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Polarized light scattering as a probe for changes in chromosome structure

Description: Measurements and calculations of polarized light scattering are applied to chromosomes. Calculations of the Mueller matrix, which completely describes how the polarization state of light is altered upon scattering, are developed for helical structures related to that of chromosomes. Measurements of the Mueller matrix are presented for octopus sperm heads, and dinoflagellates. Comparisons of theory and experiment are made. A working theory of polarized light scattering from helices is developed. The use of the first Born approximation vs the coupled dipole approximation are investigated. A comparison of continuous, calculated in this work, and discrete models is also discussed. By comparing light scattering measurements with theoretical predictions the average orientation of DNA in an octopus sperm head is determined. Calculations are made for the Mueller matrix of DNA plectonemic helices at UV, visible and X-ray wavelengths. Finally evidence is presented that the chromosomes of dinoflagellates are responsible for observed differential scattering of circularly-polarized light. This differential scattering is found to vary in a manner that is possibly correlated to the cell cycle of the dinoflagellates. It is concluded that by properly choosing the wavelength probe polarized light scattering can provide a useful tool to study chromosome structure.
Date: October 1, 1993
Creator: Shapiro, D. B.
Partner: UNT Libraries Government Documents Department

Damped and thermal motion of large, laser-aligned molecules in droplet beams

Description: We consider a monodispersed Rayleigh droplet beam of water droplets doped with proteins. An intense infrared laser is used to align these droplets. The arrangement has been proposed for electron and X-ray diffraction studies of proteins which are difficult to crystallize. This paper considers the effect of thermal fluctuations on the angular spread of alignment in thermal equilibrium, and relaxation phenomena, particularly the damping of oscillations excited as the molecules enter the field. The possibility of adiabatic alignment is also considered. We find that damping times in high pressure gas cell as used in X-ray diffraction experiments are short compared to the time taken for molecules to traverse the beam, and that a suitably shaped field might be used for electron diffraction experiments in vacuum to provide adiabatic alignment, thus obviating the need for a damping gas cell.
Date: September 29, 2005
Creator: Starodub, D; Doak, B; Schmidt, K; Weierstall, U; Wu, J; Spence, J et al.
Partner: UNT Libraries Government Documents Department

High-resolution ab initio Three-dimensional X-ray Diffraction Microscopy

Description: Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.
Date: August 19, 2005
Creator: Chapman, H N; Barty, A; Marchesini, S; Noy, A; Cui, C; Howells, M R et al.
Partner: UNT Libraries Government Documents Department

Progress in Three-Dimensional Coherent X-Ray Diffraction Imaging

Description: The Fourier inversion of phased coherent diffraction patterns offers images without the resolution and depth-of-focus limitations of lens-based tomographic systems. We report on our recent experimental images inverted using recent developments in phase retrieval algorithms, and summarize efforts that led to these accomplishments. These include ab-initio reconstruction of a two-dimensional test pattern, infinite depth of focus image of a thick object, and its high-resolution ({approx}10 nm resolution) three-dimensional image. Developments on the structural imaging of low density aerogel samples are discussed.
Date: September 30, 2005
Creator: Marchesini, S; Chapman, H N; Barty, A; Howells, M R; Cui, C; Spence, J H et al.
Partner: UNT Libraries Government Documents Department

Dose, exposure time, and resolution in Serial X-ray Crystallography

Description: Using detailed simulation and analytical models, the exposure time is estimated for serial crystallography, where hydrated laser-aligned proteins are sprayed across a continuous synchrotron beam. The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available fluxes of molecules and X-rays. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of a density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 7 {angstrom} should be possible with short (below 100 s) exposures.
Date: March 22, 2007
Creator: Starodub, D; Rez, P; Hembree, G; Howells, M; Shapiro, D; Chapman, H N et al.
Partner: UNT Libraries Government Documents Department

A camera for coherent diffractive imaging and holography with a soft-X-ray free electron laser

Description: We describe a camera to record coherent scattering patterns with a soft-X-ray free-electron laser. The camera consists of a laterally-graded multilayer mirror which reflects the diffraction pattern onto a CCD detector. The mirror acts as a bandpass filter both for wavelength and angle, which isolates the desired scattering pattern from non-sample scattering or incoherent emission from the sample. The mirror also solves the particular problem of the extreme intensity of the FEL pulses, which are focused to greater than 10{sup 14} W/cm{sup 2}. The strong undiffracted pulse passes through a hole in the mirror and propagates on to a beam dump at a distance behind the instrument rather than interacting with a beamstop placed near the CCD. The camera concept is extendable for the full range of the fundamental wavelength of the FLASH FEL (i.e. between 6 nm and 60 nm) and into the water window. We have fabricated and tested various multilayer mirrors for wavelengths of 32 nm, 16 nm, 13.5 nm, and 4.5 nm. At the shorter wavelengths mirror roughness must be minimized to reduce scattering from the mirror. We have recorded over 30,000 diffraction patterns at the FLASH free-electron laser with no observable mirror damage or degradation of performance.
Date: September 24, 2007
Creator: Bajt, S; Chapman, H N; Spiller, E; Alameda, J; Woods, B; Frank, M et al.
Partner: UNT Libraries Government Documents Department

Femtosecond Diffractive Imaging with a Soft-X-ray Free-Electron Laser

Description: Theory predicts that with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus, or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft X-ray free-electron laser. An intense 25 fs, 4 x 10{sup 13} W/cm{sup 2} pulse, containing 10{sup 12} photons at 32 nm wavelength, produced a coherent diffraction pattern from a nano-structured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling, shows no measurable damage, and extends to diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one.
Date: March 13, 2006
Creator: Chapman, H N; Barty, A; Bogan, M; Boutet, S; Frank, M; Hau-Riege, S P et al.
Partner: UNT Libraries Government Documents Department