• Why? Knowing the purpose of life is the only(?) way to achieve it. Achieving it will require from you to set up the correct priorities, optimize your work toward this achievement, since we know that our lifetime is limited (at least something definite in this quest for unknown). This means that you’ll have to (and hopefully will) do only the right things in your life and do less unneeded things. This is true for your life in general, as well as for each small piece of it: from choosing preferences for your lifestyle (health, kids, work, entertainment), to e.g. choosing a particular direction at work (for me as a scientist it would mean choosing the more valuable research interests).
• Since I don’t know the purpose of life (and nobody seems to know it yet), searching for the purpose replaces the original purpose of life, at least for the given moment of time. (I’ve heard it many times before: “If you don’t have a goal, make finding one your new goal”, but only now realize that I’m saying the same, although maybe applied to a different concept, and this as you will see turns upside down our whole life.) Note, that setting it in such a way, already provides you with the scales to judge on the value of your actions and set better priorities in your life.
• To understand the purpose of life we need to understand what is life. For me as a physicist, a physical definition of life (based on thermodynamics and, particularly, entropy) is more compelling than biological. Most of my reflections will be based on this (scientific) approach, and already show some interesting results (see below), although, take quite a bit of my time.
• While I do this, I need to sustain my current life, i.e. stay employed. So I need to make things (like thinking about life) in my free time and thus need to minimize this time, use it more optimally. I need better tools to do this. Looking for this information myself, reading it, trying to understand it and trying to decide whether the information (that I find typically on the internet) is scientifically correct, takes too much time. So I’ve decided to use the ideas of Open Science, i.e. ask the opinion from the experts in each field instead of looking for information myself.
• Thus I need to interest other people in the question (the purpose of life), I need to write down my initial thoughts and organize them. Ideally, I should not spend much time on this organization. But each person trying to help should also minimize time to find what is the most relevant to him. Moreover, if the question is very vast, then every person who is trying to help might need a different piece of the information from the post i.e. this organization of information should be different for anyone reading it i.e. the information should be self-organizing!

This line of thought defines the objective and the topics of my blog: I’ll try to understand whether this is possible conceptually, how to apply my ideas and build new tools for blogging and information aggregation, the related technical IT questions, what consequences does it have for physical view on Universe and Life, does it bring us closer to finding the ultimate purpose of life and should we correct the direction of our actions to achieve it.

Here is a highlight of interesting ideas that I come to and will try to describe in more details in my future blog posts.

• looking for existing tools (blogging platform, getting readership stats)
• improving blogging tools to save time
• communication, blogging and open science as the way to optimal aggregation (organization) of information
• open science and credit, can we protect ourselves? (learning from analogies in open-source competing with for-profit organizations)
• sharing and copyright, how to simplify the process of protecting copyright and how this leads to (self-)evaluation of information
• (self-)transforming information in real-time to present itself better for the reader
• self-organizing information as a form of artificial life
• different branches of science as different species (eating each other but not being able to live without each other)
• self-replicating and evolving information as a true new form of life
• self-generation of a new information (singularity?) and our role in it (are we the Creators of this new life or just a smaller building block in the evolution of the universe (like atoms->crystals->life and the God is equivalent to laws of physics, or God had to create the DNA?))
• simulating artificial life including the concept of neg-entropy (currently implemented methods seem to be able to touch only the evolution rather than the origin of life)
  
• wikipedia: the most condensed form of information (i.e. a digital DNA) or an artificial cell?
• is information a new form of energy? can it be converted into energy, mass, etc.?
• strings, elemental particles, atoms, crystals, life, self-organizing information - are we close to converging to Ultimate Life
• turning upside down - chaos is the true ground state of the universe (and not the minimum of the energy as we consider now). Singularity and the Big Bang is not the ground state (and not the initial state) but, on the contrary, the maximum in the evolution of Universe?
• denying infinity: “infinity” is equivalent to “the whole Universe” but it is still finite?
• analogies between reaching the absolute zero temperature and the speed of light
• accelerated expansion of the Universe is similar to accelerating ball falling to the Earth, with the Earth level being the minimum of potential energy i.e. the ground state. Will the Universe bounce back (from the Chaos) or will it stop and convert all the energy into temperature?
• if Dark Energy is somehow related to Information which is an indicator of Life, its wide distribution should mean that we are not alone, moreover non-equal distribution of it in the Universe (which should be observable) might help us find other Life
• anti-mass, would it be allowed if the new form of energy (e.g. information) existed? (analogy to Dirac antimatter)

I do. I still log on to the computational cluster via SSH, but so do people from under Linux. However, most of the programs I use, have more capabilities or are more convenient than their Unix analogues. So the need for Linux on my desktop is eliminated.

Here I would discuss some tricks/adjustments/settings that make my work more pleasant and productive. Mostly it touches my work with SIESTA, but people writing their own programs in C or Fortran may also find it useful.

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I won’t post technical specifications here - there are tons of reviews about Dell Mini 12 already. I want to share the details that you will not find anywhere else, especially given that you can hardly find it in the shops to try it yourself but can buy it only online. Particularly, the size and weight with the 6-cell battery, keyboard and trackpad comparison to other models, performance under Windows XP (browsing and say Photoshoping) compared to  notebooks with budget or older processor, and other factors that led me to choose Dell Mini 12.

Inspiron Mini 12 is still on sale in Canada ($100 off+free shipping) on Dell’s site but don’t expect to get it fast - mine, ordered on Jan 12 hasn’t yet arrived since they have to order it from US.

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Firefox smart keyword bookmarks with multiple search fields help retrieve the journal references faster

Imagine  that you could write in your address bar something like prl 52 10356 and get directly to a paper in Phys Rev Lett, Vol.52, page 10356.

This doesn’t save too much time when you do it once a week and within one journal. But what if you are reading a paper and need to get references really quick and from different journals. This is especially painful for ACS journals, where on the journal page you don’t have a search field with vol and page, but need to browse to a paper.

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Update (Dec 19, 2011): The recommended procedure now is:

Please, ask in comments for more details!

For general information about Bader analysis see this presentation.

For Bader analysis with VASP or Gaussian check Graeme Henkelman’s page.

Introduction

Analysis of charge on atoms can give a lot of interesting information in terms of understanding the nature of chemical bonding. There are different ways to do it:

• Mulliken analysis is implemented directly in SIESTA - it shows the direct population of the orbitals (basis) used in calculations.
• Natural bond orbital analysis. Similar to Mulliken in that it shows the population of the orbitals, but the interesting point is that it recalculates the population of orbitals of free atoms, i.e. in the way how we usually interpret the simplest bonds. Check the NBO program homepage for more details.
• Löwdin analysis. I don’t know too much about it. Check the original paper: On the non-orthogonality problem connected with the use of atomic wave functions in the theory of molecules and crystals. J. Chem. Phys., 18(3), p.365, 1950.
• Bader analysis. Based on the analysis of the final total charge density and division of it into basins associated with each atom. Sometime it can result in a basin non-associated with any atom which has a special physical meaning. Check this presentation for introduction.

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