I found this very interesting site about the periodic table of elements, from the University of Nottingham. For each element, there’s a video showing the characteristics of the element, and a brief commentary. Worth checking out if you always had some curiosity about the chemical elements, what they look like, and how they behave.
They also have a youtube channel for even more interesting short movies about chemistry and physics.
Of the many things I posted, I never had the chance to write something about my direct scientific activity. Recently I worked on optical properties of polyenes. A paper has been published recently on Journal of Chemical Physics. Another one is submitted right now, and a third is in preparation.
Molecules interact with light. This should come to no surprise, as (for example) the whole world of colors depends on this effect. The most trivial interaction between the light and a molecule is normally absorption of one photon followed by emission of the same photon. Nothing changes in terms of energy of the photon. A given wavelength enters, the same wavelength leaves. The molecule is unchanged and unaffected by the event, except for a brief excitation of the electrons cloud. This event is typical linear optics behavior.
However, if we increase the photon density enough, two photons can be absorbed at the same time by the same molecule. After this event takes place, the molecule has many choices to return to electronic ground state. One is to re-emit two photons again. Nothing changes, still a linear optics effect.
However, the molecule could also release a single photon, whose frequency is derived by the total amount of energy provided by the two original photons. In other words, a photon of frequency twice the original will be emitted. This is called Second Harmonic Generation and if you have seen a green laser pointer, you directly experienced this effect: the green laser diode is in reality a very strong infrared laser diode covered with a crystal of potassium titanyl phosphate. The infrared photons are absorbed and doubled by the crystal into the green wavelength we see. Exactly the same phenomenon is used with blue lasers used for Blu-ray technology.
Frequency doubling is just one of the non-linear optics effects. There are many more, and they are promising to develop optoelectronic devices, where we control light with an electric field. Unfortunately, in most cases the intensity of non-linear effects is very, very small. You need a very strong laser emission to reach a sufficient photon density for the phenomenon to be appreciable (or used for pratical, non purely instrumental purposes). Moreover, we are using inorganic crystals at the moment, but crystals are fragile, tend to degrade as they are under thermal and optical stress, and they cost a lot. As a consequence, research focused on organic compounds, carbon-based molecules able to produce sizable non-linear optics effects at a fraction of the price, better mechanical properties, and less degradation. Having a polymer able to produce strong non-linear effects would dramatically reduce the cost and increase the life of these devices.
Exploring the chemical space of organic compounds in the “wet lab” is demanding, polluting, and in some cases unachievable, so we simulate the lab on a computer, running a computational method that predicts the intensity of the non-linear effects of a molecular structure of our choice. Our task is therefore to produce a lot of molecules, feed them into this computational machinery, get the evaluation of the non-linear behavior, and try to spot some rules to guide us in maximizing the characteristics we are interested in. As it frequently happens, there’s no “perfect compound”. Instead, there’s a good trade-off, but we are interested in devising rules, not finding the perfect molecule with a brute force approach (which is unachievable, there are simply too many compounds possible out of carbon, hydrogen, nitrogen, oxygen and sulphur: infinite).
My work was focused on polyenes. It’s a nice class of compounds with a nice single-double bond alternation. This allows “almost free” flow of electrons through this kind of molecular wire.
We know that non-linear optics properties are influenced by
We explored what happened to the non-linear properties as we increase the length of the chain, and at the same time, we include different combinations of end-caps substituents groups. We chose four critically important substituents: two electron donors, one strong (NH2), one weak (OH), and two electron acceptors, one strong (NO2) and one weak (CN). In addition, we used the neutral substituent H. Results were very interesting, and in some cases unexpected. Among many other things, we found that the presence of two substituents can be approximated, in some cases, as a simple addition of two single substitutions, meaning that for certain lengths of the chain, the interaction of the two groups vanishes and they behave as they are isolated.
We also found that the presence of these groups distorts the molecule from its linear, rod-like shape to a C-shaped or S-shaped chain, depending on their nature. This is rather remarkable finding, as there was no computational report for this and very scarce experimental report only on a similar class of compounds. The shape of the molecule has both an effect on the non-linear properties, and on how the polymer crystallizes (depending how good is the packing of the various chains). A new paper on the Journal of Physical Chemistry A has just been accepted on these findings, and it will be published as soon as the editorial process is performed.
So I have something to celebrate tonight. I think I’ll go out for a nice sushi!
On a dark, clear night, if you walk far away from the city lights, you will be probably able to see a magnificent strike of light we call “the milky way”, our galaxy. It looks like this:
The Milky Way, from Wikipedia
Our sun is a small, insignificant star, sitting on one of the arms of this magnificent spiral of stars and gas clouds. Any star you can see clearly with your naked eye belongs to the Milky Way, and it’s generally very close to us: hundreds or thousands of light years, small amounts when compared with the 26.000 light years that separates us from the galactic center.
Between October 2007 and August 2009, Alex Mellinger traveled around the globe taking incredible high resolution pictures of the Milky Way. Chunk by chunk, he produced one of the most stunning visual representations of our galaxy. The image can be zoomed, panned, explored. Play with it, I’ll wait right here.
Our galaxy is definitely not alone in the dark void of the universe. On the bottom right of the image you can enjoy the vision two nearby companions, the Large Magellan Cloud and the Small Magellan Cloud. They are smaller, irregular, and quite close to us. People living in the southern hemisphere enjoy these two objects of the night sky.
If you shift your attention to the left of the picture, you will probably notice a small diagonal bit of yellow light, just a little below the Milky Way. Zoom in, it’s a good friend the Andromeda galaxy:
Andromeda galaxy by John Lanoue
The Andromeda galaxy can be seen with the naked eye on a clear night. It’s quite far: 2.2 millions light years, but still pretty close. Its shape is close to the Milky Way’s one. Being so far, the photons we see today left the galaxy 2.2 millions year ago, and traveled since then to finally reach our eyes. This means that what we see right now it is the Andromeda galaxy as it was 2.2 millions years ago. Those photons left those stars when humanity was just leaving the trees.
There are other galaxies around in the sky. Each one is full of stars, each star probably full of planets. Each one far from us, the farther they are, the more back in time we look. We developed powerful telescopes in the last decades. One of them is probably the most well known, and the one that returned the most humbling and amazing images: the Hubble Space Telescope. Far high above the turbulent atmosphere, the HST has the best view of the sky we can ask for. So one day we point it at a patch of sky no larger than a pin, and slowly accumulate the photons hitting the detector. One photon after another, an image is formed. It is the Hubble Deep Field.
Hubble Deep Field
Every bit of light in this image is a galaxy. A full galaxy, full of stars. And they are far. The more far we look, the more we approach the time of the Big Bang. So we continued looking, deeper and deeper. The Hubble Deep Field South, the Ultra Deep Field. More galaxies. Everywhere we point our telescope, in bits of sky no larger than pin tips, we find galaxies, more galaxies, again galaxies. Galaxies everywhere, with stars, some of them with planets for sure.
We pushed even more. This image has been taken a few days ago, again from Hubble
This image contains galaxies whose light left for its quest of reaching us 13 billion years ago. Yes, some of these galaxies were there after just 600 million years after the Big Bang, dated by WMAP measurements 13.7 billion years ago. They are the oldest galaxies ever seen.
This is just the beginning. We continue taking pictures of other parts of the sky. More galaxies. Very soon we are sending up a new space telescope, the James Webb telescope. We want to see more, we want to peek back in time and approach those crucial moments where everything we know began. We explore it from the immense big of the sky, and from the immense small of the Large Hadron Collider. From our tiny, insignificant water-covered rocky planet, we need to understand, we need to see, and we need to find the truth. And it will happen in our lifetime.
You have probably read or heard about the Norwegian spiral and you have probably also seen it somehow. Of course, what’s the best answer to an unexplained phenomenon ? UFOs, aliens, black holes! I won’t link any material, you can find it everywhere. I will instead link the only rational analysis of the phenomenon. Thanks to Phil Plait, which is always a pleasure to read.
So, what was it? the spiral pattern is interesting, and the fact that it was only visible from Norway as well. The first fact indicates something that rotates while ejecting something, producing therefore a spiral. The second fact indicates something that is quite low in orbit, otherwise it would have been visible from many other places. The brightness of the observed fact is due to the sun.
Ok so, a rotating object ejecting something that brightens up in sunlight and it’s quite low in altitude… something like, a spent rocket?
But no! Both Norway and Russia deny any rocket launch. Of course they are telling the truth, so it must be alien technology! Of course… yeah, right…
Update: ok, so apparently it was confirmed and known that a rocket launch was to occur. Here is a link to a NAVTEX message about a rocket launch occurring in the area.
I am currently looking for a good choice of Content Management System/EPortfolio/Social Network tool to start the activity on wavemol.org . I don’t know exactly what kind of information wavemol will provide, although I know the argument: theoretical and computational chemistry. I believe that the main objectives of wavemol should be:
So long for the features, but I ask for more
I will update this post as I try more and more. Stay tuned. At the end, I will choose what I consider the best option from the ones I tried. All my experiments were made in one hour of tinkering (for some, a bit more). Although some would consider this time probably not enough, I want to have something easy with a gradual learning curve. If the developers had this focus in mind, it gives me a clear impression of the kind of care I can find in the product.
I will update this post as I try more solutions, stay tuned.
A groundbreaking paper “Generation of long RNA chains in water” from Costanzo, Pino, Ciciriello and Di Mauro on Journal of Biological Chemistry proposes conditions for the obtainment of complex RNA chains from cyclic nucleotides. The proposed conditions are typical for the pre-biotic Earth: hot springs and puddles with water at moderate temperature (40 to 90 C), without any organic or inorganic catalysis, with simply obtainable cyclic nucleotides. This allowed the formation of long RNA chains carrying the first genetic information, starting the natural selection process of improvement. The results on this paper propose an effective and important advancement for the last piece of the puzzle of evolution: how everything started.
I am playing with rdflib, a fantastic python library to handle RDF data. I had trouble understanding how to use contexts so to partition my ConjunctiveGraph into independent subgraphs. Here is the code
import rdflib
from rdflib.Graph import Graph
conj=rdflib.ConjunctiveGraph()
NS=rdflib.Namespace("http://example.com/#")
NS_CTX=rdflib.Namespace("http://example.com/context/#")
alice=NS.alice
bob=NS.bob
charlie=NS.charlie
pizza=NS.pizza
meat=NS.meat
chocolate=NS.chocolate
loves=NS.loves
hates=NS.hates
likes=NS.likes
dislikes=NS.dislikes
love_ctx=Graph(conj.store, NS_CTX.love)
food_ctx=Graph(conj.store, NS_CTX.food)
love_ctx.add( (alice, loves, bob) )
love_ctx.add( (alice, loves, charlie) )
love_ctx.add( (bob, hates, charlie) )
love_ctx.add( (charlie, loves, bob) )
food_ctx.add( (alice, likes, chocolate) )
food_ctx.add( (alice, likes, meat) )
food_ctx.add( (alice, dislikes, pizza) )
print "Full context"
for t in conj:
print t
print ""
print "Contexts"
for c in conj.contexts():
print c
print "love context"
for t in love_ctx:
print t
print "food context"
for t in food_ctx:
print t
Running this script will produce the full graph (printing the triples in ConjunctiveGraph) but also the subgraphs as assigned for each context.
A friend of mine just reported me a very tragic event. His bag with his laptop and his backups hard drive was stolen. I can feel his pain, having experienced the very same situation once, and I am writing here hints for him and the rest of the world to protect yourself from this eventuality.
Buy cheap. Computers can be expensive to buy again, but you can tolerate more the loss of a 13 inches macbook than a 17 inches macbook pro. Of course, you should buy the minimum that satisfies your actual needs, but if you can survive without a feature, or buy it external, you can spend less money and therefore loose less in case of theft.
Encrypt everything. As our lives are more and more represented on digital media, it could be a complete and utter disaster if they fall into the wrong hands. Bank access, credit card numbers, all our online passwords, health documents, tax documents, non open intellectual property, your MP3s, movies, family photos, software licenses, emails… in the hands of a thief ? Use Truecrypt to create an encrypted area on your media. As a key, you can use “something you know”, like a passphrase or “something you have”, like a well defined file acting as your key. I strongly advise against the latter: you can loose your keyfile, meaning that under no circumstance you will be able to access your data again. If the file is accidentally modified (e.g. it’s a MP3 file and some music program changes the ID3 metadata info), the file is no longer a valid key. Ditto. A long passphrase uses your brain, which is less prone to corruption. Choose wisely: you will not use this passphrase often, so it is something that under no circumstance you can forget. Anything chosen in the bout of the moment will be long forgotten the next time you open the backup. Of course, it is strictly important that nobody (yes, I really mean it, nobody) knows, can spy on, or can guess your passphrase.
For movable storage (like SD cards, USB keys and solid state disks you use for everyday data handling) use Truecrypt to create an encrypted disk image file onto the storage device. Do not encrypt the whole card. Instead leave a readable area, and put a textfile named “RETURN_LOST_DRIVE_DETAILS.TXT” containing something like “if found please contact me at me@example.com”. Remember the TXT extension so that windows users are not intimidated by an unknown file, as these devices can be used for social engineering. Encryption cannot work for SD card aimed at cameras or MP3 players, as the hardware device won’t be able to access the encrypted area. Complain with your camera/pod producer to add Truecrypt support (don’t hold your breath). If you use the SD as a disk for your computer, there’s no problem.
Computer: use the native disk FileVault encryption of Mac, and turn off autologin. Alternatively, create a Truecrypt volume and open it every time you perform login, but remember this won’t protect some parts of your personal life, such as your browser cache, from curious eyes. Using Truecrypt has the advantage of being cross platform: you can move your encrypted disk image and read it on Linux or Windows as well, while the Mac encrypted storage format can be opened only by Mac (as far as I know).
Backups medias: For optical devices, remember that CDs and DVDs tend to become unreadable with time. It makes sense to refresh your backup media every 5 years. In this span of time, you will likely have a larger storage format, allowing you to concentrate your data (e.g. from 5 CDs to 1 DVD). Of course, you have a single point of failure in that DVD, so you have to make two exact copies of them. Use different brands for the two physical supports! This protects you from a faulty shipment. Optical devices in general don’t become completely unreadable, but tend to develop areas of unreadability. If this happens, with some doctoring and the second optical media you should be able to recreate the original archive completely. It’s a good idea to store the md5 of the files you burn. This hint however is rather obsolete, as optical devices are used less and less.
Backup hard drives: if you prefer to get rid of optical media completely, and go hard disk, my personal solution is to buy a small disk and encrypt it with Truecrypt, whole. You are not supposed to loose backup disks, and if you loose them it should not be a tragedy. If you want to feel safer, use the textfile trick, but it should not be needed for backup disks. Once you get the encrypted partition, put the contents of your computer onto the disk with the following script
#!/bin/sh SOURCE_DIRS="$HOME:/another/dir:/and/so/on" TARGET_DIR="/Volumes/Backup/laptop/" # if the external drive is not there, complain and stop if [ ! -e "$TARGET_DIR" ] then echo Target directory does not exist! exit 1 fi IFS=: date=`date +%Y%m%d-%H%M%S` pushd . cd ~/ /usr/bin/rsync --backup --suffix="-backup-$date" --progress -av $SOURCE_DIRS "$TARGET_DIR" popd
This script automatically backs up everything in your home directory onto the backup disk. New files will be added. Old files you modified since the last backup will be renamed to append the date, and the new, updated file will be stored. This command never deletes anything from your backup disk. It always adds. Run this script with some frequency, as high as you feel safe. If the backup disk breaks down or is stolen, you will have the most recent files on your computer. If the computer is stolen, you can recover the files from the backup. You will have some cleanup to do, but still…
Sooner or later the disk will fill up. Buy a new, larger disk from a different company (again, to protect you from a faulty stock). Copy all the contents of your old backup disk into the new one, and continue adding data to the new one from your computer. Eventually you can remove old, unused stuff from your computer now, because you know that at least two copies exists: one in the first disk, one in the second. When the second disk fills up, repeat the procedure with a new, larger hard drive. Store all your backup drives in a safe, fire resistant place. Banks are specialized for this.
As you can see, older files gets replicated more than recent ones, but even the most recent file is always present in at least two copies: one on the latest backup disk, one on the computer. Even if one of your backup disks breaks down in 10 years, you will have the same data duplicated on later disks.
Now, there are only two points to address. The first one is to find the sweet spot in increased hard disk size that allows you to fill it up in approximately one year, so you can archive it and move on to a newer hard drive. This depends on your usage intensity. If you put large, transitory files on your computer, remember to delete them before running the backup. Same if you move large files around, they will be copied again (remember, the script never deletes anything).
The second point is relative to the most recent files you have on your computer: they are not backed up, so unless you run your script every day, you risk to loose something more than a day worth of work. For this, you can have a small USB key. You can trash the contents at the next run of the script.
What about online backups ? Well… do you trust them ? If you do, go for it. I don’t.
Summing up, the basic rules are:
Wikimedia fundation is organizing another round of fundraising to support Wikipedia. I wish to remember that the English version currently contains more than 3 millions pages.
Wikipedia is one of the most impressive and revolutionary achievement of the internet crowd. It changed the way culture is made available. Wikipedia is important for all of us. So please consider donating. The target is currently at 7.5 million dollars, with one million already collected. It’s still quite a way to go, but it can be achieved.
I want to take this post to add a bit of information about what’s going on behind the scenes here at ForTheScience. I have two posts in preparation, plus a large set of projects to manage. I will give a sneak preview:
Yes, more indeed, but I definitely need 48 hours/day!
I must confess: I have a crush on non-newtonian fluids. They are so strange and beautiful… They defeat intuition by respecting the laws of nature… and they are fun to play with!
Fluids can be characterized by a parameter known as viscosity. We all have direct experience of viscosity, as it measures the “ease of flow”: water flows easily when compared to honey. This behavior can be measured and quantified: higher viscosity for honey (a “thick” substance) and lower viscosity for water (a “thin” one). With more rigor, the term “viscosity” is a very generic term enclosing many different types of viscosities, depending on the experimental setup and the characteristics of the fluid. For the layperson, viscosity is a measure of thickness, what technically is called “dynamic viscosity”.
The pitch drop experiment at University of Queensland
Viscosity is not constant in a fluid. It is related to various parameters, the most typical is temperature: kitchen oil is rather thick when cool. Heat it up, and it becomes thin almost like water. Same for water, although it’s less evident. Boiling water is much thinner than cold water. For gases, it happens the opposite: the higher the temperature of the gas, the higher its viscosity is. Some substances can be so thick to behave like solids, for example glass and tar pitch: smash them with a hammer, they go into a thousand pieces. Heat them up, and they flow like a liquid. The fun part is that even when apparently solid, tar is actually showing its liquid properties in the so-called “pitch drop experiment”. Pitch is flowing through the funnel, but it’s very, very slow: since the experiment started, in 1927, only 8 drops of pitch fell, an average of one drop every ten years.
In classic, so-called “newtonian” fluids, viscosity is constant at a given temperature. Non-newtonian fluids are different: the applied stress itself, or the amount of time the stress is applied alter the viscosity. A non-newtonian fluid can be thin when left alone, but it becomes thick or almost solid when shaken or hit, or vice-versa.
A popular example of kitchen-chemistry non-newtonian fluid is corn starch: take starch, add a bit of water, and you obtain this
As you can see, the result is very thick when hit, but behaves more like a (relatively) thin liquid when left undisturbed. In other words, the mixture shows dilatant (or shear thickening) properties: the viscosity depends on the amount of applied stress, increasing thickness. Although the cornstarch and water mixture does not look particularly useful except as a curiosity, the same property can be exploited to engineer a material which is soft and pliable like rubber, but becomes hard enough to substitute polycarbonate when hit. It is the case with D3O
Pushing the dilatant property even further would effectively produce a “liquid body armor”: light and flexible in normal conditions, but able to stop a bullet when needed. Military and police forces all around the world have of course a great deal of interest in something like this.
Silly putty
Another very funny application of this kind of non-newtonian behavior is my preferred toy: Silly Putty. Basically the same concept: a rubber-like polymer flowing when left undisturbed, but hard when a strain is applied. It’s very soft, but it bounces hitting the ground. If you hammer it, it goes into pieces but it slowly flows and flattens if left undisturbed on a desk. Kind of interesting, its story. As frequently happens, one man’s discard is another man’s treasure.
There are other non-newtonian fluids that show shear thinning (or pseudoplastic) behavior. When stress is applied, their viscosity becomes lower, and from solid they become liquids. One example is quicksand, whose danger comes from its property of being relatively solid until pressure is applied (like when stepping on it). Applying pressure leads to a separation between the sand and the water from the mixture. This effectively produces a very thin liquid on top, and a thicker layer of sand deposit acting as an effective trap. To liquefy again this almost solid layer, the trapped person or animal should apply a lot of pressure above him to reintroduce water without exerting pressure below, something that would drag him deeper. This is not easy, and requires considerable strength. Quicksand is very dense, so drowning is not possible, and the human body would float half way like a cork. Nevertheless, being trapped and basically unable to walk away could become a considerable issue for other reasons, such as drowning for a raising tide, lack of food, or assault from wild animals.
Another example of pseudoplastic substance is Ketchup. It flows badly in normal condition, but if stress is applied (as when shaken, squeezed, or by hitting the bottom of the bottle) it liquefies, hence the saying “first a little, then a lottle, the Ketchup bottle“.
In some cases, shear thickening or thinning depends not on the amount of stress applied, but on the amount of time this stress is applied. The longer the application, the thicker (or thinner) the result. In these cases, we talk about rheopecty and thixotrophy respectively. Saint Januarius blood, a famous relic in Naples, Italy, contains a typical thixotrophic fluid, most likely a Iron(III) hydroxide compound. When the vial is left undisturbed, the gel behaves as a solid. Applying movement for a while is sufficient to show non-newtonian properties, leading to a liquid. An article on Nature has been published on this regard.
Shear stress is not the only factor influencing the viscosity of a fluid. New smart materials are now under development, where viscosity can be altered by exposition to light.