postmodern babbler - Things to remember
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For a living, I do physics and biology.

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Shew. I passed.

Haha. Suckas! They passed me. ;) but just barely. There are still a few things before it's official, but the last major thing is done.

Sad to be leaving Stanford, but super psyched for the future and what's ahead. Thanks to all of my friends and family who were there supporting me --it means a lot to me.

(photo: my whiteboard on the day of the defense)

Comments (6)
Posted 7 days ago

Defending today ...

Instead of actually taking pictures, you can pretty much follow what's
going on today by reading PhD Comics, starting at this one:

http://www.phdcomics.com/comics/archive.php?comicid=570

I'll let y'all know how it goes!

Comments (0)
Posted 8 days ago

Arlen chilling out

Kim's new dog is awesome!

Comments (2)
Posted 11 days ago

Hot off the presses!

Just printing a few draft copies for my committee members. The countdown begins.

Comments (2)
Posted 14 days ago

Thesis Defense: How Helical Junctions Determine the Folding Stability and Allowed Conformations of Structured RNAs

Title:

“How Helical Junctions Determine the Folding Stability and Allowed Conformations of Structured RNAs”

Abstract:

Structured RNAs are inherently dynamic, exploring a diverse set of conformations within the cell. Understanding the physical origins of their folding stability, motion, and interactions with other biological actors will require characterizing the conformational landscapes they explore. The simplest motifs within structured RNAs are two helices joined by non-helical junctions. To dissect the thermodynamic properties of these fundamental helix-junction-helix (HJH) motifs, we computationally probe how junction topology, electrostatics, and tertiary contact location contribute to the folding stability of a simple tethered duplex model system. We then extend this work to construct a map of the allowed conformations of the Transactivation Response Element (TAR), a HJH motif extracted from the genome of the Human Immunodeficiency Virus. This conformational map, analogous to the Ramachandran plots for proteins, can aid in the interpretation of experiments by showing how experimental data fit into the context of the allowed conformational space. Our results indicate that the simple constraints of a single- or double-stranded junction, independent of sequence, profoundly influence the preferred location and orientation of the adjoining helices, helping to determine the folding stability and specificity of the motif. These sequence-independent effects suggest that properties as simple as a junction's topology can broadly determine the conformational landscape, stabilize desired structures, and assist in discriminating against misfolded structures, providing an additional strategy for transcending the limitations imposed by the low information content of RNA primary sequence.

Date: Thursday, October 29th, 2009 - 2pm
Location: Clark Center, S360

Filed under  //  science  
Comments (2)
Posted 17 days ago

At the Stanford Linear Accelerator Center

Here for my advisor's honorary symposium.

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Posted 19 days ago

Summer is Over ...

Summer has been pretty productive, but I didn't get out as much as I would've liked. But then there's always next summer and I'm pretty thankful for the few weekends I did take off. Ended up seeing some cool new places (Deep Springs College) and spending time in familiar ones (Tuolumne). Anyway, here's a video from a trip we took a few months ago -- just spending some nice time with friends cragging at East Cottage Dome.

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Posted 28 days ago

There I Fixed It

Comments (3)
Posted 1 month ago

Thesis writing + Sierra Nevada = Crazy Delicious

Today was good. Sat down and finally hacked ten pages. W00t.

Comments (6)
Posted 1 month ago

Haagen-Dazs x4

It's gonna be a good week. Two for $5 at mollie stones. Kim and I tried getting these last night but Mollie stones closed just as we biked up so we had to return this morning.

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Posted 1 month ago