Biomedical subjects

J C H Spence

Publications and source records attributed to J C H Spence.

At least 19 recordsLinked to original sources

PubMed2005

Damped and thermal motion of laser-aligned hydrated macromolecule beams for diffraction.

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 a high-pressure gas cell as used in x-ray-diffraction experiments are short compared with 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.

Chemistry, Physical↗

PubMed2005

Phase measurement for accurate mapping of chemical bonds in acentric space groups.

Although the electron density is fundamental to the study of chemical bonding and density-functional theory, it cannot be accurately mapped experimentally for the important class of crystals lacking inversion symmetry, since structure factor phase information is normally inaccessible. We report the combination of x-ray and electron diffraction experiments for the determination of the electron density in acentric AlN, using multiple-scattering effects in convergent-beam electron diffraction to obtain sensitivity to structure factor phases, and describe a new error metric and weighting scheme for multipole refinement using combined measurements of structure factor magnitudes and phases.

Journal Article↗

PubMed2005

Reconstruction of complex single-particle images using charge-flipping algorithm.

An iterative algorithm is developed to retrieve the complex exit-face wavefunction for a two-dimensional projection of a nanoparticle from a measurement of the oversampled modulus of its Fourier transform in reciprocal space. The algorithm does not require the support (boundary) of the object to be known. A loose support for the complex object is gradually found using the Oszlanyi-Suto charge-flipping algorithm, and a compact support is then iteratively developed using a dynamic Gerchberg-Saxton-Fienup algorithm. At the same time, the complex object is reconstructed using this compact support. The algorithm applies to the reconstruction of complex images with any distribution of phase values from 0 to 2pi. Modification of the algorithm by using real-value constraints for a complex object in the charge-flipping algorithm leads to faster reconstruction of the object whose phase value is smaller than pi/2.

Journal Article↗

PubMed2005

Diffraction and imaging from a beam of laser-aligned proteins: resolution limits.

The effect of the limited alignment of hydrated molecules is considered in a laser-aligned molecular beam, on diffraction patterns taken from the beam. Simulated patterns for a protein beam are inverted using the Fienup-Gerchberg-Saxton phasing algorithm, and the effect of limited alignment on the resolution of the resulting potential maps is studied. For a typical protein molecule (lysozyme) with anisotropic polarizability, it is found that up to 1 kW of continuous-wave near-infrared laser power (depending on dielectric constant), together with cooling to liquid-nitrogen temperatures, may be needed to produce sufficiently accurate alignment for direct observation of the secondary structure of proteins in the reconstructed potential or charge-density map. For a typical virus (TMV), a 50 W continuous-wave laser is adequate for subnanometre resolution at room temperature. The dependence of resolution on laser power, temperature, molecular size, shape and dielectric constant is analyzed.

Algorithms↗

PubMed2004

Iterative phase retrieval without support.

An iterative phase retrieval method for nonperiodic objects has been developed from the charge-flipping algorithm proposed in crystallography. A combination of the hybrid input-output (HIO) algorithm and the flipping algorithm has greatly improved performance. In this combined algorithm the flipping algorithm serves to find the support (object boundary) dynamically, and the HIO part improves convergence and moves the algorithm out of local minima. It starts with a single intensity measurement in the Fourier domain and does not require a priori knowledge of the support in the image domain. This method is suitable for general image recovery from oversampled diffuse elastic x-ray and electron-diffraction intensities. The relationship between this algorithm and the output-output algorithm is elucidated.

Journal Article↗

PubMed2004

Enhancement of the superconducting transition temperature of MgB2 by a strain-induced bond-stretching mode softening.

We report a systematic increase of the superconducting transition temperature T(c) with a biaxial tensile strain in MgB2 films to well beyond the bulk value. The tensile strain increases with the MgB2 film thickness, caused primarily by the coalescence of initially nucleated discrete islands (the Volmer-Weber growth mode.) The T(c) increase was observed in epitaxial films on SiC and sapphire substrates, although the T(c) values were different for the two substrates due to different lattice parameters and thermal expansion coefficients. We identified, by first-principles calculations, the underlying mechanism for the T(c) increase to be the softening of the bond-stretching E(2g) phonon mode, and we confirmed this conclusion by Raman scattering measurements. The result suggests that the E(2g) phonon softening is a possible avenue to achieve even higher T(c) in MgB2-related material systems.

Journal Article↗

PubMed2004

Application of a modified Oszlányi and Süto ab initio charge-flipping algorithm to experimental data.

The structures of two crystals have been solved using a new iterative phasing method. The iterative phasing algorithm is developed from the 'charge-flipping' method proposed by Oszlányi & Süto [Acta Cryst. (2004), A60, 134-141]. Positivity and point-atom constraints are incorporated within this extremely simple and effective algorithm by flipping (sign reversal) of less-positive density values during the iterations. Convergence is reliably achieved and the two structures were solved. This structure solution method does not require information on atomic scattering factors or symmetry. Heavy atoms can be distinguished from light ones by their charge-density values.

Journal Article↗

PubMed2004

Phasing diffuse scattering. Application of the SIR2002 algorithm to the non-crystallographic phase problem.

A new phasing algorithm has been used to determine the phases of diffuse elastic X-ray scattering from a non-periodic array of gold balls of 50 nm diameter. Two-dimensional real-space images, showing the charge-density distribution of the balls, have been reconstructed at 50 nm resolution from transmission diffraction patterns recorded at 550 eV energy. The reconstructed image fits well with a scanning-electron-microscope (SEM) image of the same sample. The algorithm, which uses only the density modification portion of the SIR2002 program, is compared with the results obtained via the Gerchberg-Saxton-Fienup HiO algorithm. The new algorithm requires no knowledge of the object's boundary and proceeds from low to high resolution. In this way, the relationship between density modification in crystallography and the HiO algorithm used in signal and image processing is elucidated.

Journal Article↗

PubMed2004

Single molecule diffraction.

For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.

Electrons↗

PubMed2004

Structural study of new hydrocarbon nano-crystals by energy-filtered electron diffraction.

A new brittle hydrocarbon has been successfully synthesized in polycrystalline form, and its crystal structure solved by quantitative electron diffraction. By 3D tilting of the nano-crystals, the lattice type and unit cell parameters were determined. (Triclinic, [Formula: see text] A, [Formula: see text] A, [Formula: see text] A, [Formula: see text] degrees, [Formula: see text] degrees, and [Formula: see text] degrees.) Spot diffraction patterns were obtained at -165 degrees C using the Koehler selected-area mode on a LEO 912 TEM fitted with an omega in-column elastic energy filter. The direct methods algorithm was then applied to merged intensities and a trial structure obtained assuming single scattering. This was further refined to obtain good agreement with a small residual of about 10% using multiple scattering calculations. A diagram of the proposed structure is given.

Journal Article↗

PubMed2004

Coherence and sampling requirements for diffractive imaging.

Coherent Diffractive Imaging (CDI) allows images to be reconstructed from diffraction patterns by solving the non-crystallographic phase problem for isolated nanostructures. We show that the Shannon sampling of diffraction intensities needed in CDI requires a coherence width about twice the lateral dimensions of the object, and that the linear number of detector pixels fixes the energy spread needed in the beam. The Shannon sampling, defined by the transform of the periodically repeated autocorrelation of the object, is related to Bragg scattering from an equivalent crystal, and shown to be consistent with the sampling of Young's fringes established by scattering from extreme points in the object. The results are relevant to the design of diffraction cameras for CDI and plans for femotosecond X-ray diffraction from individual proteins.

Models, Theoretical↗

PubMed2004

Convergent-beam low energy electron diffraction (CBLEED) and the measurement of surface dipole layers.

We propose the formation of LEED patterns using a highly convergent beam forming a probe of nanometer dimensions. A reflection rocking curve may then be recorded in many diffraction orders simultaneously. Multiple scattering calculations show that the intensity variations within these rocking curves is as sensitive to the parameters describing the surface dipole layer as conventional I/V scans. However the data may be collected from areas sufficiently small to avoid defects and surface steps, radiation damage controlled by use of low voltages, and the information depth selected by choice of the (constant) voltage. We briefly discuss also the application of this method to oxides and the formation of atomic-resolution scanning images in an idealized instrument in which coherent diffracted LEED orders overlap.

Crystallography↗

PubMed2003

Phase extension in crystallography using the iterative Fienup-Gerchberg-Saxton algorithm and Hilbert transforms.

A procedure for phase extension in electron crystallography is proposed based on the iterative Fienup-Gerchberg-Saxton algorithm in combination with the use of discrete Hilbert transforms. This transform is used to provide oversampling in reciprocal space, thus satisfying the Shannon sampling requirement and introducing reflections with fractional indices. When the procedure is combined with the knowledge of a small set of strong phased Bragg reflections from electron-microscope images (or direct methods), the magnitudes of many non-Bragg reflections can be calculated with useful accuracy, thus enhancing the performance of the iterative algorithm for phase extension. The effects of various constraints used in the iterative algorithm are discussed. In this way, it is shown that the iterative algorithm conventionally used for phasing diffuse scattering from non-periodic objects can also be applied to problems in conventional crystallography to find the phases of high-order (resolution) beams from a known set of low-order (resolution) phases.

Journal Article↗

PubMed2003

Structure and bonding in alpha-copper phthalocyanine by electron diffraction.

Energy-filtered quantitative electron diffraction at liquid nitrogen temperature has been used to examine the atomic structure and bonding of metastable alpha-Cu phthalocyanine crystals. Three theoretical methods (kinematic, kinematic with excitation errors and Bloch wave) were employed for the intensity calculations. The Bloch-wave method was found to account for dynamical effects by greatly reducing the residual factor between experimental and simulated results. A new method for calculating electron scattering factors for partially charged ions is proposed and the sensitivity of electron diffraction to charge transfer is discussed. The atomic charge states were analyzed for alpha-Cu phthalocyanine using a charge cloud model in which the Gaussian bond charge is positioned along the bonds. Spot patterns were collected in the Kohler mode at two beam energies to reduce error. Using the best-fitting model, a deformation charge-density map is produced and compared to the neutral-atom model. From this, the main features of atomic charge transfer in the alpha-Cu phthalocyanine structure can be seen in the (010) plane.

Journal Article↗

PubMed2003

Charge density and chemical bonding in rutile, TiO2.

The low-order structure factors of rutile (TiO(2)) have been measured with an accuracy of up to 0.09% by quantitative convergent-beam electron diffraction (QCBED). This error is an order of magnitude smaller than that in conventional Bragg X-ray diffraction and equivalent to the accuracy of the X-ray Pendellösung method. It is sufficient to distinguish atomic, covalent and ionic bonding. By refinement of the combined data of low-order reflections measured by electron diffraction with high-order reflections from X-ray diffraction, accurate charge-density maps are obtained and used to understand the role of the 3d electrons in Ti-O bonding. The results are combined with electron energy-loss spectra (EELS) in a study of the electronic structure.

Journal Article↗

PubMed2003

Solving non-periodic structures using direct methods: phasing diffuse scattering.

The problem of reconstructing the charge density of a non-periodic sample from its diffuse X-ray scattering is considered. For a sample known to be isolated, an artificial superlattice may be assumed and the numerical direct methods of crystallography applied to the continuous distribution of diffuse scattering in order to solve the phase problem. This method is applied to simulated soft-X-ray transmission speckle patterns from a two-dimensional array of gold balls of 50 nm diameter. The results are relevant to efforts to phase the scattering from many individual macromolecules that cannot be crystallized, and to the scattering from individual inorganic nanoparticles.

Journal Article↗

PubMed2003

Experimental lensless soft-X-ray imaging using iterative algorithms: phasing diffuse scattering.

Images of randomly placed two-dimensional arrays of gold balls have been reconstructed from their soft-X-ray transmission diffraction patterns. An iterative hybrid input-output (HiO) algorithm was used to solve the phase problem for the continuous distribution of diffuse X-ray scattering. Knowledge of the approximate size of the clusters was required. The images compare well with scanning electron microscope (SEM) images of the same sample. The use of micrometre-sized silicon nitride window supports is suggested, and absorption filters have been used to allow collection of low spatial frequencies often obscured by a beam stop. This method of phasing diffuse scattering may have application to scattering from individual inorganic nanostructures or single macromolecules.

Journal Article↗

PubMed2002

Kinematic and dynamical CBED for solving thin organic films at low temperature; experimental tests with anthracene.

Low-dose, low-temperature kinematic and dynamical convergent-beam electron diffraction (CBED) patterns from thin organic crystalline films have been used for the measurement of structure-factor amplitudes and phases. Kinematic conditions are identified by the observation of uniform intensity within the CBED discs and used to determine structure-factor magnitudes. CBED patterns from thicker regions affected by multiple scattering give structure-factor signs, which are varied for best fit. The use of a small probe (and the Kohler SAD mode) minimizes bending artifacts. A new method of thickness determination is evaluated. The approach is tested using experimental data from the centrosymmetric anthracene structure, the results compared with direct methods, and a potential map derived from experimental data. The faint peaks due to H-atom positions may be distinguished. Key issues influencing the validity of the method such as the appropriate dimension of the structure-factor matrix, sample thickness and crystal orientation are discussed.

Algorithms↗