Archive for May, 2011

Relative Size of Things in the Universe

Getting the relative size and distances right is not always straightforward for us – having evolved in mediocristan of middle-earth, going a few orders of magnitude larger or smaller just blows our common sense and spatial awareness to pieces (see the impressive overview of our solar system produced and donated to me by a seven-year old). I never get tired of watching good animations of zooming in and out of the world as we know it. Decades ago, it was the Powers of Ten that gave such a view for the first time – at least it was the first movie of this kind I got exposed to (the book is here).

Hence when I came across the post below on SchockWellenReiter it prompted me to search for related videos – there is a lot of good stuff out there I wish my teachers had available when I went to school! Kantel describes the Planetenweg (planetary pathway?, opened in Sptember 2003) in the honourable old University-Town Göttingen: It represents our Solar system to scale (1:2 Billion) – Two Billion Kilometres in (outer) space corresponding to one Kilometre on the Planetenweg. Planet Earth shrinks to a 6,5 Millimetre ball (approx. a quarter of an inch) while the sun is about 75 metres away and about 70 centimetres big. You have to walk about an hour to get from the sun (close to the central train station) to reach Pluto (at Bismarckturm) … I know, it’s just a dwarf planet now … relatively speaking you are walking faster than light! To reach our next neighbouring star you’d need continue walking for about half a year, about half around the earth.

The video below is based on current data from NASA – It features a sphere denoting the area that the earliest radio-wave emissions from earth (ca. 70+ years ago) have travelled. Enjoy!

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Protein Bioinformatics Tools: Sequences, Structures, Interactions, Networks

Focus on Regulatory Proteins:  Sequences, Structures, Interactions, Networks

EMBO Practical Course: Protein Bioinformatics Tools

Together with Toby Gibson and Niall Haslam, Aidan Budd is organizing an EMBO-funded course in September. It’s mostly aimed at wet-lab scientists – see below. He asked me to circulate this to other scientists who I think might be interested in the course – I thought this might be a suitable spot – the full poster can be found here.

EMBO Practical Course on Protein Bioinformatics Tools – Focus on
Regulatory Proteins: Sequences, Structures, Interactions, Networks

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A beginners guide to the galaxy

Admittedly, I have no idea about Quantum Gravity, apart that some physicists like their universe to be rather bubbly than stringy ( or just the other way around: more stringy than loopy, like Leonhard in Series 2 Episode 2 of “Big Bang Theory“).

But the caption of the above movie from the Max-Planck Institute for Gravitational Physics in Potsdam/Golm says (quote) “The following sequence visualises the quantum evolution of geometry in Loop Quantum Gravity. The colours of the faces of the tetrahedra indicate where and how much area exists at a given moment of time. The movie illustrates how these excitations of geometry change as dictated by the Quantum Einstein Equations. Technically, the faces form a complex dual to the graph of a spin network state and the colour shows the amount of spin (area) with which the edges of the graph area are charged.” (end quote).
Wow – a combination of words like evolution, network, graph, spin, state, geometry and tetrahedra in a few lines and you have my full attention! Although it was bound to appear on my radar at some point, I don’t quite see the exact connection with biomolecular networks and structures clearly – yet. Nevertheless, it’s either watching the visualisation for mere aesthetic reasons or digging deeper with the aid of “Loop and Spin Foam Quantum Gravity: A Brief Guide for Beginners” – by Hermann Nicolai, a string theorist and director of the Quantum Gravity and Unified Theories department at the MPI for Gravitational Physics / Albert Einstein Institute. The visualisation is available for download on their pages.
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Naturally obsessed – the making of a scientist

STRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX WITH COUMARIN ADP

This documentary (directed by Richard and Carole Rifkind) on the life of graduate students in a structural biology lab very nicely shows the fine line between success and failure, genius and madness, hope and despair, pressure and satisfaction when it comes to doing good science. It’s great if you’d like to convey the idea of what it’s like and what it’s about to friends and relatives who are wondering why the heck one is putting up with all of this when you could have had such a nice life as an accountant in the local bank. Also, if you are considering to go into science and eventually do a Ph.D. – this is a glimpse of the bumpy road ahead.

The page of the movie is here, and there is more in this blog-entry. (found via P212121)

A structure of the regulatory domain (fragment) of AMPK (the central protein in the movie) is here.

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Weekend Music – Feelin’ Good

I guess Feelin’ Good is a piece that stood the test of time and fits the mood of the day. Here are some of my favourite interpretations: Read the rest of this entry »

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What are you thinking about ?

Since I just get deeper into mendeley and it has the line “What’s on your mind?” on the dashboard for the Newsfeed (twitter-style) I remembered this video:

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Lively Molecules in a Crowded Cytoplasm

cytoplasm model at the end of a Brownian dynamics simulation performed with the ‘full’ energy model

Proteins are not static entities – since we live at about 300 degrees above absolute zero there is constant Brownian motion. However, looking at deposited X-Ray structures, one might get the impression that the structures are rigidly sitting in vacuum – nothing could be further from the truth! I like the analogy with early photography :

Photography, ca. 1893

because the photoplates were not that sensitive, long exposure times were necessary. Hence people had to hold very, very still for several minutes in order to get a decent picture. Photographers had special setups and chairs with neckbraces to keep the poor subject in place. This apparatus is the analogy to a protein crystal – it keeps the proteins in place, floppy and moving parts will not show up on the resulting electron-density maps.
The photographs of our great-grandfathers leave us with the impression that they were very stiff people, largely devoid of any humour. That’s probably not true, but how happy and lively would you look if you had to sit still for quite some time in your best outfit with your head squeezed onto some weird mechanical contraption? The same holds true for proteins. Read the rest of this entry »

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