Tag Archives: atom

All I know about is a bunch of damn gangs that live in a round neighborhood

Professor Venus schools Arnold on the Pros, the New Boys and the Elected Ones – the three gangs who rule the neighborhood.

Now, get back to school.

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Posted by on August 26, 2013 in Uncategorized


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The Bohr atom at 100


Bohr and Einstein having a smoke

One hundred years ago, in 1913, Niels Bohr published a trilogy of papers describing the atom in ways that we are still referring to today. These papers synthesized several previous ideas into one and presented the atom as a positive nucleus encircled by a cloud of electrons that stayed in very distinct orbits that were proportional to their energy (i.e.  electrons in low orbitals were lower energy than those that inhabited higher orbitals). 

This sounds like a simple concept, but it has some very important ideas nested in it. Probably most importantly is the idea that the orbitals are distinct. That is, there is no ‘between’ orbitals. Electrons are in one orbital or another, but never in between. Also, it takes energy input to raise an electron into a higher orbital and energy is released (as light) when an electron drops into a lower orbital. As a biologist, I find this most interesting and useful to think of when contemplating photosynthesis and considering how photons are absorbed by atoms in the reaction centers of chloroplasts. This is done by raising an electron to a higher … let’s say ‘energy level’. Once this happens, we have energy stored (at least for a while) in this electron. That energy can be used to do work, passed on to another atom or it can release the energy into the environment as light.


Bohr Model

Here’s a good representation of Bohr’s model with the different energy levels / orbitals indicated by the dotted lines labeled n=1, n=2 and n=3 .

Until now, this model has been a good, workable theory that seemed to fit  mathematically with what was observed indirectly. However, two really cool papers came out recently that have provided the first direct observations of atoms / molecules. In the first, Hydrogen atoms were observed using photoionization microscopy. This was done with a hydrogen at resting state (it’s lone electron in the lowest orbital), and in several higher energy states attained by providing energy to the atom using a laser. Below is a figure from the paper presented in Physical Review Letters 110, 213001 (2013). In each subsequent panel the electron can be seen in increasingly higher (distinct) orbitals.



Ok, I’m just going to come out and say it, ‘This is totally f’n cool.’ This means that Bohr’s totally theoretical model of a century ago has just been directly shown to be completely accurate.

But wait, there’s more. 

We’ve been using Bohr’s model and others’ ideas to model how multiple atoms come together to form molecules. Again, these structures have always been imagined from indirect observation. But, in the May 30 Science, this too has been directly observed using non-contact atomic force microscopy. Here we can see atoms in a molecule as well as the covalent bonds between them. 



Here’s to you Niels. Bang up work!! ImageNot to mention Dimas G. de Oteyza1,2,*,Patrick Gorman3,*Yen-Chia Chen1,4,*Sebastian Wickenburg1,4,Alexander Riss1Duncan J. Mowbray5,6Grisha Etkin3Zahra Pedramrazi1Hsin-Zon Tsai1,Angel Rubio2,5,6Michael F. Crommie1,4,,  and Felix R. Fischer3,4, for imaging the covalent bonds.

And A. S. Stodolna1,*A. Rouzée1,2F. Lépine3S. Cohen4F. Robicheaux5A. Gijsbertsen1J. H. Jungmann1C. Bordas3, and M. J. J. Vrakking for visualizing the orbitals of Hydrogen atoms.


Posted by on June 6, 2013 in Uncategorized


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Venus Flytrap explaining the atom

Remember when I was saying that I had seen this on WKRP? I just stumbled upon this and thought I’d share.

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Posted by on October 7, 2012 in Uncategorized


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Bio – Chapter 3


Einstein and Bohr

We’ll be continuing with Chemistry in tomorrow’s class (I’d like to get through most, if not all of what I want to cover in that day). But why is chemistry even important in a biology class?

Like I said in my previous post:

Physics –> Chemistry –> Life

It’s important to understand that chemistry is the basis of biology because it is setting the parameters within which life can function. I don’t go much further than explaining the basics of how and why the periodic table is depicted the way it is, the Bohr model of the atom, the octet rule and the three basic bonds atoms enter into.

The Bohr model is fantastic for students. So, it doesn’t depict the actual atoms as they exist in nature… not much actually does. The closer we look at their behavior, the stranger they are. So the Bohr model is just that: a model.

What it does provide is a very nice way of explaining how protons, electrons and neutrons interact. It also plants a seed of electron energy, that we will revisit when we get to photosynthesis (photons strike pigment molecules and raise an electron to a higher energy state). 

Ultimately, we lay just enough groundwork so that once we start talking about DNA and other biomolecules, these structures make some sense and students will know why the backbone of DNA sticks together, but the Hydrogen bonds between the strands are less stable and can be pulled apart and come back together in a reasonable way.

I’ll finish out the chapter on chemistry discussing these four basic biomolecules (nucleic acids, lipids, proteins and carbohydrates) as we drift into studying material that is more recognizably biology.

This week we also start our extra reading, ‘Your Inner Fish’ by Neil Shubin. I’ve been using this book for several semesters now and think it makes a good addition to the class. I’ll talk more about that later when we discuss chapter 1 on Thursday.



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Posted by on August 27, 2012 in Uncategorized


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