperature of 4 K to below 40 mK it would be able to coherently transfer quantum states At the heart of the device is a silicon nitride drum that can talk to both microwave and optical light which cannot otherwise communicate with each other Infrared laser light passes through the drum near but not touching a miniature electronic circuit Microwaves in the circuit cause the drum to vibrate which alters the phase or amplitude of the laser light Conversely changes in the phase

    Original URL path: http://jila-pfc.colorado.edu/highlights/good-vibrations-experiment (2016-04-29)
    Open archived version from archive

  • Dealing with Loss | JILA-PFC
    the molecules do not collide and react is continuous measurement of molecule loss from the simulator That it works this way is a consequence of the quantum Zeno effect also known as the watched pot effect as in the proverb A watched pot never boils In essence if researchers investigate a quantum system by continuously measuring it things stop changing altogether The strange laws of quantum mechanics are responsible for this odd behavior These laws dictate that the act of measurement itself forces the KRb molecules into a particular quantum state And if measurements occur continuously the molecules will stay in that state because the measurements themselves are collectively preventing any change in the quantum states of the molecules The idea that continuous measurements prevent a quantum system from evolving is the essence of the quantum Zeno effect named for the Greek philosopher Zeno of Elea Thus if you adjust a quantum simulator so that according to the laws of classical physics the molecules inside it get lost faster and faster because of colliding and reacting then the laws of quantum mechanics will actually make the molecules react slower and slower until they eventually just sit there forever and never get lost It s almost as if two KRb molecules know from the continuous measurements not to hop into the same place in the simulator because they would react and disappear if they did New theory by the Holland and Rey groups shows explicitly how this works It not only verifies the quantum Zeno effect but also demonstrates that older theories that attempted to explain this kind of quantum behavior incorrectly predicted loss to happen five times faster In practical terms the previous and less accurate theories suggested that the number of KRb molecules in the simulator would be about

    Original URL path: http://jila-pfc.colorado.edu/highlights/dealing-loss (2016-04-29)
    Open archived version from archive

  • Fog Island | JILA-PFC
    Holes are like bubbles created when electrons in GaAs are excited by light When it discovered the quantum droplets the Cundiff group was actually investigating the use of intense laser light to generate biexcitons which are molecule like structures in GaAs made of two excitons Excitons are hydrogen like quasi particles made of an electron and a hole But the experiment didn t behave at all in the way we expected Almand Hunter said We expected to see the energy of the biexcitons increase as the laser generated more electrons and holes But what we saw when we did the experiment was that the energy actually decreased The energy decrease meant that the researchers certainly were seeing something other than biexcitons In fact they weren t sure what they had made At this point experimentalists Hunter former research associate Hebin Li and Fellow Steve Cundiff consulted their theorist colleagues at Philipps University Marburg in Germany The German collaborators came up with the idea that the experimentalists had made quantum droplets A quantum droplet is a structure containing multiple electrons and holes for example 4 5 or 6 of each that is in between that of a traditional atom with positively charged nucleus surrounded by negatively charged electron s and an older model of the atom that viewed it as a positively charged sphere with electrons embedded in it The droplets behaved quantum mechanically because they contain only a few electrons and holes Dropletons aren t made up of multiple excitons because the electrons and holes in them are not bound into pairs In a quantum droplet all of the electrons interact equally with all of holes and vice versa In an excitonic molecule such as a biexciton the electrons and holes form excitons which then form molecules In this case

    Original URL path: http://jila-pfc.colorado.edu/highlights/fog-island (2016-04-29)
    Open archived version from archive

  • bR Phone Home | JILA-PFC
    They used a new infrared IR light imaging system with a spatial resolution and chemical sensitivity of just a few bR molecules In their experiment the tip of an atomic force microscope AFM acted like an antenna for the IR light focusing it onto the sample The AFM tip antenna then helped capture the signal emitted by the bR protein and send it back to a detector for identification and location The AFM tip antenna worked a lot like a cell phone antenna except that it talked to protein molecules The protein cell phone is actually an IR nano microscope called s SNOM scattering scanning near field optical microscope The new work has opened up imaging of biological and chemical structures 5000 fold smaller than the diameter of a human hair In particular s SNOM provides a label free method to probe the chemical composition of a material easily distinguishing proteins from other chemical constituents such as the fat molecules making up a membrane Until now such chemical distinctions were impossible to see with ordinary light microscopy and too large and complex to analyze with x ray crystallography With the new method the researchers were able to identify the bR protein with a spatial resolution of 20 nm or the length of 2 3 bR molecules Plus the researchers were able to acquire IR spectra of just a handful of protein molecules compared to about 10 000 molecules required for getting good spectra with a regular IR microscope They accomplished this feat by first using a quantum cascade laser to excite amide groups in the protein Amide groups which contain carbon oxygen and nitrogen vibrate like crazy when excited by IR light Then with the help of the AFM tip antenna in the s SNOM setup the researchers tickled the

    Original URL path: http://jila-pfc.colorado.edu/highlights/br-phone-home (2016-04-29)
    Open archived version from archive

  • A Clockwork Blue Takes the Gold | JILA-PFC
    ions This achievement was reported online in Nature this week At NIST Andrew Ludlow s group at NIST uses Yb atoms to generate ticks for its super stable atomic clock which shares many similarities with the JILA Sr lattice clock including stabilities basically at the same level Ludlow who trained at JILA under Fellow Jun Ye on earlier versions of the Sr lattice clock is now working on a comprehensive evaluation of the accuracy reproducibility and stability of the NIST Yb lattice clock The NIST Yb lattice clock team also includes Chris Oates who earned his Ph D under Fellow Jan Hall and other JILA alumni The JILA Sr lattice clock uses laser beams to trap the strontium atoms inside energy peaks and valleys created by light The result is a clock that is 30 times more accurate and 300 times more stable than the cesium based atomic clocks currently used as time standards in national laboratories around the world The most recent team responsible for developing JILA s high performing atomic clock includes graduate students Ben Bloom Travis Nicholson Sara Campbell Mike Bishof and Sarah Bromley former research associate Jason Williams research associates Xibo Zhang and Wei Zhang and Fellow Jun Ye Many former graduate students and research associates have also contributed to the development of the Sr lattice clock during the past decade The idea of using alkaline earth atoms such as calcium and Sr in atomic clocks originated in JILA and NIST in the 1980 and 1990s In the early 2000s researchers in Tokyo and JILA realized they could confine Sr atoms in optical lattices without affecting the clock ticks The lattice largely protects the critical Sr clock transition from being perturbed by outside forces This advance led to a goal of developing an ultrastable high accuracy

    Original URL path: http://jila-pfc.colorado.edu/highlights/clockwork-blue-takes-gold (2016-04-29)
    Open archived version from archive



  •