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Article ; Online: Coupled Electron-Nuclear Dynamics Induced and Monitored with Femtosecond Soft X-ray Pulses in the Amino Acid Glycine.

Schwickert, David / Przystawik, Andreas / Diaman, Dian / Kip, Detlef / Marangos, Jon P / Laarmann, Tim

The journal of physical chemistry. A

2024 Volume 128, Issue 6, Page(s) 989–995

Abstract: The coupling of electronic and nuclear motion in polyatomic molecules is at the heart of attochemistry. The molecular properties, transient structures, and reaction mechanism of these many-body quantum objects are defined on the level of electrons and ... ...

Abstract	The coupling of electronic and nuclear motion in polyatomic molecules is at the heart of attochemistry. The molecular properties, transient structures, and reaction mechanism of these many-body quantum objects are defined on the level of electrons and ions by molecular wave functions and their coherent superposition, respectively. In the present contribution, we monitor nonadiabatic quantum wave packet dynamics during molecular charge motion by reconstructing both the oscillatory charge density distribution and the characteristic time-dependent nuclear configuration coordinate from time-resolved Auger electron spectroscopic data recorded in previous studies on glycine molecules [Schwickert et al.
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.3c06517
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Article ; Online: Identification of Cofragmented Combinatorial Peptide Isomers by Two-Dimensional Partial Covariance Mass Spectrometry.

Driver, Taran / Pipkorn, Rüdiger / Averbukh, Vitali / Frasinski, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina

Journal of the American Society for Mass Spectrometry

2023 Volume 34, Issue 7, Page(s) 1230–1234

Abstract: Combinatorial post-translational modifications (PTMs), such as those forming the so-called "histone code", have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders, ...

Abstract	Combinatorial post-translational modifications (PTMs), such as those forming the so-called "histone code", have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders,
MeSH term(s)	Humans ; Peptides/chemistry ; Mass Spectrometry/methods ; Histones/chemistry ; Histone Code ; Protein Processing, Post-Translational
Chemical Substances	Peptides ; Histones
Language	English
Publishing date	2023-05-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00111
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Article ; Online: How electronic superpositions drive nuclear motion following the creation of a localized hole in the glycine radical cation.

Danilov, Don / Tran, Thierry / Bearpark, Michael J / Marangos, Jon P / Worth, Graham A / Robb, Michael A

The Journal of chemical physics

2022 Volume 156, Issue 24, Page(s) 244114

Abstract: In this work, we have studied the nuclear and electron dynamics in the glycine cation starting from localized hole states using the quantum Ehrenfest method. The nuclear dynamics is controlled both by the initial gradient and by the instantaneous ... ...

Abstract	In this work, we have studied the nuclear and electron dynamics in the glycine cation starting from localized hole states using the quantum Ehrenfest method. The nuclear dynamics is controlled both by the initial gradient and by the instantaneous gradient that results from the oscillatory electron dynamics (charge migration). We have used the Fourier transform (FT) of the spin densities to identify the "normal modes" of the electron dynamics. We observe an isomorphic relationship between the electron dynamics normal modes and the nuclear dynamics, seen in the vibrational normal modes. The FT spectra obtained this way show bands that are characteristic of the energy differences between the adiabatic hole states. These bands contain individual peaks that are in one-to-one correspondence with atom pair (+·) ↔ (·+) resonances, which, in turn, stimulate nuclear motion involving the atom pair. With such understanding, we anticipate "designer" coherent superpositions that can drive nuclear motion in a particular direction.
MeSH term(s)	Cations ; Electronics ; Electrons ; Glycine ; Motion
Chemical Substances	Cations ; Glycine (TE7660XO1C)
Language	English
Publishing date	2022-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0093780
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Article ; Online: Efficient prediction of attosecond two-colour pulses from an X-ray free-electron laser with machine learning.

Alaa El-Din, Karim K / Alexander, Oliver G / Frasinski, Leszek J / Mintert, Florian / Guo, Zhaoheng / Duris, Joseph / Zhang, Zhen / Cesar, David B / Franz, Paris / Driver, Taran / Walter, Peter / Cryan, James P / Marinelli, Agostino / Marangos, Jon P / Mukherjee, Rick

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7267

Abstract: X-ray free-electron lasers are sources of coherent, high-intensity X-rays with numerous applications in ultra-fast measurements and dynamic structural imaging. Due to the stochastic nature of the self-amplified spontaneous emission process and the ... ...

Abstract	X-ray free-electron lasers are sources of coherent, high-intensity X-rays with numerous applications in ultra-fast measurements and dynamic structural imaging. Due to the stochastic nature of the self-amplified spontaneous emission process and the difficulty in controlling injection of electrons, output pulses exhibit significant noise and limited temporal coherence. Standard measurement techniques used for characterizing two-coloured X-ray pulses are challenging, as they are either invasive or diagnostically expensive. In this work, we employ machine learning methods such as neural networks and decision trees to predict the central photon energies of pairs of attosecond fundamental and second harmonic pulses using parameters that are easily recorded at the high-repetition rate of a single shot. Using real experimental data, we apply a detailed feature analysis on the input parameters while optimizing the training time of the machine learning methods. Our predictive models are able to make predictions of central photon energy for one of the pulses without measuring the other pulse, thereby leveraging the use of the spectrometer without having to extend its detection window. We anticipate applications in X-ray spectroscopy using XFELs, such as in time-resolved X-ray absorption and photoemission spectroscopy, where improved measurement of input spectra will lead to better experimental outcomes.
Language	English
Publishing date	2024-03-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56782-z
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Article ; Online: Two-Dimensional Partial Covariance Mass Spectrometry for the Top-Down Analysis of Intact Proteins.

Driver, Taran / Averbukh, Vitali / Frasiński, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina

Analytical chemistry

2021 Volume 93, Issue 31, Page(s) 10779–10788

Abstract: Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation ... ...

Abstract	Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment-fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment-fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the
MeSH term(s)	Ions ; Peptides ; Proteins ; Proteomics ; Tandem Mass Spectrometry
Chemical Substances	Ions ; Peptides ; Proteins
Language	English
Publishing date	2021-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00332
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Article ; Online: Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry.

Driver, Taran / Bachhawat, Nikhil / Pipkorn, Rüdiger / Frasiński, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina / Averbukh, Vitali

Analytical chemistry

2021 Volume 93, Issue 45, Page(s) 14946–14954

Abstract: We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement ... ...

Abstract	We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.
MeSH term(s)	Databases, Protein ; Mass Spectrometry ; Peptides ; Proteomics ; Search Engine
Chemical Substances	Peptides
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00895
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ab Jg. 2022: Lesesaal (EG)

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Article: Two-Dimensional Partial Covariance Mass Spectrometry for the Top–Down Analysis of Intact Proteins

Driver, Taran / Averbukh, Vitali / Frasiński, Leszek J. / Marangos, Jon P. / Edelson-Averbukh, Marina

Analytical chemistry. 2021 July 26, v. 93, no. 31

2021

Abstract	Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment–fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment–fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the in silico deconvolution of the overlapping fragment ion signals from two co-isolated and co-fragmented intact proteins, demonstrating a viable new method for the concurrent mass spectrometric identification of a mixture of intact protein ions from the same fragment ion spectrum.
Keywords	analytical chemistry ; computer simulation ; covariance ; peptides ; tandem mass spectrometry
Language	English
Dates of publication	2021-0726
Size	p. 10779-10788.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00332
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Article: Delivery of stable ultra-thin liquid sheets in vacuum for biochemical spectroscopy.

Barnard, Jonathan C T / Lee, Jacob P / Alexander, Oliver / Jarosch, Sebastian / Garratt, Douglas / Picciuto, Rose / Kowalczyk, Katarzyna / Ferchaud, Clement / Gregory, Andrew / Matthews, Mary / Marangos, Jon P

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 1044610

Abstract: The development of ultra-thin flat liquid sheets capable of running in vacuum has provided an exciting new target for X-ray absorption spectroscopy in the liquid and solution phases. Several methods have become available for delivering in-vacuum sheet ... ...

Abstract	The development of ultra-thin flat liquid sheets capable of running in vacuum has provided an exciting new target for X-ray absorption spectroscopy in the liquid and solution phases. Several methods have become available for delivering in-vacuum sheet jets using different nozzle designs. We compare the sheets produced by two different types of nozzle; a commercially available borosillicate glass chip using microfluidic channels to deliver colliding jets, and an in-house fabricated fan spray nozzle which compresses the liquid on an axis out of a slit to achieve collision conditions. We find in our tests that both nozzles are suitable for use in X-ray absorption spectroscopy with the fan spray nozzle producing thicker but more stable jets than the commercial nozzle. We also provide practical details of how to run these nozzles in vacuum.
Language	English
Publishing date	2022-11-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.1044610
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Article ; Online: Attosecond soft X-ray high harmonic generation.

Johnson, Allan S / Avni, Timur / Larsen, Esben W / Austin, Dane R / Marangos, Jon P

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

2019 Volume 377, Issue 2145, Page(s) 20170468

Abstract: High harmonic generation (HHG) of an intense laser pulse is a highly nonlinear optical phenomenon that provides the only proven source of tabletop attosecond pulses, and it is the key technology in attosecond science. Recent developments in high- ... ...

Abstract	High harmonic generation (HHG) of an intense laser pulse is a highly nonlinear optical phenomenon that provides the only proven source of tabletop attosecond pulses, and it is the key technology in attosecond science. Recent developments in high-intensity infrared lasers have extended HHG beyond its traditional domain of the XUV spectral range (10-150 eV) into the soft X-ray regime (150 eV to 3 keV), allowing the compactness, stability and sub-femtosecond duration of HHG to be combined with the atomic site specificity and electronic/structural sensitivity of X-ray spectroscopy. HHG in the soft X-ray spectral region has significant differences from HHG in the XUV, which necessitate new approaches to generating and characterizing attosecond pulses. Here, we examine the challenges and opportunities of soft X-ray HHG, and we use simulations to examine the optimal generating conditions for the development of high-flux, attosecond-duration pulses in the soft X-ray spectral range. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
Language	English
Publishing date	2019-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	208381-4
ISSN	1471-2962 ; 0080-4614 ; 0264-3820 ; 0264-3952 ; 1364-503X
ISSN (online)	1471-2962
ISSN	0080-4614 ; 0264-3820 ; 0264-3952 ; 1364-503X
DOI	10.1098/rsta.2017.0468
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Article: Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry

Driver, Taran / Bachhawat, Nikhil / Pipkorn, Rüdiger / Frasiński, Leszek J. / Marangos, Jon P. / Edelson-Averbukh, Marina / Averbukh, Vitali

Analytical chemistry. 2021 Nov. 01, v. 93, no. 45

2021

Abstract	We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.
Keywords	amino acid sequences ; analytical chemistry ; covariance ; databases ; mass spectrometry ; peptides ; proteomics
Language	English
Dates of publication	2021-1101
Size	p. 14946-14954.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00895
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