2018 Nobel Prize in Physics goes to the tools of light !!

The American physicist Arthur Ashkin, Gérard Mourou from France, and Donna Strickland in Canada will share the 9M Swedish kronor (£770,000) prize announced by the Royal Swedish Academy of Sciences in Stockholm on Tuesday. Strickland is the first female physics laureate for 55 years.


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The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Physics 2018 “for groundbreaking inventions in the field of laser physics” with one half to Arthur Ashkin “for the optical tweezers and their application to biological systems” and the other half jointly to Gérard Mourou and Donna Strickland “for their method of generating high-intensity, ultra-short optical pulses.”

Optical tweezers (originally called “single-beam gradient force trap”) are scientific instruments that use a highly focused laser beam to provide an attractive or repulsive force (typically on the order of piconewtons), depending on the relative refractive index between particle and surrounding medium, to physically hold and move microscopic objects similar to tweezers. They are able to trap and manipulate small particles, typically order of micron in size, including dielectric and absorbing particles. Optical tweezers have been particularly successful in studying a variety of biological systems in recent years.

The inventions being honoured this year have revolutionised laser physics. Extremely small objects and incredibly fast processes now appear in a new light. Not only physics, but also chemistry, biology and medicine have gained precision instruments for use in basic research and practical applications.
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Arthur Ashkin (born September 2, 1922) is an American scientist who worked at Bell Laboratories and Lucent Technologies after receiving his PhD at Cornell . He started his work on manipulation of microparticles with laser light in the late 1960s which resulted in the invention of optical tweezers in 1986. He also pioneered the optical trapping process that eventually was used to manipulate atoms, molecules, and biological cells. The key phenomenon is the radiation pressure of light; this pressure can be dissected down into optical gradient and scattering forces. Arthur has been awarded by Nobel prize 2018 considering his invention of optical tweezers that grab particles, atoms and molecules with their laser beam fingers. Viruses, bacteria and other living cells can be held too, and examined and manipulated without being damaged. Ashkin’s optical tweezers have created entirely new opportunities for observing and controlling the machinery of life.

Mourou at the École Polytechnique near Paris, and Strickland at the University of Waterloo in Ontario, each receive a quarter of the prize for work that paved the way for the shortest, most intense laser beams ever created. Their technique, named chirped pulse amplification, is now used in laser machining and enables doctors to perform millions of corrective laser eye surgeries every year.

Donna Strickland and Gérard Mourou developed a technique called chirped pulse amplification, which makes it possible to generate high-intensity, ultra-short optical pulses.  Strickland is only the third woman to win the Nobel Prize in physics, following Marie Curie in 1903 and Maria Goeppert Mayer in 1963.

“Obviously we need to celebrate women physicists, because we’re out there,” Strickland said in a phone call with the academy after the prize announcement. “And hopefully in time it’ll start to move forward at a faster rate, maybe,”

 

Strickland and Mourou worked together at the University of Rochester in the 1980s. Mourou was a physics professor who headed a group researching ultra-fast lasers at UR’s Laboratory for Laser Energetics. Strickland studied under him and was the primary author of a scientific paper that first described chirped pulse amplification in 1985.

In announcing the award, the academy described that article as “revolutionary.” It was Strickland’s first scientific publication.

Mourou and Strickland demonstrated what has been described as a stunning advance in laser power, with a table-top terawatt laser. At the time, the peak power of laser pulses was limited because of the serious damage the pulses caused to the material used to amplify them.

The technique that Strickland and Mourou developed takes a short laser pulse, stretches it, amplifies it and squeezes it together again. The breakthrough made it possible to create very precise laser systems.  The applications for the technology include Lasik eye surgery, semi-conductor manufacturing, and solid state hard drives.

Strickland received her undergraduate degree in physics from McMaster University in Hamilton Ontario and a Ph.D. in optics from UR in 1989.  She currently serves as associate professor and associate chair of the physics department at the University of Waterloo in Ontario, Canada. Mourou, a native of France, came to the University of Rochester after earning his PhD in 1973. He later worked at the University of Michigan, where he was founding director of the Center for Ultrafast Optical Science in 1991. In 2004, Mourou returned to France to become director of the Laboratoire d’ Optique Appliquée at ENSTA-Ecole Polytechnique in Paris.

Surface ice at Moon’s poles

Water is the preliminary and fundamental requirement needed for everyday life. It is very unique molecule due to some important chemical properties, it has high surface tension and high value of specific heat capacity and more importantly, it is the only substance found on earth in its all three states, gas, liquid and solid.  Our planet Earth is blue planet and hence its greenery only because of presence of water in it. Earth is estimated to have approximately 1.4 x kg water in the oceans.  It is supposed that water is present over the entire universe since study reveals its presence in the interstellar medium (ISM) as well as in the spectra of stars.

 

Achieving the milestone of one of the great mission, a team of space scientists, led by Shuai Li of the University of Hawaii and Brown University & Richard Elphic from NASA’s Ames Research Center in California’s Silicon Vally, directly observed evidence of water in the form of ice on the moon’s surface which was found in the darkest and coldest parts of its polar regions. This is the very first evidence directly observed by the scientist supporting water on moon’s surface.

Image above clearly indicates the distribution of ice (blue colored locations) at the surface of moon, South Pole (left) and north pole (right). Observation has been detected by analyzing data from NASA’s Moon Mineralogy Mapper instrument called M3. M3, the Chandrayaan-1 spacecraft, launched by ISRO in 2008 significantly equipped to the confirmation of the solid ice presence on the moon. Data and direct observations have shown that the most of the ice is concentrated at lunar craters (Temperature < -250 F) at southern pole while the northern pole’s ice is more widely distributed.

Currently, a team of scientist is learning more about this ice, possible interaction with lunar environment as a key mission for NASA and commercial partners to learn our closest neighbor, Moon.

 

If you want to see the full paper published, follow the link-  Water on the surface of the Moon as seen by the Moon Mineralogy Mapper: Distribution, abundance, and origins

News source: NASA

Scientific analysis of Rudraksha seed !

Rudraksha is considered as a very sacred object in the Hindu Religion whose botanical or scientific name is Elaeocarpus Ganitrus Roxb.

Presently, 38 varieties of Rudraksha is recognized and cultivated in Nepal, Indonesia, Sri-Lanka, India and some other countries of south–east Asia.

According to the Hindu Mythology, ‘Rudra’ is other name of Lord Shiva and ‘Aksha’ means eyes or tears so rudraksha means tears of Lord Shiva. So, it considered to acquire very high cosmic force due to its link with eye of Lord Shiva in Hindu Mythology.  Roy (1993) found that Rudraksha beads possess inductive and electromagnetic properties and controls the human activities through direct action on central nervous system.

Botanically, Rudraksha seeds, or beads, are simply a plant product, containing wide range of elements like Aluminium, Chlorine, Copper, Cobalt, Nickel, Iron, Magnesium, Manganese, Phosphorus, Potassium, Sodium, Zinc, Silicon, Silver and Gold. Presence of these elements shows electromagnetic properties as well as high density value in Rudraksha seed.

Not only it contains ingredients of elements but also composed of some fraction of gaseous substances like Carbon, Nitrogen, Hydrogen and Oxygen. The percentage compositions of gaseous elements can be determined by C-H-N Analyzer and by Gas chromatography. The result obtained from above instruments was found as it consists of 50.031% carbon, 0.95% nitrogen, 17.897% hydrogen and 30.53% oxygen.

Human body can be assumed as a bio-electric circuit which contains billions of networks of nervous system and other organs which are sensitive to electrical impulses generated by continuous heart beats, blood circulation, sensory and motor impulses in nerves, contraction and relaxing of muscles. This electrical impulse generates bio-electricity inside the animal body which then produces some value of potential difference within body parts hence flow of this current is possible. But, sometimes, due to stress and other cause, this flow of bio-electric currents as well as normal body function stops working properly and we call this state as illness or abnormal psyche.

 

How Rudraksha helps in reduction of illness and regain bio-electricity flow inside the body?

 

1)  As I mention above, Rudraksha is a versatile material composed of wide range of valuable elements. Wearing Rudraksha obviously helps to control, normalize and more importantly, regulates the flow of bio-electric current inside the body.

If we talk about current then we should think of characteristic factors depending on it viz; resistance, capacitance, inductance, magnetic induction etc.

As we have the relation,

Ohm’s Law,

V= IR,   

Where, V= voltage, I= current, R= Resistance.

From above equation, resistance (R) generates some specific ampere of current flow depending on the factor of resistance.

If we correlate this concept in our case, resistance coordinated with our heartbeat and then specific impulses to the brain to generate certain bio-chemicals in the brain which brings positive mood, confidence and feel better and energetic.

 

2) We know capacitor is a device used to store an electric charge.

 

Let us impose this idea to our case again, Rudraksha can be considered as a capacitor in a sense that it can store bio-electric energy. As said above, bio-electricity flow depends on physical activity, stress, heart beats, hormonal activity, and nerve cell impulse, which gives larger value of potential difference as well.  Wearing Rudraksha seeds helps to regain normal body conditions by absorbing this excess bio-electricity.

 

 

3) Also, Rudraksha is inductor which sends out specific inductive vibrations because of its unique magnetic properties due to presence of magnetic materials.

   People wearing Rudraksha feels better even if beads do not touch them physically due to the vibrations.

4) Due to presence of variety  of elements, Rudraksha possess both paramagnetic and diamagnetic properties.

It can change its polarity called dynamic polarity due to diamagnetic property. As dia-magnetism is the ability of any substance to acquire temporary magnetic property in presence of an external magnetic field. The bio-electric flow in the body also develops bio-magnetism depending on the polarity of the induced magnetic field.

When Rudraksha comes in contact with our body it setup its polarity opposite to the inducing field. That is why it helps to proper functioning of the blood vessels better than magnets.

In one single line, Rudraksha can be considered as versatile material due to its composition as well as its use in numerous useful works.

 

“The World As I See It” an essay by Albert Einstein

“How strange is the lot of us mortals! Each of us is here for a brief sojourn; for what purpose he knows not, though he sometimes thinks he senses it. But without deeper reflection one knows from daily life that one exists for other people — first of all for those upon whose smiles and well-being our own happiness is wholly dependent, and then for the many, unknown to us, to whose destinies we are bound by the ties of sympathy. A hundred times every day I remind myself that my inner and outer life are based on the labors of other men, living and dead, and that I must exert myself in order to give in the same measure as I have received and am still receiving…

“I have never looked upon ease and happiness as ends in themselves — this critical basis I call the ideal of a pigsty. The ideals that have lighted my way, and time after time have given me new courage to face life cheerfully, have been Kindness, Beauty, and Truth. Without the sense of kinship with men of like mind, without the occupation with the objective world, the eternally unattainable in the field of art and scientific endeavors, life would have seemed empty to me. The trite objects of human efforts — possessions, outward success, luxury — have always seemed to me contemptible.

“My passionate sense of social justice and social responsibility has always contrasted oddly with my pronounced lack of need for direct contact with other human beings and human communities. I am truly a ‘lone traveler’ and have never belonged to my country, my home, my friends, or even my immediate family, with my whole heart; in the face of all these ties, I have never lost a sense of distance and a need for solitude…”

“My political ideal is democracy. Let every man be respected as an individual and no man idolized. It is an irony of fate that I myself have been the recipient of excessive admiration and reverence from my fellow-beings, through no fault, and no merit, of my own. The cause of this may well be the desire, unattainable for many, to understand the few ideas to which I have with my feeble powers attained through ceaseless struggle. I am quite aware that for any organization to reach its goals, one man must do the thinking and directing and generally bear the responsibility. But the led must not be coerced, they must be able to choose their leader. In my opinion, an autocratic system of coercion soon degenerates; force attracts men of low morality… The really valuable thing in the pageant of human life seems to me not the political state, but the creative, sentient individual, the personality; it alone creates the noble and the sublime, while the herd as such remains dull in thought and dull in feeling.

“This topic brings me to that worst outcrop of herd life, the military system, which I abhor… This plague-spot of civilization ought to be abolished with all possible speed. Heroism on command, senseless violence, and all the loathsome nonsense that goes by the name of patriotism — how passionately I hate them!

“The most beautiful experience we can have is the mysterious. It is the fundamental emotion that stands at the cradle of true art and true science. Whoever does not know it and can no longer wonder, no longer marvel, is as good as dead, and his eyes are dimmed. It was the experience of mystery — even if mixed with fear — that engendered religion. A knowledge of the existence of something we cannot penetrate, our perceptions of the profoundest reason and the most radiant beauty, which only in their most primitive forms are accessible to our minds: it is this knowledge and this emotion that constitute true religiosity. In this sense, and only this sense, I am a deeply religious man… I am satisfied with the mystery of life’s eternity and with a knowledge, a sense, of the marvelous structure of existence — as well as the humble attempt to understand even a tiny portion of the Reason that manifests itself in nature.”

 

 You can listen audio at    https://www.youtube.com/watch?v=3Y0_aNvH0Wo

 

The text of Albert Einstein’s copyrighted essay, “The World As I See It,” was shortened for our Web exhibit. The essay was originally published in “Forum and Century,” vol. 84, pp. 193-194, the thirteenth in the Forum series, Living Philosophies. It is also included in Living Philosophies (pp. 3-7) New York: Simon Schuster, 1931. For a more recent source, you can also find a copy of it in A. Einstein, Ideas and Opinions, based on Mein Weltbild, edited by Carl Seelig, New York: Bonzana Books, 1954 (pp. 8-11).

 

Organic Molecules found in interstellar space !

Since historic times, we have wondered where we came from and where life originated. As it became apparent that the Earth was just one planet orbiting the Sun, that the Sun was just one star among ∼1011 in our galaxy, and that the Galaxy itself was only one such object among ∼1011 similar systems populating the Universe out to a cosmic horizon, with perhaps countless more lying beyond, it became clear that life on other planets, near some other star, in some other galaxy was possible. The cosmological principle also makes this idea philosophically attractive. It would suggest that life is some general state of matter that prevails throughout the Universe. The probability of finding some form of life, however primitive, on other planets either within the Solar System or around nearby stars seems very high from this point of view. Nevertheless, we are unable to predict where life should exist, mainly because we do not yet understand the thermodynamics of living organisms and what different forms life may take.

As we know, things to be in equilibrium they should follow some permitted rules. Likewise, thermodynamics distinguishes between three types of systems. Isolated systems exchange neither energy nor matter with their surroundings. Closed systems exchange energy but not matter, and open systems exchange both matter and energy with the surroundings. Biological systems are always open, but in carrying out some of their functions, they may act as closed systems. Biological processes also exhibit a well-defined time dependence. Some physical processes could take place equally well whether time runs forward or backward. If we viewed a film of a clock’s pendulum, we would not be sure whether the film was running forward or back. Only if the film also showed the ratchet mechanism that advances the hands of the clock, would we be able to tell whether it was running in the right direction. The pendulum motion is reversible but the action of a ratchet is an irreversible process. Biological processes are invariably irreversible. In an irreversible process, entropy, a measure of disorder, always increases. If a cool interstellar grain absorbs visible starlight and re-emits the radiation thermally it does so by giving off a large number of low-energy photons.

The Universe is fundamentally biological. Even the Urey-Miller experiment that simulated the theorized early pre-life conditions on Earth, and produced amino acids, suggests this. The ammonia used was obtained by a process involving hydrogen of bio-origin, and the methane was also biological in origin. Non-biological catalysts would be poisoned almost instantaneously by sulfur gases under pre-life conditions. What this means is that most of the material in interstellar grains must be organic or life itself would have been impossible. The spectrum for all grains along the line of sight from the galactic center to the Earth is very much like that of dry bacteria. Either the grains are bacteria or are organic grains in proportions like bacteria (amino acids, nucleic acids, lipids and polysaccharides). Therefore, both theoretically and observationally, organic constituents fit the observations. Organic materials or bacteria would easily align in magnetic fields, and could produce superconducting surfaces that would generate filaments. Organic materials or bacteria could more easily produce the variety of objects in the Universe than inorganic or non-biological materials. As with so much of its constituents, the Universe itself is fundamentally biological. In fact, so much is this the case that life constitutes a physical law; it had to arise, it was an inevitable complexity of the real world is even more extraordinary with a hierarchy of living things.

 

Life result of the laws of physics as they exist. Moreover, the evidence indicates that the variety and permeates all of space, it is built into the very substance of the Universe, and has even brought about its own self-consciousness we humans. Yet, we have done little, in the scientific realm, to ask one ‘open’ question: Why? And the reason is that most scientists are afraid to admit that the Universe is purposeful and fundamentally biological. If electromagnetism did not exist then there would be no atoms, no chemistry, no life, and no heat and light from the Sun. If there were no strong force then nuclei would not have formed, and therefore, nothing would be. Likewise, if the weak force and gravity did not exist, then you would not be reading this, nor would any form of life be here

Yet, these four very different forces (and no others), each vital to all of the complex structures that make up the Universe, are so fine-tuned that they all combine to make a single super-force. Granted that we do not specifically know how to search for exotic forms of life, could we not find indications of extraterrestrial life in a form familiar on Earth? All terrestrial living matter contains organic molecules of some complexity proteins and nucleic acids, for example and we might expect to find either traces of such molecules or at least of their decay products. We know of two quite distinct locations in which complex molecules are found. There may be many more. First, observations of interstellar molecules by means of their microwave spectra have revealed the existence of such organic molecules as hydrogen cyanide, methyl alcohol, formaldehyde, and formic acid. Larger molecules, such as the sugar glycol-  aldehyde, CH2OHCHO, have also been found to be quite prevalent in interstellar space. Infrared observations similarly have shown the existence of the even larger, polycyclic aromatic hydrocarbon molecules.

 

References:

[1] Choudhuri A. R, Astrophysics for Physicists, Cambridge University Press (2010)

[2] Gagnon, E. et al. Soft X-ray-driven femto-second molecular Dynamic.

 

S-S Bond in Proteins

Disulfide bond also known as S-S bond, or sometimes disulfide bridge. It is a covalent bond derived from two thiol groups. More importantly, these bonds observed to play an important role in protein stability and aggregation of large biomolecules.

SS bonds are formed by a thiol/disulfide exchange reaction, and three important factors are required in the reactive groups to form this bond: accessibility, proximity, and reactivity (electrostatic environment).

 

The most common way of creating this bond is by the oxidation of sulfhydryl groups. (2 RSH → RS-SR + 2 H+ + 2 e-) This process of oxidation can produce stable protein dimers, polymers, or complexes, in which the sulfide bonds can help in protein folding.

 

Disulfide bonds can occur two ways:

·         Intramolecularly – occurs within a polypeptide chain and are usually responsible for stabilizing tertiary structures of proteins.

·         Intermolecularly- occurs between polypeptide chains and are attributed to stabilizing quaternary protein structures.

 

 

 

 

 

Following Image credit goes to Wikipedia and Maria Monica Castellanos and Coray M. Colina of Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States

Some medications and its effect on Human Kidney (Renal System)

Several research findings reveals that some medications are harmful for Kidney function and responsible for Kidney stone formation.

 

“Medications that can damage the kidneys are known as “nephrotoxic medications.”

  • As we know whenever we go to the hospital having health issues, our treatment generally starts with antibiotic prescriptions. The problem arises when some of these antibiotics help to make crystals in renal system which don’t break down and blocks urinary track and hence urine flow.

 

  • Also, antibiotics constitutes some substances that can damage certain kidney cells when they try to filter them out. Some people also have allergic reactions to antibiotics that can affect their kidneys. All these things are more likely to happen if you take antibiotics for a long time or very high dose.

Vancomycin is an antibiotic used to treat severe  infections (methicillin-resistant Staphylococcus aureus (MRSA)) but research found  it cause kidney  damage and acute interstitial nephritis, or swelling in the kidney.”

     “Aminoglycoside Antibiotics are known for causing kidney injury (nephrotoxicity), even at low doses. People with chronic kidney disease, dehydration, or those who have been taking these antibiotics for a long time are at particularly high risk. The most toxic aminoglycoside is neomycin. Although these medications are typically intravenous and used in hospitals, they are important to keep at the back of your mind”

 

  • Water pills are used to treat high blood pressure and some kinds of swelling. They help our body get rid of extra fluid. But they can sometimes dehydrate or lowers the water level of our body, which can be bad for our kidneys.

  • Non-Steroidal Anti-Inflammatory Drugs (NSAIDs)  like aspirin, ibuprofen, or naproxen  shouldn’t use them regularly for a long time or take high doses of them.

  • Some medications like omeprazole, Aciphex, Prilosec, Prevacid, Nexium are used to treat heartburn, ulcers, and acid reflux also called Proton Pump Inhibitors (PPIs).These drugs principally works by blocking the secretion of gastric acid. Although these powerful acid blockers were never designed for long-term use but unfortunately millions of peoples around the globe take these drugs indefinitely which potentially cause deadly consequences They lower the amount of acid in our stomach, but recent studies have shown that taking them for a long time can raise our chances of serious kidney problems and possibly lead to kidney failure. Researcher suggested that If you take a PPI regularly, ask your doctor about the possibility of switching to another drug which might  be far better for your health .Now, a new study from Stanford University shows these drugs double the risk of dying from a heart attack or stroke.

  • Some supplements like creatine and wormwood oil, may bad for our kidneys. It is recommended to tell your doctor about every supplement you take to make sure they’re helping or leading to damage of your body organ.

Outreach Activities

I am at the very initial phase of my career and needs more time and efforts to achieve my milestone and forth return my expertise to needy people in the Nation. There is lots more to do for my nation in coming future. Taking consideration of this theme, I am actively involving in scientific events directly or indirectly. 

Exposure, Idea exchange is always the main moto of every National or International conference which helps everyone to further furnish their skills, knowledge and more importantly networking in the common field of research. 

I have got several opportunities to learn from the experts by participating  in the following events:

 

  • “United Nations / Pakistan / Prince Sultan Bin Abdulaziz International Prize for Water – 4th International Conference on the Use of Space Technology for Water Management” in Islamabad, Pakistan on 26 Feb- 02 March, 2018 hosted by the Pakistan Space and Upper Atmosphere Research Commission, SUPARCO on behalf of Government of Pakistan. 

 

  • “International Conference on Emerging trends in Biological, Chemical & Physical Sciences” , Dec 9-11, 2016 in Kathmandu organized by Biologix research and Innovation Centre Pvt. Ltd, India. 

 

  • “South Asian  High Energy Physics Instrumentation (SAHEPI-2017) workshop on Detector Technology and Applications “held at Kathmandu University, Nepal on 20-21 June,2017 organized by CERN, the European Organization for Nuclear Research.

 

  • “4 days Workshop on LASER and its application ” held at Kathmandu on Feb 14-17,2016 organized under the collaboration of Sogang University, South Korea and St. Xavier’s college, Nepal.

 

  • “National Workshop on New Research Trends in Physics” held at St. Xavier’s college on 3 September, 2016. 

 

  • “Training Workshop on Scientific Writing ” held at Research Centre for Applied Science and Technology, RECAST jointly organized by University Grants Commission, UGC & RECAST on June 21-25, 2018.

 

  • Recently our team has organized a “National Space Meet of Nepal,2018” with the partnership with Nepal Academy of Science and Technology, NAST on July 21at NAST office.

 

  • We have conducted a general meetings of “Nepalese Society of Biomedical Physicist, NSBP”  in its office in Kathmandu and decided to organize “ Computational Biophysics Workshop” in Kathmandu this year.

 

 

  • A very fruitful meeting with energetic youths was held in July first week 2018 regarding establishment of “Research Club”  which aims to provide fundamental research knowledge on diverse range of science fields for Intermediate (+2) to graduate (B.Sc.).

   

I will always look forward to welcome every interested, active, like minded people or  those agreeing with my vision to work together for betterment of Research & Development scenario in our Nation.

Business spark

If you want to be a successful businessman you must need a great idea and clear vision… But how to understand whether your idea is great or not or it is clear enough?

“At least you should clear that for an idea to be sellable it ultimately needs to meet a customer need.”

There is no any doubt by saying customer development is key which helps scientists build high impact ventures even from single scratch.

Before startup see your product through their eyes, a customer’s eye. Your product needs to be at least 10 times better than what they have already encountering in the market and you can convince yourself that there are clients that want a service but you have to test that.

You should do prior study about targeted customers or who you’re going to sell to and why.

 

 

 

 

What happens if you don’t have an idea?

-You could be at an advantage – you can start with a problem that needs to be solved rather than a technology that needs to find a purpose.

 

“Big corporations are not very nimble. They are like dinosaurs.…They can throw a lot of money at a big project that’s more engineering. There’s not a lot of risk associated with it, but it just takes muscle. But when it takes brain and creative thought and solutions, they tend not to be that great.…Small companies are much better, much nimbler, more motivated. They are very flexible
and very fast.”

Important Secondary Structure in Protein: α-Helices and β-Sheets

α-Helices

One of the most common type of secondary structure found in proteins is the α-helix. Existence of  this type of structure was first predicted by Linus Pauling. Linus Carl Pauling was an American chemist, biochemist, peace activist, author, educator, and husband of American human rights activist Ava Helen Pauling.

But after several years of his prediction and was confirmed when the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew) was determined by X-ray crystallography.

To give you a better impression of how a helix looks like, only the main chain of the polypeptide (a linear organic polymer consisting of a large number of amino-acid residues bonded together in a chain, forming part of (or the whole of) a protein molecule)  is show in the figure, no side chains. There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). Each residue is translated 1.5 Å along the helix axis, which gives a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). The α-helix is the major structural element in proteins.

An example of an α-helix is shown on the figure below, such type of representation of a protein structure is called sticks representation.

In figure-2, When looking at the helix in the figure below, we notice how the carbonyl oxygen atoms C=O (shown in red) point in one direction, towards the amide NH groups 4 residues away (i, i+4). Together these groups form a hydrogen bond, one of the main forces in the stabilization of secondary structure in proteins. The hydrogen bonds are shown on the right figure as dashed lines. It is found that most of the alpha helices in protein are right handed

 

 

β-Sheets

The second major type of secondary structure in proteins is the β-sheet. β-sheets consist of several β-strands, stretched segments of the polypeptide chain kept together by a network of hydrogen bonds.he β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands (also β-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimer’s disease.

An example of a β-sheet with the stabilizing hydrogen bonds shown as dashed lines is shown on the figure below:

The figure shows how hydrogen bonds link different segments of the polypeptide chain. These segments do not need to follow to each other in the sequence and may be located in different regions of the polypeptide chain.

The same β-sheet is shown on the figure below, this time in the context of the 3D structure to which it belongs and in a so-called “ribbon” representation (the coloring here is according to secondary structure – β-sheets in yellow and helices in magenta). In the figure each β−strand is represented by an arrow, which defines its direction starting from the N-terminus to the C-terminus. When the strand arrows point in the same direction, we call such β-sheet parallel:

    

When the strand arrows point in opposite directions, the sheet is anti-parallel. In the next figure you can see an example of a protein structure with an anti-parallel β-sheet: