Unveiling The Natures Secrets Through A Computer Modelling,,, ------------------------------------------------------------------- If you had earlier ruminated over your estranged lover or lack of lover and got enlightened to know the reasons for your existence here through my previous Facebook posting, you may feel better, i guess,,, Far from just feeling better, please try to be an optimistic too and who knows one day you may come across the choice of your heart or if you have already one, then that one may turn favorably towards you,,, You would definitely get to hear the cliche in India - that you have to look into yourself to know the truth or whatsoever that might be,,, Though i have not understood the real meaning of that, considering the way how people utter those words ominously, i have long back realized that looking into yourself to know the truth might be somekind of important and sombre one,,, So, if you could possibly take an inner look during your rendezvous with your lover, you might realize lot of things, though it might lead to more serious problems,,, Mainly, you could feel the secretion of feel good and be happy hormone dopamine abundantly in the region VTA ( Ventral Tegmental Area ) of brain,,, if you still could concentrate into yourself, you can realize that there is an intense activity in another area of the brain - PAG ( Peri Aquaductal Gray ) too,,, And if you further concentrate into yourself, you could realized that, then deep in the brain, amygdala and ACC ( Anterior Cingulate Cortex ) were triggering something in Sympathetic Nervous System ( SNS ) and thereby turning off the neurochemicals in hypothalamus and Parasympathetic Nervous System (PNS ),,, If you are a trained yogic and could meditate amidst the most disturbing things, you may go looking deeper into you and may feel that vehicle of feeling feel good and be happy would soon travel into NAc ( Nuclus Accumbens ) where the dopamines are getting mixed with the liberal doses of Vasopressin and Testosterone ( or Estrogen and Oxytocin ) and when you are blessed with that giddy feeling of feel much better and be extremely happier, dopamine vehicle further travels into CN (Claudate Nucleus) and that is when feeling of happiness reaches its logical culmination,,, Well, if you dont feel all those hormones and their interactions as the way i have described, it is perfectly ok as we, unlike a few chemical nerds, tend to feel things much simpler way such as just feeling relaxed and inexplicably happy ( that is due to the fact that brain area for intense pleasure and pain suppression are turned on),,, I do not want to go deeper explaining the role of each of those hormones or each of those areas of the brain, as i do not intend to write the review of fifty shades of Grey here,,, If you are a saint and secretions of above hormones are so worldly to your liking, still, you should but hope your other secretons mainly from endocrine glands such as pituitary, adrenal, thyroid, parathyroid and all to work properly to carry out the day to day actvities without any hassles,,, In a way, our body is nothing but a bio-chemical factory of formidable scale, which to the aghast of many environmentalists and social activists, heavily procures and utilizes many utterly organic toxic substance like nitrous oxide and highly explosive substance such as nitroglycerine, etc,,, Of course, fortunately our body is not as bad as we, so it knows not how to misuse them,,, That toxic substance helps controlling the blood flow and energy level of cells while that explosive helps soothing the angina pains,,, Our body as a bio-chemical factory uses each one of the cells of us as its indefatigable and committed worker to produce varieties of finished products known as this protein or that protein using detailed guidelines with almost zero error,,, There are two hundred thousand proteins, our bio-chemical factory is supposed to produce and because of them, we, as human being, could spend time happily, crouching on the couch, watching TV munching potato chips,,, Then too, those work-conscious cell workers toil to convert the energy stored in that crunchy potato chips into something known as ATP (Adenosine TriPhosphate ),,, And of course, ATP are the crunchy-munchy snacks for those tireless workers,,, Like any factory, ours is also a big one with multiple discreet units coordinated well from a control room known as the brain,,, Control room is always profused with hell a lot of activitis and commands are dictated to various units through the messangers, who we genereally know as hormones,,, Sometimes, mere commands might not work and so little bit of prodding may need to be exerted,,, At such situations, catalysts are being sent, who are used to motivate the workers to do the things and these catalysts are known as enzymes,,, Let us take a little bit closer look at things that we have seen so far, ie proteins, ATPs, hormones, enzymes, etc,,, We know what is meant by an atom,,, And all the elements which we know so far in this Universe are made up of atoms with specific atomic number and atomic weight uniquely identifying them,,, If you want, you can take a peek at the periodic table,,, They contain the list of both organic ( naturally occurring ) and inorganic ( artificially made ) elements,,, Though elements are useful per se, combining them is essential to create very many new substances,,, Combining such elements are known as bonding in the lingo of chemistry,,, And the elements can be combined in more than one way ( ionic bond, covalence bond, etc ) to form a compound substance,,, And for that compound substance, a molecule is the building block as how atom is a building block to an element,,, You can now rightly guess that proteins, ATPs, hormoes and enzymes are made up of molecules,,,, Or simplistically, they all can be loosly called as molecules,,, For example, the very moment you read this article, there is a molecule known as retinal ( which is embedded in the retina of the eye ) is really overworking ( when light hits the retina, retinal molecule changes its shape and this is the first stage of human vision ) for you in your chemical factory,,, And when you relishes the tasty potato chips in between the lines, there is another molecule known as pepsin gets ready to break them down into another molecule known as peptides,,, And if you do not feel like reading fully this article, there is a molecule known as youlazymoron gets ready to cause itching through out your body until you finished reading it fully and liked the artcle in my Facebook page,,, Ok, Not to worry, there is no molecule like that as of now,,, But, by now, you would have got the point that molecules are sine qua non for the 24 by 7 running of your own chemical factory, though as a physical owner you can enjoy crouching on the couch without even worrying about what is really going over there,,, And at this point, i would like to request you to intake some nutritious food or drink but not too sugary or too salty, so that you can do a bit of favor to those tireless cell workers of your chemical factory,,, Because those food items would get broken-down into another molecule ATP and get stored inside a cell for future consumption,,, And for doing various body functionalities, they would get the required energy by breaking-down those ATPs,,, For some reasons, if those cell workers feel not so happy about the working environment, they tend to go berserk temporarily and that would send us scuttling to nearby hospitals,,, So, this is the simplistic sketch of our body as a biochemical factory,,, If you are interested, some more interesting facts about our biochemical factory are given below,,, Our body has approximately 10,000 trillion cells ie 10,000 followed by 12 zeroes,,, Our body has atleast 200,000 different types of protein,,, The size of the cell worker is 20 microns wide that is two hundreds of a millimetre,,, Each cell worker contains 20,000 different kinds of protein, and of these, 2,000 types are made up of 50,000 or more molecules,,, Then imagine what will be the size of each of those molecules,,, Virtually all the food and oxygen are delivered after processing to an exclusive area known as mitochondria ( and strangly, mitochondria is nothing but a bacteria and this benign bacteria helps us to store energy,,, and so, many even tend to call our body as nothing but a colony of bacterias ) where they are converted into a molecule, which is what we are already familiar with, known as ATP,,, ATPs are like power battery packs and at any given moment, a typical cell will have about one billion ATPs in it and in just two minutes every one of them will have been drained dry and another billion will have taken their place,,,, Everyday, our body produces and uses up a volume of ATP equivalent to about half of our body weight,,, Of course, our trillion cells need to be freshly oxygenated continuously without fail,,,For that, our heart has to pump up almost 8,000 litres of blood every day,,, Like all of us, our cells too have expiry dates,,, Once they are no longer needed, they die with dignity through process known as apoptosis,,, Unfortunately, many times, they do die quite untimely due to infection in our body,,, And around billions of our cells die every day,,, But untimely death of a cell is far better than timely undeath ( ie not dieing at right time ) because the latter condition is nothing but the dreaded cancer,,, [ For more interesting and amazing facts about us and our universe, please go through an incredibly informative book - A Short History Of Nearly Everything - by Bill Bryson,,, ] As the molecules are so essential for the functionalities, well-beingness and consumptive greed of our body and us, scientists ceaselessly tweaks and tinkers them to discover new molecules, medicines, utility substances and industrial usage materials etc,,, But it is not an easy task in creating new combinations and anlayzing individual reactions of combined molecules as that kind of experiments can not merely be carried out with a few test tubes and stacks of chemical substances,,, What chemists and pharmacologists require is a reliable computer modelling to simulate the experiments innumerable times on the LCD monitors and see the resultant compounds and their chemical structures,,, As we all know that the mechanics of tiny and petit elements such as atoms are very finicky ( atoms of the molecules are dynamic and bonding of the molecules are tricky ), the computer model should be based on firm foundations of proven scientific frameworks ie it needs to be based on both classical and Quantum mechanics,,, [ Though a thorough understanding of classical mechanics and Quantum mechanics would be required for such modelling, we, common folks, would not require such deep knowledge on them to know what is happening, but knowing something about the fundamentals of them is essential to understand the underlying complexities of such modelling,,, Classical mechanics are mainly based on Newtons laws of motion and thermodynamics laws,,, At one point of time, when everything about the cosmos was misunderstood, an unassailable genius - Newton - postulated the theories on the working of our earth and its planet system which have been empirically proven in later centuries to be accurate,,, Newton, a multi-faceted personality ( an alchemist, scientist, skilled mathematician and the one who invented the new domain of mathematics - calculus - for explaining his scientific principles ) so rightly guessed about the gravity ( though he could not satisfactory guess how it worked ) and without surprise, his laws of motion of earthly objects so rightly created so much sensation,,, For him, this universe is nothing more than a big mechanical device with discreet parts and each one of them could be explained in isolated manner,,, Time and space are so absolute ones to him,,, And any movement of an object could not have happened without a Force,,, So, obviously he firmly believed in the prime-mover the God,,, And, as he thought that this universe was an ordained one with permanent and unchangeable mathematically precise laws, the nature of the laws, if could be discovered, should be applied invariably to all earthly ( and near earth ) phenomenons,,, To be brief, he was so deterministic about the way the mechanics of the matters worked,,, Of course, thermodynamics laws along with Newtonian laws held the primary place in the science domain of that time and worked as unassailable ones untill certain natural phenomenons such as black-body radiation ( in quantum physics, it would be famoulsy known as ultraviolet catostrophe ), matter particles with energy bundles ( duality of particle and wave properties ) and discreet emission of energy by the particles as packets known as quanta, etc could not have been satisfactorily explained by the classical laws,,, Then scientists started thinking that Newton may be Newton but he may still be wrong,,,, I dont want to further delve into these matters as they require more effort and hell a lot of readings to understand them fully, but understanding that while Classical mechanisms are still valid and relevant for the matters that we are dealing with in our day-to-day life and our immediate observable things including planets ( Of course, for understanding that kind of macroscopic level objects, modern theories such as Einsteins are required, because Einstein was the one who successfully explained how gravitational force works through his general theory of relativity by warping the time-space continuum ),,, But for the things such as elementary and sub-atomic particles of microscopic level , classical laws ceased to be relevant and adoption of Quantum laws are essential as those particles are no more just pointed masses so that their characteristics such as the location, velocity and momentum etc could be exactly predicted by newtonian laws,,, In Quantum world, a particle dons a dual role of both particle and wave and because of its quirky nature, we can only statistically guess where it may tend to be rather than where exactly it would be,,, Not only that but the role of observer is kind of intermingled with the result of observables,,, I know that head might start to swirl,,, So briefly what it means is that if space related character ( eg. location ) of the particle is observed, there is no way to exactly find out its time related ( eg. velocity and momentum ) properties,,, ] If you have survived this far, i can definitely say that you could go through various popular science books dealing with those subjects as those authors, unlike me are the masters of the lauguage, so they would explain arcane things in comprehensible manner,,, Anyway, point to be noted here is that formulation of computer modelling based on these classical, modern and quantum mechanics was a tremendous achievement,,, And so, the credits should duly go to the scientists who left no stone unturned to form that modelling,,, Martin Karplus, Universite de Strasbourg, France & Harvard University, Michael Levitt, Stanford University School of Medicine and Arien Warshel, University of Southern California developed computer model that would simulate chemical reactions using quantum as well as classical physics,,, They also found ingenious way to reduce the computing power by merging several atoms in the not-so-significant parts of the molecule during simulations,,, Those ingenious minds no doubt deserved the Nobel prize for Chemistry,,,, And it is a great achievement to the field of software engineering too as their model has successfully replaced the labs and test tubes atleast in this case,,,, What CERNs LHC has done to the betterment of physics, Computer Software has definitley done to the betterment of chemistry,,, Thanks for being in the game of appreciating the noble efforts of the greatest thinkers of our time in understanding the minuscule elements such as atoms, cells, molecules which we need not think and care about much in our ordinary lives,,,, In order to end this trilogy of Unveiling The Natures Secrets, in lighter vein, let us think about this scenario,,, Three Higgs Bosons formed during the collision of high velocity protons in LHC were vehimently discussing about the superiority of their respective ideologies - Advaitha ( monism ), Dwaitha ( dualism ) and Vishistadhwaitha ( qualified dualism ), in their livetimes of split seconds,,,,
Posted on: Thu, 17 Oct 2013 03:33:01 +0000
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