In an attempt to image the acoustic fields emerging from ultrasound transducers we’ve built a small Schlieren setup with stroboscopic LED illumination. There’s a 10-cycle 7.5 MHz sound-wave coming in from the top at a velocity of around 1500 m/s, and if you illuminate it at just the right time with a 500 ns pulse of light you see the change in refractive index due to the pressure change. In the videos we are adjusting the delay between the acoustic pulse and the light-pulse from about 0 us up to 10 us to see how the sound propagates through the ~15 mm field of view.
Here’s another one with a reflecting metal piece at the bottom. The reflected pulse shows quite nicely! If you look carefully between 3 and 4 s you can see an interference pattern between the incoming and reflected pulse.
Optical tweezers use light to trap dielectric particles in an approximately harmonic potential. If the position of the bead is X, the position of the trap Xtrap, and the stiffness of the trap k then the equation of motion looks like this:
where Beta is the drag coefficient and Ft is a random white-noise thermal force (the bead is so small that kicks and bumps by surrounding water-molecules matter!). If the trap stays in one place all the time (Xtrap is constant) the power-spectral-density (PSD) of the bead fluctuations turns out to be Lorentzian.
But if there’s a fast way of steering the trap, we might try feedback control where we actively steer Xtrap based on some feedback signal:
This is a position-clamp where we use proportional feedback with gain Kp to keep the bead bead at some fixed set-point Xset. Tau accounts for some delay in measuring the bead position and in steering the trap. Inspired by a magnetic-tweezers paper by Gosse et al. we inserted this into the equation of motion to find the PSD:
So how do we go about verifying this experimentally? Well, you build something like this:
The idea is to use a powerful laser at 1064 nm for trapping. It can be steered with about a 10 us delay using AODs. Then we use another laser at 830 nm to detect the position of the trapped particle using back-focal-plane interferometry. But since in-loop measurements in feedback loops can give funny results it’s best to verify the position measurement with a third laser at 785 nm. The feedback control is performed by a PCI-7833R DAQ card from National Instruments which houses an AD converter for reading in the position signals at 200 kS/s and 16-bit precision, and then we do the feedback algorithm on a 3 Mgate FPGA. We output the steering command as 30 bit numbers in parallel to DDSs that drive the AODs. The 10 us delay in the AOD (the acoustic time-of-flight in the crystal) combined with the AD-conversion time of 5 us gives a total loop-delay of around 15 us in our setup.
It all works quite nicely! The colored PSD traces are experimental data at increasing feedback gain starting from the blue trace at the top (zero gain, Lorentzian shape as expected) down to the black trace at the bottom (gain 24.8). When increasing the gain further trapping becomes unstable due to the peak at ~12 kHz (think about what’s usually termed ‘feedback’: pointing a microphone at a loudspeaker). The theoretical PSDs are shown as solid lines and they agree pretty well with the experiment. The inset shows the effective trap stiffness calculated from the integral of the PSD. We’re able to increase the lateral effective trap stiffness around 10-13 fold compared to the no-feedback situation.
This video shows a time-series of the bead position (left) and the trap position (right) first with no feedback where we see the bead fluctuating a lot and the trap stationary, and then with feedback gain applied (gain=7) where we see the bead-noise significantly reduced and the trap moving around.
These results appear as a 3-page write-up in today’s Applied Physics Letters:
We’re not the first ones to perform this experiment, but I would argue that our paper is the first one to do all steps in the experiment properly, and we get the nice agreement between theory and experiment.
An early paper by Simmons et al. claims a 400-fold improvement in effective trap stiffness using an analog feedback circuit. There’s no discussion about the feedback bandwidth or the PSD when position-clamping. Perhaps a case of undersampling?
Simulations by Ranaweera et al. indicate that a 65-fold increase in effective trap stiffness can be achieved, but there’s no discussion about how the delays in the feedback loop affect this, and there’s no experimental verification.
More recently, Wulff et al. used steering mirrors to do the same thing, but they used the position detection signal from the trapping laser itself for feedback control. I’m not sure what this achieves since the coordinate-system in which you do position measurements is going to be steered around as you try to minimize fluctuations. Their PSDs don’t look like ours, and the steering mirror has a bandwidth of only a few hundred Hz so you cannot control the high frequency noise like this.
Increasing the stiffness of optical tweezers by other means seems like a fashionable topic. A recent paper from Alfons van Blaaderen’s group uses counter propagating beams to trap high-index (n>2) particles effectively, while simulations by Halina Rubinsztein-Dunlop’s group indicate that anti-reflection coating the beads also improves trapping efficiency.
A test of the 8-channel 0-7 kPa microfluidic pressure controller today. We’re looking through a 100x inverted microscope. There’s a 2 um latex bead in a ~40 um wide channel formed between a glass coverslip and a PDMS layer. I’m hitting the keyboard to either increase or decrease the pressure in steps of +/-35 Pa which allows me to just barely keep the bead within the field of view during the 1 min video. The controller has plenty more resolution, down to about 1-2 Pa, so it should be possible to control flows down to <1 um/s. Stay tuned for more of the same later…
Saw some supercontinuum (a better explanation here) generation in the lab today. At the top there’s a diode laser at 808 nm (the bright white light in the pic, try photographing your TV-remote with a digicam!) that pumps a YAG laser which outputs a 1064 nm pulse. This is then converted to a 532 nm pulse through second harmonic generation and directed into a very fancy holey-fiber in which the supercontinuum is created. In the middle of the pic there are two reflections from a diffraction grating. To the right the zero order diffraction which looks like mostly 532nm to the camera/eye, and to the left the 1st order diffraction where you see a fair bit of blue to the right of the 532nm peak and a bit of yellow/red(ish) to the left of the peak.
I got some new microfluidic chips to play with today (courtesy of the Microfabrication Group at TKK). This must be cutting-edge research, since there’s an article about using laminar flow cells for single molecule experiments in the latest issue of Nature Methods. I’m testing our custom-built pressure controller which controls the inlet and outlet pressures between 0 and 7 kPa with about 2 Pa resolution. There are three inlet channels (~40 um wide) with blue fluid in the top channel, clear fluid in the middle, and red fluid in the bottom channel. They all meet in the middle of the chip and there’s a wider (120 um) outlet channel.
The video shows a sinusoidally modulated pressure applied to each of the input channels as well as varying the pressures manually between zero and maximum.
I used this Sallen-Key design to build an 8-channel 4th order low-pass anti-alias filter for a 16-bit 200 kS/s +/- 10 V AD-Converter. I calculated the components for the 60 kHz low-pass Butterworth design with this on-line calculator. Previously I’ve used the MAX274, but that component is limited to +/- 5 V signals. Here I really need the +/- 10 V voltage swing. The exact design calls for 2872 pF, 2452 pF, 6935 pF, and 1016 pF capacitors, but I looked at the transfer function with what values were available in 1% tolerance from Farnell, and the response looked fine with (R= 1 k, C1=C2= 2700 pF for the first stage and C1=6800 pF, C2=1000 pF for the second stage). Both the resistors and capacitors (~1.5 eur/pcs!) have a tolerance of 1 %, which according to a monte-carlo simulation should not affect the response that much. I’m using OP42 op-amps with a unity-gain bandwidth of 10 MHz, which should be adequate (100x the cut-off frequency was recommended in a guide I read, that would be 6 MHz in this case).
For testing I hooked up a signal generator and an oscilloscope and wrote a LabVIEW program to loop trough around 250 different frequencies while recording the peak-to-peak value of the filter input and output signals. The oscilloscope only has an 8-bit AD converter, but I adjusted the analogue gain between 5 V/div and 2 mV/div to achieve effectively around 16-bit dynamic range.
This is the result of testing all channels with a 20 Vpp sine wave between 100 Hz and 10 MHz. The blue curve shows the design response and the red and green curves show the maximum and minimum expected response from the monte-carlo simulation (I drew all component values from normal distributions with 1 % standard deviations). Pretty nice agreement until ~500 kHz. Here’s another view of the data:
This figure shows the deviation of the real filters from the design response, again confirming that everything works as it should up to 500 kHz.
Log-log plots can be confusing, so here’s a semilog plot and a linear plot of the same data:
This 8-channel pressure-gauge card is a step towards proper control of fluid flow in microfluidic devices. The transducers (0-1 psi) are around 30 eur each and made by Honeywell. The mV-level signal from a Wheatstone bridge in the transducer is amplified by an instrumentation amplifier (INA111) to around 0-10 V for input to a 16-bit AD-converter.
I’m trying to keep up with the ever increasing volume of scientific publications in my own and related fields. I’ve been using the Biophysical Journal’s email based service for some time, but lately it has been very unreliable - often alerting me about supposedly ‘new’ papers that have been published in 1994 or so. Another way is to subscribe to the RSS/Atom feeds many journals provide, and I’ve been doing that also with Google reader, but it easily means wading through 100s of papers per week.
It’s clear I need a better solution, something that first aggregates all the new papers into one big feed from the journals I am interested in, and then in a second step filters the big feed down to the few new papers that contain interesting keywords. Yahoo pipes could do that, but the LabVIEW-ish editor doesn’t scale very well to a situation where you have 20+ feeds and 20+ keywords you are looking for. There’s also google-mashup, but it isn’t open for the public yet.
A complex solution would be to set up my own Planet, but it doesn’t have web-based setup and administration so requires tinkering with config files etc. which I want to avoid.
So far I’ve only come up with this Thunderbird-based solution:
On the left I’ve subscribed to a number of journal feeds and put them in a folder of their own. On the right is a list of filters I am running. Each journal feed needs its own ‘dummy filter’ which does nothing but moves all the entries into the ‘all papers’ folder. Then I can run a filter of my own that looks for things in the subject or body of the paper. It’s simple, ugly, but seems to work somehow.
Please tell me there is a simpler way to do this in Thunderbird! Or is there already a good web-based service like this around?
My requirements would be:
able to read and aggregate: RSS/Atom etc. (whatever the journals provide)
set up filters that look for keywords in any field or in only one field (title, author, abstract etc.)
output an RSS feed with all papers, and the filtered papers that I can read with Thunderbird or Google-reader.
So far I haven’t found anything that would do this in a pain-free way. The aggregation part is handled by most web-based services, but there aren’t many that allow searching/filtering and can provide the results as a separate feed.
Something like this is already going on with ‘virtual-journals’ that aggregate papers across journals in one field (e.g. Virtual Journal of Biological Physics Research or Virtual Journal of Nanoscale Science & Technology). Papers get selected to these ‘VJs’ by their editors, but I’m thinking my aggregator+filter idea will be able to cover a broader range of journals and look for more specific search terms.
I’ve been playing around with a microfluidic channel, to be used with optical tweezers experiments later. There’s clear fluid coming in from the left in the wide (ca 30um) channel, and I’ve colored the fluid from the top red and the fluid coming in from the bottom blue. The top and bottom channels are narrower, ca 10um.
Here all the channels are on at first, then the red channel is switched on/off two times. Here’s the same thing, but switching the blue channel on/off. Here the clear channel is switched off, and the main channel fills with red/blue fluid. It’s interesting to follow the laminar flow at these very small Reynolds numbers - the fluids effectively don’t mix at all (they do mix by diffusion, but very slowly) and there’s a clear boundary between red and blue. At the end the clear channel is switched on again.I’m using pressurized air to drive the fluid flow, similar to a product from French company Fluigent (nice videos here and here). Their product sells for around the price of a small car, so I’m thinking I can come up with a DIY solution for slightly less. Switching is by solenoid valves that switch either high pressure or ambient pressure to the fluid bottles (2ml Eppendorfs). The pressures required are surprisingly small, here I’m using the smallest pressure my regulator will output, 5 psi, but I have a feeling this is too much… so I’ll need a pressure regulator with fine control between 0 and 5 psi, any ideas?The other option is using gravity to drive fluid flow, 0.5m H2O is around 5 kPa or 0.7 psi which could be OK. The problem is you then have to switch the fluid lines directly. I tried this with solenoid pinch-valves, and the valves create huge pressure transients when switching off - completely flushing the channel with rapid flow. So the gravity driven solution requires valves that open and close very gently.
Some promising results yesterday with trying to stretch DNA molecules. The molecule is attached between two microspheres, and we are actively moving the smaller sphere while the force acting on the bigger sphere is being measured. The image and video shows the view through a 100x microscope objective on the optical tweezers instrument I am building. Towards the end you can see the construct breaking in two stages, so that probably means there were two molecules of DNA between the beads and not one as intended. This is a control experiment and will hopefully set the stage for bigger and better things to come…
