Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
23,537
result(s) for
"transition state"
Sort by:
The demographic imagination and the nineteenth-century city : Paris, London, New York
\"In this provocative book, Nicholas Daly tracks the cultural effects of the population explosion of the nineteenth century, the 'demographic transition' to the modern world. As the crowded cities of Paris, London and New York went through similar transformations, a set of shared narratives and images of urban life circulated among them, including fantasies of urban catastrophe, crime dramas, and tales of haunted public transport, refracting the hell that is other people. In the visual arts, sentimental genre pictures appeared that condensed the urban masses into a handful of vulnerable figures: newsboys and flower-girls. At the end of the century, proto-ecological stories emerge about the sprawling city as itself a destroyer. This lively study excavates some of the origins of our own international popular culture, from noir visions of the city as a locus of crime, to utopian images of energy and community\"-- Provided by publisher.
Book
Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions
This article surveys the empirical information which originated both by laboratory experiments and by computational simulations, and expands previous understanding of the rates of chemical processes in the low-temperature range, where deviations from linearity of Arrhenius plots were revealed. The phenomenological two-parameter Arrhenius equation requires improvement for applications where interpolation or extrapolations are demanded in various areas of modern science. Based on Tolman's theorem, the dependence of the reciprocal of the apparent activation energy as a function of reciprocal absolute temperature permits the introduction of a deviation parameter d covering uniformly a variety of rate processes, from those where quantum mechanical tunnelling is significant and d < 0, to those where d > 0, corresponding to the Pareto-Tsallis statistical weights: these generalize the Boltzmann-Gibbs weight, which is recovered for d = 0. It is shown here how the weights arise, relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermion-like or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.
This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Journal Article
The Nature of the Enthalpy–Entropy Compensation and “Exotic” Arrhenius Parameters in the Denaturation Kinetics of Proteins
Protein unfolding is a ubiquitous process responsible for the loss of protein functionality (denaturation), which, in turn, can be accompanied by the death of cells and organisms. The nature of enthalpy–entropy compensation (EEC) in the kinetics of protein unfolding is a subject of debate. In order to investigate the nature of EEC, the “completely loose” transition state (TS) model has been applied to calculate the Arrhenius parameters for the unfolding of polyglycine dimers as a model process. The calculated Arrhenius parameters increase with increasing dimer length and demonstrate enthalpy–entropy compensation. It is shown that EEC results from the linear correlations of enthalpy and entropy of activation with dimer length, which are derived directly from the properties of the transition state. It is shown that EEC in solvated (hydrated, etc.) proteins is a direct consequence of EEC in proteins themselves. The suggested model allows us also to reproduce and explain “exotic” very high values of the pre-exponential factor measured for the proteins unfolding, which are drastically higher than those known for unimolecular reactions of organic molecules. A similar approach can be applied to analyzing the nature of EEC phenomena observed in other areas of chemistry.
Journal Article
Developing an expert elicited simulation model to evaluate invasive species and fire management alternatives
Invasive species can alter ecosystem properties and cause state shifts in landscapes. Resource managers charged with maintaining landscapes require tools to understand implications of alternative actions (or inactions) on landscape structure and function. Simulation models can serve as a virtual laboratory to explore these alternatives and their potential impacts on a landscape. To be useful, however, managers need to participate in model development to ensure that model structure can evaluate the response of key resources to plausible actions. Here, we detail development of a state‐and‐transition simulation model (STSM) to evaluate buffelgrass (Cenchrus ciliaris L. syn Pennisetum ciliare (L.) Link) in Saguaro National Park (SNP), Arizona, USA, through collaboration between managers and researchers. We integrate expert knowledge and research to create and parameterize a stochastic, spatially explicit STSM to evaluate specific management objectives. We also develop a dynamic link between the STSM and a fire behavior model to allow exploration of potential novel processes introduced to the ecosystem by buffelgrass invasion. Our projections show that buffelgrass can be expected to increase on the landscape and that the integration of fire into the model accelerates the projected rate of invasion and increases degradation of resources of management concern. We highlight the benefit of engaging end users in the modeling process so that the model is targeted to evaluate management objectives, in this case retention of saguaro cacti (Carnegiea gigantea (Engelm.) Britton & Rose) on the landscape. Being able to integrate an external model that can help address the unique characteristics of a problem such as the introduction of fire into the SNP desert ecosystem increases the ability of simulations to address complex ecological and management questions.
Journal Article
Effectiveness, benefit harm and cost effectiveness of colorectal cancer screening in Austria
Background
Clear evidence on the benefit-harm balance and cost effectiveness of population-based screening for colorectal cancer (CRC) is missing. We aim to systematically evaluate the long-term effectiveness, harms and cost effectiveness of different organized CRC screening strategies in Austria.
Methods
A decision-analytic cohort simulation model for colorectal adenoma and cancer with a lifelong time horizon was developed, calibrated to the Austrian epidemiological setting and validated against observed data. We compared four strategies: 1) No Screening, 2) FIT: annual immunochemical fecal occult blood test age 40–75 years, 3) gFOBT: annual guaiac-based fecal occult blood test age 40–75 years, and 4) COL: 10-yearly colonoscopy age 50–70 years. Predicted outcomes included: benefits expressed as life-years gained [LYG], CRC-related deaths avoided and CRC cases avoided; harms as additional complications due to colonoscopy (physical harm) and positive test results (psychological harm); and lifetime costs. Tradeoffs were expressed as incremental harm-benefit ratios (IHBR, incremental positive test results per LYG) and incremental cost-effectiveness ratios [ICER]. The perspective of the Austrian public health care system was adopted. Comprehensive sensitivity analyses were performed to assess uncertainty.
Results
The most effective strategies were FIT and COL. gFOBT was less effective and more costly than FIT. Moving from COL to FIT results in an incremental unintended psychological harm of 16 additional positive test results to gain one life-year. COL was cost saving compared to No Screening. Moving from COL to FIT has an ICER of 15,000 EUR per LYG.
Conclusions
Organized CRC-screening with annual FIT or 10-yearly colonoscopy is most effective. The choice between these two options depends on the individual preferences and benefit-harm tradeoffs of screening candidates.
Journal Article
Application of the Dynamical Network Biomarker Theory to Raman Spectra
The dynamical network biomarker (DNB) theory detects the early warning signals of state transitions utilizing fluctuations in and correlations between variables in complex systems. Although the DNB theory has been applied to gene expression in several diseases, destructive testing by microarrays is a critical issue. Therefore, other biological information obtained by non-destructive testing is desirable; one such piece of information is Raman spectra measured by Raman spectroscopy. Raman spectroscopy is a powerful tool in life sciences and many other fields that enable the label-free non-invasive imaging of live cells and tissues along with detailed molecular fingerprints. Naïve and activated T cells have recently been successfully distinguished from each other using Raman spectroscopy without labeling. In the present study, we applied the DNB theory to Raman spectra of T cell activation as a model case. The dataset consisted of Raman spectra of the T cell activation process observed at 0 (naïve T cells), 2, 6, 12, 24 and 48 h (fully activated T cells). In the DNB analysis, the F-test and hierarchical clustering were used to detect the transition state and identify DNB Raman shifts. We successfully detected the transition state at 6 h and related DNB Raman shifts during the T cell activation process. The present results suggest novel applications of the DNB theory to Raman spectra ranging from fundamental research on cellular mechanisms to clinical examinations.
Journal Article
Applicability of Transition State Theory to the (Proton-Coupled) Electron Transfer in Photosynthetic Water Oxidation with Emphasis on the Entropy of Activation
Recent advancements in the study of the protein complex photosystem II have clarified the sequence of events leading to the formation of oxygen during the S3 → S4 → S0 transition, wherein the inorganic Mn4Ca(µ-O)6(OHx)4 cluster finishes photo-catalyzing the water splitting reaction (Greife et al., Nature 2023, 617, 623–628; Bhowmick et al., Nature 2023, 617, 629–636). During this final step, a tyrosine radical (TyrZ), stable for a couple of milliseconds, oxidizes a cluster-bound oxygen while the hydrogen bonding patterns of nearby waters shift a proton away. A treatment of this redox reaction within the context of accepted transition state theories predicts rate constants that are significantly higher than experimentally recovered values (1012 s−1 versus 103 s−1). In an effort to understand this disparity, temperature-dependent experiments have revealed large entropic contributions to the rates with only a moderate enthalpy of activation. We suggest that the entropic source may be related to the observed proton rearrangements, and further possible near isoenergetic variations in the nearby extended H-bonding network delaying the realization of an ‘ideal’ transition state. In the following, we explore this relation in the context of Eyring’s transition state theory and Marcus’ electron transfer theory and evaluate their compatibility with the experimental evidence.
Journal Article
Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation
A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC). This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche) and sandpile-type critical behavior. Genome avalanche patterns—competition between order (scaling) and disorder (divergence) reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control) in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality). This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state) occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i) the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii) essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.
Journal Article
Before the oath : how George W. Bush and Barack Obama managed a transfer of power
An expert on presidential transitions illuminates the factors necessary for a successful handoff.
Winner of the CHOICE Outstanding Academic Title of the Choice ACRL
It's one of the hallmarks of American democracy: on inauguration day, the departing president heeds the will of the people and hands the keys to power to a successor. The transition from one administration to the next sounds simple, even ceremonial. But in 2009, as President George W. Bush briefed President-elect Barack Obama about the ongoing wars and plummeting economy he'd soon inherit, the Bush team revealed that they were grappling with a late-breaking threat to the presidency: U.S. intelligence sources believed that a terror group with links to Al Qaeda planned to attack the National Mall during the inaugural festivities. Although this violence never materialized, its possibility made it clear that well-laid contingency plans were essential.
Political scientist Martha Joynt Kumar uncovered this secret peril while interviewing senior Bush and Obama advisers for her latest book. In Before the Oath, Kumar documents how two presidential teams—one outgoing, the other incoming—must forge trusting alliances in order to help the new president succeed in his or her first term.
Kumar enjoyed unprecedented access to several incumbent and candidate transition team members, and she combines in-depth scholarship with one-on-one interviews to put readers squarely behind the scenes. Using the Bush-Obama handoff as a lens through which to examine the presidential transition process, Kumar interweaves examples from previous administrations as far back as Truman-Eisenhower. Her subjects describe in vivid detail the challenges of sowing campaign ideals across a sprawling executive branch as Congress, the media, and external events press in. Kumar's lively account of lessons learned and pitfalls encountered during past presidential transitions provides an essential road map for presidential aspirants and their advisers, as well as campaign workers, federal employees, and political appointees.
eBook
PSB33 sustains photosystem II D1 protein under fluctuating light conditions
On Earth, solar irradiance varies as the sun rises and sets over the horizon, and sunlight is thus in constant fluctuation, following a slow dark–low–high–low–dark curve. Optimal plant growth and development are dependent on the capacity of plants to acclimate and regulate photosynthesis in response to these changes of light. Little is known of regulative processes for photosynthesis during nocturnal events. The nucleus-encoded plant lineage-specific protein PSB33 has been described as stabilizing the photosystem II complex, especially under light stress conditions, and plants lacking PSB33 have a dysfunctional state transition. To clarify the localization and function of this protein, we used phenomic, biochemical and proteomics approaches in the model plant Arabidopsis. We report that PSB33 is predominantly located in non-appressed thylakoid regions and dynamically associates with a thylakoid protein complex in a light-dependent manner. Moreover, plants lacking PSB33 show an accelerated D1 protein degradation in nocturnal periods, and show severely stunted growth when challenged with fluctuating light. We further show that the function of PSB33 precedes the STN7 kinase to regulate or balance the excitation energy of photosystems I and II in fluctuating light conditions.
Journal Article