Sirocco Research Labs

Archive: Science

• Telepathic Devices

  Not every­one gets to live in the same city, unfor­tu­nately.  What’s worse, this even applies to friends who really wish they did.  Pos­si­bil­i­ties are mul­ti­plied by prox­im­ity; inten­tion­ally or not, pos­i­tively or oth­er­wise, things nat­u­rally grow in the same direc­tion when they’re near to one another. Granted, this is the great­est time in human his­tory to not live in the same city, what with all the oppor­tu­ni­ties for sleepy phone calls and care­fully crafted e-mails to let all the far away friends know they’re #1.  But, what tech­nol­ogy has never been able to dupli­cate is the sacred alone-but-together time.

  My friend Nora and I found our­selves in this sit­u­a­tion just recently.  Not being the types to wal­low in pas­siv­ity, we took it upon our­selves to dab­ble in invent­ing our own tech­nol­ogy to make expanses of geog­ra­phy eas­ier to shoul­der.  The result is what we’re now refer­ring to as the Tele­pathic Device.

  

  Nora mod­el­ing the Yel­low and White Tele­pathic Devices

  The Tele­pathic Device DOES NOT allow the wear­ers to com­mu­ni­cate with their minds in direct and secret con­ver­sa­tion.  For exam­ple, by using the Tele­pathic Device a sub­ject could not say to another sub­ject, “I wish we were hang­ing right now.”  The Tele­pathic Device is much, much more nuanced than this.  It oper­ates in a more sim­i­lar way to lying with your friend in a field, pos­si­bly a beach, or moun­tain top,  and gaz­ing at some­thing very big and remain­ing very quiet.  The Tele­pathic Device guides two thoughts in the same direc­tion, allow­ing the users to grow and develop their own thoughts inde­pen­dently, while shar­ing an experience.

  Finally, here are four exam­ples of the Tele­pathic Device in action:

  

  

  

  

  The Tele­pathic Device remains in beta test­ing.  But, we feel as though we have struck a major break­through for Friend­ships around the world.  We will con­tinue our work on per­fect­ing this impor­tant new discovery.

  XO

  J&N

  Published August 16th, 2010 by Jimmy Marble

• Algorithms for Multiscale Characterization of Equilibrium Protein Motions

  Find­ings by Andrej Savol

  
  
  
  

  Con­for­ma­tional motions rel­e­vant to pro­tein func­tion span an enor­mous range of tem­po­ral scales. While the appro­pri­ate method for under­stand­ing these fluc­tu­a­tions may be spe­cific to a par­tic­u­lar timescale and detail level, the char­ac­ter­i­za­tion of spa­tial and ener­getic tran­si­tions pro­vides our lab’s over­ar­ch­ing focus. To that aim, we have devel­oped advanced machine learn­ing tech­niques for extract­ing non-Gaussian and rare behav­ior in MD tra­jec­to­ries. Although out­comes of purely spa­tial fluc­tu­a­tions, QAA basis vec­tors seg­ment ubiquitin’s hier­ar­chi­cal inter­nal energy space with sur­pris­ing clar­ity, and we give insight for why pur­su­ing such rare events pro­vides use­ful bio­chem­i­cal infor­ma­tion, espe­cially when com­pared with estab­lished principal-component and full-(de)correlation based approaches.

  Longer tem­po­ral win­dows and larger spa­tial motions are con­sid­ered with Struc­ture–from–FRET, an algo­rithm that answers the fol­low­ing ques­tion: given a time-evolving dis­tance con­straint between two pro­tein residues, what is the most likely tra­jec­tory of the entire pro­tein? Our Kalman-Filter based approach gen­er­ates ensem­bles of tra­jec­to­ries that agree with sin­gle mol­e­cule Forster Res­o­nance Energy Trans­fer data. We high­light its util­ity with Adeny­late Kinase, a model hinge pro­tein, and describe how this appar­ently under­de­ter­mined prob­lem is made tractable by incor­po­rat­ing stan­dard bio­chem­i­cal con­straints (bond-length, bond-angle) into the state-space update algorithm.

  Published June 28th, 2010 by Jimmy Marble