Solid-state nanopore animations for all occasions

If a picture is worth a thousand words, then an animation is worth so much more. Here are some simplified animations to explain various translocation scenarios which often arise in solid-state nanopore experiments. These animations were made during the course of my PhD at the Cees Dekker lab at TUDelft. Vectorized Flash SWF versions can be found here. Please contact me if you would like a copy of the Adobe Flash source files. Everything is released under a CC BY-SA licence. Enjoy!

DNA translocation through a solid-state nanopore:
DNA translocation through a solid-state nanopore

Translocation of a DNA molecule with bound protein through a solid-state nanopore, assuming high-salt conditions (See Plesa et al.):
Translocation of a DNA molecule with bound protein through a solid-state nanopore

Recapturing a DNA molecule through a solid-state nanopore by alternating the electric field (ping-pong) (See Gershow & Golovchenko; Plesa et al.):
Recapturing a DNA molecule through a solid-state nanopore by alternating the electric field

Translocation of membrane bound protein through a lipid-coated solid-state nanopore (See Yusko et al.):
Translocation of membrane bound protein through a lipid-coated solid-state nanopore

Translocation of a DNA molecule with bound protein through a lipid-coated solid-state nanopore:
Translocation of a DNA molecule with bound protein through a lipid-coated solid-state nanopore

Translocation protein through a solid-state nanopore (See Plesa et al.):
Translocation protein through a solid-state nanopore

Translocation of a DNA molecule containing a trefoil knot through a solid-state nanopore (knot region shaded magenta for clarity) (See Plesa et al.):
Translocation of a DNA molecule containing a trefoil knot through a solid-state nanopore

Behind the scenes. Most of these were made using stop motion animation of a small chain:

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Thoughts on Books #5

Fooled by Randomness by Nassim Nicholas Taleb

The book focuses on a number of cognitive biases and how people tend to assign explanations to the products of random processes. It draws examples from the financial world where Taleb worked for many years, although many concepts could be generalized to other areas.

The World is Flat by Thomas L. Friedman

How a number of recent technological innovations and events, combined with globalization are changing the nature of and competition within the global economic landscape. The book focuses heavily on the emergence of India and China and how this will affect the US economy. At times the book feels dated and just a series of smaller stories which helped to reinforce the authors perceptions.

Cloud Atlas by David Mitchell

This had been on my reading pile for a while and luckily I was able to get to it before the release of the movie it inspired. I found the book to be an intricately woven thread of a number of stories, with many subtle features linking each one. The themes, roles, and relationships in the book are constantly repeated and reflected even within the structure of the book itself. With this the author manages to draw the reader into a brilliant and well-crafted tale spanning centuries.

If on a winter’s night a traveler by Italo Calvino

A reader gets pulled into a complex puzzle in the process of trying to finish reading an incomplete book. Each time thinking he has found the lost part of the book, he merely stumbles into a different story which itself finishes early leaving the reader even more frustrated.

Tipping Point by Malcom Gladwell

An interesting book investigating the proliferation of memes and why some spread like fire while others fall into oblivion. Gladwell attributes success to three factors and provides a number of examples of how each of these factors contributed to the sudden spread of something.

The Sunbird by Wilbur Smith

An archaeological/historical thriller taking place in both modern and ancient times. The story surrounds a long lost civilization in Africa, how it is rediscovered and how it became lost in the first place.

A Short History of Nearly Everything by Bill Bryson

A history of some of the greatest discoveries in science and the people who made them.

SuperFreakonomics by Steven D. Levitt and Stephen J. Dubner

A follow-up to Freakonomics, overall entertaining but somehow lacking when compared to the prequel.

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Thoughts on Books #4

Rubicon: The Triumph and Tragedy of the Roman Republic by Tom Holland

Excellent look at the slow decline of the Roman Republic and the people in the upper echelon who brought this about. The roles of all the major players from  Sulla to Cicero are discussed in detail. It would seem that in 2000 years, the game of politics hasn’t changed too much.

The Difference Engine by William Gibson and Bruce Sterling

A great Steampunk novel based around the idea that Charles Babbage’s difference engine was successful and started the information revolution over 100 years ahead of time.

The Bottomless Well: The Twilight of Fuel, the Virtue of Waste, and Why We Will Never Run Out of Energy by Peter Huber, Mark P. Mills

The authors of this book attempt to paint a picture of why we will not have a energy crisis. A major portion of the book focuses on how most of our energy is in fact spent towards extracting and purifying more energy, and this so called ‘wasted energy’ will always be present. They also discuss how increasing efficiency usually ends up using more energy as the demand for the more efficient source increases. Although I may not agree with all of their conclusions, this book was an excellent read and had a very technological perspective.

Island by Aldous Huxley

This is Huxley’s last novel, and it provides a forum for him to explore a variety of ideas which are scattered throughout his previous novels. The primary focus of this book revolves around what an ideal society would look like and how it would be structured, in this case on a small tropical island. Against this backdrop we see if such a society would be able to survive given the nature of modern civilization in the rest of the world.

The Story of Philosophy: The Lives and Opinions of the World’s Greatest Philosophers by Will Durant

I picked this book up in the amazing Beijing Books Building near Xidan station (see the basement). It manages to go through all of the major thinkers of the last two millennia, and gives a short biography to provide a background context into which the ideas were developed, as well as the thinkers main idea’s themselves.

Binary by Michael Crichton as John Lange

A short thriller written by Michael Crichton in his early days.

The Death Of Ivan Ilych by Leo Tolstoy

I don’t think there is anything I can say about this book which hasn’t already been said, and in more eloquent prose.

The Metamorphosis by Franz Kafka

Wow! Read it if you haven’t done so already.

On the Edge by Jon E. Lewis

A compilation of 28 firsthand accounts of some of the most famous accents in mountaineering history. An amazing and chilling account of man vs the elements and life at the edge of survival.

Logic of Life by Tim Harford

Thought I would give this a go as I had heard it was very similar to Freakonomics. Overall I did not think it was as well written, although the content and conclusions were interesting.

Guns, Germs, and Steel: The Fates of Human Societies by Jared Diamond

A logical investigation into why human history turned out as it did, with a particular focus on the development of civilizations and its technological achievements. While at times this book can have a glacial pace, it is well worth hanging in until the very end.

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Thoughts on Books #3

The Black Swan: The Impact of the Highly Improbable By Nassim Nicholas Taleb

A brilliant book dealing with several cognitive biases and our understanding of risk. Many interesting ideas are explored within and they raise even more questions. I think I’ll do a dedicated post on this later.

Baudolino By Umberto Eco

This book was a slight deviation from what I was expecting after Name of the Rose and Foucault’s Pendulum, but still fascinating in its own way. The plot is woven into various historical events in the Middle Ages. The novel has an interesting point to make about the accuracy of historical texts and the authenticity of artifacts and relics. That is, people who “recorded” history may have not written down what really happened but altered it to manipulate the opinions of future historians.

Fatal Misconception: The Struggle to Control World Population By Matthew Connelly

The intricate history of the population control movement. This is a well written, comprehensive book on the subject. Although the author has a bias, and declares so himself, I felt he did a great job in presenting the facts and events objectively. The history of this movement reads like a soap opera at times, with interest groups, NGOs, the church, and governments all vying for control and influence. While I don’t necessarily agree with some of the author’s conclusions, I do think it is very important to note, in the authors own words: The only factor that has consistently and convincingly been found to correlate with lower fertility is increasing women’s education.

The Fortune Tellers: Inside Wall Street’s Game of Money, Media and Manipulation By Howard Kurtz

An interesting, though dated, book which outlines why you should not trust any analyst you see on TV or any of the personalities appearing on financial channels such as CNBC. While historically interesting I would not characterize this as essential reading, although its central arguments remain true today.

The Last River: The Tragic Race for Shangri-la By Todd Balf

Unfortunately I did not get to see Solo at the International Documentary Film Festival Amsterdam but I’m sure it would have been a good companion to this book, which documents the tragic 1998 kayaking expedition to the Yarlung Tsangpo gorge. One of the most remote places on Earth. It provides an interesting glimpse into the psyche of adventurers and practitioners of extreme sports.

The Arraignment By Steve Martini

A legal thriller / mystery novel. While entertaining, I wouldn’t recommend it.

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What happened to our dreams of phage?

I want to talk about bacteriophages and more specifically phage therapy, that is using phages to treat bacterial infections. While I have known about phages for several years, I’ve only recently gained enough knowledge in biochemistry to better appreciate the elegance of the solution they provide. Simply put bacteria evolve, chemicals (antibiotics) don’t. A changing threat requires an adaptive solution.

I will not go into the details, except to say that phages are just viruses that infect specific bacteria. Similarly, the full history of phage therapy is long and interesting but beyond the scope of this post.

Back in 1997 the BBC program Horizon (episode “The Virus that Cures”) introduced many people to phage and sparked much interest in the West. So here we are 11 years later and it seems that very little has happened. So where did things go wrong?

First it must be realized that a phage is VERY specific in which bacteria strain it targets. This property is very useful medically but very problematic for companies looking to deploy phage based treatments. The specificity leads to two possible types of treatment:

  1. The first would be a highly personalized approach where the particular strain affecting a patient is determined and a phage collection is checked to see if there is an existing phage which targets that particular bacteria. If the matching phage is not in the existing collection, a new lytic phage must be found, although this could take quite some time.
  2. The second option is to just create a cocktail of different types of phages for common bacteria, and hope you get lucky. This would probably be very effective for a majority of cases. Of course if your cocktail is ineffective, you would have to go to the personalized approach.

Now it important to note that it is very difficult to get the FDA to approve a cocktail. In the domain of personalized treatments, it is not exactly clear how a company would have to get approval from the FDA (which takes about 12 years on average) if they wanted to treat a single person with a brand new phage. Add to this that fact that single biophages can not be patented and you get a perfect regulatory storm.

My research seems to indicate that several pharmaceutical companies which have tried to test the FDA waters (Targanta Therapeutics [formerly PhageTech] and Exponential Biotherapies) have met with little success. Although the FDA has allowed the use of phages on meat products in the food industry to prevent food poisoning.

So from an investor’s perspective the best policy seems to be just sitting back and waiting for some big changes in FDA regulation. In the mean time it would be a good idea to keep an eye on developments outside the US, particularly on countries with much more relaxed regulation. Depending on the exact change in regulation which will come inevitably, a company’s large collection of phages may go from being just scientifically priceless to a valuable capital asset as well. Of course this change in policy may only come about once the antibiotic resistance situation is way out of control. Until then, the bacteria will divide as they always do and the FDA will sleep as it always does.

Here are the companies I looked at:

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Ubuntu / Vista dual boot installation on a Sony VGN-FZ

So you want to dual boot Ubuntu and Windows on your Sony VAIO VGN-FZ** laptop? Here is a quick guide to help you through the procedure. It will assume you are starting on a brand new laptop with Vista pre-installed. If this is not a new laptop then backup, backup, backup.

  1. Remove all the useless bloatware which Sony has installed.
  2. Create recovery DVDs. Sony does not provide any recovery disks so you should make some in case….
  3. Use the Start Menu > Computer > Manage > Disk Management to “Shrink Volume” of the main system partition. Note that Sony will have a 9 Gb EISA recovery partition at the start of the drive (I would recommend leaving this alone).
  4. Yes, the Shrink Volume feature will only let you shrink it to about half, if you want to get by this then disable system restore, the pagefile, and hibernaion. With these disabled you can shrink the Vista partition to 48 Gb after defragmenting the drive. This allowed me to have the following partition setup on a 250 Gb drive:
    1. 9 Gb EISA recovery partition
    2. 48 Gb Vista partition
    3. 30 Gb FAT32 partition to share data between Windows and Ubuntu (created using Visa)
    4. 140 Gb Ext3 Linux partition (created by Ubuntu installer)
    5. 6 Gb Linux SWAP space (created by Ubuntu installer)
  5. If you want to be able to read your Linux data from Vista have a look at http://www.fs-driver.org/ or http://sourceforge.net/projects/ext2fsd
  6. Download the Ubuntu ISO for 64bit AMD and Intel computers from http://www.ubuntu.com/getubuntu/download
  7. Although you could burn it to a CD to install it, I would recomend using a USB key:
  8. Download UNetbootin from http://unetbootin.sourceforge.net/
  9. Get a USB key that is at least 1 Gb and backup the data on it.
  10. Run UNetbootin, point it to the Ubuntu ISO you just downloaded, and select the location of the USB key.
  11. Once UNetbootin has created the bootable USB key reboot the computer.
  12. Ubuntu will go into live CD mode.
  13. Select Install and follow the instructions.
  14. Selecting the manual partition choice will allow you to create the 140 Gb Ext3 partition which will be mounted as root and the 6 Gb Linux Swap partition (double the RAM size).
  15. If all goes well you will see the Grub menu upon restart. Select the first choice.
  16. The Grub menu will have two identical choices listed at the bottom. The second to last choice is pointing to the VAIO recovery partition. This confusion can be cleared up by changing the Grub menu using “su gedit /boot/grub/menu.lst
  17. Go down until you see:

    title Windows Vista/Longhorn (loader)

    root (hd0,0)

  18. Change the title to “VAIO Recovery Center EISA Partition” to clear up any confusion.

Next we come to Sony VAIO specific problems in Hardy Heron (Ubuntu 8.04):

  1. The backlight is stuck at full intensity.
  2. Download the xbacklight package using the System > Administration > Synaptic Packag Manager
  3. Write a small script which has the following two lines:

    xrandr –output LVDS –set BACKLIGHT_CONTROL native

    xbacklight -set 50

    where 50 is the percentage intensity.

  4. Headphones dont work without some modifications. Add the folowing line at the end of the file /etc/modprobe.d/alsa-base

    options snd-hda-intel model=vaio

  5. To get mic working edit your /etc/init.d/alsa-utils as described here: http://ubuntuforums.org/showpost.php?p=4502727&postcount=4
  6. Switch to the internal mic then enable Capture in the volume control panel and set your mic recording level as explained here: http://ubuntufs.wordpress.com/2006/06/08/trouble-with-your-microphone/
  7. Get your Motion Eye Webcam working by following the steps outlined at this site: http://www.palmix.org/r5u870-en.html

Enjoy Ubuntu!

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More books reviewed

The Alchemist by Paulo Coelho

This book has come with very high recommendations from several people I’ve met while travelling. Earlier this year I heard that a big-budget movie was being developed based on the book and knowing Hollywood’s terrible track record for movie adaptations, I definitely wanted to read the book before any movie came out. While short at under 180 pages, the book certainly lived up to its expectations. The plot centers around the journey of a boy as he journeys in search of a treasure in Egypt. Along the way he meets many interesting characters and learns some important lessons about life. An excellent read, highly recommended.

The Future of an Illusion By Sigmund Freud (1927) (http://en.wikipedia.org/wiki/The_Future_of_an_Illusion)

James Strachey 1961 Translation

An excellent essay by Freud on the nature of religion and why it is needed (for now) to ensure the survival of civilization. Although this was written in German originally, even in English the ideas presented are integrated into a beautiful smooth structural flow. Freud is able to predict many of the criticisms the reader may develop and address them. Perhaps Freud’s biggest strength is his ability to logically take on subjects which to this day are somewhat taboo in society (eg. People’s fear of death).


Slipping into Paradise: Why I Live in New Zealand By Jeffrey Moussaieff Masson

An interesting book comparing life and society in New Zealand with the rest of the world.

A Shortcut Through Time: The Path to the Quantum Computer By George Johnson

A generalized introduction to quantum computers, the problems where they would succeed over classical computers, and some of the algorithms developed for these problems.

Hacking Matter: Levitating Chairs, Quantum Mirages, and the Infinite Weirdness of Programmable Atoms By Wil Mccarthy

Perhaps a bit old now, this book gives an overview of the research being done towards the goal of creating a type of programmable matter which would allow us to fully control a variety of properties normally in the hands of nature.

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Tutorial: 3d Visualization for MEMS

Several months ago I was asked to comment on how I created the 3D visualizations for several MEMS designs. What follows is a step by step description of the process used.


Tools Needed:

First, begin by exporting your model in GDSII format. I have found that for best results the exported GDSII model should be a single cell (flatten the hierarchy if necessary). Both KLayout and LayoutEditor can be used to view the GDSII file, which will look something like this:

Layout

Next the process file used to fabricate the device must be written. Each layer is described in a similar fashion:

LayerStart: POLY0 (layer name)
Layer: 13 (the layer number in the GDSII file)
Height: 2000 (uses the same units as the GDSII file; starting height of the layer)
Thickness: 5000
Red: 1
Green: 0.9
Blue: 0.75
Filter: 0
Metal: 0
Show: 1
LayerEnd

Once you have written your process file, run gds2pov from the command line:

> gds2pov -i model.gds -o model.pov -p process.txt

This will generate a .pov file for your model. Open this using POV-Ray and set the render image size under the “Render > Edit Settings” menu. Finally, set your camera angles in the pov file:

camera {
location <188,257,-279>
sky <0,0,-1>
look_at <8,27,0>
}

The camera angles may need some adjustments based on your particular model. Running the script will render the model as seen from the camera angle chosen. This is the final rendering of the layout shown above:

Enjoy!

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Book reviews

I’ve compiled some short reviews of the books I’ve read recently.

Adventure Capitalist by Jim Rogers (http://www.jimrogers.com)

Good book chronicling one of the world’s longest road-trips by famed investor Jim Rogers at the turn of the millennium. While overall a great read, some countries are only briefly mentioned and he could have added more discussion on the various predictions and conclusions he makes as a result of the trip including:

• The new commodity bull market has started.
• The twenty-first century will belong to China.
• There is a dramatic shortage of women developing in Asia.
• Pakistan is on the verge of disintegrating.
• India, like many other large nations, will break into several countries.
• The Euro is doomed to fail.
• There are fortunes to be made in Angola.
• Nongovernmental organizations (NGOs) are a scam.
• Bolivia is a comer after decades of instability, thanks to gigantic amounts of natural gas.

Tai-Pan by James Clavell

A true classic which is hard to put down once started. A fascinating look at the opium trade, founding of Hong Kong, and international relations with China in the 1800s all wrapped around an excellent plot. It also got me looking at the history of Malaria (http://www.malariasite.com/MALARIA/History.htm).

Freakonomics by Steven D. Levitt and Stephen J. Dubner (http://freakonomics.blogs.nytimes.com)

I first heard about this when Prof. Steven Levitt went on the Daily Show to discuss some of his interesting findings. Simply put, when given access to rare types of datasets an economist can come up with many interesting insights into the world.

White Gold: The Extraordinary Story of Thomas Pellow by Giles Milton

In early April there was an article titled “Freedom of the Cyber Seas” over at CSO Online (http://www.csoonline.com/article/print/329164) which compared piracy on the high seas in the late 18th century with the current security problems on the internet. This book provides further insight into how the European powers attempted to deal with the Barbary states and centers around the story of Thomas Pellow who was captured on the high seas and served Sultan Moulay Ismail for over 20 years.

Ambassador without Credentials by Sergei Snegov

Written in 1977 by Soviet SF author Sergei Snegov, this is a collection of 12 short stories exploring various ideas being researched by two brilliant brothers as they attempt to solve various mysteries. One of the stories lays out the same fundamental ideas explored in Michael Crichton’s Sphere over 10 years later.

Heart of Darkness by Joseph Conrad

The inspiration for the film Apocalypse Now, follows a journey up a river in the Congo to an ivory trading station. Complex, dark, psychological, it succeeds in putting the reader into the same state of mind Conrad must have experienced in his own journey up the Congo River in 1890.

Coalescent by Stephen Baxter

Average SF book exploring the possibility of humans using a hive type social structure as seen in beehives or ant colonies.

Tales from the White Heart by Sir Arthur C. Clark

A great collection of short stories centered around discussions at a small London bar in the 1950s.

Hyperspace: A Scientific Odyssey Through Parallel Universes, Time Warps, and the 10th Dimension by Michio Kaku (http://www.mkaku.org)

An excllent look at the historical development and implications of theories based on a multidimensional universe.

The Fourth Protocol by Frederick Forsyth

Good thriller centered around a plot by the Soviets to destabilize the UK government.

Hunting Al Qaeda by Anonymous

An account of the time spent in Afghanistan by a special forces unit of the US National Guard which tends to focus on the bureaucratic nightmare they encountered.

Chasing Shakespeares by Sarah Smith

A fictional book about two scholars investigating the Shakespeare authorship question in London. (http://en.wikipedia.org/wiki/Shakespeare_authorship_question)

The Trudeau Vector by Juris Jurjevics

A good thriller about an epidemiologist sent to determine the vector for a pathogen which is killing researchers at a remote Arctic station.

The Camel Club by David Baldacci

A decent thriller about a high-level conspiracy in Washington.

The Broker by John Grisham

Another decent thriller about a Washington lawyer being chased by various intelligence services.

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