28 results on '"Jonathan M. Dilger"'
Search Results
2. Mapping the co-evolution of artificial intelligence, robotics, and the internet of things over 20 years (1998-2017).
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Katy Börner, Olga Scrivner, Leonard E. Cross, Michael Gallant, Shutian Ma, Adam S. Martin, Elizabeth Record, Haici Yang, and Jonathan M. Dilger
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- 2020
3. From the laboratory to the field: Chemical analysis of colored smoke pyrotechnic formulations via mass spectrometry techniques
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Patrick W. Fedick, Kelly M. Thoreson, Benjamin P. Wilkins, Douglas M. Papenmeier, Brian C. Bohrer, and Jonathan M. Dilger
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Spectroscopy - Published
- 2023
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4. COMPARISON OF CORRELATION PERFORMANCE FOR VARIOUS MEASUREMENT SCHEMES IN QUANTUM BIPARTITE RADAR AND COMMUNICATION SYSTEMS
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Rory A. Bowell, Matthew J. Brandsema, Ram M. Narayanan, Stephen W. Howell, and Jonathan M. Dilger
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Radiation ,Electrical and Electronic Engineering ,Condensed Matter Physics - Published
- 2022
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5. Microwave-assisted modulation of light emission intensity in alkali-pyrotechnic plumes
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Stuart J. Barkley, James B. Michael, Travis R. Sippel, Jonathan M. Dilger, Joel E. Lynch, William Crespo, Shankar Subramaniam, and Eric J. Miklaszewski
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Materials science ,Infrared ,General Chemical Engineering ,Population ,General Physics and Astronomy ,Energy Engineering and Power Technology ,Astrophysics::Cosmology and Extragalactic Astrophysics ,02 engineering and technology ,01 natural sciences ,020401 chemical engineering ,0103 physical sciences ,Emission spectrum ,0204 chemical engineering ,Chromaticity ,education ,Astrophysics::Galaxy Astrophysics ,education.field_of_study ,010304 chemical physics ,business.industry ,General Chemistry ,Wavelength ,Fuel Technology ,Excited state ,Optoelectronics ,Light emission ,business ,Microwave - Abstract
Creating next-generation pyrotechnic emitters capable of dynamically controllable light output requires a paradigm shift away from emission control via formulation. This work demonstrates the ability to modulate light emission intensity of a pyrotechnic flame with 2.46 GHz microwave energy within a multimodal cavity. Stoichiometric mixtures of three pyrotechnic systems are investigated: magnesium fuel with oxidizers of NaNO3, KNO3, or CsNO3. Using time-resolved visible and infrared emission spectroscopy and high-speed color videography, microwave illumination of flames is found to produce enhanced atomic photo emission from the alkali species. Emission increases of up to ~120% are demonstrated, which are predominantly in the visible and near-infrared wavelengths and have little effect on flame emission chromaticity. At near- and mid-IR wavelengths, gray body continuum enhancement is observed with moderate enhanced emission from CO2 and H2O bands. Sustained light emission from microwave illumination of combustion products long after pyrotechnic extinguishment was also demonstrated. A simplified model of microwave-enhanced visible and near-IR emission is presented and shown to be consistent with the observed trend of elevated emission enhancement for lower wavelength alkali transitions. Sensitivity analysis is performed which suggests a lower equilibrium population of electronically excited alkali atoms is primarily responsible for maximizing the degree of light emission enhancement of applied microwave fields, especially in extinguished low-temperature pyrotechnic plumes. These findings suggest microwave illumination of alkali-containing pyrotechnic flames may be a useful strategy to achieve dynamic control of light emission intensity.
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- 2021
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6. Tripartite correlation performance for use in quantum radar systems
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Stephen W. Howell, Matthew J. Brandsema, Jonathan M. Dilger, Ram M. Narayanan, and Rory A. Bowell
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Physics ,Correlation ,Bipartite graph ,Quantum radar ,Quantum entanglement ,Covariance ,Topology ,Signal ,Bottleneck ,Squeezed coherent state - Abstract
In recent years, quantum radar has focused entirely on using bipartite squeezed states of light as a mechanism for target detection. This paper studies the performance of a quantum radar that uses a tripartite squeezed state, whereby two signal beams are sent out towards the target which both correlate with the idler. It is found that for very low signal strengths, the bipartite has better performance. As the signal strength increases however, the tripartite becomes dominant. This result suggests that quantum radar (declared useful only in the low SNR regime) may possess more possibilities of increased performance at higher SNRs when different states are used for correlation. The bottleneck, of course, is the ability to generate transmit powers necessary to utilize.
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- 2021
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7. Mapping the co-evolution of artificial intelligence, robotics, and the internet of things over 20 years (1998-2017)
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Lisel Record, Adam S. Martin, Katy Börner, Olga Scrivner, Michael Gallant, Haici Yang, Shutian Ma, Jonathan M. Dilger, and Leonard E. Cross
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FOS: Computer and information sciences ,Institutional Funding of Science ,Research program ,Computer and Information Sciences ,Computer science ,Science Policy ,Science ,Internet of Things ,050905 science studies ,Research and Analysis Methods ,Research Funding ,Computer Science - Information Retrieval ,Machine Learning ,Data visualization ,Citation analysis ,Artificial Intelligence ,0502 economics and business ,Digital Libraries (cs.DL) ,Government Funding of Science ,Computer networks ,Data Management ,Social and Information Networks (cs.SI) ,Internet ,Multidisciplinary ,business.industry ,Mechanical Engineering ,Data Visualization ,05 social sciences ,Publications ,Computer Science - Digital Libraries ,Computer Science - Social and Information Networks ,Robotics ,Research Assessment ,Data science ,Citation Analysis ,Medicine ,Engineering and Technology ,Convergence (relationship) ,Artificial intelligence ,0509 other social sciences ,business ,050203 business & management ,Information Retrieval (cs.IR) ,Research Article - Abstract
Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. The resulting data-driven decision support helps set proper research and development (R&D) priorities; develop future S&T investment strategies; monitor key authors, organizations, or countries; perform effective research program assessment; and implement cutting-edge education/training efforts. This paper presents new funding, publication, and scholarly network metrics and visualizations that were validated via expert surveys. The metrics and visualizations exemplify the emergence and convergence of three areas of strategic interest: artificial intelligence (AI), robotics, and internet of things (IoT) over the last 20 years (1998-2017). For 32,716 publications and 4,497 NSF awards, we identify their conceptual space (using the UCSD map of science), geospatial network, and co-evolution landscape. The findings demonstrate how the transition of knowledge (through cross-discipline publications and citations) and the emergence of new concepts (through term bursting) create a tangible potential for interdisciplinary research and new disciplines., 10 figures
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- 2020
8. Remote sensing performance enhancement due to quantum + classical cooperative sensor
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Ram M. Narayanan, Stephen W. Howell, Rory A. Bowell, Bilal M. Ahmed, Jonathan M. Dilger, and Matthew J. Brandsema
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Photon entanglement ,Field (physics) ,law ,Remote sensing (archaeology) ,Computer science ,ComputerSystemsOrganization_MISCELLANEOUS ,Quantum system ,Waveform ,Quantum radar ,Radar ,Quantum ,law.invention ,Remote sensing - Abstract
Within the last decade, the field of quantum remote sensing has garnered a lot of interest from the radar and communication community. Many papers on this topic have compared the performance of a classical system versus a quantum system. However, the concept of a system using both classical and quantum components in conjunction has not been explored thoroughly. This paper documents the design and simulation of a quantum + classical cooperative remote sensing design in the optical regime. The arrangement uses quantum correlations created by entangled photons in addition to conventional classical waveform correlations. We show that the composite quantum + classical system exhibits increased performance compared to a pure classical system alone.
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- 2020
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9. Electric field correlations in quantum radar and the quantum advantage
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Ram M. Narayanan, Matthew J. Brandsema, Rory A. Bowell, Stephen W. Howell, Jonathan M. Dilger, and Bilal M. Ahmed
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Physics ,Photon ,Cross-correlation ,Covariance matrix ,Quantum radar ,Coherent states ,Covariance ,Quantum ,Noise (electronics) ,Computational physics - Abstract
In this paper, we derive the electric field covariance matrix of the signal and idler beams from an entangled source for applications involving quantum radar. We also derive the corresponding covariance matrix for a classical matched filtering remote sensing system and compare to the quantum result. We use this comparison to derive an expression for the quantum enhancement factor as a function of the mean photon number per mode, Ns. This result is significant because it allows one to exactly calculate the predicted quantum enhancement as a function of transmit power, rather than only having an upper bound. Additionally, we look into previous analog correlation techniques using an optical parametric amplifier (OPA) and show that immediately detecting the idler produces the same cross correlation terms. However, the actual measurements needed to harness these correlations is enhanced when one immediately detects the idler because it minimizes the added noise caused by the additional length of the idler path in the conventional method. Finally, our results also show that one does not need to count photons to harness these correlations, but rather, perform electric field measurements.
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- 2020
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10. Pyrolysis/GC/MS as a Method to Rapidly Profile Pyrotechnic Formulations for Objectionable Gaseous Emissions
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Eric J. Miklaszewski, Jonathan M. Dilger, Brian C. Bohrer, Kelly M. Thoreson, Patrick W. Fedick, Douglas M. Papenmeier, and Jessica E. Coleman
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Pollutant ,Pyrotechnic composition ,Renewable Energy, Sustainability and the Environment ,Chemistry ,General Chemical Engineering ,010401 analytical chemistry ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Nitrogen ,Decomposition ,0104 chemical sciences ,law.invention ,law ,Environmental Chemistry ,Gas chromatography ,Pyrolysis ,Flare - Abstract
A method to empirically determine the gaseous emissions produced from a pyrotechnic flare composition through the combination of gas chromatography and mass spectrometry is described. In this approach, milligram quantities of a model yellow signal flare composition and its individual polymeric constituents were subjected to pyrolysis at conditions that were guided via thermal analysis. Many volatile organic compounds and polycyclic aromatic hydrocarbons were identified as emission products even though thermochemical calculations fail to anticipate such products. Thus, these data may complement characterization of emission products predicted in silico. Pyrolysis of this pyrotechnic composition also demonstrated unique products formed via donation of nitrogen to aromatic fragments originating from resinous portions of the formulation. These products included EPA priority pollutants that were not formed by decomposition from staple ingredients. This work demonstrates that a variety of EPA priority pollutants...
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- 2018
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11. Analysis of Residual Explosives by Swab Touch Spray Ionization Mass Spectrometry
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Jonathan M. Dilger, Patrick W. Fedick, R. Graham Cooks, and Ryan M. Bain
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Materials science ,Chromatography ,Explosive material ,General Chemical Engineering ,010401 analytical chemistry ,General Chemistry ,Ionization mass spectrometry ,010402 general chemistry ,Mass spectrometry ,Residual ,01 natural sciences ,0104 chemical sciences ,Ambient ionization - Published
- 2018
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12. Detection and toxicity modeling of anthraquinone dyes and chlorinated side products from a colored smoke pyrotechnic reaction
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Patrick W. Fedick, Benjamin P. Wilkins, Brian C. Bohrer, Todd M. Martin, Jonathan M. Dilger, and Kelly M. Thoreson
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Pollutant ,Exothermic reaction ,Colored smoke ,Environmental Engineering ,Chemistry ,Health, Toxicology and Mutagenesis ,Chlorate ,Public Health, Environmental and Occupational Health ,Pyrotechnics ,Anthraquinones ,General Medicine ,General Chemistry ,Pollution ,Anthraquinone ,Article ,chemistry.chemical_compound ,Smoke ,Tobacco ,Smoke composition ,Environmental Chemistry ,Organic chemistry ,Coloring Agents ,Pyrolysis ,Mutagens - Abstract
“Green” pyrotechnics seek to remove known environmental pollutants and health hazards from their formulations. This chemical engineering approach often focuses on maintaining performance effects upon replacement of objectionable ingredients, yet neglects the chemical products formed by the exothermic reaction. In this work, milligram quantities of a lab-scale pyrotechnic red smoke composition were functioned within a thermal probe for product identification by pyrolysis-gas chromatography-mass spectrometry. Thermally decomposed ingredients and new side product derivatives were identified at lower relative abundances to the intact organic dye (as the engineered sublimation product). Side products included chlorination of the organic dye donated by the chlorate oxidizer. Machine learning quantitative structure-activity relationship models computed impacts to health and environmental hazards. High to very high toxicities were predicted for inhalation, mutagenicity, developmental, and endocrine disruption for common military pyrotechnic dyes and their analogous chlorinated side products. These results underscore the need to revise objectives of “green” pyrotechnic engineering.
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- 2022
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13. Melting proteins confined in nanodroplets with 10.6 μm light provides clues about early steps of denaturation
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Yoni Toker, David E. Clemmer, Christopher R. Conant, David H. Russell, Daniel W. Woodall, Shannon A. Raab, Jonathan M. Dilger, Tarick J. El-Baba, Evan R. Williams, and Daniel R. Fuller
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Co2 laser ,Chemistry ,Ion-mobility spectrometry ,010401 analytical chemistry ,Metals and Alloys ,A protein ,General Chemistry ,010402 general chemistry ,Mass spectrometry ,Photochemistry ,01 natural sciences ,Article ,Catalysis ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Ion formation ,Solvent evaporation ,Materials Chemistry ,Ceramics and Composites ,Denaturation (biochemistry) ,Irradiation - Abstract
Ubiquitin confined within nanodroplets was irradiated with a variable-power CO(2) laser. Mass spectrometry analysis shows evidence for a protein “melting”-like transition within droplets prior to solvent evaporation and ion formation. Ion mobility spectrometry reveals that structures associated with early steps of denaturation are trapped because of short droplet lifetimes.
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- 2018
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14. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues
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David E. Clemmer, Matthew S. Glover, and Jonathan M. Dilger
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chemistry.chemical_classification ,Spectrometry, Mass, Electrospray Ionization ,Database ,Ion-mobility spectrometry ,Chemistry ,010401 analytical chemistry ,Solvation ,Protonation ,Peptide ,010402 general chemistry ,computer.software_genre ,01 natural sciences ,0104 chemical sciences ,Ion ,Cross section (geometry) ,Residue (chemistry) ,Transition metal ,Structural Biology ,Metals, Heavy ,Amino Acids ,Databases, Protein ,Peptides ,computer ,Spectroscopy - Abstract
Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases.
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- 2017
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15. Development of a Sustainable Perchlorate-Free Yellow Pyrotechnic Signal Flare
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Jonathan M. Dilger, Christina Yamamoto, and Eric J. Miklaszewski
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Smoke ,Materials science ,010304 chemical physics ,Potassium perchlorate ,Dominant wavelength ,Renewable Energy, Sustainability and the Environment ,General Chemical Engineering ,Analytical chemistry ,Mineralogy ,General Chemistry ,Luminous intensity ,010402 general chemistry ,01 natural sciences ,Signal ,0104 chemical sciences ,law.invention ,Ignition system ,chemistry.chemical_compound ,Perchlorate ,chemistry ,law ,0103 physical sciences ,Environmental Chemistry ,Flare - Abstract
Novel yellow-light emitting pyrotechnic compositions absent perchlorate oxidizers were investigated for use in the Mk 144 marine smoke and illumination signal. In laboratory-scale testing, three candidate formulations met or surpassed performance metrics of luminous intensity, dominant wavelength, color purity, and burn time when compared to a mock Mk 144 formulation which currently utilizes the environmentally hazardous potassium perchlorate. Also, one identified formulation does not utilize any barium compounds which may be the focus of future regulations. Furthermore, these candidate systems exhibited similar insensitivity to electrostatic, friction, and impact ignition stimuli in comparison to the mock Mk 144 formulation. Therefore, replacement formulations for the Mk 144 marine smoke and illumination signal have been identified with increased performance, environmental sustainability, and acceptable safety characteristics.
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- 2016
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16. Resolution of Stepwise Cooperativities of Copper Binding by the Homotetrameric Copper-Sensitive Operon Repressor (CsoR): Impact on Structure and Stability
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Vicki H. Wysocki, Feng-Ming James Chang, Lindsay J. Morrison, Alexander D. Jacobs, David E. Clemmer, David P. Giedroc, and Jonathan M. Dilger
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Models, Molecular ,chemistry.chemical_classification ,genetic structures ,Protein Conformation ,Protein Stability ,Chemistry ,Operon ,Allosteric regulation ,Geobacillus ,Repressor ,Cooperativity ,General Medicine ,General Chemistry ,Article ,Catalysis ,Repressor Proteins ,Crystallography ,Metalloprotein ,Biophysics ,A-DNA ,Protein Multimerization ,Biological regulation ,Conformational ensembles ,Copper - Abstract
The cooperativity of ligand binding is central to biological regulation and new approaches are needed to quantify these allosteric relationships. Herein, we exploit a suite of mass spectrometry (MS) experiments to provide novel insights into homotropic Cu-binding cooperativity, gas- phase stabilities and conformational ensembles of the D2- symmetric, homotetrameric copper-sensitive operon repressor (CsoR) as a function of Cu I ligation state. Cu I binding is overall positively cooperative, but is characterized by distinct ligation state-specific cooperativities. Structural transitions occur upon binding the first and fourth Cu I , with the latter occurring with significantly higher cooperativity than previous steps; this results in the formation of a holo-tetramer that is markedly more resistant than apo-, and partially ligated CsoR tetramers toward surface-induced dissociation (SID). The structural, dynamic and thermodynamic origins of cooperativity of ligand binding (allostery) is a subject of considerable interest, motivated by the central role this process plays in the regulation of biological activity. (1) Cooperativity can be positive or negative and involve the binding of the same (homotropic) or different (heterotropic) ligands, often to an homooligomeric protein. (2, 3) Bacterial repressors that function to control transition metal bioavail- ability in cells are typically homodimeric or homotetrameric and minimally bind two "ligands": a DNA operator found upstream of metal-regulated genes and a specific (cognate) transition metal ion(s). (4) Although a robust thermodynamic framework capable of quantifying both homo- and hetero- tropic cooperativity in these systems is available, (5) these ensemble-based methods suffer from the limitation that a specific, partially ligated state can not be studied independ- ently of other states. Such step-wise insights are required to understand allosteric coupling beyond a generally phenom- enological description. (1)
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- 2015
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17. Isotope Labeling Study of Retinal Chromophore Fragmentation
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Jonathan M. Dilger, Shany Ytzhak, Amiram Hirshfeld, Noga Friedman, Yoni Toker, Lihi Musbat, Mordechai Sheves, and Maria Nihamkin
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Rhodopsin ,Isotope ,biology ,010405 organic chemistry ,Chemistry ,Stereoisomerism ,010402 general chemistry ,Photochemistry ,Tandem mass spectrometry ,Polyene ,01 natural sciences ,Retina ,0104 chemical sciences ,Photoexcitation ,chemistry.chemical_compound ,Fragmentation (mass spectrometry) ,Cyclization ,Tandem Mass Spectrometry ,Isotope Labeling ,biology.protein ,Single bond ,Physical and Theoretical Chemistry - Abstract
Previous studies have shown that the gas-phase fragmentation of the retinal chromophore after S0-S1 photoexcitation results in a prominent fragment of mass 248 which cannot be explained by the cleavage of any single bond along the polyene chain. It was therefore theorized that the fragmentation mechanism involves a series of isomerizations and cyclization processes, and two mechanisms for these processes were suggested. Here we used isotope labeling MS-MS to provide conclusive support for the fragmentation mechanism suggested by Coughlan et al. (J. Phys. Chem. Lett. 2014, 5, 3195).
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- 2016
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18. The binding of Ca2+, Co2+, Ni2+, Cu2+, and Zn2+ cations to angiotensin I determined by mass spectrometry based techniques
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Jonathan M. Dilger, David E. Clemmer, Matthew S. Glover, and Feifei Zhu
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Collision-induced dissociation ,Chemistry ,Ion-mobility spectrometry ,Analytical chemistry ,Condensed Matter Physics ,Mass spectrometry ,Dissociation (chemistry) ,Ion ,Metal ,A-site ,Crystallography ,Transition metal ,visual_art ,visual_art.visual_art_medium ,Physical and Theoretical Chemistry ,Instrumentation ,Spectroscopy - Abstract
The interaction of a series of doubly charged metal cations (M2+ = Ca, Co, Ni, Cu, and Zn) with angiotensin I (AngI, Asp1-Arg2-Val3-Tyr4-Ile5-His6-Pro7-Phe8-His9-Leu10) is examined by collision-induced dissociation (CID) and ion mobility spectrometry–mass spectrometry (IMS–MS). The series of CID patterns combined with IMS–MS data for [AngI+M+H]3+ ions provides information about the metal–peptide binding sites. Overall, Ca2+ favors association with oxygen atoms spanning the peptide backbone; whereas, the transition metals favor binding at a site that involves association at the His6 and His9 sites. From these experiments, it is possible to derive insight into the populations of different metal coordination sites that are sampled in solution prior to introduction of species into the gas phase.
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- 2013
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19. Measurements of the stabilities of isolated retinal chromophores
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Yoni Toker, Soumyajit Sarkar, Maria Nihamkin, and Amiram Hirshfeld, Jonathan M. Dilger, David E. Clemmer, Tarick J. El-Baba, Leeor Kronik, Lihi Musbat, Mordechai Sheves, Daniel R. Fuller, and Noga Friedman
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Rhodopsin ,Molecular Structure ,010405 organic chemistry ,Chemistry ,Protein Stability ,Retinal ,Chromophore ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Mass Spectrometry ,Retina ,0104 chemical sciences ,Delocalized electron ,chemistry.chemical_compound ,Fragmentation (mass spectrometry) ,Isomerism ,Molecule ,Animals ,Ground state ,Isomerization ,Schiff Bases ,Methyl group - Abstract
The barrier energies for isomerization and fragmentation were measured for a series of retinal chromophore derivatives using a tandem ion mobility spectrometry approach. These measurements allow us to quantify the effect of charge delocalization on the rigidity of chromophores. We find that the role of the methyl group on the C13 position is pivotal regarding the ground state dynamics of the chromophore. Additionally, a correlation between quasi-equilibrium isomer distribution and fragmentation pathways is observed.
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- 2016
20. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry
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Randy J. Arnold, Predrag Radivojac, Jonathan M. Dilger, Matthew D. Acton, Matthew S. Glover, and David E. Clemmer
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0301 basic medicine ,Phosphopeptides ,Proline ,Stereochemistry ,Peptide ,Mass spectrometry ,01 natural sciences ,Article ,Mass Spectrometry ,03 medical and health sciences ,Isomerism ,Structural Biology ,Structural isomer ,Organic chemistry ,Peptide bond ,Phosphorylation ,Spectroscopy ,Polyproline helix ,chemistry.chemical_classification ,Ions ,Phosphopeptide ,010401 analytical chemistry ,Phosphorylated Peptide ,0104 chemical sciences ,030104 developmental biology ,Ion-mobility spectrometry–mass spectrometry ,chemistry - Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/trans orientation of Xaa-Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.
- Published
- 2016
21. A database of alkali metal-containing peptide cross sections: Influence of metals on size parameters for specific amino acids
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Stephen J. Valentine, Michael A. Ewing, David E. Clemmer, Jonathan M. Dilger, and Matthew S. Glover
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chemistry.chemical_classification ,Database ,Chemistry ,Ion-mobility spectrometry ,Tryptic peptide ,Peptide ,Protonation ,Condensed Matter Physics ,Mass spectrometry ,Alkali metal ,computer.software_genre ,Ion ,Amino acid ,Physical and Theoretical Chemistry ,Instrumentation ,computer ,Spectroscopy - Abstract
Ion mobility/mass spectrometry techniques have been used to generate a cross section database containing 1772 entries (147 singly-, 1325 doubly-, and 300 triply-charged) for protonated and alkalated tryptic peptide ions. Such a large number of values make it possible to assess the influence of alkali metal cations [where the cation (M+) corresponds to Li+ ,N a + ,K + ,o r Cs +] on peptide ion conformation. Peptide ion sizes generally increase with increasing cation size relative to the respective singly- or doublyprotonated species. Intrinsic size parameters for individual amino acid residues for alkali [Pep+M+H] 2+
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- 2012
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22. Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters
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Matthew S. Glover, Chris Hughes, Scott J. Geromanos, Michael A. Ewing, Jonathan M. Dilger, Stephen J. Valentine, and David E. Clemmer
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Proteomics ,chemistry.chemical_classification ,Quantitative Biology::Biomolecules ,Ion Transport ,Ion-mobility spectrometry ,Analytical chemistry ,Peptide ,General Chemistry ,Mass spectrometry ,Biochemistry ,Mass Spectrometry ,Article ,Ion ,Amino acid ,chemistry ,Research Design ,Amino Acids ,Peptides ,Biological system ,Peptide sequence ,Ion transporter ,Chromatography, Liquid - Abstract
A new method for enhancing peptide ion identification in proteomics analyses using ion mobility data is presented. Ideally, direct comparisons of experimental drift times (tD) with a standard mobility database could be used to rank candidate peptide sequence assignments. Such a database would represent only a fraction of sequences in protein databases and significant difficulties associated with the verification of data for constituent peptide ions would exist. A method that employs intrinsic amino acid size parameters to obtain ion mobility predictions that can be used to rank candidate peptide ion assignments is proposed. Intrinsic amino acid size parameters have been determined for doubly-charged peptide ions from an annotated yeast proteome. Predictions of ion mobilities using the intrinsic size parameters are more accurate than those obtained from a polynomial fit to tD versus molecular weight data. More than a two-fold improvement in prediction accuracy has been observed for a group of arginine-terminated peptide ions twelve residues in length. The use of this predictive enhancement as a means to aid peptide ion identification is discussed and a simple peptide ion scoring scheme is presented.
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- 2011
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23. Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides
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Jonathan M. Dilger, Zhiyu Li, David L. Smiley, David E. Clemmer, Vikas Pejaver, Predrag Radivojac, Randy J. Arnold, Sean D. Mooney, and Suchetana Mukhopadhyay
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chemistry.chemical_classification ,Peptide modification ,Chemistry ,Tryptic peptide ,Peptide ,Condensed Matter Physics ,Peptide ions ,humanities ,Article ,Biochemistry ,Palmitoylation ,Physical and Theoretical Chemistry ,Amino acid residue ,Instrumentation ,Peptide sequence ,Spectroscopy ,Cysteine - Abstract
Cross sections for 61 palmitoylated peptides and 73 cysteine-unmodified peptides are determined and used together with a previously obtained tryptic peptide library to derive a set of intrinsic size parameters (ISPs) for the palmitoyl (Pal) group (1.26 ± 0.04), carboxyamidomethyl (Am) group (0.92 ± 0.04), and the 20 amino acid residues to assess the influence of Pal- and Am-modification on cysteine and other amino acid residues. These values highlight the influence of the intrinsic hydrophobic and hydrophilic nature of these modifications on the overall cross sections. As a part of this analysis, we find that ISPs derived from a database of a modifier on one amino acid residue (Cys Pal ) can be applied on the same modification group on different amino acid residues (Ser Pal and Tyr Pal ). Using these ISP values, we are able to calculate peptide cross sections to within ±2% of experimental values for 83% of Pal-modified peptide ions and 63% of Am-modified peptide ions. We propose that modification groups should be treated as individual contribution factors, instead of treating the combination of the particular group and the amino acid residue they are on as a whole when considering their effects on the peptide ion mobility features.
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- 2015
24. Frontispiz: Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore
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Yoni Toker, Mordechai Sheves, Anastasia V. Bochenkova, Jonathan M. Dilger, Lihi Musbat, and David E. Clemmer
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Chemistry ,General Medicine ,Chromophore ,Photochemistry ,Isomerization ,Retinal chromophore - Published
- 2015
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25. Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore
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Jonathan M. Dilger, Lihi Musbat, Anastasia V. Bochenkova, David E. Clemmer, Y. Toker, and Mordechai Sheves
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Opsin ,History ,Rhodopsin ,spectroscopy ,gas-phase reactions ,Mass spectrometry ,Photochemistry ,Catalysis ,Retina ,isomerization ,Education ,Ion ,ion mobility ,Fragmentation (mass spectrometry) ,Isomerism ,medicine ,Molecule ,chromophores ,Spectroscopy ,Schiff Bases ,Retinal chromophore ,Chemistry ,Photodissociation ,General Chemistry ,General Medicine ,Chromophore ,proteins ,Computer Science Applications ,medicine.anatomical_structure ,Spectrophotometry ,Excited state ,Protons ,Isomerization - Abstract
Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined. The energy barrier for a single cis–trans isomerization is (0.64±0.05) eV, which is significantly lower than that observed for the reaction within opsin proteins.
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- 2015
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26. A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure
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Stephen J. Valentine, Matthew S. Glover, Jonathan M. Dilger, and David E. Clemmer
- Subjects
Databases, Factual ,Stereochemistry ,Ion-mobility spectrometry ,Molecular Sequence Data ,Protonation ,Peptide ,computer.software_genre ,Mass Spectrometry ,Ion ,Structural Biology ,Coordination Complexes ,Cations ,Metals, Alkaline Earth ,Amino Acid Sequence ,Amino Acids ,Peptide sequence ,Spectroscopy ,chemistry.chemical_classification ,Alkaline earth metal ,Database ,Alkali metal ,Peptide backbone ,chemistry ,Calcium ,Peptides ,computer ,Hydrogen - Abstract
A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.
- Published
- 2012
27. Negatively-charged helices in the gas phase
- Author
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Erin E. Carlson, David E. Clemmer, Matthew S. Glover, Andrew R. Johnson, and Jonathan M. Dilger
- Subjects
Models, Molecular ,Static Electricity ,Peptide ,Mass spectrometry ,Mass Spectrometry ,Protein Structure, Secondary ,Catalysis ,Ion ,Gas phase ,Residue (chemistry) ,Materials Chemistry ,Protein secondary structure ,chemistry.chemical_classification ,Physics::Biological Physics ,Quantitative Biology::Biomolecules ,Hydrogen bond ,Chemistry ,Metals and Alloys ,Hydrogen Bonding ,General Chemistry ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Crystallography ,Dipole ,Ceramics and Composites ,Gases ,Peptides - Abstract
A polyalanine-based peptide which forms a stable, negatively-charged α-helix in the gas phase is reported. Addition of an N-terminal acidic residue forms a stabilizing hydrogen bond network and an electrostatic interaction with the helical dipole. Formation of this secondary structure was demonstrated using ion mobility-mass spectrometry and molecular modelling techniques.
- Published
- 2014
- Full Text
- View/download PDF
28. Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters.
- Author
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Stephen J. Valentine, Michael A. Ewing, Jonathan M. Dilger, Matthew S. Glover, Scott Geromanos, Chris Hughes, and David E. Clemmer
- Published
- 2011
- Full Text
- View/download PDF
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