51,561 research outputs found
Optimization problems in electron microscopy of single particles
The final publication is available at Springer via http://dx.doi.org/10.1007/s10479-006-0078-8Electron Microscopy is a valuable tool for the elucidation of the three-dimensional structure of macromolecular complexes. Knowledge about the macromolecular structure provides important information about its function and how it is carried out. This work addresses the issue of three-dimensional reconstruction of biological macromolecules from electron microscopy images. In particular, it focuses on a methodology known as “single-particles” and makes a thorough review of all those steps that can be expressed as an optimization problem. In spite of important advances in recent years, there are still unresolved challenges in the field that offer an excellent testbed for new and more powerful optimization techniques.We acknowledge partial support from the “Comunidad Autónoma de Madrid” through
grants CAM-07B-0032-2002, GR/SAL/0653/2004 and GR/SAL/0342/2004, the “Comisión Interministerial de
Ciencia yTecnologia” of Spain through grants BIO2001-1237, BIO2001-4253-E, BIO2001-4339-E, BIO2002-
10855-E, BFU2004-00217/BMC, the Spanish FIS grant (G03/185), the European Union through grants QLK2-
2000-00634, QLRI-2000-31237, QLRT-2000-0136, QLRI-2001-00015, FP6-502828 and the NIH through
grant HL70472. Alberto Pascual and Roberto Marabini acknowledge support by the Spanish Ramon y Cajal
Program
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images
In cryo-electron microscopy (EM), molecular structures are determined from
large numbers of projection images of individual particles. To harness the full
power of this single-molecule information, we use the Bayesian inference of EM
(BioEM) formalism. By ranking structural models using posterior probabilities
calculated for individual images, BioEM in principle addresses the challenge of
working with highly dynamic or heterogeneous systems not easily handled in
traditional EM reconstruction. However, the calculation of these posteriors for
large numbers of particles and models is computationally demanding. Here we
present highly parallelized, GPU-accelerated computer software that performs
this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI
parallelization combined with both CPU and GPU computing. The resulting BioEM
software scales nearly ideally both on pure CPU and on CPU+GPU architectures,
thus enabling Bayesian analysis of tens of thousands of images in a reasonable
time. The general mathematical framework and robust algorithms are not limited
to cryo-electron microscopy but can be generalized for electron tomography and
other imaging experiments
Phase Retrieval with Application to Optical Imaging
This review article provides a contemporary overview of phase retrieval in
optical imaging, linking the relevant optical physics to the information
processing methods and algorithms. Its purpose is to describe the current state
of the art in this area, identify challenges, and suggest vision and areas
where signal processing methods can have a large impact on optical imaging and
on the world of imaging at large, with applications in a variety of fields
ranging from biology and chemistry to physics and engineering
Alignment of cryo-EM movies of individual particles by optimization of image translations
Direct detector device (DDD) cameras have revolutionized single particle
electron cryomicroscopy (cryo-EM). In addition to an improved camera detective
quantum efficiency, acquisition of DDD movies allows for correction of movement
of the specimen, due both to instabilities in the microscope specimen stage and
electron beam-induced movement. Unlike specimen stage drift, beam-induced
movement is not always homogeneous within an image. Local correlation in the
trajectories of nearby particles suggests that beam-induced motion is due to
deformation of the ice layer. Algorithms have already been described that can
correct movement for large regions of frames and for > 1 MDa protein particles.
Another algorithm allows individual < 1 MDa protein particle trajectories to be
estimated, but requires rolling averages to be calculated from frames and fits
linear trajectories for particles. Here we describe an algorithm that allows
for individual < 1 MDa particle images to be aligned without frame averaging or
linear trajectories. The algorithm maximizes the overall correlation of the
shifted frames with the sum of the shifted frames. The optimum in this single
objective function is found efficiently by making use of analytically
calculated derivatives of the function. To smooth estimates of particle
trajectories, rapid changes in particle positions between frames are penalized
in the objective function and weighted averaging of nearby trajectories ensures
local correlation in trajectories. This individual particle motion correction,
in combination with weighting of Fourier components to account for increasing
radiation damage in later frames, can be used to improve 3-D maps from single
particle cryo-EM.Comment: 11 pages, 4 figure
Production of carbon nanotubes by PECVD and their applications to supercapacitors
Mà ster en Nanociència i NanotecnologiaPlasma enhanced chemical vapor deposition (PECVD) is a versatile technique to obtain vertically dense-aligned carbon nanotubes (CNTs) at lower temperatures than chemical vapor deposition (CVD). In this work, we used magnetron sputtering to deposit iron layer as a catalyst on silicon wafers. After that, radio frequency (rf) assisted PECVD reactor was used to grow CNTs. They were treated with water plasma and finally covered by MnO2 as dielectric layer in order to use CNTs as electrode for supercapacitors. Optimization of annealing time, reaction time and temperature, water plasma time and MnO2 deposition time were performed to find appropriate conditions to improve the characteristics of supercapacitors. SEM (Scanning Electron Microscopy), TEM (Transmission Electron Microscopy), AFM (Atomic Force Microscopy) and Raman spectroscopy were used to characterize obtained electrodes
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