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Computational challenges in high-resolution cryo-electron microscopy

Citation

Leong, Peter Anthony (2009) Computational challenges in high-resolution cryo-electron microscopy. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechETD:etd-08072008-171049

Abstract

To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), two of the key obstacles are the large computational requirements of high-resolution reconstructions and the curvature of the Ewald sphere, which leads to a breakdown of the projection theorem used by conventional 3D reconstruction programs. Here, two solutions to these obstacles are presented. First, a simple distributed processing system named Peach was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific cryo-EM applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster. Second, an iterative refinement reconstruction algorithm, Prec, is described that overcomes the curvature of the Ewald sphere resolution limitation by averaging information from images recorded from different points of view, as are present in typical micrographs. Prec was implemented in the popular software packages IMIRS, EMAN, and Bsoft. In preliminary tests with both simple and multi-slice simulated images, Prec overcame the curvature problem even in the presence of noise. Prec was then used to refine the three recently published, ~ 4 Å resolution, icosahedral virus reconstructions from experimental cryo-EM images, but unfortunately no significant improvements in resolution were realized. Further simulations showed that limitations other than the Ewald sphere curvature problem must still be dominant in these experimental studies.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Cryo-Electron Microscopy; Depth of Field; Distributed Computation; Ewald Sphere Curvature; Parallel Computation; Three-Dimensional Reconstruction
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Applied Physics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Jensen, Grant J.
Thesis Committee:
  • Fraser, Scott E. (chair)
  • Rees, Douglas C.
  • Jensen, Grant J.
  • Phillips, Robert B.
  • Zhou, Z. Hong
  • Fultz, Brent T.
Defense Date:4 August 2008
Author Email:peter.a.leong (AT) gmail.com
Record Number:CaltechETD:etd-08072008-171049
Persistent URL:http://resolver.caltech.edu/CaltechETD:etd-08072008-171049
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5245
Collection:CaltechTHESIS
Deposited By: Imported from ETD-db
Deposited On:13 Aug 2008
Last Modified:26 Dec 2012 03:16

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