Computational Studies of Molecules Adsorbed on Surfaces

This dissertation contains the results of two different computational studies of adsorbed species. The dissertation is composed of two parts. In the first part we present research aimed at understanding the structural and dynamical properties of a single, partially adsorbed, model polymer chain. In the second part, we present research aimed at determining the minimum energy configuration of a single methane molecule adsorbed on the (100) face of MgO. These two studies are independent of each other, but both contribute to the general understanding of molecules adsorbed on surfaces. Here we provide a brief overview for each study. In the polymer study we simulated the dynamics of a single polymer chain partially adsorbed on an impenetrable surface using a Monte Carlo method. Two sets of simulations were performed. In one set we used the Local Jump (LJ) algorithm to simulate the motion of the polymer chain and in the other we used the Bond Fluctuation (BF) algorithm to simulate the chain’s motion. The objectives of this research were three-fold: (1) to determine the structural and dynamical scaling exponents for a partially adsorbed polymer chain; (2) to determine if the Rouse normal coordinates are the appropriate normal coordinates for a partially adsorbed chain; (3) to determine if the LJ and BF algorithms provide similar descriptions of the dynamics of the partially adsorbed polymer chain. The results of our polymer research show that the scaling exponents for the mean square end-to-end distance, the mean square radius of gyration and the diffusion constant are nearly the same for chains simulated using the LJ and BF algorithms. The scaling exponents for the relaxation times of the Rouse modes indicate the internal dynamics of a chain is different for the chains simulated using the LJ and BF algorithms. Using both algorithms we determined that the Rouse normal coordinates are not the appropriate normal coordinates for a partially adsorbed polymer chain. In the methane-MgO(100) study we used the electronic structure methods and empirical potential energy functions to investigate the minimum energy configurations of a single methane molecule adsorbed on a model MgO(100) surface. The primary goal of this research was to understand why the minimum energy configuration obtained using the electronic structure methods is different than the minimum energy configuration obtained using empirical potential energy functions. The results of our electronic structure calculations indicate that the electronic energy of the edge-down (C2v axis perpendicular to the MgO(100) surface) configuration of methane is significantly lower than that of the face-down (C3v axis perpendicular to the MgO(100) surface) configuration. Furthermore, our electronic structure results indicate that a single methane molecule in the near-surface electric field of MgO experiences significant polarization effects. Using the electronic structure results as our standard we assessed the accuracy of three empirical potential energy functions. We have shown that an empirical potential which treats the electrostatic component of the potential energy using a point charge model cannot accurately describe the electrostatic energy of both the edge-down and the face-down geometries using the same set of point charges. If we extend this approach by including the polarization of the methane adsorbate due to the electric field and field gradients of the MgO surface, we are still unable to account for all of the electrostatic and induction contributions obtained from the electronic structure calculations. Additionally, we show the charge equilibration method of Rappé and Goddard does not reproduce the induction effects indicated by the electronic structure calculations

Miniaturized Ion Mobility Spectrometer

By utilizing the combination of a unique electronic ion injection control circuit in conjunction with a particularly designed drift cell construction, the instantly disclosed ion mobility spectrometer achieves increased levels of sensitivity, while achieving significant reductions in size and weight. The instant IMS is of a much simpler and easy to manufacture design, rugged and hermetically sealed, capable of operation at high temperatures to at least 250.degree. C., and is uniquely sensitive, particularly to explosive chemicals

Analysis of model Titan atmospheric components using ion mobility spectrometry

The Gas Chromatograph-Ion Mobility Spectrometer (GC-IMS) was proposed as an analytical technique for the analysis of Titan's atmosphere during the Cassini Mission. The IMS is an atmospheric pressure, chemical detector that produces an identifying spectrum of each chemical species measured. When the IMS is combined with a GC as a GC-IMS, the GC is used to separate the sample into its individual components, or perhaps small groups of components. The IMS is then used to detect, quantify, and identify each sample component. Conventional IMS detection and identification of sample components depends upon a source of energetic radiation, such as beta radiation, which ionizes the atmospheric pressure host gas. This primary ionization initiates a sequence of ion-molecule reactions leading to the formation of sufficiently energetic positive or negative ions, which in turn ionize most constituents in the sample. In conventional IMS, this reaction sequence is dominated by the water cluster ion. However, many of the light hydrocarbons expected in Titan's atmosphere cannot be analyzed by IMS using this mechanism at the concentrations expected. Research at NASA Ames and PCP Inc., has demonstrated IMS analysis of expected Titan atmospheric components, including saturated aliphatic hydrocarbons, using two alternate sample ionizations mechanisms. The sensitivity of the IMS to hydrocarbons such as propane and butane was increased by several orders of magnitude. Both ultra dry (waterless) IMS sample ionization and metastable ionization were successfully used to analyze a model Titan atmospheric gas mixture

Effectiveness of Occupational Therapy’s Role in Promotion of Role Fulfillment with Aviation Students in Higher Education who are Experiencing Mental Health Conditions

This critically appraised topic paper focuses on occupational therapy’s role and the interventions for improving the mental health of aviation students in higher education. Aviation students are higher education student pilots learning to become pilots within various roles. Stress and fatigue among students in higher education are prominent problems (Beiter, 2015; Kalmakis et al., 2021). The focus on aviation students for this critically appraised topic paper reveals the unique stressors relating to flight training that is added on top of the normal academic stress load that university students face (Robertson & Ruiz, 2010). Due to these stress factors, the mental health of aviation students is negatively impacted and can affect their role fulfillment as aviation students. Higher level education has been defined in this critically appraised topic paper as institutions providing study beyond the level of secondary education, such as colleges and universities, community colleges, and vocational and technical schools (National Center on Safe Supportive Learning Environments, 2023)

A digital boxcar integrator for IMS spectra

When trying to detect or quantify a signal at or near the limit of detectability, it is invariably embeded in the noise. This statement is true for nearly all detectors of any physical phenomena and the limit of detectability, hopefully, occurs at very low signal-to-noise levels. This is particularly true of IMS (Ion Mobility Spectrometers) spectra due to the low vapor pressure of several chemical compounds of great interest and the small currents associated with the ionic detection process. Gated Integrators and Boxcar Integrators or Averagers are designed to recover fast, repetitive analog signals. In a typical application, a time 'Gate' or 'Window' is generated, characterized by a set delay from a trigger or gate pulse and a certain width. A Gated Integrator amplifies and integrates the signal that is present during the time the gate is open, ignoring noise and interference that may be present at other times. Boxcar Integration refers to the practice of averaging the output of the Gated Integrator over many sweeps of the detector. Since any signal present during the gate will add linearly, while noise will add in a 'random walk' fashion as the square root of the number of sweeps, averaging N sweeps will improve the 'Signal-to-Noise Ratio' by a factor of the square root of N

Lead immobilization in thermally remediated soils and igneous rocks

This is the final report for a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The principal goal of this project was to investigate the speciation of lead in the environment at LANL and to determine the feasibility of using thermal remediation methods to immobilize lead in the environment. Lead occurs as pyromorphite [Pb(PO{sub 4}){sub 3}(Cl, OH)], cerussite (PbCO{sub 3}) and galena (PbS) in vapor-phase-altered Bandelier Tuff samples. LANL soils primarily contain cerussite and PbO. Thermal remediation experiments at high temperatures (up to 400 C) suggest that thermal immobilization of highly-reactive Pb compounds in the environment may be feasible, but that this technique is not optimal for more refractory lead phases such as cerussite and PbO

Developing an instrument to assess the endoscopic severity of ulcerative colitis : The Ulcerative Colitis Endoscopic Index of Severity (UCEIS)

Full list of Investigators is given at the end of the article.Background: Variability in endoscopic assessment necessitates rigorous investigation of descriptors for scoring severity of ulcerative colitis (UC). Objective: To evaluate variation in the overall endoscopic assessment of severity, the intra- and interindividual variation of descriptive terms and to create an Ulcerative Colitis Endoscopic Index of Severity which could be validated. Design: A two-phase study used a library of 670 video sigmoidoscopies from patients with Mayo Clinic scores 0-11, supplemented by 10 videos from five people without UC and five hospitalised patients with acute severe UC. In phase 1, each of 10 investigators viewed 16/24 videos to assess agreement on the Baron score with a central reader and agreed definitions of 10 endoscopic descriptors. In phase 2, each of 30 different investigators rated 25/60 different videos for the descriptors and assessed overall severity on a 0-100 visual analogue scale. κ Statistics tested inter- and intraobserver variability for each descriptor. A general linear mixed regression model based on logit link and β distribution of variance was used to predict overall endoscopic severity from descriptors. Results: There was 76% agreement for 'severe', but 27% agreement for 'normal' appearances between phase I investigators and the central reader. In phase 2, weighted κ values ranged from 0.34 to 0.65 and 0.30 to 0.45 within and between observers for the 10 descriptors. The final model incorporated vascular pattern, (normal/patchy/ complete obliteration) bleeding (none/mucosal/luminal mild/luminal moderate or severe), erosions and ulcers (none/erosions/superficial/deep), each with precise definitions, which explained 90% of the variance (pR2, Akaike Information Criterion) in the overall assessment of endoscopic severity, predictions varying from 4 to 93 on a 100-point scale (from normal to worst endoscopic severity). Conclusion: The Ulcerative Colitis Endoscopic Index of Severity accurately predicts overall assessment of endoscopic severity of UC. Validity and responsiveness need further testing before it can be applied as an outcome measure in clinical trials or clinical practice.publishersversionPeer reviewe

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis

Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.Fil: Trilling, Mirko. Universitat Duisburg - Essen; AlemaniaFil: Bellora, Nicolás. Parque de Investigación Biomédica de Barcelona; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; ArgentinaFil: Rutkowski, Andrzej J.. University of Cambridge; Reino UnidoFil: de Graaf, Miranda. University of Cambridge; Reino UnidoFil: Dickinson, Paul. University Of Edinburgh; Reino UnidoFil: Robertson, Kevin. University Of Edinburgh; Reino UnidoFil: Da Costa, Olivia Prazeres. Universitat Technical Zu Munich; AlemaniaFil: Ghazal, Peter. University Of Edinburgh; Reino UnidoFil: Friedel, Caroline C.. Ludwig-Maximilians-University Munich; AlemaniaFil: Albà, M. Mar. Institució Catalana de Recerca I Estudis Avancats; España. Parque de Investigación Biomédica de Barcelona; EspañaFil: Dölken, Lars. University of Cambridge; Reino Unid