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

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.
  • Enjoy your PhD! Celebrate your successes and enjoy yourself.

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


Miller-Urey Experiment; Origin of Life

Miller-Urey Experiment; Origin of Life
















Astrobiology: An Introduction

Astrobiology: An Introduction

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.


Molecular Dynamics: Bridge between Theory and Experiment !

Molecular Dynamics: Bridge between Theory and Experiment !

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.



[1] The Nobel Prize in Chemistry., 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

Chetanath Neupane: Journal Editor of {iaps}, 2019

Mr. Chetanath Neupane is a M.Sc. graduate of St. Xavier’s College (affiliated on Tribhuvan University, Nepal) and is currently working as an editor of {jIAPS}. He has a prior experience of working as a managing editor of his physics department publication called New Dimension for 2017 edition — he is very excited to work with people around the world !

Have a look:

He is continuously supporting {iaps} activities conducted by LC Kathmandu, Nepal. Unfolding his academic interests, he is highly motivated in the search for an answer to the question “are we alone in the universe?” To reach this answer, Chetanath studied Astrophysics (major) & Biophysics (non-credit), exploring the tiniest living organisms up to the largest object to date: the Universe. In order to give justice to this question, he is looking forward to doing a PhD in Astrobiology.

Chetanath has also been actively involved in scientific activities in Nepal for the last 10 years, and has participated and organized more than two dozen national & international conferences / seminars / workshops held in Nepal and abroad.

He has never been in ICPS –and is very eager to meet peoples working in IAPS in coming ICPS 2019 to be held in Germany !

Documentation for Visual Molecular Dynamics (VMD)

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.





  • 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:



<<< Register Here >>>





More details on the program on the website!

Deadline for application: 25 Nov 2018 (now closed).

Dates: 20 Dec – 30 Dec 2018

Women are highly encouraged to apply!


This event is powered by generous sponsorship from NCELL.
















Surface ice at Moon’s poles

Surface ice at Moon’s poles








News source: NASA

Kathmandu humanitarian Mini Maker Faire (KMMF)

Kathmandu humanitarian Mini Maker Faire (KMMF)

Nepal Communitere, with Rural Development Initiative, is organizing the second installment of Kathmandu humanitarian Mini Maker Faire (KMMF) on September 22-23, 2018.
The Kathmandu Humanitarian Mini Maker Faire is a unique gathering of global innovators who are solving some of the greatest social challenges facing by our communities. It’s a festival of invention, creativity and resourcefulness which can lead to transformative change.

The KMMF 2018 will bring together communities, entrepreneurs, makers, international and national non-governmental organizations (I/NGOs), and government agencies to celebrate the Maker Movement and showcase an array of incredible projects and new technologies.

The event will celebrate the Maker Movement – a movement that brings together tech innovators, tinkerers, and artisans – and showcase an array of new technologies and innovative projects that promote STEAM (Science, Technology, Engineering, Art, and Math) learning.

Apply at :

This year, we will bring together makers from Nepal and
beyond, specifically highlighting global innovations that
inspire communities to “Design the Future”.

The two day celebration will have displays and booths, speaker sessions, and interactive workshops where makers can come together to ideate, co-create and MAKE!

KMMF 2018 aims to

01 | Highlight the growth & impact of global humanitarian makers
02 | Create a platform to apply design thinking in building a better future
03 | Showcase innovative approaches to Health, Education and
Environmental challenges
04 | Foster partnerships between global humanitarian makers
05 | Provide seed funding to incubate promising projects in Nepal