scholarly journals Quantum aspects of roaming dynamics

2020 ◽  
Author(s):  
◽  
Casey D. Foley

Decades of experimental and theoretical achievements built on the foundations of thermochemistry and quantum mechanics have birthed the field of molecular dynamics where intimate details of individual reactive events can be mapped. On the ground state of formaldehyde, two dissociation pathways are commonly known, one proceeding over a high barrier through a three-center, tight transition state to give molecular products, and another via homolytic simple bond fission to radical products. A third, distinct ground state dissociation pathway first seen in formaldehyde 15 years ago, the 'roaming' mechanism, involves incipient radicals, but the H atom samples a large, flat region of the PES, roaming in the van der Waals region, leading to an intramolecular H + HCO reaction. Roaming reactions have been visualized from a classical perspective with only a few exceptions in the literature despite the likely quantum nature of the process. A major objective of the presented work is to reveal quantum aspects of roaming reactions. Here, a few different molecules (C3H3Cl, HDCO, and H2CO) were investigated with the goal of characterizing roaming radicals on the ground state, where roaming observations have primarily occurred. Knowledge of the excited states of propargyl chloride was necessary to understand the experimental observations from investigation of its ground state. Ultraviolet (UV) photodissociation and state-specific detection with velocity map imaging of Cl, Cl*, and C3H3 were interpreted with the aid of multireference calculations to characterize the nature of the electronic excitations. A series of triplet states were identified to preferentially dissociate to Cl or Cl*. Infrared multiphoton excitation and infrared multiphoton dissociation (IRMPD) of propargyl chloride enhanced UV processes and allowed for radical dissociation at threshold. IRMPD on the ground state produced HCl following isomerization to 1-chloroallene, where a roaming-like transition state with Cl in an abstraction geometry is adopted. Accurate H and D atom ground state radical thresholds of singly deuterated formaldehyde, HDCO, were obtained from velocity map imaging to aid future studies HDCO dynamics studies. The different radical thresholds, arising from the difference in zero-point energies, is a purely quantum phenomenon. PHOFEX spectra over a wide range were collected, creating a library of known frequencies of rotational lines that can be used to study the dynamics of different vibrational bands and the energy dependence of different processes. Heats of formation of HDCO and DCO were also determined. Finally, a detailed examination of the photochemical dynamics in both ortho and para nuclear spin isomers of formaldehyde is provided, exploring the full range of parent rotational levels from J = 0 to 4, initially prepared via excitation of specific rotational lines of a range of vibrational bands on the first singlet excited state (2141, 2161, 2143, 2241, 2243). Measurements of the entire CO (v = 0) product rotational distributions are combined with velocity map imaging of selected CO product states to obtain a complete picture of the photochemical dynamics for each specific parent rotational level. Distributions are found to vary dramatically with small changes in total energy, effects not captured at all by classical treatments. Full quantum state correlations reveal interactions among three formaldehyde dissociation continua, yielding rich insight into the dynamics of this highly excited molecule as it decays to products. An orbiting resonance dominates the dynamics, though other possible dynamical phenomena are noted.

Author(s):  
John Maynard Smith ◽  
Eors Szathmary

Over the history of life there have been several major changes in the way genetic information is organized and transmitted from one generation to the next. These transitions include the origin of life itself, the first eukaryotic cells, reproduction by sexual means, the appearance of multicellular plants and animals, the emergence of cooperation and of animal societies, and the unique language ability of humans. This ambitious book provides the first unified discussion of the full range of these transitions. The authors highlight the similarities between different transitions--between the union of replicating molecules to form chromosomes and of cells to form multicellular organisms, for example--and show how understanding one transition sheds light on others. They trace a common theme throughout the history of evolution: after a major transition some entities lose the ability to replicate independently, becoming able to reproduce only as part of a larger whole. The authors investigate this pattern and why selection between entities at a lower level does not disrupt selection at more complex levels. Their explanation encompasses a compelling theory of the evolution of cooperation at all levels of complexity. Engagingly written and filled with numerous illustrations, this book can be read with enjoyment by anyone with an undergraduate training in biology. It is ideal for advanced discussion groups on evolution and includes accessible discussions of a wide range of topics, from molecular biology and linguistics to insect societies.


Oxford Studies in Medieval Philosophy annually collects the best current work in the field of medieval philosophy. The various volumes print original essays, reviews, critical discussions, and editions of texts. The aim is to contribute to an understanding of the full range of themes and problems in all aspects of the field, from late antiquity into the Renaissance, and extending over the Jewish, Islamic, and Christian traditions. Volume 6 includes work on a wide range of topics, including Davlat Dadikhuda on Avicenna, Christopher Martin on Abelard’s ontology, Jeremy Skrzypek and Gloria Frost on Aquinas’s ontology, Jean‐Luc Solère on instrumental causality, Peter John Hartman on Durand of St.‐Pourçain, and Kamil Majcherek on Chatton’s rejection of final causality. The volume also includes an extended review of Thomas Williams of a new book on Aquinas’s ethics by Colleen McCluskey.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. P. M. Marques ◽  
D. Gonçalves ◽  
A. P. Mamede ◽  
T. Coutinho ◽  
E. Cunha ◽  
...  

AbstractComplementary optical and neutron-based vibrational spectroscopy techniques (Infrared, Raman and inelastic neutron scattering) were applied to the study of human bones (femur and humerus) burned simultaneously under either aerobic or anaerobic conditions, in a wide range of temperatures (400 to 1000 °C). This is the first INS study of human skeletal remains heated in an oxygen-deprived atmosphere. Clear differences were observed between both types of samples, namely the absence of hydroxyapatite’s OH vibrational bands in bone burned anaerobically (in unsealed containers), coupled to the presence of cyanamide (NCNH2) and portlandite (Ca(OH)2) in these reductive conditions. These results are expected to allow a better understanding of the heat effect on bone´s constituents in distinct environmental settings, thus contributing for an accurate characterisation of both forensic and archaeological human skeletal remains found in distinct scenarios regarding oxygen availability.


Author(s):  
Yogi Sheoran ◽  
Bruce Bouldin ◽  
P. Murali Krishnan

Inlet swirl distortion has become a major area of concern in the gas turbine engine community. Gas turbine engines are increasingly installed with more complicated and tortuous inlet systems, like those found on embedded installations on Unmanned Aerial Vehicles (UAVs). These inlet systems can produce complex swirl patterns in addition to total pressure distortion. The effect of swirl distortion on engine or compressor performance and operability must be evaluated. The gas turbine community is developing methodologies to measure and characterize swirl distortion. There is a strong need to develop a database containing the impact of a range of swirl distortion patterns on a compressor performance and operability. A recent paper presented by the authors described a versatile swirl distortion generator system that produced a wide range of swirl distortion patterns of a prescribed strength, including bulk swirl, twin swirl and offset swirl. The design of these swirl generators greatly improved the understanding of the formation of swirl. The next step of this process is to understand the effect of swirl on compressor performance. A previously published paper by the authors used parallel compressor analysis to map out different speed lines that resulted from different types of swirl distortion. For the study described in this paper, a computational fluid dynamics (CFD) model is used to couple upstream swirl generator geometry to a single stage of an axial compressor in order to generate a family of compressor speed lines. The complex geometry of the analyzed swirl generators requires that the full 360° compressor be included in the CFD model. A full compressor can be modeled several ways in a CFD analysis, including sliding mesh and frozen rotor techniques. For a single operating condition, a study was conducted using both of these techniques to determine the best method given the large size of the CFD model and the number of data points that needed to be run to generate speed lines. This study compared the CFD results for the undistorted compressor at 100% speed to comparable test data. Results of this study indicated that the frozen rotor approach provided just as accurate results as the sliding mesh but with a greatly reduced cycle time. Once the CFD approach was calibrated, the same techniques were used to determine compressor performance and operability when a full range of swirl distortion patterns were generated by upstream swirl generators. The compressor speed line shift due to co-rotating and counter-rotating bulk swirl resulted in a predictable performance and operability shift. Of particular importance is the compressor performance and operability resulting from an exposure to a set of paired swirl distortions. The CFD generated speed lines follow similar trends to those produced by parallel compressor analysis.


2018 ◽  
Vol 64 (4) ◽  
pp. 656-679 ◽  
Author(s):  
Jeffrey D Freeman ◽  
Lori M Rosman ◽  
Jeremy D Ratcliff ◽  
Paul T Strickland ◽  
David R Graham ◽  
...  

Abstract BACKGROUND Advancements in the quality and availability of highly sensitive analytical instrumentation and methodologies have led to increased interest in the use of microsamples. Among microsamples, dried blood spots (DBS) are the most well-known. Although there have been a variety of review papers published on DBS, there has been no attempt at describing the full range of analytes measurable in DBS, or any systematic approach published for characterizing the strengths and weaknesses associated with adoption of DBS analyses. CONTENT A scoping review of reviews methodology was used for characterizing the state of the science in DBS. We identified 2018 analytes measured in DBS and found every common analytic method applied to traditional liquid samples had been applied to DBS samples. Analytes covered a broad range of biomarkers that included genes, transcripts, proteins, and metabolites. Strengths of DBS enable its application in most clinical and laboratory settings, and the removal of phlebotomy and the need for refrigeration have expanded biosampling to hard-to-reach and vulnerable populations. Weaknesses may limit adoption in the near term because DBS is a nontraditional sample often requiring conversion of measurements to plasma or serum values. Opportunities presented by novel methodologies may obviate many of the current limitations, but threats around the ethical use of residual samples must be considered by potential adopters. SUMMARY DBS provide a wide range of potential applications that extend beyond the reach of traditional samples. Current limitations are serious but not intractable. Technological advancements will likely continue to minimize constraints around DBS adoption.


1992 ◽  
Vol 15 (3) ◽  
pp. 425-437 ◽  
Author(s):  
Allen Newell

AbstractThe book presents the case that cognitive science should turn its attention to developing theories of human cognition that cover the full range of human perceptual, cognitive, and action phenomena. Cognitive science has now produced a massive number of high-quality regularities with many microtheories that reveal important mechanisms. The need for integration is pressing and will continue to increase. Equally important, cognitive science now has the theoretical concepts and tools to support serious attempts at unified theories. The argument is made entirely by presenting an exemplar unified theory of cognition both to show what a real unified theory would be like and to provide convincing evidence that such theories are feasible. The exemplar is SOAR, a cognitive architecture, which is realized as a software system. After a detailed discussion of the architecture and its properties, with its relation to the constraints on cognition in the real world and to existing ideas in cognitive science, SOAR is used as theory for a wide range of cognitive phenomena: immediate responses (stimulus-response compatibility and the Sternberg phenomena); discrete motor skills (transcription typing); memory and learning (episodic memory and the acquisition of skill through practice); problem solving (cryptarithmetic puzzles and syllogistic reasoning); language (sentence verification and taking instructions); and development (transitions in the balance beam task). The treatments vary in depth and adequacy, but they clearly reveal a single, highly specific, operational theory that works over the entire range of human cognition, SOAR is presented as an exemplar unified theory, not as the sole candidate. Cognitive science is not ready yet for a single theory – there must be multiple attempts. But cognitive science must begin to work toward such unified theories.


2012 ◽  
Vol 58 (12) ◽  
pp. 1703-1710 ◽  
Author(s):  
Yeo-Min Yun ◽  
Julianne Cook Botelho ◽  
Donald W Chandler ◽  
Alex Katayev ◽  
William L Roberts ◽  
...  

BACKGROUND Testosterone measurements that are accurate, reliable, and comparable across methodologies are crucial to improving public health. Current US Food and Drug Administration–cleared testosterone assays have important limitations. We sought to develop assay performance requirements on the basis of biological variation that allow physiologic changes to be distinguished from assay analytical errors. METHODS From literature review, the technical advisory subcommittee of the Partnership for the Accurate Testing of Hormones compiled a database of articles regarding analytical and biological variability of testosterone. These data, mostly from direct immunoassay-based methodologies, were used to specify analytical performance goals derived from within- and between-person variability of testosterone. RESULTS The allowable limits of desirable imprecision and bias on the basis of currently available biological variation data were 5.3% and 6.4%, respectively. The total error goal was 16.7%. From recent College of American Pathologists proficiency survey data, most currently available testosterone assays missed these analytical performance goals by wide margins. Data from the recently established CDC Hormone Standardization program showed that although the overall mean bias of selected certified assays was within 6.4%, individual sample measurements could show large variability in terms of precision, bias, and total error. CONCLUSIONS Because accurate measurement of testosterone across a wide range of concentrations [approximately 2–2000 ng/dL (0.069–69.4 nmol/L)] is important, we recommend using available data on biological variation to calculate performance criteria across the full range of expected values. Additional studies should be conducted to obtain biological variation data on testosterone from women and children, and revisions should be made to the analytical goals for these patient populations.


2021 ◽  
Author(s):  
Subhadeep Sarkar ◽  
Mathias Horstmann ◽  
Tore Oian ◽  
Piotr Byrski ◽  
George Lawrence ◽  
...  

Abstract One of the crucial components of well integrity evaluation in offshore drilling is to determine the cement bond quality assuring proper hydraulic sealing. On the Norwegian Continental Shelf (NCS) an industry standard as informative reference imposes verification of cement length and potential barriers using bonding logs. Traditionally, for the last 50 years, wireline (WL) sonic tools have been extensively used for this purpose. However, the applicability of logging-while-drilling (LWD) sonic tools for quantitative cement evaluation was explored in the recent development drilling campaign on the Dvalin Field in the Norwegian Sea, owing to significant advantages on operational efficiency and tool conveyance in any well trajectory. Cement bond evaluation from conventional peak-to-peak amplitude method has shown robust results up to bond indexes of 0.6 for LWD sonic tools. Above this limit, the casing signal is smaller than the collar signal and the amplitude method loses sensitivity to bonding. This practical challenge in the LWD realm was overcome through the inclusion of attenuation rate measurements, which responds accordingly in higher bonding environments. The two methods are used in a hybrid approach providing a full range quantitative bond index (QBI) introduced by Izuhara et al. (2017). In order to conform with local requirements related to well integrity and to ascertain the QBI potential from LWD monopole sonic, a wireline cement bond log (CBL) was acquired in the first well of the campaign for comparison. This enabled the strategic deployment of LWD QBI service in subsequent wells. LWD sonic monopole data was acquired at a controlled speed of 900ft/h. The high-fidelity waveforms were analyzed in a suitable time window and both amplitude- and attenuation-based bond indexes were derived. The combined hybrid bond index showed an excellent match with the wireline reference CBL, both in zones of high as well as lower cement bonding. The presence of formation arrivals was also in good correlation with zones of proper bonding distinguishable on the QBI results. This established the robustness of the LWD cement logging and ensured its applicability in the rest of the campaign which was carried out successfully. While the results from LWD cement evaluation service are omnidirectional, it comes with a wide range of benefits related to rig cost or conveyance in tough borehole trajectories. Early evaluation of cement quality by LWD sonic tools helps to provide adequate time for taking remedial actions if necessary. The LWD sonic as part of the drilling BHA enables this acquisition and service in non-dedicated runs, with the possibility of multiple passes for observing time-lapse effects. Also, the large sizes of LWD tools relative to the wellbore ensures a lower signal attenuation in the annulus and more effective stabilization, thereby providing a reliable bond index.


Author(s):  
Ik-Hwan Um ◽  
Seungjae Kim

Second-order rate constants (kN) for reactions of p-nitrophenyl acetate (1) and S-p-nitrophenyl thioacetate (2) with OH‒ have been measured spectrophotometrically in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. The kN value increases from 11.6 to 32,800 M‒1s‒1 for the reactions of 1 and from 5.90 to 190,000 M‒1s‒1 for those of 2 as the reaction medium changes from H2O to 80 mol % DMSO, indicating that the effect of medium on reactivity is more remarkable for the reactions of 2 than for those of 1. Although 2 possesses a better leaving group than 1, the former is less reactive than the latter by a factor of 2 in H2O. This implies that expulsion of the leaving group is not advanced in the rate-determining transition state (TS), i.e., the reactions of 1 and 2 with OH‒ proceed through a stepwise mechanism, in which expulsion of the leaving group from the addition intermediate occurs after the rate-determining step (RDS). Addition of DMSO to H2O would destabilize OH‒ through electronic repulsion between the anion and the negative-dipole end in DMSO. However, destabilization of OH‒ in the ground state (GS) is not solely responsible for the remarkably enhanced reactivity upon addition of DMSO to the medium. The effect of medium on reactivity has been dissected into the GS and TS contributions through combination of the kinetic data with the transfer enthalpies (ΔΔHtr) from H2O to DMSO-H2O mixtures for OH‒ ion.


2018 ◽  
Vol 115 (47) ◽  
pp. 11958-11963 ◽  
Author(s):  
Christian Kubitza ◽  
Florian Bittner ◽  
Carsten Ginsel ◽  
Antje Havemeyer ◽  
Bernd Clement ◽  
...  

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.


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