Advice- one need to receive before getting admitted to any PhD programs

Chetanath Neupane

Lucy Taylor is a PhD graduate from the University of Oxford in 2018 who shared her experiences earned throughout her PhD life- advice- which one need to obtain before getting admitted to any kind of PhD projects as to end up with successful PhD outcome. She suggested following advice:

  • Maintain a healthy work–life balance.
  • Discuss expectations with your supervisor and communicate them early on, so you can work productively together.
  • Invest much time in literature reviews.                                                                                                                                Credit: Susanne Vogel
  • Decide on your goals early- goals can change later, but a clear plan will help you to maintain focus.
  • Write down everything you do- even if it doesn’t work (-meeting notes, method details, code annotations, among other things).
  • Organize your work and workspace.
  • It’s never too early to start writing your thesis- it’s good practice and a way to get ideas more organized in your head.
  • Split your thesis down into SMART (specific, measurable, attainable, relevant and timely) goals instead of writing chapter-1, write “draft first paragraph of the results”.
  • The best thesis is a finished one which will be obtained by multiple corrections.
  • Be honest with your supervisor.
  • Back up your work!
  • Socialize with your lab group and other students
  • Attend departmental seminars and lab-group meetings,
  • Present your research it gets easier as you practise, and it’s a fantastic way of networking and get feedback at the same time.
  • Aim to publish your research- drafting articles and submitting them to journals is a great way to learn new skills and enhance your CV.
  • Have a life outside work – it’s great for your mental health to be able to escape work.
  • Don’t compare yourself with others.
  • Keep calm, take a break and then carry on. Those experiments which are failed can still be written up as part of a successful PhD.
  • Never struggle on your own. Talk to other students and have frank discussions with your supervisor.
  • Enjoy your PhD! Celebrate your successes and enjoy yourself.

Source: Nature Careers Community (doi: 10.1038/d41586-018-07332-x)

 

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Miller-Urey Experiment and its correlation to the Origin of Life

Miller-Urey Experiment and its correlation to the Origin of Life

Chetanath Neupane

The Miller and Urey experiment,  it was conducted in 1952 and published in 1953 by Stanley Miller and Harold Urey at the University of Chicago. It has been considered as a breakthrough  that made organic compounds out of inorganic ones by applying a form of energy. Their  idea was based on simulation of  hypothetical conditions on the early Earth as to test the biochemical origins of life.

Urey and Miller were testing the hypothesis of Alexander Oparin’s and J.B.S Haldane’s hypothesis, as they said that “conditions on the primitive earth favored chemical reactions that synthesized organic compounds from inorganic precursors.” This is consider to be classical experiment on the origin of life.

The reason that this experiment is consider a significant since after Miller’s death in 2007, scientists examined sealed vials preserved from the original experiments. They were able to show that there were well over 20 different amino acids produced in Miller’s original experiments. That is considerably more than those Miller originally reported, and more than the 20 that naturally occur in life.

Possibly one of the most important experiments was one conducted in 1952, when the scientists Urey and Miller, who were interested in the origin of life, and they carried out an experiment, to simulate an early Earth atmosphere. And you can see this rather ingenious apparatus where they’ve got some water boiling away inside a flask, being circulated into another container that’s got an electrical discharge apparatus. And this electrical discharge is discharging across an ancient simulated Earth atmosphere.
And they circulated this water round and round. And after a period of time, they found that the gases in this container, once they had been electrically sparked, transform themselves into amino acids, that we saw, are the building blocks of life. So, in this simple experiment, using only water and the constituents of early Earth atmosphere, these scientists managed to create the building blocks of life. This was a truly remarkable experiment, a breakthrough in astrobiology that allowed scientists to go from speculation about the origin of life, to thinking about how those early building blocks might well have formed. Nowadays we think that the atmosphere of early Earth is actually slightly different from the atmosphere that was used by Urey and Miller in the early experiments. But nevertheless this remains a remarkable and landmark experiment in the early history of Astrobiology, at least in the twentieth century. And taking our understanding of the origin of life to a new, empirical level.

 

References

[1] Hill H.G. & Nuth J.A. (2003). “The catalytic potential of cosmic dust: implications for prebiotic chemistry in the solar nebula and other protoplanetary systems”. Astrobiology 3 (2): 291–304. doi:10.1089/153110703769016389. PMID 14577878.

[2] Balm S.P; Hare J.P. & Kroto H.W. (1991). “The analysis of comet mass spectrometric data”. Space Science Reviews 56: 185–9. doi:10.1007/BF00178408.

[3] Miller, Stanley L. (1953). “Production of amino acids under possible primitive Earth conditions” (PDF). Science 117 (3046): 528. doi:10.1126/science.117.3046.528. PMID 13056598.

[4] Miller, Stanley L.; Harold C. Urey (1959). “Organic ccompound synthesis on the primitive Earth”. Science 130 (3370): 245. doi:10.1126/science.130.3370.245. PMID 13668555. Miller states that he made “A more complete analysis of the products” in the 1953 experiment, listing additional results.

[5] A. Lazcano, J.L. Bada (2004). “The 1953 Stanley L. Miller experiment: fifty years of prebiotic organic chemistry”. Origins of Life and Evolution of Biospheres 33 (3): 235–242. doi:10.1023/A:1024807125069. PMID 14515862.

[6] Bada, Jeffrey L. (2000). “Stanley Miller’s 70th Birthday”. Origins of life and evolution of the biosphere (Netherlands: Kluwer) 30: 107–12.

[7] BBC: The spark of life. TV documentary, BBC 4, 26 August 2009.

[8] “Right-handed amino acids were left behind”. New Scientist (2554). Reed Business Information Ltd. 2006-06-02. p. 18. Retrieved 2008-07-09.

[9] Brooks D.J. et al (2002). “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code”. Molecular Biology and Evolution 19 (10): 1645–55. PMID 12270892

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Astrobiology: An Introduction

Astrobiology: An Introduction

Chetanath Neupane

Astrobiology is a very new, exciting and very rapidly developing area of science that addresses the question of the origin, the evolution and the distribution of life in the universe. There’s little doubt in saying that one of the most exciting questions in Astrobiology is, “Are we alone in the universe? “And I should say right at the beginning of this course, we don’t have an answer to this question, but we do know that the answer is either yes or no. And either one of those answers has profound implications for our understanding of our own place in the universe. If the answer to this question is “Yes, we are alone in the universe.” then we need to ask the question, “Why are we alone in the universe?”, “What is missing on other planets that was present on Earth and allowed life to originate and evolve here?”. We would have to find out about the origin and evolution of life on Earth in order to find out why life on earth is so special. It would also raise fundamental philosophical questions. If there’s no other life in the rest of the universe, there’s no one else to talk to. Then, why have we spent the last 40 thousand years building a civilization? Is it just so that we can be lonely in greater luxury? Astrobiology forces us to address philosophical questions that strike at the very core of our civilization. If the answer to this question is “No, we’re not alone in the universe.” we are also faced with some very fascinating questions: What is the nature of this other life on other planets? Is it microbial life? Life like bacteria? And if so, how does it compare to life on Earth and where is it? Or is it intelligent life? And if it is intelligent life, what is the nature of this other intelligence? Can we communicate with it? And, what will be the consequences if we do communicate with it? Are we alone in the universe is unquestionably the one question in Astrobiology that fires the imagination of the general public and is probably the question that brought you along to this course. It’s a very reasonable question to ask when you think about the universe that we live in.The planet on which we live orbits a single star and this star is one of about 200 billion stars in the Milky Way galaxy and our own galaxy is probably one of many many billions of galaxies throughout the universe. In truth, we don’t know how many galaxies there are in the universe. It may be something on the order of a hundred billion galaxies, maybe more. But if you think about it, 200 billion stars in our own galaxy. Possibly a hundred billion galaxies throughout the universe. It seems reasonable to ask the question: Is there life on other planets?

And that is why Astrobiology is concerned with a question for which we do not yet have an answer but which scientifically, empirically looks like a reasonable question to ask. To search for life on other planets, we first of all have to understand something about life on our own home planet, Earth..

The fact that scientists propose that the extinction of the dinosaurs was caused by an asteroid shows that in order to understand the past history of life on Earth, we have to understand its connection with the cosmic environment. So, to understand the past history of life on Earth, we have to understand Astrobiology, how life fits in to its cosmic environment. We also know that the future of life on Earth is going to change. This is a rather dramatic image of the Crab Nebula, the result of a supernova explosion. An exploding star that exploded thousands of years ago. Our own sun may not end its life in quite such a dramatic matter but in a few billion years from now, our sun will come to the end of its life and at that point our own planet will be completely destroyed and all life on it will be extinguished. That’s not for a long time to come. But we do know that in order to understand the future of life on a planet, its long term future, we must think about the connection of a planet, again, with its cosmic environment. How it connects with the history of its parent star and how long that star lives and therefore, how long you can expect life to survive on a planet. So in order to understand life on Earth, we have to understand the past history of life and its connection with the cosmic environment and we have to understand the future of life on Earth and its connection with the cosmic environment. In other words, an understanding of life on Earth is really about studying Astrobiology, the connection of life with its astronomical or cosmic environment. So astrobiology has many areas that we will look at in this course and many questions that it wants to address.

Let’s have a look at some of these questions and see what we’re going to look at throughout this course. Astrobiology is first interested with understanding the origin of life on this planet, how did it come about? And the sorts of questions that Astrobiologists ask and that we’ll be looking at in this course are: how did life originate on this planet? Where did life originate? What were the locations of the first organisms to emerge on this planet? When might they have first evolved? Is life an inevitable process on any planet where the conditions are good enough? Do you always get an evolution of life? Is this a common process throughout the universe? When did this happen? Did it happen very quickly after the earth was formed? Or did it take rather a long time for those chemical reactions to lead to the earliest types of life? And, what is the evidence for early life on Earth? What is the evidence for the origin of life on this planet and its emergence into early single-celled organisms that first occupied this planet many billions of years ago? Once we’ve established the presence of life on the planet, we want to know about its limits. How far can you push it and what sort of extremes can it live in? This is important if we are to try and understand the possibilities of life on other planets, to assess that habitability as we call it. And the sorts of questions that Astrobiologists want to address are: what are the limits of life? What are the most extreme physical and chemical environments that life can survive and grow in? How does life survive extremes? What are the sorts of mechanisms that evolves? What sort of biochemistry? What sort of physiology do organisms evolve in order to be able to cope with some of the most extreme environments on the earth? And all these limits universal? If we do find life on another planet out there in the universe, will it be living in completely different conditions from life on Earth or will we in fact find similar life living in similar types of environments? And once we’ve looked at life in extremes, what does that tell us about the prospects for life elsewhere- about the possibilities for going to extreme environments on other planets and finding life there? So by studying life on our planet today and looking at the way in which it lives in different types of environments and different extremes, we can learn something about the prospects for life elsewhere. Astrobiology as I’ve already mentioned is also concerned with trying to understand the history of life on Earth once it did emerge. It’s concerned with questions like: how is life related? When you walk around outside you see a whole diversity of life from dogs to giraffes to trees.

How are all these different creatures related? And how did they come to be on the surface of the earth? How did they evolve? Astrobiology is interested in trying to understand the connections between these different creatures and how they came to be and evolved from one another over time. We also want to know about multicellular life- complex life. We’ll see later in this course that when you look around you, most of the life that you and I are familiar with are things like dogs and giraffes that are multicellular creatures, complex larger organisms that we can see with the naked eye. But in fact, much of life on earth is bacteria- archaea- simple single celled organisms. And we want to understand as Astrobiologists how life emerged from those more simple organisms in the early history of life on Earth to the more complex life that you and I see on a day-to-day basis on the surface of the planet. And another question that concerns astrobiology this is catastrophes and extinctions. How does life go extinct? How do these catastrophes affect life throughout its history whether that be asteroid or comet impacts, giant volcanic eruptions? And, what sort of catastrophes might befall life along its long tenure on life on Earth?

Astrobiology is concerned with taking this information and looking for life elsewhere. And as I said earlier, there’s no doubt this is the most interesting question in Astrobiology, at least the one that captures the public imagination and the sorts of questions that Astrobiologists ask, once it began to get an understanding of life on the Earth is, is there life elsewhere in the universe?

Are we unique experiments in biological evolution or is it repeated on other planets? And if there is life elsewhere, what does it look like? What sort of life is it? Is it microbial life, single-celled life or is it intelligent life? And if there isn’t any life out there in the universe, why not? What’s missing in the rest of the universe that was present on the Earth that allowed life to originate and evolve on this planet? Of course, following on from that question, another interest for Astrobiologist, certainly for the general public is: are there other intelligences in the universe? If there is life out there, could it be intelligent life? And the sorts of questions that Astrobiologists want to address is: is intelligence inevitable? Wherever we get life on a planet, is it inevitable that it will eventually progress to intelligent types of lifeforms? Can we communicate with life on other planets? And if we do communicate with it, what will be the consequences for society? What would happen to us if we made contact with another intelligences ? How would that affect religion and our social structures?

And we’ll answer some of those questions in this course. Of course, it’s all very well looking for alien life and studying the evolution of life on the Earth and going out and hunting for life elsewhere. But of course, we may eventually ourselves leave the earth and travel beyond and establish permanent settlements. Some places like the moon and Mars.

And Astrobiology is also concerned with the technical question of how human beings will establish themselves in space. What is the future of human life beyond the Earth? The sorts of questions that Astrobiologists are concerned with spanned from science to technology to philosophy. And the sort of questions of things like: will humans leave the Earth? Is it inevitable that we will move out beyond the Earth and establish a permanent human presence beyond our home planet? And if we do make this choice to leave the Earth, how will we do it? How will we establish self-sustaining settlements on other planets? And, if we are going to spend money and human resources establishing other branches of civilization beyond the Earth on other planets, how do we do that but at the same time preserve the earth? How do we look after our own planet, live sustainably on the earth but establish sustainable settlements on other planets and planetary bodies such as the moon and Mars? And how will we adapt to space? If we move out beyond the Earth, what will be the social implications for humanity? How will we change as a species? How will our societies develop as we move out beyond the earth and establish settlements on other planetary bodies? These are just some of the questions, some of the diversity of questions that astrobiology seek to ask.

We’re going to learn about how we search for life on other planets. How we use our knowledge of life on the earth to go beyond the Earth and send out missions to Mars and other planets and seek out signatures of life on other planetary bodies. We’re going to look a little bit about the future of human life beyond the Earth and the establishment of a permanent human presence beyond Earth. We are going to look at some of the social implications of Astrobiology, more difficult to define than some of the scientific research associated with Astrobiology but nevertheless very important to understand the way in which science can affect society and the way in which we think about the universe around us. We’re also going to look at the difference between science and sensationalism. And you may have noticed that in some of the publicity for this course, there was even talk about UFOs, alien autopsies and all sorts of crazy but nevertheless interesting material that captures the imagination of many people. And in this course, we want to learn about what is empirical science. What is evidence that allows us to address scientific questions in Astrobiology. And what areas of Astrobiology are not underpinned at the moment by any empirical evidence that make it difficult to address particular questions. Astrobiology is a very good vehicle, particularly when we talk about extraterrestrial intelligences for thinking about the difference between science and sensationalism. And we’ll touch upon some of those problems throughout this course. So what have we learnt in this brief introduction to Astrobiology? Hopefully, what you’ve learned is that Astrobiology covers many fields. It’s a very diverse subject that goes from physics to chemistry, biology and even, philosophy and sociology when we think about the implications of discoveries in Astrobiology. Astrobiology as a subject as its name suggests,

Astrobiology that sets life in its cosmic context. It seeks to understand how life on a planet evolves in the context of its changing astronomical environment and how life changes through its origin, its evolution on the planet and eventually the end of that planet as it is destroyed perhaps by its parent star.

Astrobiology seeks to understand life from how it arose to how intelligent life might one day colonize other planets from Earth possibly to the moon or Mars and beyond. And as you’ll see throughout this course, Astrobiology as well as being a science in its own right is actually an outstanding vehicle for learning many of the common principles that underpin different parts of science. It’s a way to learn about different disciplines as well as to understand the possibility of the origin, evolution and distribution of life in the universe.

 

By Charles Cockell,

Professor of Astrobiology at the University of Edinburgh.

 

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Molecular Dynamics: Bridge between Theory and Experiment !

Molecular Dynamics: Bridge between Theory and Experiment !

Chetanath Neupane

Molecular dynamics (MD) is a technique of computer simulation in which time evolution of large set of interacting atoms is followed by tracing their trajectory so that their corresponding equation of motion can be understood.  Molecular dynamics is becoming a celebrating technique which is now being used routinely, mostly in applied investigation of a wide range of dynamic properties and processes by researchers in numerous fields, including structural biochemistry, biophysics, molecular biology, pharmaceutical chemistry, and biotechnology. So the number of publications regarding MD theory and application of MD to biological systems is growing at an extraordinary pace. Using MD simulations, one is able to study thermodynamic properties and time-dependent (i.e., kinetic) phenomena of infinitely large complex structure of interacting atoms. Understanding the thermodynamics of the system one can develop various dynamic simulations using variety of algorithms in computer. In the simulation procedure, it has been considered the systems as small as an atom and a diatomic molecule undergoing a chemical reaction as large as a galaxy. Before doing MD simulation one needs to have knowledge of interaction potential for the particles, force due to these interactions, and the equation of motion that leads the particle dynamics. The interaction potential may vary with the mass and the distance between the interaction particles i.e the simple gravitational interaction between stars to the complex many-body forces between atoms and molecules. In conventional MD simulations, the energy function for non-bonded interactions tends to be a simple pair wise additive function (for computational reasons) of nuclear coordinates only. This use of a single nuclear coordinate to represent atoms is justified in terms of the Born-Oppenheimer approximation.The basic idea of molecular dynamics is the solution of the Newton’s law of motion in classical dynamics.

It has been noticed that the classical Newtonian equations of motion are adequate for many systems, including large biomolecules but for the systems with tunneling reactions, quantum corrections are important and need to include relativistic effects if we consider evolution of galaxy. In the MD simulation and its algorithm, it is supposed that the single particle motions as a function of time so they can be understood more easily than experiments to answer lots of properties of the system. To run the MD simulation, energy of the system is taken as a function of the atomic co-ordinates. We know, forces acting on the atoms of any system can be calculated by taking first derivative of the potential with respect to the atom positions. The force thus calculated gives dynamic behavior of the system by solving Newton’s equations of motion for the atoms as a function of time (M. Karplus, 1990). So, the major component in MD simulations is the force evaluation, specifically the long-range van der Waals and electrostatic interactions that must be computed for each pair of interacting components.

MD simulations are designed such a way that the result/simulation obtained is largely consistent with basic physical principles which can be validated by experiments. It is therefore, the Nobel Prize for Chemistry in 2013 [1] was awarded to Marin Karplus, Micheal Leavitt, and Arieh Warshall, who pioneered the MD simulations methodology for bimolecular systems. They explored that MD simulations evaluate the interactions between particles as a function of the coordinates of their individual substituent particles (e.g., atoms, residues/nucleotides, etc.). The foundation of MD is several theories from mathematics, physics, and chemistry, and it contains algorithms from computer science and information theory. The idea was originally conceived within theoretical physics but is applied today mostly in materials science and modeling of biomolecules. Before it became possible to simulate molecular dynamics with computers, some undertook the hard work of trying it with physical models such as macroscopic spheres.

Molecular dynamics is a specialized discipline of molecular modeling and computer simulation based on statistical mechanics; the main justification of the MD method is that statistical ensemble averages are equal to time averages of the system, known as the ergodic hypothesis. As stated by ergodic hypothesis, statistical ensemble averages are equal to time averages of the system if integration is performed to higher order. However, it is found that long MD simulations are mathematically limited because of cumulative errors in numerical integration of equations of motion. This error can be minimized with proper selection of algorithms and parameters, but cannot eliminate entirely. Furthermore, current potential functions are, in many cases, not sufficiently accurate to reproduce the dynamics of molecular systems, so researchers are taking use of computationally demanding Ab-Initio Molecular Dynamics method. Nevertheless, MD method allows detailed time and space resolution into representative behavior in phase space and thermodynamic properties of the large system.

It is found that there is a significant difference between the focus and methods used by various chemists and physicists while doing MD simulation and this is the key differences in the way used by the different fields. In chemistry and biophysics, the interaction between the particles is either described by a force field (classical MD), a quantum chemical model, or a mix between these two as a hybrid.

In applied mathematics and theoretical physics, molecular dynamics is considered as part of the research realm of dynamical systems i.e ergodic theory and statistical mechanics in general. So, theories of thermodynamics can be used to analyze the concepts of energy conservation and molecular entropy.

Some techniques to calculate conformational entropy such as principal components analysis come from information theory. Mathematical techniques such as the transfer operator become applicable when MD is seen as a Markov chain. Also, there is a large community of mathematicians working on volume preserving, symplectic integrators for more computationally efficient MD simulations. MD can also be seen as a special case of the discrete element method (DEM) in which the particles have spherical shape (e.g. with the size of their van der Waals radii.) Some authors in the DEM community employ the term MD rather loosely, even when their simulations do not model actual molecules.

 

References:

[1] The Nobel Prize in Chemistry. http://www.nobelprize.org, 2013.

[2] Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning,    Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 497(7451):643–646, May 2013.

Image Copyright: Universität Stuttgart, IMWF

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Documentation for Visual Molecular Dynamics (VMD)

Chetanath Neupane

The VMD Installation Guide, User’s Guide, and Programmer’s Guide are available which describe how to install, use, and modify VMD.   All three guides are available from the main web site. Online help may be accessed via the “Help” menu in the main VMD window or by typing help in the VMD command window.  This will bring up the VMD quick help page in a browser, and will lead you to several other VMD help files and manuals.

Quick Installation Instructions

Detailed instructions for compiling VMD from source code can be found in the programmer’s guide.

 

The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self-explanatory.

 

The native MacOS X version of VMD is packaged as a disk image and is extracted by opening the disk image, and dragging the “VMD” application contained inside into an appropriate directory.

 

 

For quick installation of the binary distribution for Unix do the following:

 

  • Uncompress and untar the distribution into a working directory, being sure to do this and subsequent steps as a non-root user. In this working directory, there are several subdirectories such as bin, src, doc, data, as well as this README and a configure script. Change to this working directory after the unpacking is complete.

 

  • Edit the file ‘configure’; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed, be sure that you installing into a clean target directory and not overwriting an existing version of VMD (which would otherwise give problems):

 

  • $install_bin_dir is the location of the startup script ‘vmd’. It should be located in the path of users interested in running VMD.

 

  • $install_library_dir is the location of all other VMD files. This included the binary and helper scripts. It should not be in the path.

 

  • A Makefile must be generated based on these configuration variables by running “./configure”.

 

  • After configuration is complete, cd to the src directory, become root or use sudo if necessary, e.g., for installation of VMD into /usr/local or other permission-protected system directories and type “make install”.

 

  • This will install VMD in the two directories listed above. Note that running “make install” twice will print error messages because you are attempting to overwrite some read-only files.  Similarly, if you have incorrectly specified the target installation directories or attempt to overwrite an existing VMD installation, you will get error messages.

 

  • When installed, type ‘vmd’ to start (make sure the $install_bin_dir directory is in your path).

 

 

Required Libraries

——————

VMD requires several libraries and programs for several of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD’s optional features.

 

Please visit the VMD web site for more information: http://www.ks.uiuc.edu/Research/vmd/

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

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

Chetanath Neupane

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.

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Surface ice at Moon’s poles

Surface ice at Moon’s poles

Chetanath Neupane

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

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Scientific analysis of Rudraksha seed !

Scientific analysis of Rudraksha seed !

Chetanath Neupane

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.

Fig: Magnetic field.
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.

References: To be uploaded soon.

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

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

Chetanath Neupane

“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).

 

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Organic Molecules found in interstellar space !

Organic Molecules found in interstellar space !

Chetanath Neupane

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.

 

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