Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

The Kineticist's Workbench is a computer program currently under development whose purpose is to help chemists understand, analyze, and simplify complex chemical reaction mechanisms. This paper discusses one module of the program that numerically simulates mechanisms and constructs qualitative descriptions of the simulation results. These descriptions are given in terms that are meaningful to the working chemist (e.g., steady states, stable oscillations, and so on); and the descriptions (as well as the data structures used to construct them) are accessible as input to other programs.

Different mechanisms for the formation of acetaldehyde and ethanol on the Rh-based catalysts

Different mechanisms for the formation of acetaldehyde and ethanol on the Rh-based catalysts were investigated by the TPR (temperature programmed reaction) method, and the active sites were studied by CO-TPD, TPSR (temperature programmed surface reaction of preadsorbed CO by H-2) and XPS techniques. The TPR results indicated that ethanol and acetaldehyde might be formed through different intermediates, whereas ethanol and methanol might result from the same intermediate. Results of CO-TPD, TPSR, and XPS showed that on the Rh-based catalyst, the structure of the active sites for the formation of C-2-oxygenates is ((RhxRhy+)-Rh-0)-O-Mn+ (M=Mn or Zr, x>>y, 2 less than or equal ton less than or equal to4). The tilt-adsorbed CO species is the main precursor for CO dissociation and the precursor for the formation of ethanol and methanol. Most of the linear and geminal adsorbed CO species desorbed below 500 K. Based on the suggested model of the active sites, detailed mechanisms for the formation of acetaldehyde and ethanol are proposed. Ethanol is formed by direct hydrogenation of the tilt-adsorbed CO molecules, followed by CH2 insertion into the surface CH2-O species and the succeeding hydrogenation step. Acetaldehyde is formed through CO insertion into the surface CH3-Rh species followed by hydrogenation, and the role of the promoters was to stabilize the intermediate of the surface acetyl species. (C) 2000 Academic Press.

The Role of Chemical Mechanisms in Neural Computation and Learning

Most computational models of neurons assume that their electrical characteristics are of paramount importance. However, all long-term changes in synaptic efficacy, as well as many short-term effects, are mediated by chemical mechanisms. This technical report explores the interaction between electrical and chemical mechanisms in neural learning and development. Two neural systems that exemplify this interaction are described and modelled. The first is the mechanisms underlying habituation, sensitization, and associative learning in the gill withdrawal reflex circuit in Aplysia, a marine snail. The second is the formation of retinotopic projections in the early visual pathway during embryonic development.

Hypothesizing Device Mechanisms: Opening Up the Black Box

I describe an approach to forming hypotheses about hidden mechanism configurations within devices given external observations and a vocabulary of primitive mechanisms. An implemented causal modelling system called JACK constructs explanations for why a second piece of toast comes out lighter, why the slide in a tire gauge does not slip back inside when the gauge is removed from the tire, and how in a refrigerator a single substance can serve as a heat sink for the interior and a heat source for the exterior. I report the number of hypotheses admitted for each device example, and provide empirical results which isolate the pruning power due to different constraint sources.

Dynamical Systems in the Sensorimotor Loop: On the Interrelation Between Internal and External Mechanisms of Evolved Robot Behavior

Huelse, M., Wischmann, S., Manoonpong, P., Twickel, A.v., Pasemann, F.: Dynamical Systems in the Sensorimotor Loop: On the Interrelation Between Internal and External Mechanisms of Evolved Robot Behavior. In: M. Lungarella, F. Iida, J. Bongard, R. Pfeifer (Eds.) 50 Years of Artificial Intelligence, LNCS 4850, Springer, 186 - 195, 2007.

Exploring knowledge transfer mechanisms: The case of a UK-based group within a high-tech global corporation

Jasimuddin, Sajjad, 'Exploring knowledge transfer mechanisms: The case of a UK-based group within a high-tech global corporation', International Journal of Information Management (2007) 27(4) pp.294-300 RAE2008

The Terrorism Virus: Contemporary Traits and Mechanisms

In order to present and understand the nature of modern terrorism it is important to realize its key properties as well the mechanisms that shape terrorism. Selected properties and mechanisms shaping modern terrorism which can be exemplified by the following: evolutionary nature of terrorism, asymmetry of terrorism, interferentiality of terrorism, multitude of components of terrorism, diffusion of terrorism, duality of terrorism, positive dimension of terrorism, terrorist as the system, diversity of terrorist activity goals, changeability of terrorist threat, the broad and narrow dimension of terrorism, counter-anti-terrorism, the confrontational and cooperational character of relations, calculation and operational strategy, disintegrational nature of terrorism, multidisciplinarity of terrorism, horizontal and vertical dimension of terrorism and a the few other traits or mechanisms.

How Does Binocular Rivalry Emerge from Cortical Mechanisms of 3D Vision?

Under natural viewing conditions, a single depthful percept of the world is consciously seen. When dissimilar images are presented to corresponding regions of the two eyes, binocular rivalyr may occur, during which the brain consciously perceives alternating percepts through time. How do the same brain mechanisms that generate a single depthful percept of the world also cause perceptual bistability, notably binocular rivalry? What properties of brain representations correspond to consciously seen percepts? A laminar cortical model of how cortical areas V1, V2, and V4 generate depthful percepts is developed to explain and quantitatively simulate binocualr rivalry data. The model proposes how mechanisms of cortical developement, perceptual grouping, and figure-ground perception lead to signle and rivalrous percepts. Quantitative model simulations include influences of contrast changes that are synchronized with switches in the dominant eye percept, gamma distribution of dominant phase durations, piecemeal percepts, and coexistence of eye-based and stimulus-based rivalry. The model also quantitatively explains data about multiple brain regions involved in rivalry, effects of object attention on switching between superimposed transparent surfaces, and monocular rivalry. These data explanations are linked to brain mechanisms that assure non-rivalrous conscious percepts. To our knowledge, no existing model can explain all of these phenomena.

Does Binocular Rivalry Emerge from Cortical Mechanisms of 3D Vision

Under natural viewing conditions, a single depthful percept of the world is consciously seen. When dissimilar images are presented to corresponding regions of the two eyes, binocular rivalry may occur, during which the brain consciously perceives alternating percepts through time. Perceptual bistability can also occur in response to a single ambiguous figure. These percepts raise basic questions: What brain mechanisms generate a single depthful percept of the world? How do the same mechanisms cause perceptual bistability, notably binocular rivalry? What properties of brain representations correspond to consciously seen percepts? How do the dynamics of the layered circuits of visual cortex generate single and bistable percepts? A laminar cortical model of how cortical areas V1, V2, and V4 generate depthful percepts is developed to explain and quantitatively simulate binocular rivalry data. The model proposes how mechanisms of cortical development, perceptual grouping, and figure-ground perception lead to single and rivalrous percepts.

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

Molecular analysis of virulence mechanisms associated with adherent-invasive Escherichia coli (AIEC)

Crohn's Disease (CD) is a chronic inflammatory bowel disease of unknown etiology. Recent work has shown that a new pathotype of Escherichia coli, Adherent Invasive E. coli (AIEC) may be associated with CD. AIEC has been shown to adhere to and invade epithelial cells and to replicate within macrophages (together this is called the AIEC phenotype). In this thesis, the AIEC phenotype of 84 E. coli strains were determined in order to identify the prevalence of this phenotype within the E. coli genus. This study showed that a significant proportion of E. coli strains (approx. 5%) are capable of adhering to and invading epithelial cells and undergoing intramacrophage replication. Moreover, the results presented in this study indicate a correlation between survival in macrophage and resistance to grazing by amoeba supporting the coincidental evolution hypothesis that resistance to amoebae could be a driving force in the evolution of pathogenicity in some bacteria, such as AIEC. In addition, this study has identified an important regulatory role for the CpxA/R two component system (TCS) in the invasive abilities of AIEC HM605, a colonic mucosa-associated CD isolate. A mutation in cpxR was shown to be defective in the invasion of epithelial cells and this defect was shown to be independent of motility or the expression of Type 1 fimbriae, factors that have been shown to be involved in the invasion of another strain of AIEC, isolated from a patient with ileal CD, called LF82. The CpxA/R TCS responds to disturbances in the cell envelope and has been implicated in the virulence of a number of Gram negative pathogens. In this study it is shown that the CpxA/R TCS regulates the expression of a potentially novel invasin called SinH. SinH is found in a number of invasive strains of E. coli and Salmonella. Moreover work presented here shows that a critical mechanism underpinning AIEC persistence in macrophages is the repair of DNA bases damaged by macrophage oxidants. Together these findings provide evidence to suggest that AIEC are a diverse group of E. coli and possess diverse molecular mechanisms and virulence factors that contribute to the AIEC phenotype. In addition, AIEC may have gone through different evolutionary histories acquiring various molecular mechanisms ultimately culminating in the AIEC phenotype. The gastrointestinal (GI) tract harbors a diverse microbiota; most are symbiotic or commensal however some bacteria have the potential to cause disease (pathobiont). The work presented here provides evidence to support the model that AIEC are pathobionts. AIEC strains can be carried as commensals in healthy guts however, when the intestinal homeostasis is disrupted, such as in the compromised gut of CD patients, AIEC may behave as opportunistic pathogens and cause and/or contribute to disease by driving intestinal inflammation.