G. Bunker | Illinois Institute of Technology (original) (raw)

Papers by G. Bunker

Research paper thumbnail of Determination by X-Ray Absorption of Redox Induced Structural Changes in Iron-Sulfur Cluster Fxin Photosystem I

Acta Physica Polonica A, 1997

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Research paper thumbnail of Double crystal bent Laue “beam cleaner”

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Research paper thumbnail of Tests of a multilayer analyzer x-ray fluorescence array detector

It is a concern that multi-element solid-state detectors commonly used in x-ray fluorescence dete... more It is a concern that multi-element solid-state detectors commonly used in x-ray fluorescence detection for dilute systems will not be suitable at the third-generation sources such as the Advanced Photon Source (APS), Argonne National Laboratory. Indeed, with the more than 10–13 photon flux available at the Bio-CAT insertion device (ID) beamline, a solid state detector (e.g., the Canberra 13element Ge detector) will not work efficiently because of count rate limitations. It is estimated that only a few percent of the beam can be utilized by such a detector. In other words, elements in the order of thousands are needed on the detector to use the whole beam effectively. Thus, we have proposed the development of x-ray fluorescence detectors using multilayers [1, 2]. Acting as an analyzer, the mutilayers select x-ray fluorescence signals from background photons when the Bragg condition is met at the fluorescence energy. The data can be collected using a nonenergyresolving detector. Thus,...

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Research paper thumbnail of Introduction to XAFS: References

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Research paper thumbnail of Multiple scattering in the XANES of tetrahedral Ge gases

Physical review. B, Condensed matter

X-ray absorption fine structure (XAFS) measurements of GeCl4, GeH3Cl, and GeH4 were made. We expe... more X-ray absorption fine structure (XAFS) measurements of GeCl4, GeH3Cl, and GeH4 were made. We experimentally isolate the single- and multiple-scattering terms in the XAFS of GeCl4 by comparison of the spectra of the three compounds. The multiple scattering (MS) amplitude is comparable to the single-scattering (SS) amplitude only to within 15 eV of the edge. Beyond 40 eV the MS to SS ratio is less than 0.06. Calculations are in qualitative agreement with experiment. Our results suggest that XAFS data in the range 1 < k < 3 Å-1 can be analyzed in a SS picture in many cases.

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Research paper thumbnail of Initial results on logarithmic spiral bent Laue analyzer for fluorescence x-ray absorption spectroscopy (abstract)

Review of Scientific Instruments, 2002

We have previously described [Z. Zhong, D. Chapman, B. A. Bunker, G. B. Bunker, R. Fischetti, and... more We have previously described [Z. Zhong, D. Chapman, B. A. Bunker, G. B. Bunker, R. Fischetti, and C. U. Segre, J. Synchrotron Radiat. 6, 212 (1999); C. Karanfil et al., AIP Conf. Proc. 521, 178 (2000)] a novel concept of using highly bent single crystals in Laue geometry for wide bandwidth monochromatization of fluorescence x rays emerging from a point source, such as the sample in fluorescence x-ray absorption spectroscopy (XAFS) experiments. In this article we describe the first measurements (summer 2000) of the fluorescence XAFS of millimolar solutions of several elements. The potential of this type of analyzer is clearly demonstrated.

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Research paper thumbnail of Single and multiple scattering XAFS Debye-Waller factors for crystalline materials using periodic Density Functional Theory

ABSTRACT We present an accurate and efficient technique for calculating thermal X-ray absorption ... more ABSTRACT We present an accurate and efficient technique for calculating thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) applicable to crystalline materials. Using Density Functional Theory on a 3×3×3 supercell pattern of MnO structure, under the nonlocal hybrid B3LYP functional paired with Gaussian local basis sets, we obtain the normal mode eigenfrequencies and eigenvectors; these parameters are in turn used to calculate single and multiple scattering XAFS DWFs. The DWFs obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters, when experimental spectra are fitted with a hypothetical structure. The size of the supercell size limits the R-space range that these parameters could be used. Therefore corresponding DWFs for paths outside of this range are calculated using the correlated Debye model. Our method is compared with prior cluster calculations and with corresponding values obtained from fitting experimental XAFS spectra on manganosite with simulated spectra.

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Research paper thumbnail of A ‘beam cleaner’ for harmonic selection/rejection

AIP Conference Proceedings, 2000

A ‘beam cleaner’ for selection of a harmonic from the beamline monochromator and rejection of oth... more A ‘beam cleaner’ for selection of a harmonic from the beamline monochromator and rejection of other harmonics has been developed using a bent Laue crystal post-monochromator. This is a set of cylindrically bent Si (111) crystals that are aligned to diffract the 2nd harmonic (3× fundamental) from the beamline Si (111) monochromator. This device will reject the fundamental and other

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Research paper thumbnail of An X-ray Harmonic Selection and Rejection Device

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Research paper thumbnail of A device for selecting and rejecting X-ray harmonics in synchrotron radiation beams

Journal of Synchrotron Radiation, 2004

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Research paper thumbnail of Introduction to XAFS: References

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Research paper thumbnail of A bent Laue analyzer for fluorescence EXAFS detection

Journal of Synchrotron Radiation, 1999

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Research paper thumbnail of Quantitative performance measurements of bent crystal Laue analyzers for X-ray fluorescence spectroscopy

Journal of Synchrotron Radiation, 2012

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Research paper thumbnail of GPU Computing in XAFS

Journal of Physics: Conference Series, 2013

Modern graphics processing units (GPUs) are powerful parallel computers. Porting the mathematical... more Modern graphics processing units (GPUs) are powerful parallel computers. Porting the mathematically intense, parallelizable algorithms of XAFS to run on GPUs should expand the scale of tractable XAFS calculations. Part of a time-limiting subroutine in FEFF 8.4 (fms) was converted to run on a GPU, showing significant performance gains. With parallel CPUs sharing GPU resources, the runtime of the modules calling fms should accelerate by one or two orders of magnitude versus a single-threaded CPU process (at least for large atomic clusters,). New or existing XAFS algorithms and programs (e.g. FEFF 9) should show similar acceleration when ported to GPUs, as long as they meet certain criteria (outlined in detail).

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Research paper thumbnail of Multiple scattering in the x-ray-absorption near-edge structure of tetrahedral Ge gases

Physical Review B, 1988

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Research paper thumbnail of Bent Laue Crystal Analyzers for X-ray Fluorescence Detection

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Research paper thumbnail of Extended X-ray absorption fine structure studies of Zn2Fe2 hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry, 1986

Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized b... more Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized by extended X-ray absorption structure (EXAFS) studies. Since Zn and Fe have very different K absorption edge energies, the structures of the ligated (Fe) and unligated (Zn) sites could be examined independently within a single molecule that mimics an intermediate ligation state. The observed EXAFS spectra and associated structural parameters are compared among the ligand free (alpha Zn)2(beta Zn)2, half-ligated (alpha FeCO)2(beta Zn)2 and (alpha Zn)2(beta FeCO)2, and fully ligated (alpha FeCO)2(beta FeCO)2 systems.

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Research paper thumbnail of Extended X-ray absorption fine structure studies of ZnâFeâ hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry, 1986

Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized b... more Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized by extended X-ray absorption structure (EAFS) studies. Since Zn and Fe have very different K absorption edge energies, the structures of the ligated (Fe) and unligated (Zn) sites could be examined independently within a single molecule that mimics an intermediate ligation state. The observed EXAFS spectra and associated

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Research paper thumbnail of Extended X-ray absorption fine structure studies of ZnâFeâ hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry Usa, 1986

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Research paper thumbnail of Extended x-ray absorption fine structure studies on the iron-containing subunit of ribonucleotide reductase from Escherichia coli

Biochemistry Usa, Aug 1, 1987

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Research paper thumbnail of Determination by X-Ray Absorption of Redox Induced Structural Changes in Iron-Sulfur Cluster Fxin Photosystem I

Acta Physica Polonica A, 1997

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Research paper thumbnail of Double crystal bent Laue “beam cleaner”

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Research paper thumbnail of Tests of a multilayer analyzer x-ray fluorescence array detector

It is a concern that multi-element solid-state detectors commonly used in x-ray fluorescence dete... more It is a concern that multi-element solid-state detectors commonly used in x-ray fluorescence detection for dilute systems will not be suitable at the third-generation sources such as the Advanced Photon Source (APS), Argonne National Laboratory. Indeed, with the more than 10–13 photon flux available at the Bio-CAT insertion device (ID) beamline, a solid state detector (e.g., the Canberra 13element Ge detector) will not work efficiently because of count rate limitations. It is estimated that only a few percent of the beam can be utilized by such a detector. In other words, elements in the order of thousands are needed on the detector to use the whole beam effectively. Thus, we have proposed the development of x-ray fluorescence detectors using multilayers [1, 2]. Acting as an analyzer, the mutilayers select x-ray fluorescence signals from background photons when the Bragg condition is met at the fluorescence energy. The data can be collected using a nonenergyresolving detector. Thus,...

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Research paper thumbnail of Introduction to XAFS: References

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Research paper thumbnail of Multiple scattering in the XANES of tetrahedral Ge gases

Physical review. B, Condensed matter

X-ray absorption fine structure (XAFS) measurements of GeCl4, GeH3Cl, and GeH4 were made. We expe... more X-ray absorption fine structure (XAFS) measurements of GeCl4, GeH3Cl, and GeH4 were made. We experimentally isolate the single- and multiple-scattering terms in the XAFS of GeCl4 by comparison of the spectra of the three compounds. The multiple scattering (MS) amplitude is comparable to the single-scattering (SS) amplitude only to within 15 eV of the edge. Beyond 40 eV the MS to SS ratio is less than 0.06. Calculations are in qualitative agreement with experiment. Our results suggest that XAFS data in the range 1 < k < 3 Å-1 can be analyzed in a SS picture in many cases.

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Research paper thumbnail of Initial results on logarithmic spiral bent Laue analyzer for fluorescence x-ray absorption spectroscopy (abstract)

Review of Scientific Instruments, 2002

We have previously described [Z. Zhong, D. Chapman, B. A. Bunker, G. B. Bunker, R. Fischetti, and... more We have previously described [Z. Zhong, D. Chapman, B. A. Bunker, G. B. Bunker, R. Fischetti, and C. U. Segre, J. Synchrotron Radiat. 6, 212 (1999); C. Karanfil et al., AIP Conf. Proc. 521, 178 (2000)] a novel concept of using highly bent single crystals in Laue geometry for wide bandwidth monochromatization of fluorescence x rays emerging from a point source, such as the sample in fluorescence x-ray absorption spectroscopy (XAFS) experiments. In this article we describe the first measurements (summer 2000) of the fluorescence XAFS of millimolar solutions of several elements. The potential of this type of analyzer is clearly demonstrated.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Single and multiple scattering XAFS Debye-Waller factors for crystalline materials using periodic Density Functional Theory

ABSTRACT We present an accurate and efficient technique for calculating thermal X-ray absorption ... more ABSTRACT We present an accurate and efficient technique for calculating thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) applicable to crystalline materials. Using Density Functional Theory on a 3×3×3 supercell pattern of MnO structure, under the nonlocal hybrid B3LYP functional paired with Gaussian local basis sets, we obtain the normal mode eigenfrequencies and eigenvectors; these parameters are in turn used to calculate single and multiple scattering XAFS DWFs. The DWFs obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters, when experimental spectra are fitted with a hypothetical structure. The size of the supercell size limits the R-space range that these parameters could be used. Therefore corresponding DWFs for paths outside of this range are calculated using the correlated Debye model. Our method is compared with prior cluster calculations and with corresponding values obtained from fitting experimental XAFS spectra on manganosite with simulated spectra.

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Research paper thumbnail of A ‘beam cleaner’ for harmonic selection/rejection

AIP Conference Proceedings, 2000

A ‘beam cleaner’ for selection of a harmonic from the beamline monochromator and rejection of oth... more A ‘beam cleaner’ for selection of a harmonic from the beamline monochromator and rejection of other harmonics has been developed using a bent Laue crystal post-monochromator. This is a set of cylindrically bent Si (111) crystals that are aligned to diffract the 2nd harmonic (3× fundamental) from the beamline Si (111) monochromator. This device will reject the fundamental and other

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Research paper thumbnail of An X-ray Harmonic Selection and Rejection Device

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Research paper thumbnail of A device for selecting and rejecting X-ray harmonics in synchrotron radiation beams

Journal of Synchrotron Radiation, 2004

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Research paper thumbnail of Introduction to XAFS: References

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Research paper thumbnail of A bent Laue analyzer for fluorescence EXAFS detection

Journal of Synchrotron Radiation, 1999

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Research paper thumbnail of Quantitative performance measurements of bent crystal Laue analyzers for X-ray fluorescence spectroscopy

Journal of Synchrotron Radiation, 2012

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Research paper thumbnail of GPU Computing in XAFS

Journal of Physics: Conference Series, 2013

Modern graphics processing units (GPUs) are powerful parallel computers. Porting the mathematical... more Modern graphics processing units (GPUs) are powerful parallel computers. Porting the mathematically intense, parallelizable algorithms of XAFS to run on GPUs should expand the scale of tractable XAFS calculations. Part of a time-limiting subroutine in FEFF 8.4 (fms) was converted to run on a GPU, showing significant performance gains. With parallel CPUs sharing GPU resources, the runtime of the modules calling fms should accelerate by one or two orders of magnitude versus a single-threaded CPU process (at least for large atomic clusters,). New or existing XAFS algorithms and programs (e.g. FEFF 9) should show similar acceleration when ported to GPUs, as long as they meet certain criteria (outlined in detail).

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Research paper thumbnail of Multiple scattering in the x-ray-absorption near-edge structure of tetrahedral Ge gases

Physical Review B, 1988

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Research paper thumbnail of Bent Laue Crystal Analyzers for X-ray Fluorescence Detection

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Extended X-ray absorption fine structure studies of Zn2Fe2 hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry, 1986

Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized b... more Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized by extended X-ray absorption structure (EXAFS) studies. Since Zn and Fe have very different K absorption edge energies, the structures of the ligated (Fe) and unligated (Zn) sites could be examined independently within a single molecule that mimics an intermediate ligation state. The observed EXAFS spectra and associated structural parameters are compared among the ligand free (alpha Zn)2(beta Zn)2, half-ligated (alpha FeCO)2(beta Zn)2 and (alpha Zn)2(beta FeCO)2, and fully ligated (alpha FeCO)2(beta FeCO)2 systems.

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Research paper thumbnail of Extended X-ray absorption fine structure studies of ZnâFeâ hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry, 1986

Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized b... more Metal hybrid hemoglobins, in which Zn(II) replaces Fe(II), have been structurally characterized by extended X-ray absorption structure (EAFS) studies. Since Zn and Fe have very different K absorption edge energies, the structures of the ligated (Fe) and unligated (Zn) sites could be examined independently within a single molecule that mimics an intermediate ligation state. The observed EXAFS spectra and associated

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Research paper thumbnail of Extended X-ray absorption fine structure studies of ZnâFeâ hybrid hemoglobins: absence of heme bond length changes in half-ligated species

Biochemistry Usa, 1986

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Research paper thumbnail of Extended x-ray absorption fine structure studies on the iron-containing subunit of ribonucleotide reductase from Escherichia coli

Biochemistry Usa, Aug 1, 1987

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