Dilano Saldin - Academia.edu (original) (raw)
Papers by Dilano Saldin
Physical review. B, Condensed matter, 1994
We report a study of the x-ray-absorption near-edge structure of the Bi [ital L][sub 3] and O [it... more We report a study of the x-ray-absorption near-edge structure of the Bi [ital L][sub 3] and O [ital K] edges in Bi[sub 2]Sr[sub 2]CaCu[sub 2]O[sub 8]. A comparison with the Bi [ital L][sub 3] edges of Bi[sub 2]O[sub 3] and KBiO[sub 3] indicates that the Bi atoms are in a state close to a formal valency of +3 in the
Physical Review B, 1998
Following on the success of the recent application of holographic LEED to the determination of th... more Following on the success of the recent application of holographic LEED to the determination of the threedimensional atomic geometry of Si adatoms on a SiC(111)p(3ϫ3) surface, which enabled that structure to be solved, we show in this paper that a similar technique allows the direct recovery of the local geometry of adsorbates forming superstructures as small as p(2ϫ2), even in the presence of a local substrate reconstruction.
Surface Science, 2008
The structure, formation and decomposition pathways of 2-butoxide species formed on a Pd(111) sur... more The structure, formation and decomposition pathways of 2-butoxide species formed on a Pd(111) surface following the adsorption of 2-butanol is studied by a combination of density functional theory (DFT), analysis of the low-energy electron intensity versus beam energy curves (LEED I/E) and temperature-programmed desorption (TPD). Both DFT calculations and LEED I/E measurements reveal that 2-butoxide adsorbs with the oxygen atom located in the three-fold hollow sites on Pd(111) with the C–O bond almost perpendicular to the surface with the 2-butyl group in the trans configuration. At coverages below ∼0.11 monolayers, adsorbed 2-butoxide species completely thermally decompose to desorb hydrogen and carbon monoxide. The 2-butoxide species present at higher coverages either hydrogenate to reform 2-butanol or undergo a β-hydride elimination reaction to form 2-butanone.
Tribology International, 2005
Calculation of X-ray absorption near-edge structure (XANES) has been used to investigate the chem... more Calculation of X-ray absorption near-edge structure (XANES) has been used to investigate the chemical nature of zinc in thermal films formed on the surfaces of steel coupons by the additive zinc dialkyl dithiophosphate (ZDDP) in oil solution. Carbon K, oxygen K, and zinc L edge XANES spectra were used to characterize the thermal films and a model film formed by addition of cumene hydroperoxide (CHP) to the ZDDP. Thermal films formed by heating at up to 100 v C for 5 h showed little change from unreacted ZDDP. At 160 v C for 5 h, the ZDDP underwent thermal solution decomposition with similarities to the oxidation induced by CHP. The Zn L edge XANES spectra were compared to calculated spectra of the model surface species ZnO and ZnS in the wurtzite structure and ZnS in the zinc blende structure. Agreement between experiment and simulation is found for the 160 v C thermal film with a roughly two monolayer film of ZnO and for oxidation by CHP with a three to four monolayer film of ZnS. #
Surface Science, 2008
... scattering. Zhenjun Li a , Octavio Furlong a , Florencia Calaza a , Luke Burkholder a , Hin C... more ... scattering. Zhenjun Li a , Octavio Furlong a , Florencia Calaza a , Luke Burkholder a , Hin Cheuk Poon b , Dilano Saldin b and Wilfred T. Tysoe a , Corresponding Author Contact Information , E-mail The Corresponding Author. ...
Surface Science, 2006
A structural study has been performed on the MgO(1 1 1)-(1 · 1) surface by low energy electron di... more A structural study has been performed on the MgO(1 1 1)-(1 · 1) surface by low energy electron diffraction (LEED) using experimental data obtained with a delay-line-detector LEED (DLD-LEED) system to minimize electron damage. It was found that the surface is terminated by a hydroxide layer with the top O-Mg interlayer spacing equal to 1.02 Å , which is close to the spacings between Mg and O planes in bulk brucite crystals (Mg(OH) 2 ). This is in good agreement with a recent study using photoelectron diffraction (PhD) spectroscopy and density functional theory calculation (DFT) [V.K. Lazarov, R. Plass, H.-C. Poon, D.K. Saldin, M. Weinert, S.A. Chambers, M. Gajdardziska-Josifovska, Phys. Rev. B 71 (2005) 115434]. The second interlayer spacing shows a small expansion of 3% and the third is bulk-like, while the DFT calculation predicted that the spacings below the top one are all bulk-like. This result clearly favors hydroxylation [K. Refson, R.A. Wogelius, D.G. Fraser, M.C. Payne, M.H. Lee, V. Milman, Phys. Rev. B 52 (1995) 10823] as a way of stabilizing the MgO(1 1 1) surface at low temperature over metallization, which has a top layer spacing of 0.86 Å for O termination and 1.25 Å for Mg termination [Lazarov et al.
Surface Science, 2009
A structural study has been performed on the TiO 2 (0 1 1)(2Â1) surface by quantitative low energ... more A structural study has been performed on the TiO 2 (0 1 1)(2Â1) surface by quantitative low energy electron diffraction (LEED), using a delay-line-detector (DLD-LEED) system. The atomic coordinates obtained are in good agreement with recent studies using surface X-ray diffraction (SXRD). The best-fit Pendry R factor is 0.29. This effectively rules out the other models previously proposed, which have significantly higher R factors. Despite the good agreement, however, a key feature of the bonding in this model, which has been suggested as the origin of the photo-catalytic activity of this surface, is not supported by the current analysis. Contrary to a previous study for the TiO 2 (1 1 0)(1Â1) surface, it was also found that calculating the sample potentials self-consistently had little effect on the results.
In about an hour, 10 5 "shots" from the LCLS XFEL should scatter ~10 3 photons into each pixel of... more In about an hour, 10 5 "shots" from the LCLS XFEL should scatter ~10 3 photons into each pixel of the high-q regions of a diffraction pattern from a 500 kDa biological molecule -if only we could integrate the scattered photons from successive shots. In the absence of orientational alignment, each single-shot diffraction pattern will emanate from an unknown random orientation of the molecule. A key problem therefore concerns determining the relative orientations of the individual diffraction patterns in the presence of noise; a "high-q pixel" of a single-shot diffraction pattern is expected to contain an average of ~10 -2 photons.
Physical Review Letters, 2011
We report on the first experimental ab initio reconstruction of an image of a single particle fro... more We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
Physical Review B, 2005
The surface structure of MgO(111)-(1×1) bulk and thinned single crystals have been investigated b... more The surface structure of MgO(111)-(1×1) bulk and thinned single crystals have been investigated by transmission and reflection high-energy electron diffraction, low-energy electron diffraction (LEED), and x-ray photoelectron and Auger electron diffraction. The (1×1) polar surface periodicity is observed both after 800 °C annealing in air and also after oxygen plasma cleaning and annealing in ultrahigh vacuum. The x-ray photoelectron spectroscopy and diffraction results were analyzed by simulations based on path-reversed LEED theory and by first-principles calculations to help distinguish between different mechanisms for the stabilization of this extremely polar oxide surface: (1) stabilization by adsorption of a hydrogen monolayer; maintaining the insulating nature of the surface and (2) stabilization of the clean O or Mg terminated 1×1 surface by interlayer relaxations and two-dimensional surface metallization. The analysis favors stabilization by a single OH layer, where hydrogen sits on top of the O ions with O-H bond distance of 0.98Å. The in-plane O and Mg positions fit regular rocksalt sites, the distance between the topmost O and Mg plane is 1.04 Å, contracted by ˜14% with respect to bulk MgO distance of 1.21 Å, while the interlayer separation of the deeper layers is close to that of bulk, contracted by less than 1%. The presence of a monolayer of H associated with the terminal layer of oxygen reduces significantly the surface dipole and stabilizes the surface.
Physical Review B, 2010
We propose a method for determining the projected electron density of an individual molecule from... more We propose a method for determining the projected electron density of an individual molecule from diffraction patterns of many such simultaneously illuminated molecules, randomly oriented about an axis parallel to an incident x-ray beam. We illustrate the idea with a simulation of a structure determination of a K-channel membrane protein in situ.
Physical Review B, 2007
We report on the structural determination of the surface of TiO 2 -terminated SrTiO 3 ͑001͒ using... more We report on the structural determination of the surface of TiO 2 -terminated SrTiO 3 ͑001͒ using surface x-ray diffraction. The detailed analysis of two surface diffraction data sets are presented, one ͑cold͒ taken at room temperature in vacuum, and the other ͑hot͒ under typical conditions used for thin film growth. 49 different combinations of possible surface terminations are described for the cold structure, from which the final structure was chosen, consisting of a weighted mixture of a ͑1 ϫ 1͒ relaxation and ͑2 ϫ 1͒ and ͑2 ϫ 2͒ reconstructions, simultaneously present at the surface. The structures are best modeled by a TiO 2 -rich surface similar to that proposed by Erdman et al. ͓Nature ͑London͒ 419, 55 ͑2002͔͒. The reconstructions are energetically favorable according to density functional theory. They disappear within several minutes upon heating to the hot conditions, forming a termination very similar to the cold ͑1 ϫ 1͒, but more puckered and higher in energy. Six additional models, suggested by direct methods and the literature, to describe the hot surface are also discussed. Direct methods confirm the TiO 2 -rich termination and the atomic positions of the hot surface. The atomic coordinates for the two TiO 2 -rich surfaces exhibit significant displacements down to three unit cells, which may have important implications on possible surface ferroelectric phenomena in SrTiO 3 . Surface energy considerations suggest a temperature-induced order-disorder transition, produced by a mixing of the ͑2 ϫ 1͒ and ͑2 ϫ 2͒ reconstructions, to form the hot pseudo ͑1 ϫ 1͒ structure. Electrostatic stability arguments provide circumstantial support for the experimentally determined TiO 2 -rich surfaces.
New Journal of Physics, 2010
In this paper is demonstrated a complete algorithm for determining the electron density of an ind... more In this paper is demonstrated a complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles, randomly oriented about a single axis. The algorithm operates on angular correlations among the measured intensity distributions. We also demonstrate the ability to recover the angular correlation functions of a single particle from measured diffraction patterns.
Nature Physics, 2009
Moves are afoot to illuminate particles in flight with powerful X-ray bursts, to determine the st... more Moves are afoot to illuminate particles in flight with powerful X-ray bursts, to determine the structure of single molecules, viruses and nanoparticles. This would circumvent important limitations of current techniques, including the need to condense molecules into pure crystals. Proposals to reconstruct the molecular structure from diffraction 'snapshots' of unknown orientation, however, require ∼1,000 times more signal than available from next-generation sources. Using a new approach, we demonstrate the recovery of the structure of a weakly scattering macromolecule at the anticipated next-generation X-ray source intensities. Our work closes a critical gap in determining the structure of single molecules and nanoparticles by X-ray methods, and opens the way to reconstructing the structure of spinning, or randomly oriented objects at extremely low signal levels.
Microscopy and Microanalysis, 2010
Journal of Physics: Condensed Matter, 2009
Amongst the promised capabilities of fourth-generation x-ray sources currently under construction... more Amongst the promised capabilities of fourth-generation x-ray sources currently under construction is the ability to record diffraction patterns from individual biological molecules. One version of such an experiment would involve directing a stream of molecules into the x-ray beam and sequentially recording the scattering from each molecule of a short, but intense, pulse of radiation. The pulses are sufficiently short that the diffraction pattern is that due to scattering from identical molecules 'frozen' in random orientations. Each diffraction pattern may be thought of as a section through the 3D reciprocal space of the molecule, of unknown, random, orientation. At least two algorithms have been proposed for finding the relative orientations from just the measured diffraction data. The 'common-line' method, also employed in 3D electron microscopy, appears not best suited to the very low mean photon count per diffraction pattern pixel expected in such experiments. A manifold embedding technique has been used to reconstruct the 3D diffraction volume and hence the electron density of a small protein at the signal level expected of the scattering of an x-ray free electron laser pulse from a 500 kD biomolecule. In this paper, we propose an alternative algorithm which raises the possibility of reconstructing the 3D diffraction volume of a molecule without determining the relative orientations of the individual diffraction patterns. We discuss why such an algorithm may provide a practical and computationally convenient method of extracting information from very weak diffraction patterns. We suggest also how such a method may be adapted to the problem of finding the variations of a structure with time in a time-resolved pump-probe experiment.
The Journal of Chemical Physics, 2009
We investigate the molecular structure information contained in the x-ray diffraction patterns of... more We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.
Acta Crystallographica Section A Foundations of Crystallography, 2010
Author(s) of this paper may load this reprint on their own web site or institutional repository p... more Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.
Nature Photonics, 2009
Resonant energy transfer from an optically excited donor molecule to a non-excited acceptor molec... more Resonant energy transfer from an optically excited donor molecule to a non-excited acceptor molecule residing nearby is widely used to detect molecular interactions in living cells. To date, resonant energy transfer has been used to obtain stoichiometric information, such as the number of proteins forming a complex, for a handful of proteins, but only after performing sequential scans of the emission wavelengths, excitation wavelengths, or sometimes both. During this lengthy process of measurement, the molecular makeup of a cellular region may change, limiting the applicability of resonant energy transfer to the determination of cellular averages. Here, we demonstrate a method for the determination of protein complex size, configuration, and spatial distribution in single living cells. It relies on a spectrally resolved two-photon microscope, a simple but competent theory, and a judicious selection of fluorescent tags. This approach eventually may lead to tracking the dynamics of individual molecular complexes inside living cells.
Physical review. B, Condensed matter, 1994
We report a study of the x-ray-absorption near-edge structure of the Bi [ital L][sub 3] and O [it... more We report a study of the x-ray-absorption near-edge structure of the Bi [ital L][sub 3] and O [ital K] edges in Bi[sub 2]Sr[sub 2]CaCu[sub 2]O[sub 8]. A comparison with the Bi [ital L][sub 3] edges of Bi[sub 2]O[sub 3] and KBiO[sub 3] indicates that the Bi atoms are in a state close to a formal valency of +3 in the
Physical Review B, 1998
Following on the success of the recent application of holographic LEED to the determination of th... more Following on the success of the recent application of holographic LEED to the determination of the threedimensional atomic geometry of Si adatoms on a SiC(111)p(3ϫ3) surface, which enabled that structure to be solved, we show in this paper that a similar technique allows the direct recovery of the local geometry of adsorbates forming superstructures as small as p(2ϫ2), even in the presence of a local substrate reconstruction.
Surface Science, 2008
The structure, formation and decomposition pathways of 2-butoxide species formed on a Pd(111) sur... more The structure, formation and decomposition pathways of 2-butoxide species formed on a Pd(111) surface following the adsorption of 2-butanol is studied by a combination of density functional theory (DFT), analysis of the low-energy electron intensity versus beam energy curves (LEED I/E) and temperature-programmed desorption (TPD). Both DFT calculations and LEED I/E measurements reveal that 2-butoxide adsorbs with the oxygen atom located in the three-fold hollow sites on Pd(111) with the C–O bond almost perpendicular to the surface with the 2-butyl group in the trans configuration. At coverages below ∼0.11 monolayers, adsorbed 2-butoxide species completely thermally decompose to desorb hydrogen and carbon monoxide. The 2-butoxide species present at higher coverages either hydrogenate to reform 2-butanol or undergo a β-hydride elimination reaction to form 2-butanone.
Tribology International, 2005
Calculation of X-ray absorption near-edge structure (XANES) has been used to investigate the chem... more Calculation of X-ray absorption near-edge structure (XANES) has been used to investigate the chemical nature of zinc in thermal films formed on the surfaces of steel coupons by the additive zinc dialkyl dithiophosphate (ZDDP) in oil solution. Carbon K, oxygen K, and zinc L edge XANES spectra were used to characterize the thermal films and a model film formed by addition of cumene hydroperoxide (CHP) to the ZDDP. Thermal films formed by heating at up to 100 v C for 5 h showed little change from unreacted ZDDP. At 160 v C for 5 h, the ZDDP underwent thermal solution decomposition with similarities to the oxidation induced by CHP. The Zn L edge XANES spectra were compared to calculated spectra of the model surface species ZnO and ZnS in the wurtzite structure and ZnS in the zinc blende structure. Agreement between experiment and simulation is found for the 160 v C thermal film with a roughly two monolayer film of ZnO and for oxidation by CHP with a three to four monolayer film of ZnS. #
Surface Science, 2008
... scattering. Zhenjun Li a , Octavio Furlong a , Florencia Calaza a , Luke Burkholder a , Hin C... more ... scattering. Zhenjun Li a , Octavio Furlong a , Florencia Calaza a , Luke Burkholder a , Hin Cheuk Poon b , Dilano Saldin b and Wilfred T. Tysoe a , Corresponding Author Contact Information , E-mail The Corresponding Author. ...
Surface Science, 2006
A structural study has been performed on the MgO(1 1 1)-(1 · 1) surface by low energy electron di... more A structural study has been performed on the MgO(1 1 1)-(1 · 1) surface by low energy electron diffraction (LEED) using experimental data obtained with a delay-line-detector LEED (DLD-LEED) system to minimize electron damage. It was found that the surface is terminated by a hydroxide layer with the top O-Mg interlayer spacing equal to 1.02 Å , which is close to the spacings between Mg and O planes in bulk brucite crystals (Mg(OH) 2 ). This is in good agreement with a recent study using photoelectron diffraction (PhD) spectroscopy and density functional theory calculation (DFT) [V.K. Lazarov, R. Plass, H.-C. Poon, D.K. Saldin, M. Weinert, S.A. Chambers, M. Gajdardziska-Josifovska, Phys. Rev. B 71 (2005) 115434]. The second interlayer spacing shows a small expansion of 3% and the third is bulk-like, while the DFT calculation predicted that the spacings below the top one are all bulk-like. This result clearly favors hydroxylation [K. Refson, R.A. Wogelius, D.G. Fraser, M.C. Payne, M.H. Lee, V. Milman, Phys. Rev. B 52 (1995) 10823] as a way of stabilizing the MgO(1 1 1) surface at low temperature over metallization, which has a top layer spacing of 0.86 Å for O termination and 1.25 Å for Mg termination [Lazarov et al.
Surface Science, 2009
A structural study has been performed on the TiO 2 (0 1 1)(2Â1) surface by quantitative low energ... more A structural study has been performed on the TiO 2 (0 1 1)(2Â1) surface by quantitative low energy electron diffraction (LEED), using a delay-line-detector (DLD-LEED) system. The atomic coordinates obtained are in good agreement with recent studies using surface X-ray diffraction (SXRD). The best-fit Pendry R factor is 0.29. This effectively rules out the other models previously proposed, which have significantly higher R factors. Despite the good agreement, however, a key feature of the bonding in this model, which has been suggested as the origin of the photo-catalytic activity of this surface, is not supported by the current analysis. Contrary to a previous study for the TiO 2 (1 1 0)(1Â1) surface, it was also found that calculating the sample potentials self-consistently had little effect on the results.
In about an hour, 10 5 "shots" from the LCLS XFEL should scatter ~10 3 photons into each pixel of... more In about an hour, 10 5 "shots" from the LCLS XFEL should scatter ~10 3 photons into each pixel of the high-q regions of a diffraction pattern from a 500 kDa biological molecule -if only we could integrate the scattered photons from successive shots. In the absence of orientational alignment, each single-shot diffraction pattern will emanate from an unknown random orientation of the molecule. A key problem therefore concerns determining the relative orientations of the individual diffraction patterns in the presence of noise; a "high-q pixel" of a single-shot diffraction pattern is expected to contain an average of ~10 -2 photons.
Physical Review Letters, 2011
We report on the first experimental ab initio reconstruction of an image of a single particle fro... more We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
Physical Review B, 2005
The surface structure of MgO(111)-(1×1) bulk and thinned single crystals have been investigated b... more The surface structure of MgO(111)-(1×1) bulk and thinned single crystals have been investigated by transmission and reflection high-energy electron diffraction, low-energy electron diffraction (LEED), and x-ray photoelectron and Auger electron diffraction. The (1×1) polar surface periodicity is observed both after 800 °C annealing in air and also after oxygen plasma cleaning and annealing in ultrahigh vacuum. The x-ray photoelectron spectroscopy and diffraction results were analyzed by simulations based on path-reversed LEED theory and by first-principles calculations to help distinguish between different mechanisms for the stabilization of this extremely polar oxide surface: (1) stabilization by adsorption of a hydrogen monolayer; maintaining the insulating nature of the surface and (2) stabilization of the clean O or Mg terminated 1×1 surface by interlayer relaxations and two-dimensional surface metallization. The analysis favors stabilization by a single OH layer, where hydrogen sits on top of the O ions with O-H bond distance of 0.98Å. The in-plane O and Mg positions fit regular rocksalt sites, the distance between the topmost O and Mg plane is 1.04 Å, contracted by ˜14% with respect to bulk MgO distance of 1.21 Å, while the interlayer separation of the deeper layers is close to that of bulk, contracted by less than 1%. The presence of a monolayer of H associated with the terminal layer of oxygen reduces significantly the surface dipole and stabilizes the surface.
Physical Review B, 2010
We propose a method for determining the projected electron density of an individual molecule from... more We propose a method for determining the projected electron density of an individual molecule from diffraction patterns of many such simultaneously illuminated molecules, randomly oriented about an axis parallel to an incident x-ray beam. We illustrate the idea with a simulation of a structure determination of a K-channel membrane protein in situ.
Physical Review B, 2007
We report on the structural determination of the surface of TiO 2 -terminated SrTiO 3 ͑001͒ using... more We report on the structural determination of the surface of TiO 2 -terminated SrTiO 3 ͑001͒ using surface x-ray diffraction. The detailed analysis of two surface diffraction data sets are presented, one ͑cold͒ taken at room temperature in vacuum, and the other ͑hot͒ under typical conditions used for thin film growth. 49 different combinations of possible surface terminations are described for the cold structure, from which the final structure was chosen, consisting of a weighted mixture of a ͑1 ϫ 1͒ relaxation and ͑2 ϫ 1͒ and ͑2 ϫ 2͒ reconstructions, simultaneously present at the surface. The structures are best modeled by a TiO 2 -rich surface similar to that proposed by Erdman et al. ͓Nature ͑London͒ 419, 55 ͑2002͔͒. The reconstructions are energetically favorable according to density functional theory. They disappear within several minutes upon heating to the hot conditions, forming a termination very similar to the cold ͑1 ϫ 1͒, but more puckered and higher in energy. Six additional models, suggested by direct methods and the literature, to describe the hot surface are also discussed. Direct methods confirm the TiO 2 -rich termination and the atomic positions of the hot surface. The atomic coordinates for the two TiO 2 -rich surfaces exhibit significant displacements down to three unit cells, which may have important implications on possible surface ferroelectric phenomena in SrTiO 3 . Surface energy considerations suggest a temperature-induced order-disorder transition, produced by a mixing of the ͑2 ϫ 1͒ and ͑2 ϫ 2͒ reconstructions, to form the hot pseudo ͑1 ϫ 1͒ structure. Electrostatic stability arguments provide circumstantial support for the experimentally determined TiO 2 -rich surfaces.
New Journal of Physics, 2010
In this paper is demonstrated a complete algorithm for determining the electron density of an ind... more In this paper is demonstrated a complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles, randomly oriented about a single axis. The algorithm operates on angular correlations among the measured intensity distributions. We also demonstrate the ability to recover the angular correlation functions of a single particle from measured diffraction patterns.
Nature Physics, 2009
Moves are afoot to illuminate particles in flight with powerful X-ray bursts, to determine the st... more Moves are afoot to illuminate particles in flight with powerful X-ray bursts, to determine the structure of single molecules, viruses and nanoparticles. This would circumvent important limitations of current techniques, including the need to condense molecules into pure crystals. Proposals to reconstruct the molecular structure from diffraction 'snapshots' of unknown orientation, however, require ∼1,000 times more signal than available from next-generation sources. Using a new approach, we demonstrate the recovery of the structure of a weakly scattering macromolecule at the anticipated next-generation X-ray source intensities. Our work closes a critical gap in determining the structure of single molecules and nanoparticles by X-ray methods, and opens the way to reconstructing the structure of spinning, or randomly oriented objects at extremely low signal levels.
Microscopy and Microanalysis, 2010
Journal of Physics: Condensed Matter, 2009
Amongst the promised capabilities of fourth-generation x-ray sources currently under construction... more Amongst the promised capabilities of fourth-generation x-ray sources currently under construction is the ability to record diffraction patterns from individual biological molecules. One version of such an experiment would involve directing a stream of molecules into the x-ray beam and sequentially recording the scattering from each molecule of a short, but intense, pulse of radiation. The pulses are sufficiently short that the diffraction pattern is that due to scattering from identical molecules 'frozen' in random orientations. Each diffraction pattern may be thought of as a section through the 3D reciprocal space of the molecule, of unknown, random, orientation. At least two algorithms have been proposed for finding the relative orientations from just the measured diffraction data. The 'common-line' method, also employed in 3D electron microscopy, appears not best suited to the very low mean photon count per diffraction pattern pixel expected in such experiments. A manifold embedding technique has been used to reconstruct the 3D diffraction volume and hence the electron density of a small protein at the signal level expected of the scattering of an x-ray free electron laser pulse from a 500 kD biomolecule. In this paper, we propose an alternative algorithm which raises the possibility of reconstructing the 3D diffraction volume of a molecule without determining the relative orientations of the individual diffraction patterns. We discuss why such an algorithm may provide a practical and computationally convenient method of extracting information from very weak diffraction patterns. We suggest also how such a method may be adapted to the problem of finding the variations of a structure with time in a time-resolved pump-probe experiment.
The Journal of Chemical Physics, 2009
We investigate the molecular structure information contained in the x-ray diffraction patterns of... more We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.
Acta Crystallographica Section A Foundations of Crystallography, 2010
Author(s) of this paper may load this reprint on their own web site or institutional repository p... more Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.
Nature Photonics, 2009
Resonant energy transfer from an optically excited donor molecule to a non-excited acceptor molec... more Resonant energy transfer from an optically excited donor molecule to a non-excited acceptor molecule residing nearby is widely used to detect molecular interactions in living cells. To date, resonant energy transfer has been used to obtain stoichiometric information, such as the number of proteins forming a complex, for a handful of proteins, but only after performing sequential scans of the emission wavelengths, excitation wavelengths, or sometimes both. During this lengthy process of measurement, the molecular makeup of a cellular region may change, limiting the applicability of resonant energy transfer to the determination of cellular averages. Here, we demonstrate a method for the determination of protein complex size, configuration, and spatial distribution in single living cells. It relies on a spectrally resolved two-photon microscope, a simple but competent theory, and a judicious selection of fluorescent tags. This approach eventually may lead to tracking the dynamics of individual molecular complexes inside living cells.