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Mighty Oaks from Little Acorns Grow…

Tue, February 05, 2013 - 11:20pm


Paul Whitford

One of I2CAM’s programs is exchange awards, facilitating new research collaborations between labs as graduate students or postdocs move between the groups. These awards pay costs for travel and lodging/meals for a relatively short duration (normally 2-12 months). 


Vitor Leite                       Jose Onuchic

In 2007, graduate student Paul Whitford received one of our exchange awards to travel for six weeks from José  Onuchic’s group at UC San Diego to visit Vitor Leite’s lab at Universidade Estadual Paulista in São José do Rio Preto, Brazil.  The goal was to use computer simulations to study coordinate-dependent diffusion in protein folding. .


Paul’s work with Prof. Leite, Prof. Onuchic, and Ronaldo Oliveira from Prof. Leite’s group, carried out two pieces of work directly resulting from the exchange visit.  One of these compared the folding rates from a semianalytic theory against the values obtained from the simulations (“Coordinate and time-dependent diffusion in protein folding” Oliveira, PCW, et al. Methods 2010 ) as shown below.


The science in Paul’s collaboration with the Leite group and Onuchic groups expanded further.  Paul & collaborators realized that the approaches they had used to study small proteins could be put together to help understand diffusion processes of tRNAs (the pieces of RNA which carry amino acids into the ribosomes for protein assembly) within the ribosomes, a gigantic bio-molecular machine in the cell.  (Whitford et al, JACS Communication, 2010).  The plots below show the linear dependence upon time of the relevant squared coordinates associated with the tRNA motion within the ribosome. These results shed quantitative impact on the kinetic barriers for motion within the ribosomes.


Now, as an Assistant Professor at Northeastern University, Paul continues to collaborate with the Leite and Onuchic groups, where they are extending investigations into diffusion in molecular machines. This includes seeking funds for graduate students in the Leite group (including Mr. Contessoto) to visit Northeastern for extended collaborations. Paul and Vitor have, in addition, parlayed this collaboration into adventures with state of the art supercomputing.  In 2013, they received a large computing allocation on the Stampede and Kraken supercomputing systems (+petaflop machines). Additionally, Paul became the chief liaison to the University of São Paulo on behalf of Rice University for a new BlueGene supercomputer (shown below),  jointly operated by the two universities.  This high performance parallel computer runs at 84 teraflops, and has >24000 compute cores.

Paul’s experience that grew from his exchange award and subsequent blossoming of a collaboration helped make this possible.


Success stories like this are a delight to the ICAM directors and ICAM community.  Who knows what mighty forests lie ahead?

Daniel L Cox


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