NEETHI - fundamental fun !

Why is the sea blue?

2010-01-10T20:18:00.004-05:00

It is well known in the history of science that study of some natural phenomenon has been a starting-point in the development of a new branch of knowledge. One such example is the following. In 1919, Sir C.V. Raman was studying the phenomenon of diffraction and molecular light scattering, especially in the context of liquids. His interest in this topic was aroused by an interesting experiment: a beam of white light was passed through a tank containing a solution. Certain chemicals were then added to this solution so that it gradually changed from a clear liquid into a turbid one. This was due to the production of particles which then remained suspended in the liquid. Naturally, the intensity of the transmitted light decreased as the turbidity increased, and at one stage the light was almost cut off. Interestingly, it was found that with the further passage of time, not only the intensity of the transmitted light increased, but also its colour went through a series of changes — indigo, blue, blue-green, greenish-yellow, and finally white. Why did such a thing happen? An explanation was necessary. Lord Rayleigh was able to explain the initial decrease in intensity of the transmitted light but had no answer for the strange appearance of colours later. Raman was able to explain this. First, he considered the way the light wave is diffracted by the individual particles, and then how these different diffracted waves combined together, either constructively or destructively, to produce an overall effect. There was one more intriguing question: What if the diffraction is not by a suspended particle but by a molecule? In 1921, Raman was returning to India via sea after his first ever visit abroad. He was fascinated by the deep blue colour of the Mediterranean and began to wonder why the sea is blue. Earlier, Lord Rayleigh who had successfully explained the blue colour of the sky had declared, "The much-admired dark blue of the deep sea has nothing to do with the colour of water but is simply the blue of the sky seen in reflection." In short, the sea is blue because it is merely reflecting the blue sky — this was Lord Rayleigh's explanation. Raman was not satisfied with this explanation, and further investigated this matter in detail . His observations revealed the following: (i) light can be scattered by the molecules of water just as it can be by the molecules of air, and (ii) that the blue colour of the sea is due to such molecular scattering just as the blue of the sky is. In his seminal paper on the molecular scattering of light, Raman concluded the following: "In this phenomenon, as in the parallel case of the colour of the sky, molecular diffraction determines the observed luminosity and in great measure also its colour." Raman thus proved that the sea is blue because the molecules of water scatter light just the same way molecules of air do. This was an important result which not only disproved Lord Rayleigh's explanation, but also had further implications in understanding the interaction of light with molecules, especially in the context of Raman effect.

The 'HOLE'Y light

2009-11-18T20:15:00.007-05:00

A French scientist working in Japan had problems communicating in Japanese. He had asked the technician in the lab to drill 100 holes in square centimeter of a metal sheet, but the technician drilled 10000 holes in the same area. Then the French scientist performed the following experiment –

He shined light of intensity A through the perforated metal film and obtained light of intensity B at the other end. To his surprise, intensity B was far greater than intensity A (B >>>> A) This is the remarkable story of Thomas W. Ebbesen, who discovered the extraordinary transmission through sub-wavelength apertures.

What is a sub-wavelength aperture ?

It means that the diameter of the hole drilled in the metal film is lesser than the wavelength of the incident light. See the picture above…

Why does this extraordinary transmission happen?

This amazing effect is due to the interaction of the light with electronic resonances in the surface of the metal film, and they can be controlled by adjusting the size and geometry of the holes.

This knowledge is opening up exciting new opportunities in applications ranging from subwavelength optics and optoelectronics to chemical sensing and biophysics. If the output surface surrounding the aperture is also corrugated, a surprisingly narrow beam can be generated, having a divergence of less than a few degrees, which is far smaller than that of the single apertures. This is because the light emerging from the hole couples to the periodic structure of the exit surface and to the modes existing in the grooves—which in turn scatter the surface waves into freely propagating light. This then interferes with the light that has travelled directly through the hole generating the focused beam.

What’s the use of this ?

In the field of opto-electronics for instance, studies are being carried out to extract more light from light-emitting devices. The metal electrodes of such devices, which are normally a source of loss, can be structured with holes to help extract the light from the diode. The need for ever-smaller features on electronic chips is pushing photolithography to use shorter wavelengths, with the associated increased costs and complications. The use of extraordinary optical transmission could perhaps circumvent this problem by using plasmon-activated lithography masks. Thes holes might find use in quantum optics. For instance, hole arrays are promising tools in the study of the physical nature—quantum versus classical—of plasmons as collective excitations when implemented in quantum entanglement experiments. They can also be harnessed for bio-detection where the molecule of interest can be specifically illuminated with a subwavelength aperture. The high optical contrast of these holes, their small sizes and their simplicity make them ideal candidates for integration on biochips as sensing elements. As in all plasmon enhanced phenomena, both the input and output optical fields can be strengthened, with the additional feature that the structure can potentially focus the signal towards a detector.

Recently, an opposite trend has also been observed. Say, you have very thin metal film which is so thin (nanometer thickness) that it is transparent. If you incident light through this film, most of the light passes through it, which is quite obvious. Now, if you perforate same kind of holes as mentioned above in them, then the intensity of the out coming light is drastically decreased! This observation has further led to excitement in the field…

It’s indeed amazing that how the everlasting light continues to awe us…

SINGLE DYE MOLECULE AS AN OPTICAL TRANSISTOR

2009-07-05T20:06:00.003-04:00

During 2nd year of my Ph.D.(2005-06) at JNCASR, I had the privilege of presenting a general seminar on ELECTROMAGNETICALLY INDUCED TRANSPARENCY. One of tricks I came across during the preparation of the talk was to modulate electronic transition of an atom or a molecule by intelligently choosing a pump and a probe laser beam. Based on the same principle, a letter in NATURE reports ‘A SINGLE MOLECULE OPTICAL TRANSISTOR’

Following are the highlights of the paper for a science enthusiast:

1. Just as electrons in an electronic device can be modulated by transistor, photons radiated from a single dye molecule can be modulated (i.e., amplified or attenuated) using laser beams, which makes the whole system an optical transistor.

2. A pump laser beam (a pulsed laser) acts as gate and a probe beam (continuous wave laser) acts as the source.

3. By varying the power of the gate laser, the absorption and emission of light from a dye molecule can be modulated.

Following are some of the advantages of an optical transistor:

1. Photons are better candidates for long distance communication.

2. Unlike electronic signals, photonic signals do not perturb each other.

3. Coherence of photons can be maintained at a relatively higher temperature than electrons, which make them better candidates for quantum computation.

This recent report is indeed a breakthrough, and it is worth prusuing further research on the same lines. Ultimate goal can be an OPTICAL COMPUTER……

Catalytic Motors

2009-05-22T10:31:00.003-04:00

Research on nanoscale robots is opening a completely new trend in the way we look at the world, and has derived interest from various quarters of science and technology. If the robots at nanoscale do their job as desired, their potential and utility are unbound. One of the major hurdles towards such a design is the interaction of the robots with its local environment. It is well know that when things shrink to the nanoscale, the Brownian motion plays a vital role in the movement of such nanoscale object, and an ‘extra’ amount of force has to be spent by the object to overcome the ‘random walk’. At these scales, Brownian motion makes it all but impossible to keep a steady direction of motion while immersed in a fluid. In fact, all molecular-scale motors in nature—including muscle proteins and the enzymes that produce ATP—are either constrained to run along a track or embedded in a membrane due to this. But this does not discourage us from building motors at nanoscale. In fact, there are now many smart methods to overcome the above disadvantage.

One such method is the Catalytic motor. The idea behind this is very simple: create a chemical reaction at the surface of an object which is coated with a catalyst. When the reaction takes place, the product will escape the surface, which further propels the object in the opposite direction. Let’s see an example of this.

In 2001, Rustem Ismagilov (now at Chicago) and George Whitesides, both then at Harvard University found that centimeter-scale “boats” with catalytic platinum strips on their stern would spontaneously move on the surface of a tank of water and hydrogen peroxide ( H₂O₂). The platinum promotes the breakup of H₂O₂ into oxygen and water, and bubbles of oxygen formed that seemed to push the boats ahead by recoil, the way the exhaust coming out the back of a rocket gives it forward thrust.

Wonderful !.....isn’t it….now the question is how do you bring this down to nanoscale. Ayusman Sen and coworkers at Penn State University came up with a smart idea: Their miniaturized version of the Harvard engine was a gold-platinum rod about as long as a bacterial cell (two microns) and half as wide (350 nanometers). The rods were mixed into the solution, rather than floating on the surface. Like the ATP-powered molecular motors inside the cell, these tiny catalytic cylinders were essentially immersed in their own fuel. And they did indeed move autonomously, at speeds of tens of microns per second ! But the reason why they moved was different from the Harvard engine. The way these nanorods actually work is that they apply a continuous force to prevail over the drag with no need for gliding. At the platinum end, each H₂O₂molecule is broken down into an oxygen molecule, two electrons and two protons. At the gold end, electrons and protons combine with each H₂O₂ molecule to produce two water molecules. These reactions generate an excess of protons at one end of the rod and a dearth of protons at the other end; consequently, the protons must move from platinum to gold along the surface of the rod. Like all positive ions in water, protons attract the negatively charged regions of water molecules and thus drag water molecules along as they move, propelling the rod in the opposite direction as dictated by Newton’s law of motion that every action has an equal and opposite reaction. And thus a catalytic motor works…..still there are plenty of things to venture, and am sure more progress will be made in this field in coming years.

Every time I come across these nano-excitements in science, a quote by Feynman always resonates in my mind “There is plenty of room at the bottom”, and what a prophetic statement it has turned out to be !

Jellyfish, GFP and Douglas Prasher

2009-05-14T09:35:00.009-04:00

Nobel Prize in Chemistry for the year 2008 was awarded "for the discovery and development of the green fluorescent protein, GFP". Three scientists shared this prize: Osamu Shimomura, Martin Chalfie and Roger Tsien, and I was awestruck to learn the stories behind their discoveries.

Now, coming to the molecule, GFP is a fluorescent protein with it's emission maxima at 509nm, and has been one of the vastly used visual markers in molecular biology today.

Shimomura was one of the earliest to discover the significance of GFP when he was studying the bioluminescence property of jellyfish. Many of us would have observed a spectacular image of a glowing jellyfish, which is due to the emission of a specific kind of a protein expressed in these organisms. When Shimomura isolated the protein from the jellyfish, to his surprise, he observed that the proteins emitted blue light instead of green. Further studies showed that jellyfish contains another protein which absorbed the blue light and emitted green light, which led to its bioluminescence. This phenomenon is nothing but Forster's Resonance Energy Transfer (FRET), and I was trilled to know that jellyfish too makes use of it !

In 1988, Chalfie heard about GFP, and realized that it can be harnessed for in vivo bioimaging. He further came up with molecular biology methods to introduce GFP gene into the DNA of a small worm called C. elegans. His methods showed self expression of GFP by cells, and led to it's usage in imaging various organelles and organisms.

The real mechanism of the fluorescence emission was unveiled by Tsien. He showed a one to one correspondence with the structure and emission of GFPs. He further tweaked the structure of GFP to vary the emission maxima of the fluorescence, and thus engineered the emission mechanism. In time, his group also added further fluorescent molecules from other natural sources to the tag collection, which continues to expand.

I like to mention another key person who was involved in this discovery - Douglas C. Prasher. In fact, Prasher was the first to clone and sequence the gene of GFP, but unfortunately, he lost his tenure as a professor and could not continue his research on GFP. It was sad to know that he is now a courtesy shuttle-bus driver. It highlights that a so-called 'good system' can still err in making the right choice.

To conclude, in today's molecular biology, one cannot imagine the absence of fluorescent markers. It has now become integral part of biological research, and has led to deeper insights in understanding biology at the molecular scale. This prize was a celebration for basic science, and signifies the importance of analytical methods, and shows that revealing secrets of nature always leads to enlightenment.

Seeing minus infinity…almost!

2009-05-07T22:16:00.008-04:00

On 23^rd April 2009, NASA’s SWIFT satellite recorded the farthest star burst ever in the history of astronomy. The observation with acronym GRB 090423 (GRB is gamma ray burst) recorded a red shift of 8.2, which corresponds to an event in the universe as early as 630 million years since big bang. The accompanying picture is from Gemini North Telescope in Hawaii, USA. On the electromagnetic spectrum, gamma rays are at the blue end, which makes them most energetic radiation. The gamma ray bursts essentially occur due to collapse of a massive star at a distant galaxy to form a black hole. Tremendous amount of energy is released during this event which acts a window to decipher many of the puzzles of early universe. These bursts are also dubbed as novas and supernovas depending on their intensity. One of the spectacular aspects of these bursts is the relativistic jets along the axis of the rotation of the collapsing star. These jets are collimated emission of radiation, which arise due to the frictional collapse of matter towards the center of the black hole. It has been estimated that energy as much as 10⁴⁴ J is released during this process. However, the mechanism of the collimated emission is still under debate in astrophysics. The initial burst of gamma rays is followed by an afterglow of other electromagnetic radiation like x-rays, UV, visible etc. which unveil a wealth of information about the collapsing stars in other galaxies. It is indeed a wonder that what we see in these burst is not only an event which is very, very far from us, but also something which happend when the universe was a mere one-twentieth of its current age. Well, for me, this is almost as good as seeing minus infinity !

Introduction to NEETHI

2009-04-29T23:47:00.003-04:00

Ever since I started as a student of science, I have been deeply influenced by the fundamental concepts of it, and have realized that no matter how sophisticated my research turns out to be, it finally bogs down to be a massive knot of basic concepts which has to be disentangled. My gurus Prof. Srinivasan and Prof. Ranganath (both at RRI) always emphasized the importance of ‘keeping in touch’ with the fundamentals of science because at every phase of a researcher’s life they play a priceless role. With this advice in the hindsight, I begin NEETHI, in which I shall frequently share with you an interesting concept/law in science, which may be either new or old. Inhere; I shall not discriminate between physics, maths, chemistry or biology, as I believe that they are all different colours of the same scientific rainbow.

I hope this blogsite will serve as a good platform for us to share scientific knowledge, and stay in touch with our fundamentals...so below blog is a simple example..

Colour of a shadow

2009-04-29T23:25:00.005-04:00

Ever wondered what is the colour of a shadow in sunlight ? At first we may think either black or grey as the answer, but that is NOT TRUE! There was a recent article in Physics Education titled "What colour is a shadow?" which proves that in bright sunlight, the dominant colour of a shadow is BLUE ! Although this fact may be non-trivial to our eyes, the author of this paper proves this by the following experiment :He takes a digital photograph of a white sheet of paper in sunlight and shadow, and further analyzes them using a shareware called ImageJ(which is free to download). He quantifies the pixel intensity of the RED, GREEN and BLUE, and finds that 50% of the light intensity constitutes blue colour.

It is a simple and elegant experiment, and reveals an interesting fact....shadows have their colour blue !