Kim G. L. Pedersen

On Molecules, Molecular Junctions, Quantum Interference in Transport and Quantum Pumping

Just recently I defended my PhD Thesis entitled “Theoretical Investigations Regarding Single Molecules”. The title is so generic because the thesis contains work in different fields:

  • An introduction to the PPP model (an extended Hubbard model) and the numerical solution using exact diagonalization.
  • Neoclassical Valence Bond Theory as an effective tool for calculating and describing molecular quantum states.
  • Another main topic of the thesis is transport through gated molecular junctions, including work on:
    • Quantum interference in transport through interacting electronic systems (e.g. molecules).
    • AFM and FM Kondo Effect in transport through molecular junctions.
    • Quantum pumping in molecules using a general Floquet formalism.

If you are interested, my thesis can be downloaded here:

Improve Your Ssh-foo: Quick Way to Bridge Multiple Ssh-servers

While I work from my trustworthy Macbook Pro, everything in this tutorial should translate easily to any Unix-variant OS.

This document explains how to access a ssh-enabled server by using another server as a bridge. This may be relevant if you must access server S2, say, in order to to carry out some calculations, but S2 is only connected to a university network S1. From your home computer you would have to first ssh into S1 and then ssh into S2. This quickly becomes messy, when you wish to do anything remotely complicated like transferring files between different machines.

In the end of this tutorial you should be able to simply write ssh S2. And then end up immediately in S2. Similarly you can use any ssh-based technology like the terminal-based scp S2:file ., or drag-and-drop based solutions like MacFusion without ever thinking about the complicated two stage ssh-connection.


The ssh program must of course be installed on your home computer and both servers, and publickey authentication must be enabled.

You also need server names, usernames and passwords for both servers S1 and S2.

Set up password-less login

Generate public keys on your home computer, by issuing the command:

ssh-keygen -t rsa

Leave everything blank. If you wish, you can generate different keys for logging into S1 and S2, and in that case you should save the keys in different files likes id1_rsa and id2_rsa.

Move the generated keys to the server:

scp ~/.ssh/

Create the .ssh directory and append the key to the authorized_keys file.

ssh username1@S1                            # access S1
mkdir -p ~/.ssh                             # create .ssh directory
touch ~/.ssh/authorized_keys                # create file
chmod 644 ~/.ssh/authorized_keys            # give correct permissions
cat >> ~/.ssh/authorized_keys    # add public-key to file

Repeat this procedure for S2, making sure to move the relevant files all the way through S1 first. Remember to delete the file after you have added it to the authorized_keys file.


You should then be able to log in to S1 from your home computer without using your password. Test that this work seamlessly before moving on.

On your computer

Create ~/.ssh/config file to manage your connections. In the config file you should put the following:

Host S1nick
    Hostname S1
    port 22
    PreferredAuthentications publickey
    IdentityFile ~/.ssh/id1_rsa
    User username1

Host S2nick
    HostName S2
    port 22
    PreferredAuthentications publickey
    IdentityFile ~/.ssh/id2_rsa
    User username2
    ProxyCommand ssh -A S1nick nc %h %p

The variables S1nick and S2nick are some short nick names for the two servers. This is convenient because servernames tend to be long and tedious to type. If you are using a university network you could e.g. set S1nick to “uni” and S2nick to “calc”.

Now you can access S1 with the command

ssh S1nick

And server S2 with,

ssh S2nick


Self-referential First Post: Why the First Post Exists

Welcome to the first post. If you read this retrospectively in a world where this is no longer the first post… Then I am sorry to inform you that you have reached the end of this blog archive. Feel free to be sad or move along to something more meaningful.

If you indeed happened upon this blog in its infancy, when this is the only post… Then I am sorry to inform you that there are no more posts, and this post is also quite boring. Move along, nothing to see here.

To really get started with this first post I would like to entertain you with some bits and pieces of homespun philosophy:

  • In the beginning of a project, simply starting is the most difficult part you have encountered so far. Many projects die even before they begin.
  • Doing something while you are still not very good at it, is an important trait of the young enrepreneur. A trait I hope to have advertised quite perfectly with this first post.
  • If the beginning was the best part of the project, you have clearly done something wrong. While this should not be an encouragement to start in the crappiest possible way… It is an encouragement not to worry too much about crap in the beginning. It gets better (hopefully).
  • Writing is the invention which have made the biggest impact on human history. Period. Just writing ideas down make them double their value. Documenting your daily life, thoughts and reasoning is the single most inspiring and productive thing you can do.
  • Do not try to apply the above reasoning to anything profound… like e.g. the Bible where the beginning really do represent the pinnacle of human niceness.
  • Homespun philosophy is really only the work of drunk or bored people. And of little interest to anyone at all. Do not divulge yourself in reading other peoples ramblings. Simply don’t.

Having started on this rather silly note… Allow me to contrast with a very serious picture of me:

I am a physicist by education, and the blood of the natural sciences runs deep in my veins. However, as a scout I have flirted quite a bit with project management, leadership and administration.

I have a strange fascination with writing computer code. I have been told that my grandfather – who was an engineer using early mainframe computers – could suddenly stop whatever he was doing, and then try to solve a computer problem for hours before returning to the task at hand… like eating or clothing. I do not think I have inherited that character flaw, but the fascination is definitely there.

I also have a small family. My girlfirend and I have a 2-year old daughter, which in the most wonderful way takes up most of our spare time.

I tell you all this to warn you that any subsequent posts are probably going to center around the four themes: Physics, Scouting, Programming and Parenting. In what proportions these themes will feature, I am not quite sure as of yet.

To finish this post let me tell you the reason for actually writing this blog. It is in fact somewhat lame (as is the reasons for most real world projects). So let me divulge you in my lameness:

I used to have a static html homepage which mainly hosted my wish-list. I then stumbled upon Octopress which works by compiling all posts to static content, and in my case serves it to you via github. I became fascinated with the setup and one sleepless night later my old site was migrated to Octopress. The blog was baked into Octopress, but I do not know why I did not remove it then.

Over time I got annoyed with the empty homepage… so slowly, in the back of my brain, I began to consider the possibility of actually writing a blog… and this night then just happened to be the time where this possibility was violently born into the world as a fact…

I know that this is quite a silly first post, and I do apologize. Instead I hope that you may value the incoherent and silly character of this piece. I believe when pushing a text towards the incoherent and rambling, there is a turning point where meaning will change and suddenly the test makes sense on a completely new level and in a completely new way.

If not then hopefully the post is silly enough to force me to quickly write more posts to cover this up…

See you later.