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New PGP Key

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

This is a quick message to those who communicate with me over PGP or who verify my signatures, I am now using a new key and I am retiring (but not yet revoking) the old 1954fed2 key. Many things I have written are still signed with the old key and many software packages I wrote are signed by that key so it will remain secret hopefully for a year or two. The reason I'm changing keys is because the 1954fed2 key is 1024-bit El-Gamal and is 9 years old. How many keys are 9 years old? The longevity of my key probably has to do with my trust in El-Gamal and my distrust of RSA. Over the past few months I have factored a handful of weak RSA keys and I have done a little bit of cryptanalysis. There are many weaknesses in cryptographic keys and many weaknesses in the computer systems that protect them. We hope that we will avoid these and that our random number generators are strong enough to keep the NSA from reading our personal and business conversations that we choose to encrypt with PGP. We also hope that the NSA isn't able to sign malicious software with our keys or the keys of people we rely upon to provide us with software. But in all, we can only do so much and if RSA is broken or SHA-2 is broken, then we just have to deal with the consequences. Until we know better, we have to use the best judgement we have.

So now for the key. It's been signed by 1954fed2. The key id is CBA783EF. As always, only trust fingerprints or keys signed by keys you have checked the fingerprints for.

- -----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG v2

mQINBFR5XEwBEADZugzJdRuD2WROStTqK88UhMjEs+Y2CMrztHavacyJj7b299FB
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=ua9y
- -----END PGP PUBLIC KEY BLOCK-----

For those who are interested in the OpenPGP format. Here is a parsing of the above public key:

Read more.

Protein Tutorial with PyMOL and GROMACS

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Hash: SHA1

You may have been patiently waiting for the first installment of my nanotechnology blog and you're right to expect great things. I have found myself pushing more and more stuff onto my stack and there will be a time for popping all those off the stack. The first one is what I've been working on the past three weeks.

There are plenty of tutorials for GROMACS but because I had a bunch of problems using it, I thought I would write another one. My tutorial is based on this one, so if you want the original, look there.

First, we need a molecule to minimize*. We could use 1OEI, but let's start with a blank slate. Minimizing an already minimized protein is kinda boring.

Read much more.

Plans for March 2014

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Hash: SHA1

Dear friends,

I've told some of you about my big plans in March, but I wanted to write a big open letter to everyone for good measure. When I graduated college, I feel really silly for not sending an e-mail to everyone I knew telling them that I had graduated and was looking for a job. Now that I'm switching careers, I thought it'd be wise to send an e-mail. This time I'm not looking for a job.

I'm leaving the security industry in a few months to pursue independent research in nanotechnology. It's taken a long time for me to achieve my goal of feeling confident about my financial situation so that I can pursue research without spending years in academia as a grad student or as a researcher working on someone else's project in industry. It's not that I think those things are bad, in fact they can be great, just not a good fit for me. I've been very independent for pretty much all my life and I'm impatient waiting for nanotechnology which I predicted would be in full swing years ago. If you're not familiar with nanotechnology, there's a lot of very cool science going on which is headed toward the molecular scale, smaller even than Intel's new 14nm resolution CPUs. Applications are wide-ranging and could change the way we make things. Not just computers, not just medicine, and not just solar panels. It's the reason I got my Bachelor of Science in Physics and had I been smarter about it, I may have gotten a research job back then and be where I am right now but with 10 years of research behind me. So this is me righting myself.

Read much more.

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