Sunday, November 23, 2008

Viva le lost foam technique

After almost three months of playing with the silly stuff at work it finally dawned to test the lost foam technique - massive success. To the left are homey's initials carved in blue foam. To the right are those initials in aluminum. Absolutely wicked.
Lessons learned: Don't pack the sand too hard or air bubbles get in there. Too loose and the metal may pour out the side of the foam (especially when you pack it up around the edges of the design... This piece came out great and the little dude tore outta there 30 seconds after completion to show his bros. Most excellent.

Friday, September 19, 2008

Dr. Kolossavary, DESMOND, bilipid membranes, and other great ways to spend a weekend

I am behind the times so often it is startling. Dr. Kretsinger took some time on a recent hike to up it to me bluntly "It would help if you caught up to physics 1908." With that in the background, attendance at the Chem E. lecture - arranged by the Shirts Group - made for an enjoyable blitz-crash.

One of my favorite facets of America is the influx of great minds generated of great cultures. Kolossvary is of Hungarian descent, and very much looks the part - broad shoulders, thin mustache, and Mediterranean complexion... with one notable exception... the fingers of a programmer. Much like a pianist, a programmers fingers, albeit strong, are often long and dextrose. In any case Dr. Istvan fits the part of the guy who has sledge-hammered on a chemo-physio-computer engineering project around for the past 17 years. My guess is this guy's keyboards last ~3-5 months max.

At first blush DESMOND has some impressive stats. Dr. Shirts of folding@home fame chuckled throughout the lecture. At this slide he cited the first microsecond of modeling required 6 months to calculate.
Towards the bottom of the slide note the Anton - this processor, also developed by D. E. Shaw Research, works in tandem with Desmond to crunch up to 14 microseconds per day.

To facilitate we amateurs Desmond comes with a free downloadable Desmond GUI merged with Schrodinger's Maestro software. An impressive and thorough package a full license for Maestro runs in the $30K+ realm. The academic license, however, is free and provides an excellent platform to enjoy Desmond from. The pros: In fifteen minutes or so I had gone through some basic protein preparation wizard and was running Desmond through operations and getting a bi-lipid membrane like the pictured above. Amazing stuff that might have taken every bit of a month a few years ago to understand and initiate now accomplished in minutes.

Beneath the GUI hood there are even more features. To access these Desmond also comes with a command line interface - this provides additional algorithms for more in depth view and control. Navigating between the gui and command line is helped greatly by Maestro's process and file management that creates files prior to executing actions that are very simple to read and modify. Shirt enthusiastically likened these unto a voting paper trail, and I must agree it's a handy feature.

Cons: well it's not too big a deal, however there's no 64 bit binary yet, and for simplicities sake I ended up running Maestro in a virtual 32 bit machine to get everything more stable. Dr. Kolossvary indicated that this upgrade might be coming as early as this month - so stay tuned. Another planned feature includes direct reading of OPM's protein database files.

This week is finally calming down and am going to start running some simulations - stay tuned for part 2 some time in the next week or so.

The Making of Membranes
  1. After importing a PDB file go to the protein preparation wizard under "workflows" on the far right hand side
  2. Dr. Kosovarry recommended assigning bond orders, adding hydrogens, treating metals, capping the termini, and detecting the disulfide bonds. In his example he did not feel it necessary to delete waters... there are some other options below that are only available with the full version.... ah well... it's a start. Also there appear to be some missing AA groups and I am yet to figure out how to fix that...
  3. Now under "Applications" go to "Desmond" and go to the System Builder. There are 3 solvent models available, with more on the command line - There's an ion placement submenu perhaps a ligand placement menu may appear in future versions.
  4. The membrane builder menu let's you autoposition the membrane using selected atoms or amino acids - I've had moderate success in this using the selection tool to grab a bunch of atoms around the disc created by the OPM database, If you're not satisfied with the initial placement modify it clicking the "Adjust..." checkbox.
  5. When you're ready to see your model click "Start" - depending on a 2cpu 3.2 ghz machine you'll see a model like the above in a minute or two with ~120k atoms in the case of FAAH.

Friday, September 05, 2008

charlottesville police lady rocks a "cha-ching" for the camera while writing a ticket

Parking on some frat kid's lawn - $20
Tickets to the game - $50
Police lady writing a ticket, dancing, and rocking a "cha-ching" cause your lazy butt couldn't find a parking spot.... priceless (+$15 and towing fees...)

(and yeah, I put her up to it, we were both laughing pretty hard - thank you Ma'am for being a good sport)

Wednesday, September 03, 2008

mexican jesus

His name is Jesus - as appears on his name tag. On his helmet, where many others put their names for clear view, he has typed "Mexican." That's right- he's our Mexican Jesus... but seriously ya'll as our nation debates as to "what to do with all these immigrants" I would encourage the following line of reasoning these "Mexicans" are vastly more "American" than your average honky walking on the street. Their ancestors were here 25,000+ years before most of the people reading this got here. Jesus here speaks some of the original Aztec language... how many "Americans" speak ONE WORD of native tongue. Most "Americans" have been in the USA less than 100 years, and are now trying to perform a repeat of the conquistadors actions. Viva la revolucion, and to all you "Mexicans" - please move to Charlottesville. We need more of you. Ya'll are way cooler than most of these immigrants from the North.

Para aquellos hablando espanol - por favor vengan todos a Charlottesville, Virginia -es la mejor ciudad en EEUU- ademas todo el mundo habla un poco de espanol aca. Hay de buen trabajo, la tierra es buena para la agricultura, la gente es bastante rica, y la clima es excelente - siqguen rockirollando amigos ;)

Sunday, July 20, 2008

quick chemistry video

Well thanks to VMD, Pubchem + Pubchem Edit + Blender 3d + Biocyc.orghere's a test video of a hypothesized cannabigerolic acid synthase (aka the geranyl diphosphate transferase) that converts olivetolic acid (painted in blue + gray) into cannabigerolic acid (painted with red) need to get the gpp in there correctly and for those who must know the protein is 1U0V - I picked it for a couple reasons, however it's sorta silly cause it hasn't been structured. It's for illustration.

Charlottesville Community Bikes, Aluminum Foundries, and Bling

Had a rad time at the Cville community bike shop this weekend. We melted a bunch of aluminum and one lucky gal got some handmade hard core bling for her wheelz. And every one got to hear a bunch about aluminum, aluminum oxide, steel, slag, and a bunch of other stuff that makes the whole thing so what it is... rad.

Here's a video of the whole thing... may have said aluminum oxide 10+ times... ah well.... metallurgical chemistry = BONUS!

Saturday, March 22, 2008

our daily bread board

Today working for the third week on the Arduino Diecimila chip - combined with a GM862 and a one-wire temp sensor -
From Our Daily Bre...

and so now I gotta connect that diecmila on the left to the one wire sensor to the 50 pin break-out board to get a SMS message to a buddy when the temperature drops below 26 degrees farenheit.

The software employed is arduino sdk and the One wire + arduino tutorial

Wednesday, February 13, 2008

taste of eli cook + some train graffiti

walking down the tracks to see eli cook rock out durty nelly's passed a train with almost 50 cars in a row of awesome tag art + graffiti - a mobile museum, festival of colors - wait until the end to see this really gnarly chick painted in amazing detail....

the track is light that gasoline from eli cooks new album electric holy fire water

it's what those of us who dig eli's rock blues van halen meets muddy water have been waiting for.... and well worth the wait. dead man is an awesome fist pounder boot stomp and santeria shakedown is straight badass.... eli's only getting better, badder, and radder - maybe we'll get a rundmc aerosmith moment one of these days... here's hoping

Tuesday, January 15, 2008

android v1

android rocks - a fun sdk with simple plugins to eclipse. brief little tidbit - the subclipse plugin is great too

to get svn access in eclipse get the subclipse svn plugin

be careful when installing to avoid buckminster & mylyn errors - all you need to do is click into the plugin to get to the second menu where those dependencies are visible. there's a forum thread somewhere on this - can't find it now.... it's the second step in the plugin installation process though...

after that you can access it by right clicking on your source , go to the "team" menu and "share" button - ='s all the rest of the instructions for getting svn access...

get your password that google creates for your code, and you're done