a national resource for computational science education

HOME BWPEP Shodor Blue Waters

View Position
Project TitleMolecular Modeling of Plant Hormone Receptors
SummaryPlant hormone receptors are proteins involved in perception of hormones that play a critical role in helping plant adapt to the changes in environmental conditions such as high temperature, water or nutrient scarcity. Despite the tremendous progress has been achieved in elucidating the mechanisms of plant hormone perception, the molecular mechanisms of their perception remain elusive. In this project, the intern will work closely with a graduate student in the Shukla group at Illinois to perform extensive molecular simulations of all 9 plant hormone receptors using Blue Waters to elucidate their mechanism of perception.
Job DescriptionIntern will be expected to set up and perform simulations on Blue Waters, analyze data and prepare report for submission to NCSI at the end of the internship period. Interns will use NAMD molecular dynamics package to perform simulations and use MSMBuilder, MDTraj and other related softwares to build Markov state model of receptor dynamics using the simulation data.
Use of Blue WatersProject is related to a Blue waters allocation awarded to the PI via the Blue Waters Professor program. The interns will learn and employ large scale adaptive sampling protocols, which can be efficiently performed on the Blue Waters Supercomputer.
Conditions/QualificationsMust be an undergrad at University of Illinois at Urbana-Champaign.
Start Date05/31/2018
End Date05/31/2019
LocationShukla Group, Department of chemical & biomolecular engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
Faisal Aldukhi