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BE5592010Symposium1

Molecular Systems Biology Laboratory (PI: Ravi Radhakrishnan, PhD)
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In-Class Presentation Topics and Sign-up

This is a list of topics for in-class presentations in march/april 2010. Presentations will be held on some tuesdays and thursdays. Each lecture will consist of 3 presentations of 20 minutes each (conference style timimg will be strictly enforced) with additional five minutes for questions and change-over.

Each student should select one topic from methods and one topic from applications. The list of topics and the field for sign-up are given below. Link to all papers (for all topics) is also given given below. These are large zipped files so do not dare to venture a download unless you have a high-speed connection! You can download and browse/read the topics/papers now, but you cannot sign-up until you receive a password (see below).

Your selection is on a first-come-first-serve basis and is finalized when you enter your name next to the topic. To do this, click the edit button on the wiki page and enter the password given to you through a separate email on Tuesday March 16.

Important: after you enter your name, click Save button to confirm. The page should immediately update with your selection.

You may chose to present one or more of the papers provided to you for the two topics you have chosen. You may also substitute the papers to others that are closely related should you find more revelant articles than the one given to you, but they need to be closely related to your topic and the original set of papers. In your presentation, you must emphasize the following (in the introduction and the conclusion, you should make efforts to relate the topic to the contents covered in the course):

  • Outline
  • Introduction and Background
  • Methods
  • Results
  • Conclusions and Summary

Your two presentations will be each be scheduled on different days. You need to bring your presentation in a USB stick in powerpoint or pdf format. You should also submit your presentation in an electronic format at the end of class in which you present.

Audience Participation with questions in a constructive and timely manner is a requirement. The audience must also read the articles for the topics prior to class. This will determine the class-participation component of your final grade.

Thank you in advance for your active and timely participation.

Sincerely Yours, Ravi Radhakrishnan Symposium Organizer and Instructor BE559

Link to compressed files for methods.zip (~26 MB) and applications.zip (~42 MB)

Methods

DateTopicPresenter
 accelerated-md-
4/1coarse-grainingDua
 continuum-membrane-
 dosmc-
 elastic-network-
4/1expanded-ensembleRamanan
4/8fepKatherine Wu
 finite-temperature-string-
4/13metadynamicsRuonan Wu
5/5milestoningBarr, R.Wu
4/13multiscale network biologyNg
4/15multiscale-hmmDolan
 multiscale-hydrodynamics-
4/6nebH-C Ko
4/20path-sampling-theoryBarr
4/20parallel-temperingShesh
4/27single-molecule-jarzynskiMakadia
4/22single-molecule-phenomenologyColace
5/5Crystal GrowthDua
5/5Genetic AlgorithmsTom, Andrew

Applications

DateTopicPresenter
4/1abl-her3Katherine Wu
4/8antibody-designRamanan
4/8coarse-grained-membranesDua
 continuum-cell-
 continuum-membrane-
4/13dynamicsBarr
5/5electrostaticsWu, Ramanan
 electrostatics-langevin-dna-
4/15ion-channelRuonan Wu
5/5nucleosome-pore-complexDaphne
4/ 27path-sampling-application1H-C Ko
 path-sampling-application2-
4/15protein-foldingShesh
4/20signaling-immunologyDolan
4/22signaling-spatial-stochasticMakadia
4/22signaling-stochastic_vs_deterministicNg
4/27single-molecule-applicationsColace
5/5srcShesh
5/5PolymeraseMakadia
5/5Materials SimulationKo
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Page last modified on May 03, 2010, at 03:55 PM