Global dynamic optimization

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2004.Includes bibliographical references (p. 247-256).(cont.) on a set composed of the Cartesian product between the parameter bounds and the state bounds. Furthermore, I show that the solution of the differential equations is affine in the parameters. Because the feasible set is convex pointwise in time, the standard result that a convex function composed with an affine function remains convex yields the desired result that the integrand is convex under composition. Additionally, methods are developed using interval arithmetic to derive the exact state bounds for the solution of a linear dynamic system. Given a nonzero tolerance, the method is rigorously shown to converge to the global solution in a finite time. An implementation is developed, and via a collection of case studies, the technique is shown to be very efficient in computing the global solutions. For problems with embedded nonlinear dynamic systems, the analysis requires a more sophisticated composition technique attributed to McCormick. McCormick's composition technique provides a method for computing a convex underestimator for for the integrand given an arbitrary nonlinear dynamic system provided that convex underestimators and concave overestimators can be given for the states. Because the states are known only implicitly via the solution of the nonlinear differential equations, deriving these convex underestimators and concave overestimators is a highly nontrivial task. Based on standard optimization results, outer approximation, the affine solution to linear dynamic systems, and differential inequalities, I present a novel method for constructing convex underestimators and concave overestimators for arbitrary nonlinear dynamic systems ...My thesis focuses on global optimization of nonconvex integral objective functions subject to parameter dependent ordinary differential equations. In particular, efficient, deterministic algorithms are developed for solving problems with both linear and nonlinear dynamics embedded. The techniques utilized for each problem classification are unified by an underlying composition principle transferring the nonconvexity of the embedded dynamics into the integral objective function. This composition, in conjunction with control parameterization, effectively transforms the problem into a finite dimensional optimization problem where the objective function is given implicitly via the solution of a dynamic system. A standard branch-and-bound algorithm is employed to converge to the global solution by systematically eliminating portions of the feasible space by solving an upper bounding problem and convex lower bounding problem at each node. The novel contributions of this work lie in the derivation and solution of these convex lower bounding relaxations. Separate algorithms exist for deriving convex relaxations for problems with linear dynamic systems embedded and problems with nonlinear dynamic systems embedded. However, the two techniques are unified by the method for relaxing the integral in the objective function. I show that integrating a pointwise in time convex relaxation of the original integrand yields a convex underestimator for the integral. Separate composition techniques, however, are required to derive relaxations for the integrand depending upon the nature of the embedded dynamics; each case is addressed separately. For problems with embedded linear dynamic systems, the nonconvex integrand is relaxed pointwise in timeby Adam Benjamin Singer.Ph.D

Multi-Attribute Tradespace Exploration for Survivability

Multi-Attribute Tradespace Exploration for Survivability is a system design and analysis methodology that incorporates survivability considerations into the tradespace exploration process (i.e., a solution-generating and decision-making framework that applies decision theory to model-based design). During the concept generation phase of tradespace exploration, the methodology applies seventeen empirically validated survivability design principles spanning susceptibility reduction, vulnerability reduction, and resilience enhancement. During subsequent concept evaluation, the methodology adds value-based survivability metrics to traditional architectural evaluation criteria of mission utility and lifecycle cost. Applied to a satellite radar mission, the methodology allowed operational survivability to be statistically evaluated across representative distributions of naturally occurring disturbances in the space environment and for survivability to be incorporated as a decision factor earlier in the design process. Constellations in the illustrative example are shown to be the most survivable, mitigating disturbances architecturally, rather than through additive features.Massachusetts Institute of Technology (Systems Engineering Advancement Research Initiative (SEAri))Massachusetts Institute of Technology. Program on Emerging Technologie

Mean first-passage time of surface-mediated diffusion in spherical domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: to appear in J. Stat. Phy

Interpretation of positive troponin results among patients with and without myocardial infarction.

Measuring cardiac troponins is integral to diagnosing acute myocardial infarction (AMI); however, troponins may be elevated without AMI, and the use of multiple different assays confounds comparisons. We considered characteristics and serial troponin values in emergency department chest pain patients with and without AMI to interpret troponin excursions. We compared serial troponin in 124 AMI and non-AMI patients from the observational Performance of Triage Cardiac Markers in the Clinical Setting (PEARL) study who presented with chest pain and had at least one troponin value exceeding the 99th percentile of normal. Because 8 assays were used during data collection, we employed a method of scaling the troponin value to the corresponding assay\u27s 99th percentile upper reference limit to standardize the results. In 81 AMI patients, 96% had elevated troponin at the first test following initial elevation, compared to 73% of the 43 non-AMI patients

Kinetics of active surface-mediated diffusion in spherically symmetric domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: Published online in J. Stat. Phy

GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms

This database includes thermal tolerance metrics for 2,133 species of multicellular algae, plants, fungi, and animals in 43 classes, 203 orders and 525 families from both aquatic, and terrestrial realms, extracted from published studies. Abbreviated citations are included in the 'REF_min' and 'REF_max' variable in the data file. For full citations, please see the attached workbook, "References_1_09_2017.xlsx". The data are available in both Excel and CSV formats in the Dryad Digital Repository (doi:10.5061/dryad.1cv08). Updates to the data and metadata will be curated through the iDiv data portal (https://idata.idiv.de/). For example, in the future we plan to include interspecific variation in the dataset, to provide multiple estimates of thermal tolerance limits for a given species where estimates determined using the best possible methods will be more highly ranked

GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms

CITATION: Bennett, J. M., et al. 2018. GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms. Scientific Data, 5:180022, doi:10.1038/sdata.2018.22.The original publication is available at https://www.nature.comHow climate affects species distributions is a longstanding question receiving renewed interest owing to the need to predict the impacts of global warming on biodiversity. Is climate change forcing species to live near their critical thermal limits? Are these limits likely to change through natural selection? These and other important questions can be addressed with models relating geographical distributions of species with climate data, but inferences made with these models are highly contingent on non-climatic factors such as biotic interactions. Improved understanding of climate change effects on species will require extensive analysis of thermal physiological traits, but such data are both scarce and scattered. To overcome current limitations, we created the GlobTherm database. The database contains experimentally derived species’ thermal tolerance data currently comprising over 2,000 species of terrestrial, freshwater, intertidal and marine multicellular algae, plants, fungi, and animals. The GlobTherm database will be maintained and curated by iDiv with the aim to keep expanding it, and enable further investigations on the effects of climate on the distribution of life on Earth.https://www.nature.com/articles/sdata201822Publisher's versio

Identification of Giardia lamblia DHHC Proteins and the Role of Protein S-palmitoylation in the Encystation Process

Protein S-palmitoylation, a hydrophobic post-translational modification, is performed by protein acyltransferases that have a common DHHC Cys-rich domain (DHHC proteins), and provides a regulatory switch for protein membrane association. In this work, we analyzed the presence of DHHC proteins in the protozoa parasite Giardia lamblia and the function of the reversible S-palmitoylation of proteins during parasite differentiation into cyst. Two specific events were observed: encysting cells displayed a larger amount of palmitoylated proteins, and parasites treated with palmitoylation inhibitors produced a reduced number of mature cysts. With bioinformatics tools, we found nine DHHC proteins, potential protein acyltransferases, in the Giardia proteome. These proteins displayed a conserved structure when compared to different organisms and are distributed in different monophyletic clades. Although all Giardia DHHC proteins were found to be present in trophozoites and encysting cells, these proteins showed a different intracellular localization in trophozoites and seemed to be differently involved in the encystation process when they were overexpressed. dhhc transgenic parasites showed a different pattern of cyst wall protein expression and yielded different amounts of mature cysts when they were induced to encyst. Our findings disclosed some important issues regarding the role of DHHC proteins and palmitoylation during Giardia encystation.Fil: Merino, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Zamponi, Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Vranych, Cecilia Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Touz, Maria Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Ropolo, Andrea Silvana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin

The Evaluation of a Rapid In Situ HIV Confirmation Test in a Programme with a High Failure Rate of the WHO HIV Two-Test Diagnostic Algorithm

BACKGROUND: Concerns about false-positive HIV results led to a review of testing procedures used in a Médecins Sans Frontières (MSF) HIV programme in Bukavu, eastern Democratic Republic of Congo. In addition to the WHO HIV rapid diagnostic test algorithm (RDT) (two positive RDTs alone for HIV diagnosis) used in voluntary counselling and testing (VCT) sites we evaluated in situ a practical field-based confirmation test against western blot WB. In addition, we aimed to determine the false-positive rate of the WHO two-test algorithm compared with our adapted protocol including confirmation testing, and whether weakly reactive compared with strongly reactive rapid test results were more likely to be false positives. METHODOLOGY/PRINCIPAL FINDINGS: 2864 clients presenting to MSF VCT centres in Bukavu during January to May 2006 were tested using Determine HIV-1/2 and UniGold HIV rapid tests in parallel by nurse counsellors. Plasma samples on 229 clients confirmed as double RDT positive by laboratory retesting were further tested using both WB and the Orgenics Immunocomb Combfirm HIV confirmation test (OIC-HIV). Of these, 24 samples were negative or indeterminate by WB representing a false-positive rate of the WHO two-test algorithm of 10.5% (95%CI 6.6-15.2). 17 of the 229 samples were weakly positive on rapid testing and all were negative or indeterminate by WB. The false-positive rate fell to 3.3% (95%CI 1.3-6.7) when only strong-positive rapid test results were considered. Agreement between OIC-HIV and WB was 99.1% (95%CI 96.9-99.9%) with no false OIC-HIV positives if stringent criteria for positive OIC-HIV diagnoses were used. CONCLUSIONS: The WHO HIV two-test diagnostic algorithm produced an unacceptably high level of false-positive diagnoses in our setting, especially if results were weakly positive. The most probable causes of the false-positive results were serological cross-reactivity or non-specific immune reactivity. Our findings show that the OIC-HIV confirmation test is practical and effective in field contexts. We propose that all double-positive HIV RDT samples should undergo further testing to confirm HIV seropositivity until the accuracy of the RDT testing algorithm has been established at programme level

River ecosystem conceptual models and non‐perennial rivers: A critical review

Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.info:eu-repo/semantics/publishedVersio